10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2020

OR

☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from              to

Commission File Number: 001-34885

AMYRIS, INC.

(Exact name of registrant as specified in its charter) 

Delaware	55-0856151
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

(510) 450-0761

(Address and telephone number of principal executive offices)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, $0.0001 par value per share	AMRS	The Nasdaq Stock Market, LLC

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  o

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files).    Yes  x    No  o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and "emerging growth company" in Rule 12b-2 of the Exchange Act.

Large accelerated filer	☐	Accelerated filer	☒
Non-accelerated filer	☐	Smaller reporting company	☒
Emerging growth company	☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  ☐    No  x

Shares outstanding of the Registrant's common stock:

        Class Outstanding as of August 4, 2020

        Common Stock, $0.0001 par value per share 204,730,979

AMYRIS, INC.

TABLE OF CONTENTS

		Page
	PART I
Item 1.	Financial Statements (unaudited)	4
	Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019	5
	Condensed Consolidated Statements of Operations for the Three and Six Months Ended June 30, 2020 and 2019	7
	Condensed Consolidated Statements of Comprehensive Loss for the Three and Six Months Ended June 30, 2020 and 2019	8
	Condensed Consolidated Statements of Stockholders’ Deficit and Mezzanine Equity for the Three Months Ended March 31, 2020 and 2019, and the Three Months Ended June 30, 2020 and 2019	9
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2020 and 2019	11
	Notes to Condensed Consolidated Financial Statements	15
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	50
Item 4.	Controls and Procedures	61
	PART II
Item 1.	Legal Proceedings	62
Item 1A.	Risk Factors	62
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	63
Item 3.	Defaults Upon Senior Securities	63
Item 5.	Other Information	64
Item 6.	Exhibits	65
SIGNATURES

2

PART I

ITEM 1. FINANCIAL STATEMENTS (UNAUDITED)

3

AMYRIS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(Unaudited)

(In thousands, except shares and per share amounts)	June 30, 2020		December 31, 2019
Assets
Current assets:
Cash and cash equivalents	$	99,998	$	270
Restricted cash	362		469
Accounts receivable, net of allowance of $102 and $45, respectively	22,029		16,322
Accounts receivable - related party, net of allowance of $0 and $0, respectively	94		3,868
Contract assets	11,724		8,485
Contract assets - related party	1,203		—
Inventories	33,059		27,770
Deferred cost of products sold - related party	7,709		3,677
Prepaid expenses and other current assets	14,531		12,750
Total current assets	190,709		73,611
Property, plant and equipment, net	27,394		28,930
Contract assets, noncurrent - related party	—		1,203
Deferred cost of products sold, noncurrent - related party	14,260		12,815
Restricted cash, noncurrent	960		960
Recoverable taxes from Brazilian government entities	5,725		7,676
Right-of-use assets under financing leases, net (Note 2)	11,422		12,863
Right-of-use assets under operating leases (Note 2)	11,662		13,203
Other assets	5,557		9,705
Total assets	$	267,689	$	160,966
Liabilities, Mezzanine Equity and Stockholders' Deficit
Current liabilities:
Accounts payable	$	22,779	$	51,234
Accrued and other current liabilities	49,110		36,655
Financing lease liabilities (Note 2)	3,605		3,465
Operating lease liabilities (Note 2)	4,893		4,625
Contract liabilities	5,180		1,353
Debt, current portion (includes instrument measured at fair value $36,624 and $24,392, respectively)	43,482		45,313
Related party debt, current portion	—		18,492
Total current liabilities	129,049		161,137
Long-term debt, net of current portion (includes instrument measured at fair value of $0 and $26,232, respectively)	23,532		48,452
Related party debt, net of current portion (includes instrument measured at fair value of $81,551 and $0, respectively)	138,898		149,515
Financing lease liabilities, net of current portion (Note 2)	2,305		4,166
Operating lease liabilities, net of current portion (Note 2)	12,457		15,037
Derivative liabilities	5,833		9,803
Other noncurrent liabilities	15,254		23,024
Total liabilities	327,328		411,134
Commitments and contingencies (Note 8)
Mezzanine equity:
Contingently redeemable common stock (Note 5)	5,000		5,000
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of June 30, 2020 and December 31, 2019; 110,436 and 8,280 shares issued and outstanding as of June 30, 2020 and December 31, 2019, respectively	—		—
Common stock - $0.0001 par value, 350,000,000 and 250,000,000 shares authorized as of June 30, 2020 and December 31, 2019, respectively; 204,618,423 and 117,742,677 shares issued and outstanding as of June 30, 2020 and December 31, 2019, respectively	20		12
Additional paid-in capital	1,935,252		1,543,668
Accumulated other comprehensive loss	(48,708)		(43,804)
Accumulated deficit	(1,953,919)		(1,755,653)
Total Amyris, Inc. stockholders’ deficit	(67,355)		(255,777)
Noncontrolling interest	2,716		609
Total stockholders' deficit	(64,639)		(255,168)
Total liabilities, mezzanine equity and stockholders' deficit	$	267,689	$	160,966

4

See the accompanying notes to the unaudited condensed consolidated financial statements.

5

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(Unaudited)

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Revenue:
Renewable products (includes related party revenue of $56, $0, $105 and $2, respectively)	$	25,188	$	12,120	$	43,042	$	24,004
Licenses and royalties (includes related party revenue of $0, $40,682, $3,750 and $40,302, respectively)	990		40,964		6,151		41,082
Grants and collaborations (includes related party revenue of $1,251, $2,646, $4,269 and $3,042, respectively)	3,827		9,610		9,942		11,982
Total revenue (includes related party revenue of $1,307, $43,328, $8,124 and $43,346, respectively)	30,005		62,694		59,135		77,068
Cost and operating expenses:
Cost of products sold	23,098		15,121		34,888		32,828
Research and development	16,965		19,222		34,091		37,061
Sales, general and administrative	30,503		30,862		62,517		59,115
Total cost and operating expenses	70,566		65,205		131,496		129,004
Loss from operations	(40,561)		(2,511)		(72,361)		(51,936)
Other income (expense):
Interest expense	(20,118)		(15,217)		(35,120)		(27,751)
Loss from change in fair value of derivative instruments	(11,779)		—		(8,497)		(2,039)
Loss from change in fair value of debt	(14,949)		(14,444)		(31,452)		(16,574)
Loss upon extinguishment of debt	(22,029)		(5,875)		(49,348)		(5,875)
Other income (expense), net	1,497		(41)		1,501		(156)
Total other expense, net	(67,378)		(35,577)		(122,916)		(52,395)
Loss before income taxes and loss from investment in affiliate	(107,939)		(38,088)		(195,277)		(104,331)
Provision for income taxes	(99)		—		(190)		—
Loss from investment in affiliate	(277)		—		(692)		—
Net loss	(108,315)		(38,088)		(196,159)		(104,331)
Less: income attributable to noncontrolling interest in Aprinnova	(2,107)		—		(2,107)		—
Net loss attributable to Amyris, Inc.	(110,422)		(38,088)		(198,266)		(104,331)
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D	—		(34,964)		—		(34,964)
Add: losses allocated to participating securities	6,361		2,255		7,435		4,690
Net loss attributable to Amyris, Inc. common stockholders	$	(104,061)	$	(70,797)	$	(190,831)	$	(134,605)
Loss per share attributable to common stockholders, basic and diluted	$	(0.56)	$	(0.76)	$	(1.12)	$	(1.59)
Weighted-average shares of common stock outstanding used in computing loss per share of common stock, basic and diluted	184,827,330		92,785,752		169,946,482		84,831,269

See the accompanying notes to the unaudited condensed consolidated financial statements.

6

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

(Unaudited)

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Comprehensive loss:
Net loss	$	(108,315)	$	(38,088)	$	(196,159)	$	(104,331)
Foreign currency translation adjustment	(2,355)		(1,100)		(4,904)		(136)
Total comprehensive loss	(110,670)		(39,188)		(201,063)		(104,467)
Income attributable to noncontrolling interest	(2,107)		—		(2,107)		—
Comprehensive loss attributable to Amyris, Inc.	$	(112,777)	$	(39,188)	$	(203,170)	$	(104,467)

See the accompanying notes to the unaudited condensed consolidated financial statements.

7

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' DEFICIT AND MEZZANINE EQUITY

(Unaudited)

	Preferred Stock			Common Stock
(In thousands, except number of shares)	Shares	Amount		Shares	Amount		Additional Paid-in Capital		Accumulated Other Comprehensive Loss		Accumulated Deficit		Noncontrolling Interest		Total Stockholders' Deficit		Mezzanine Equity - Common Stock
Balances at December 31, 2019	8,280	$	—	117,742,677	$	12	1,543,668		$	(43,804)	$	(1,755,653)	$	609	$	(255,168)	$	5,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	—	—		6,337,594	1		21,259		—		—		—		21,260		—
Issuance of common stock in private placement	—	—		3,484,321	—		10,000		—		—		—		10,000		—
Issuance of common stock in private placement - related party	—	—		10,505,652	1		27,188		—		—		—		27,189		—
Issuance of common stock upon exercise of warrants	—	—		1,160,929	—		3,332		—		—		—		3,332		—
Issuance of common stock upon exercise of warrants - related party	—	—		24,165,166	2		68,763		—		—		—		68,765		—
Exercise of common stock rights warrant - related party	—	—		—	—		15,000		—		—		—		15,000		—
Issuance of common stock right warrant - related party	—	—		—	—		8,904		—		—		—		8,904		—
Modification of previously issued common stock warrants	—	—		—	—		1,286		—		—		—		1,286		—
Derecognition of liability warrants to equity	—	—		—	—		5,200		—		—		—		5,200		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		495,581	—		(8)		—		—		—		(8)		—
Stock-based compensation	—	—		—	—		3,504		—		—		—		3,504		—
Foreign currency translation adjustment	—	—		—	—		—		(2,549)		—		—		(2,549)		—
Net loss attributable to Amyris, Inc.	—	—		—	—		—		—		(87,844)		—		(87,844)		—
Balances at March 31, 2020	8,280	$	—	163,891,920	$	16	$	1,708,096	$	(46,353)	$	(1,843,497)	$	609	$	(181,129)	$	5,000
Issuance of preferred and common stock in private placement, net of issuance costs	72,156			32,614,573	3		160,014								160,017		—
Issuance of preferred stock in private placement - related party, net of issuance costs	30,000			—	—		30,000								30,000		—
Issuance of common stock upon exercise of warrants				132,746	—		—								—		—
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party				5,226,481	1		(1)								—		—
Fair value of pre-delivery shares released to holder in connection with debt amendment				—	—		10,478								10,478		—
Derecognition of liability warrants to equity				—	—		6,550								6,550		—
Fair value of modification to previously issued common stock warrants				—	—		1,067								1,067		—
Return of pre-delivery shares previously issued in connection with debt agreement				(1,363,636)	—		—								—		—
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity				3,246,489	—		15,778								15,778		—
Stock-based compensation				—	—		2,931								2,931		—
Issuance of common stock upon ESPP purchase				144,523	—		421								421		—
Issuance of common stock upon exercise of stock options				5,227	—		16								16		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock				720,100	—		(98)								(98)		—
Foreign currency translation adjustment				—	—		—		(2,355)						(2,355)		—
Net loss attributable to Amyris, Inc.				—	—		—				(110,422)		2,107		(108,315)		—
Balances at June 30, 2020	110,436	$	—	204,618,423	$	20	$	1,935,252	$	(48,708)	$	(1,953,919)	$	2,716	$	(64,639)	$	5,000
	Preferred Stock			Common Stock
(In thousands, except number of shares)	Shares	Amount		Shares	Amount		Additional Paid-in Capital		Accumulated Other Comprehensive Loss		Accumulated Deficit		Noncontrolling Interest		Total Stockholders' Deficit		Mezzanine Equity - Common Stock
Balances at December 31, 2018	14,656	$	—	76,564,829	$	8	$	1,346,996	$	(43,343)	$	(1,521,417)	$	937	$	(216,819)	$	5,000
Cumulative effect of change in accounting principle for ASU 2017-11	—	—		—	—		32,512		—		8,531		—		41,043		—
Issuance of common stock upon exercise of warrants	—	—		450,568	—		1		—		—		—		1		—
Issuance of common stock upon exercise of stock options	—	—		3,612	—		13		—		—		—		13		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		191,672	—		(9)		—		—		—		(9)		—
Stock-based compensation	—	—		—	—		3,452		—		—		—		3,452		—
Fair value of bifurcated embedded conversion feature in connection with debt modification	—	—		—	—		398		—		—		—		398		—
Foreign currency translation adjustment	—	—		—	—		—		964		—		—		964		—

8

Net loss	—	—		—	—		—	—		(66,243)		—		(66,243)		—
Balances at March 31, 2019	14,656	—		77,210,681	8		1,383,363	(42,379)		(1,579,129)		937		(237,200)		5,000
Issuance of common stock in private placement	—	—		3,610,944	1		14,221	—		—		—		14,222		—
Issuance of common stock in private placement - related party	—	—		10,478,338	—		39,499	—		—		—		39,499		—
Issuance of common stock upon conversion of debt	—	—		7,101,468	1		34,650	—		—		—		34,651		—
Issuance of common stock upon ESPP purchase		—		131,460	—		464	—		—		—		464		—
Issuance of common stock upon exercise of warrants	—	—		2,064,606	—		—	—		—		—		—		—
Issuance of common stock and payment of minimum employee taxes withheld upon net share settlement of restricted stock	—	—		589,241	—		(347)	—		—		—		(347)		—
Issuance of warrants in connection with debt accounted for at fair value	—	—		—	—		4,428	—		—		—		4,428		—
Stock-based compensation	—	—		—	—		3,375	—		—		—		3,375		—
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock	—	—		—	—		34,964	—		—		—		34,964		—
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock	—	—		—	—		(34,964)	—		—		—		(34,964)		—
Other	—	—		—	—		(238)	—		—		—		(238)		—
Foreign currency translation adjustment	—	—		—	—		—	(1,100)		—		—		(1,100)		—
Net loss	—	—		—	—		—	—		(38,088)		—		(38,088)		—
Balances at June 30, 2019	14,656	$	—	101,186,738	$	10	1,479,415	$	(43,479)	$	(1,617,217)	$	937	$	(180,334)	$	5,000

See the accompanying notes to the unaudited condensed consolidated financial statements.

9

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(Unaudited)

10

	Six Months Ended June 30,
(In thousands)	2020		2019
Operating activities
Net loss	$	(196,159)	$	(104,331)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss upon extinguishment of debt	49,348		5,875
Loss from change in fair value of debt	31,452		16,574
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	10,478		—
Loss from change in fair value of derivative instruments	8,497		2,039
Stock-based compensation	6,435		6,827
Depreciation and amortization	4,115		1,722
Accretion of debt discount	2,308		7,260
Amortization of right-of-use assets under operating leases	1,336		5,846
Non-cash interest expense in connection with modification of warrants	1,066		—
Loss in equity-method investee	692		—
Non-cash interest expense added to debt principal	100		—
Loss (gain) on disposal of property, plant and equipment	42		(4)
Impairment of property, plant and equipment	13		438
Expense for warrants issued for debt covenant waivers	—		4,428
Gain on foreign currency exchange rates	(327)		(36)
Changes in assets and liabilities:
Accounts receivable	(1,971)		(2,147)
Contract assets	(3,239)		—
Accounts receivable, unbilled - related party	—		8,021
Inventories	(6,229)		(4,310)
Deferred cost of products sold - related party	(5,477)		(14,066)
Prepaid expenses and other assets	868		(1,000)
Accounts payable	(27,934)		4,532
Accrued and other liabilities	12,580		7,659
Lease liabilities	(2,153)		(8,096)
Contract liabilities	3,827		4,512
Net cash used in operating activities	(110,332)		(58,257)
Investing activities
Purchases of property, plant and equipment	(5,494)		(5,951)
Net cash used in investing activities	(5,494)		(5,951)
Financing activities
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs	170,017		14,221
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs - related party	45,000		39,500
Proceeds from exercises of warrants	3,332		1
Proceeds from exercises of warrants - related party	13,998		—
Proceeds from exercise of common stock rights warrant - related party	15,000		—
Proceeds from issuance of debt, net of issuance costs	15,279		18,614
Proceeds from issuance of common stock upon ESPP purchase	421		464
Proceeds from exercises of common stock options	16		13
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(106)		(356)
Principal payments on financing leases	(1,721)		(258)
Principal payments on debt	(45,949)		(52,145)
Net cash provided by financing activities	215,287		20,054
Effect of exchange rate changes on cash, cash equivalents and restricted cash	160		(507)
Net increase (decrease) in cash, cash equivalents and restricted cash	99,621		(44,661)
Cash, cash equivalents and restricted cash at beginning of period	1,699		47,054
Cash, cash equivalents and restricted cash at end of the period	$	101,320	$	2,393
Reconciliation of cash, cash equivalents and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	$	99,998	$	940
Restricted cash, current	362		493
Restricted cash, noncurrent	960		960
Total cash, cash equivalents and restricted cash	$	101,320	$	2,393

11

See the accompanying notes to the unaudited condensed consolidated financial statements.

12

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS, Continued

(Unaudited)

	Six Months Ended June 30,
(In thousands)	2020		2019
Supplemental disclosures of cash flow information:
Cash paid for interest	$	8,281	$	7,986
Supplemental disclosures of non-cash investing and financing activities:
Accrued interest added to debt principal	$	1,702	$	448
Unpaid property, plant and equipment balances in accounts payable and accrued liabilities at end of period	$	708	$	1,026
Acquisition of right-of-use assets under operating leases	$	—	$	1,675
Cumulative effect of change in accounting principle for ASU 2017-11	$	—	$	41,043
Derecognition of derivative liabilities to equity upon extinguishment of debt	$	6,461	$	—
Derecognition of derivative liabilities upon authorization of shares	$	6,550	$	—
Derecognition of derivative liabilities upon exercise of warrants	$	5,200	$	—
Exercise of common stock warrants in exchange for debt principal and accrued interest reduction	$	69,918	$	—
Fair value of embedded features in connection with private placement	$	2,962	$	—
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances	$	188	$	—
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances - related party	$	747	$	—
Fair value of warrants recorded as debt discount in connection with debt modification	$	—	$	398
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$	27,650	$	34,650
Lease liabilities recorded upon adoption of ASC 842	$	—	$	33,552
Right-of-use assets under operating leases recorded upon adoption of ASC 842	$	—	$	29,713

See the accompanying notes to the unaudited condensed consolidated financial statements.

13

AMYRIS, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1. Basis of Presentation and Summary of Significant Accounting Policies

Amyris, Inc. (Amyris or the Company) is a leading synthetic biotechnology company in Clean Health and Beauty markets through its consumer brands, and is a supplier of sustainable and natural ingredients. Amyris applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably sourced products into the Health, Beauty, and Flavor & Fragrance end-markets. The Company's technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume ingredients. This platform, combined with our proprietary fermentation process, replaces existing complex and oftentimes expensive manufacturing processes, resulting in our successful development and production of many distinct molecules at commercial volumes.

The accompanying unaudited condensed consolidated financial statements of Amyris, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2019 (the 2019 Form 10-K), from which the condensed consolidated balance sheet as of December 31, 2019 is derived. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP) for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the accompanying interim condensed consolidated financial statements do not include all of the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are not necessarily indicative of results for a full year.

Raizen Joint Venture Agreement

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into a joint venture agreement relating to the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products. In connection with the formation of the joint venture, among other things, (i) the joint venture will construct a manufacturing facility on land owned by Raizen and leased to the joint venture (the Sweetener Plant), (ii) the Company will grant to the joint venture an exclusive, royalty-free, worldwide, license to certain technology owned by the Company relevant to the joint venture’s business, and (iii) the Company and Raizen will enter into a shareholders agreement setting forth the rights and obligations of the parties with respect to, and for the management of, the joint venture. The formation of the joint venture is subject to certain conditions, including certain regulatory approvals, and the achievement of certain technological and economic milestones relating to the Company’s existing production of its alternative sweetener product. The COVID-19 pandemic caused a disruption in the production campaign of the Company’s alternative sweetener product. The disruption delayed the generation of the requisite data required to complete technological and economic analysis underpinning the joint venture agreement between the parties. Therefore, the parties have agreed to extend the previous July 2020 deadline to conduct the relevant analysis of the sweetener production data in order to determine potential next steps for the joint venture. In addition, notwithstanding the satisfaction of the closing conditions, Raizen may elect not to consummate the formation and operation of the joint venture, in which event, the Company will retain the right to construct and operate the Sweetener Plant. The Company is evaluating the accounting treatment for its future interest in the joint venture under ASC 810, Consolidations and ASC 323, Equity Method and Joint Ventures and will conclude once the corporate governance and economic participation structure is finalized and the formation of the joint venture is consummated.

Potential Impact of COVID-19 on the Company's Business

With the global spread of the COVID-19 pandemic beginning in the first quarter of 2020 and anticipated continuation throughout 2020, and the resulting shelter-in-place orders covering the Company’s corporate headquarters, primary research and development laboratories, and employees, the Company has implemented policies and procedures to continue its operations under applicable minimum business operations guidelines. The extent to which the COVID-19 pandemic impacts the Company’s business, financial condition or results of operations will depend on future developments, which are highly uncertain and cannot be accurately predicted. New information may emerge concerning the severity of the COVID-19 pandemic and the actions to contain the pandemic or treat COVID-19, such as the ultimate geographic spread of the disease, the duration of the pandemic, continued travel restrictions, social distancing, business closures or disruptions, and the effectiveness of actions taken to contain or treat COVID-19 in the United States and in other countries. As the COVID-19 pandemic continues to evolve, to the extent it adversely affects our business and financial results, it may also impact other risks to which the Company is subject as set forth in the “Risk Factors” section (Part I, Item 1A) of the 2019 Form 10-K.

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Going Concern

The Company has incurred significant operating losses since its inception and expects to continue to incur losses and negative cash flows from operations over the course of at least the next 12 months following the issuance of these condensed consolidated financial statements. As of June 30, 2020, the Company had working capital of $61.7 million (compared to negative working capital of $87.5 million as of December 31, 2019), and an accumulated deficit of $2.0 billion.

As of June 30, 2020, the Company's outstanding debt principal (including related party debt) totaled $175.8 million, of which $37.0 million is classified as current. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as restrictions on additional indebtedness, material adverse effect and cross default provisions. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of a substantial portion of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of such other outstanding indebtedness. At December 31, 2019, the Company failed to meet certain covenants under several credit arrangements, including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. Further, at March 31, 2020, the Company failed to meet certain covenants and provisions under several credit arrangements, including those associated with cross-default provisions (as discussed below). In March 2020 and again in May 2020, these lenders (except Schottenfeld Group LLC and certain of its affiliates (Schottenfeld)) provided waivers to the Company for breaches of all past covenant violations and cross-default payment failures, under the respective credit agreements (discussed in the paragraph below) through the earlier of the closing of a significant equity offering or May 31, 2020. The Company cured these defaults with the closing of the $200 million equity offering described below and the repayment of these past due amounts. As of June 30, 2020, the Company failed to achieve the minimum revenue thresholds under the Foris LSA, Naxyris LSA and Senior Convertible Notes Due 2022, which are described in more detail in Note 4, “Debt”, and obtained a waiver from each of these lenders to cure the June 30, 2020 minimum revenue covenant violation.

Between March 31, 2020 and April 30, 2020, the Company failed to pay (i) Total Raffinage Chimie (Total), Nikko Chemicals Co. Ltd (Nikko) and certain affiliates of Schottenfeld an aggregate of $17.6 million of maturing promissory notes, (ii) failed to pay Ginkgo $7.2 million of past due interest, waiver fees and partnership payments and (iii) failed to make interest payments to all of its lenders totaling $2.8 million. These payment failures resulted in an event of default under the respective agreements and triggered cross-defaults under other debt instruments that permitted each of the affected debt holders (the Cross-Default Lenders) to accelerate the amounts owing under such cross-defaulted instruments. In May 2020, the Company obtained waivers from the lenders, except Schottenfeld, to extend the due date for all payments due under the respective agreements to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020; and amended the credit arrangements with Total and Nikko to extend the maturity dates of the original respective promissory notes to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. Also, the Company received waivers from each of the affected Cross-Default Lenders to waive the right to accelerate due to the event-specific cross-defaults.

Beginning in May 2020 and continuing through June 2020, the Company executed a series of financial transactions to minimize cash outflows related to debt service payments and to increase operating cash. On May 1, 2020, the Company amended the Senior Convertible Notes Due 2022 to eliminate the monthly amortization payments and change the interest payment frequency from monthly to quarterly. On May 7, 2020, the Company received a $10 million Paycheck Protection Plan loan (PPP Loan). On June 1, 2020, the Company amended the Foris LSA to eliminate the quarterly principal payments and defer all interest payments until maturity on July 1, 2022, and to provide for the conversion of all outstanding indebtedness under the LSA at a $3.00 per share conversion price, which conversion is subject to stockholder approval. Further, on June 1, 2020 and June 4, 2020, the Company entered into securities purchase agreements with investors for the private placement of an aggregate of $200 million of common and preferred stock, resulting in the Company receiving approximately $190 million of net proceeds. A portion of the proceeds from the offering was used to pay down approximately $37.1 million of debt principal (which included $10 million to repay the PPP Loan) and $6.1 million of accrued interest. Also, on June 2, 2020, Total converted approximately $9.3 million of debt principal and accrued interest into common stock under the terms of the 2014 Rule 144A Convertible Note, further reducing the Company’s outstanding indebtedness. As a result of closing the equity offering, making all past due payments, converting the $9.1 million 2014 Rule 144A Convertible Note principal into equity, and executing amendments to the Foris LSA and the Senior Convertible Notes Due 2022, the Company cured all payment defaults and other events of default, including cross-defaults under the Company’s various debt instruments as of June 30, 2020. Although the Company has been able to obtain waivers in the past for substantially all of its prior defaults to date and was able to cure the existing payment defaults, it may not be able to cure or obtain a waiver for any defaults in the future.

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Further, the Company's cash and cash equivalents of $100.0 million as of June 30, 2020 may not be sufficient to fund expected cash flows requirements from operations and cash debt service obligations through August 2021. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date these condensed consolidated financial statements are issued. The condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. The Company's ability to continue as a going concern will depend, in large part, on its ability to eliminate or minimize the anticipated negative cash flows from operations during the 12 months from the date of this filing and to either raise additional cash proceeds through financings or refinance the debt maturities occurring in June 2021, all of which are uncertain and outside the control of the Company. Further, the Company's operating plan for the remainder of 2020 contemplates (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) reduced spending in general and administrative areas, and (iv) continued cash inflows from collaborations and grants. If the Company is unable to complete these actions, it may be unable to meet its operating cash flow needs and its obligations under its existing debt facilities over the next 12 months. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and the Company may be forced to obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all, and/or liquidate its assets. In such a scenario, the value received for assets in liquidation or dissolution could be significantly lower than the value reflected in these financial statements.

Significant Accounting Policies

Note 1, "Basis of Presentation and Summary of Significant Accounting Policies", to the audited consolidated financial statements in the 2019 Form 10-K includes a discussion of the significant accounting policies and estimates used in the preparation of the Company’s consolidated financial statements. There have been no material changes to the Company's significant accounting policies and estimates during the six months ended June 30, 2020.

Accounting Standards or Updates Recently Adopted

In the six months ended June 30, 2020, the Company adopted these accounting standards or updates:

Fair Value Measurement In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement, which amends ASC 820, Fair Value Measurement. ASU 2018-13 modifies the disclosure requirements for fair value measurements by removing, modifying or adding certain disclosures. ASU 2018-13 became effective in the first quarter of fiscal 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The adoption of this standard did not have a material impact on the Company’s condensed consolidated financial statements.

Collaborative Revenue Arrangements In November 2018, the FASB issued ASU 2018-18, Clarifying the Interaction between Topic 808 and Topic 606, that clarifies the interaction between the guidance for certain collaborative arrangements and Topic 606, the new revenue recognition standard. A collaborative arrangement is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. The ASU provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. ASU 2018-18 became effective in the first quarter of fiscal year 2020 retrospectively. The adoption of this standard did not have any impact on the Company’s condensed consolidated financial statements.

Accounting Standards or Updates Not Yet Adopted

Credit Losses In June 2016, the FASB issued ASU 2016-13, Financial Instruments—Credit Losses (Topic 326), Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires entities to measure all expected credit losses for most financial assets held at the reporting date based on an expected loss model which includes historical experience, current conditions, and reasonable and supportable forecasts. Entities will now use forward-looking information to better form their credit loss estimates. ASU 2016-13 also requires enhanced disclosures to help financial statement users better understand significant estimates and judgments used in estimating credit losses, as well as the credit quality and underwriting standards of an entity's portfolio. ASU 2016-13 is effective for the Company in the first quarter of 2021. The Company is currently evaluating the impact this standard will have on its condensed consolidated financial statements.

Accounting for Income Taxes In December 2019, the FASB issued ASU 2019-12, “Simplifying the Accounting for Income Taxes” (“ASU 2019-12”). The amendments in ASU 2019-12 simplify the accounting for income taxes by removing certain exceptions to the general principles in ASC Topic 740, Income Taxes. The amendments also improve consistent application of and simplify U.S. GAAP for other areas of ASC Topic 740 by clarifying and amending existing guidance. ASU

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2019-12 will be effective for the Company commencing in the first quarter of fiscal year 2021. The transition requirements are dependent upon each amendment within this update and will be applied either prospectively or retrospectively. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Convertible Debt, and Derivatives and Hedging On August 5, 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity, to improve financial reporting associated with accounting for convertible instruments and contracts in an entity’s own equity. ASU 2020-06 is effective for the Company in the first quarter of 2022. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Use of Estimates and Judgements

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates, judgements and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates, and such differences may be material to the condensed consolidated financial statements.

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2. Balance Sheet Details

Allowance for Doubtful Accounts

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Period
Six months ended June 30, 2020	$	45	$	57	$	—	$	102
Year ended December 31, 2019	$	642	$	110	$	(707)	$	45

Inventories

(In thousands)	June 30, 2020		December 31, 2019
Raw materials	$	4,487	$	3,255
Work-in-process	8,204		7,204
Finished goods	20,368		17,311
Inventories	$	33,059	$	27,770

Deferred cost of products sold - related party

(In thousands)	June 30, 2020		December 31, 2019
Deferred cost of products sold - related party	$	7,709	$	3,677
Deferred cost of products sold, noncurrent - related party	14,260		12,815
Total	$	21,969	$	16,492

In November 2018, the Company amended the supply agreement with DSM to secure capacity at the Brotas 1 facility for sweetener production through December 2022. See Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K for information regarding the November 2018 Supply Agreement Amendment. As part of the amendment, the Company made a series of manufacturing capacity fee payments from November 2018 to March 31, 2020. Of these payments $17.4 million was recorded as deferred cost of products sold. In June 2020, the Company paid an additional $6.9 million manufacturing capacity fee, which represents the final payment under the amendment. The capitalized deferred cost of products sold asset is expensed to cost of products sold on a units of production basis as the Company's sweetener product is produced and sold over the five-year term of the supply agreement. Each quarter, the Company evaluates its estimated future production volumes through the end of the agreement and adjusts the unit cost to be expensed over the remaining estimated production volume. During the three and six months ended June 30, 2020, the Company expensed $1.1 million and $1.3 million, respectively, of the deferred cost of products sold asset to cost of products sold. Inception to date amortization through June 30, 2020 totaled $2.3 million.

Prepaid expenses and other current assets

(In thousands)	June 30, 2020		December 31, 2019
Non-inventory production supplies	$	4,687	$	5,376
Prepayments, advances and deposits	6,423		4,726
Other	3,421		2,648
Total prepaid expenses and other current assets	$	14,531	$	12,750

Property, Plant and Equipment, Net

(In thousands)	June 30, 2020		December 31, 2019
Machinery and equipment	$	46,568	$	48,041
Leasehold improvements	41,479		41,478
Computers and software	9,700		9,822
Furniture and office equipment, vehicles and land	3,496		3,510
Construction in progress	8,985		9,752
	110,228		112,603
Less: accumulated depreciation and amortization	(82,834)		(83,673)
Property, plant and equipment, net	$	27,394	$	28,930

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During the three and six months ended June 30, 2020 and 2019, depreciation and amortization expense was as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Depreciation and amortization expense	$	1,675	$	873	$	3,395	$	1,722

Leases

Operating Leases

The Company has operating leases primarily for administrative offices, laboratory equipment and other facilities. The operating leases have remaining terms that range from 1 to 5 years, and often include one or more options to renew. These renewal terms can extend the lease term from 1 to 5 years and are included in the lease term when it is reasonably certain that the Company will exercise the option. The operating leases are classified as ROU assets under operating leases on the Company's condensed consolidated balance sheets and represent the Company’s right to use the underlying asset for the lease term. The Company’s obligation to make operating lease payments is included in "Lease liabilities" and "Lease liabilities, net of current portion" on the Company's condensed consolidated balance sheets. Operating lease right-of-use assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. The Company had $11.7 million and $13.2 million of right-of-use assets as of June 30, 2020 and December 31, 2019, respectively. Operating lease liabilities were $17.4 million and $19.7 million as of June 30, 2020 and December 31, 2019, respectively. During the three and six months ended June 30, 2020 and 2019, respectively, the Company recorded $1.5 million, $3.0 million, $3.0 million and $5.8 million of operating lease amortization that was charged to expense, of which $0.3 million, $0.6 million, $0.2 million and $0.4 million was recorded to cost of products sold.

Because the rate implicit in each lease is not readily determinable, the Company uses its incremental borrowing rate to determine the present value of the lease payments. The Company has certain contracts for real estate and marketing which may contain lease and non-lease components which it has elected to treat as a single lease component.

Information related to the Company's right-of-use assets and related lease liabilities were as follows:

	Six Months Ended June 30,
	2020	2019
Cash paid for operating lease liabilities, in thousands	$3,807	$10,660
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$—	$31,293
Weighted-average remaining lease term	2.9	2.6
Weighted-average discount rate	18.0%	18.0%

(1) 2019 amount includes $29.7 million for operating leases existing on January 1, 2019 and $1.7 million for operating leases that commenced during the six months ended June 30, 2019.

Financing Leases

The Company has financing leases primarily for laboratory and computer equipment. Assets purchased under financing leases are included in "Right-of-use assets under financing leases, net" on the condensed consolidated balance sheets. For financing leases, the associated assets are depreciated or amortized over the shorter of the relevant useful life of each asset or the lease term. Accumulated amortization of assets under financing leases totaled $3.1 million and $1.7 million as of June 30, 2020 and December 31, 2019, respectively.

Maturities of Financing and Operating Leases

Maturities of lease liabilities as of June 30, 2020 were as follows:

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Years ending December 31: (In thousands)	Financing Leases		Operating Leases		Total Leases
2020 (remaining six months)	$	2,185	$	3,918	$	6,103
2021	4,566		7,478		12,044
2022	—		7,654		7,654
2023	—		3,318		3,318
2024	—		152		152
Total lease payments	6,751		22,520		29,271
Less: amount representing interest	(841)		(5,170)		(6,011)
Total lease liability	$	5,910	$	17,350	$	23,260
Current lease liability	$	3,605	$	4,893	$	8,498
Noncurrent lease liability	2,305		12,457		14,762
Total lease liability	$	5,910	$	17,350	$	23,260

Other Assets

(In thousands)	June 30, 2020		December 31, 2019
Equity-method investment	$	4,043	$	4,734
Deposits	277		295
Contingent consideration	—		3,303
Other	1,237		1,373
Total other assets	$	5,557	$	9,705

In connection with the December 2017 sale of its subsidiary Amyris Brasil Ltda. (Amyris Brasil), the Company recorded a long-term receivable related to certain contingent consideration to be received from DSM upon DSM’s realization of certain Brazilian value-added tax benefits it acquired with its purchase of Amyris Brasil. In the three months ended June 30, 2020, the Company received the $3.3 million remaining balance of contingent consideration due to the Company under the 2017 asset purchase agreement.

Accrued and Other Current Liabilities

(In thousands)	June 30, 2020		December 31, 2019
Accrued interest	$	10,810	$	8,209
Ginkgo partnership payments obligation	10,134		4,319
Equity issuance costs	9,983		—
Payroll and related expenses	6,718		7,296
Contract termination fees	5,490		5,347
Asset retirement obligation	2,447		3,184
Professional services	1,595		2,968
Tax-related liabilities	—		1,685
Other	1,933		3,647
Total accrued and other current liabilities	$	49,110	$	36,655

Other noncurrent liabilities

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(In thousands)	June 30, 2020		December 31, 2019
Liability for unrecognized tax benefit	$	7,384	$	7,204
Liability in connection with acquisition of equity-method investment	5,962		5,249
Ginkgo partnership payments, net of current portion	725		4,492
Contract liabilities, net of current portion	245		1,449
Refund liability(1)	—		3,750
Other	938		880
Total other noncurrent liabilities	$	15,254	$	23,024

(1) In April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" in Part II, Item 8 of the 2019 Form 10-K for further information. The assignment was accounted for as a contract modification under ASC 606 that resulted in $12.5 million of prepaid variable consideration to the Company. The $12.5 million was recorded as a refund liability. During the three months ended March 31, 2020, the Company concluded that it would not be required to return any portion of the remaining refund liability to DSM, and recorded $3.8 million of royalty revenue related to this change in estimate and reduction of the refund liability.

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3. Fair Value Measurement

Liabilities Measured and Recorded at Fair Value on a Recurring Basis

The following tables summarize liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

(In thousands)	June 30, 2020								December 31, 2019
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Foris Convertible Note (LSA Amendment)	$	—	$	—	$	81,551	$	81,551	$	—	$	—	$	—	$	—
Senior Convertible Notes	—		—		36,624		36,624		—		—		50,624		50,624
Embedded derivatives bifurcated from debt instruments	—		—		5,833		5,833		—		—		2,832		2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		—		—		—		—		6,971		6,971
Total liabilities measured and recorded at fair value	$	—	$	—	$	124,008	$	124,008	$	—	$	—	$	60,427	$	60,427

The Company did not hold any financial assets to be measured and recorded at fair value on a recurring basis as of June 30, 2020 and December 31, 2019. Also, there were no transfers between the levels during the three months ended June 30, 2020 or the year ended December 31, 2019.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgements and consider factors specific to the asset or liability. The method of determining the fair value of embedded derivative liabilities is described subsequently in this note. Market risk associated with embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

Changes in fair value of derivative liabilities are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of derivative instruments".

Changes in the fair value of debt that is accounted for at fair value are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of debt".

Fair Value of Debt — Foris Convertible Note (LSA Amendment)

On June 1, 2020, the Company and Foris entered into an Amendment No. 1 to the Amended and Restated Foris LSA (LSA Amendment), pursuant to which, among other provisions, Foris will have the option in its sole discretion to convert all or a portion of the secured indebtedness, including accrued interest, into shares of Common Stock at a $3.00 conversion price (Conversion Option), which Conversion Option is subject to stockholder approval. See Note 4, “Debt” for further information regarding the LSA Amendment and related extinguishment accounting treatment. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). The LSA Amendment also contains certain change in control embedded derivatives and a contingent beneficial conversion feature and management believes the fair value option best reflects the underlying economics of new convertible note. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the LSA Amendment.

At June 1, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $72.1 million. The Company measured the initial fair value of the LSA Amendment using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $3.73 stock price, (ii) 26% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year. At June 30, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $81.6 million. The Company remeasured the fair value of the LSA Amendment using the following inputs: (i) $4.27 stock price, (ii) 25% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year. The Company recorded a $9.5 million loss related to the change in fair value of the LSA Amendment for the three months ended June 30, 2020.

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Fair Value of Debt — Senior Convertible Notes

On January 14, 2020, the Company exchanged the $66 million Senior Convertible Notes (or the Prior Notes) for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (ii) an aggregate of 2,742,160 shares of common stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of common stock, (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of common stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, (v) accrued and unpaid interest on the Senior Convertible Notes (payable on or prior to January 31, 2020) and (vi) cash fees in an aggregate amount of $1.0 million (payable on or prior to January 31, 2020). Due to the legal extinguishment and exchange of the Prior Notes and significantly different cash flows contained in the New Notes, the Company accounted for the exchange as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt, which was comprised of the $4.1 million fair value of the Warrants, the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and Rights over the $2.87 per share contractual value. See Note 4, "Debt” for further information regarding the transaction.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported as "Gain (loss) from change in fair value of debt" in the consolidated statements of operations in each reporting period subsequent to the issuance of the New Notes.

At January 14, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $51.0 million and the fair value was $35.8 million. The Company measured the fair value at January 14, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $2.90 stock price, (ii) 226% discount yield, (iii) 1.59% risk free interest rate (iv) 45% equity volatility, (v) 25% / 75% probability of principal repayment in cash or stock, respectively and (vi) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year.

At June 30, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $30.0 million and the fair value was $36.6 million. The Company measured the fair value at June 30, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $4.27 stock price, (ii) 232% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility, and (v) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year.

For the three and six months ended June 30, 2020, the Company recorded a $5.5 million loss and a $22.0 million loss from change in fair value of debt, respectively, in connection with the fair value remeasurement of the Prior Notes and the New Senior Convertible Notes, as follows:

In thousands
Fair value at December 31, 2019	$	50,624
Less: principal paid	(35,980)
Loss from change in fair value	21,980
Fair value at June 30, 2020	$	36,624

A binomial lattice model was used to determine whether the LSA Amendment and the Senior Convertible Notes (Debt Instruments) would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible note will be converted early if the conversion value is greater than the holding value and (ii) the convertible note will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible note is called, the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible note. Using this lattice method, the Company valued the Debt Instruments using the "with-and-without method", where the fair value of the Debt Instruments including the embedded and freestanding features is defined as the "with," and the fair value of the Debt Instruments excluding the embedded and freestanding features is defined as the "without." This method estimates the fair value of the Debt Instruments by looking at the difference in the values of the Debt Instruments with the embedded and freestanding derivatives and the fair value of the Debt Instruments without the embedded and freestanding features. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility, estimated credit spread and other instrument-specific

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assumptions. The Company remeasures the fair value of the Debt Instruments and records the change as a gain or loss from change in fair value of debt in the statement of operations for each reporting period.

Derivative Liabilities Recognized in Connection with the Issuance of Debt Instruments

The following table provides a reconciliation of the beginning and ending balances for the Company's derivative liabilities recognized in connection with the issuance of debt instruments, either freestanding or embedded, measured at fair value using significant unobservable inputs (Level 3):

(In thousands)	Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2019	$	9,803	$	9,803
Fair value of derivative liabilities issued during the period	8,752		8,752
Change in fair value of derivative instruments	8,496		8,496
Derecognition on settlement or extinguishment	(21,218)		(21,218)
Balance at June 30, 2020	$	5,833	$	5,833

Freestanding Derivative Instruments

In connection with the January 14, 2020 issuance of the New Senior Convertible Notes as discussed above and in Note 4, “Debt” (which was accounted for as an extinguishment of the original $66 million Senior Convertible Notes), the Company issued warrants (the Warrants) to purchase up to an aggregate of 3.0 million shares of common stock (the Warrant Shares). Due to stock exchange ownership limitations, which if exceeded would require stockholder approval and possibly require cash settlement for failure to deliver shares upon exercise, the Company concluded that a portion of the Warrant Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Warrant Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Warrants had an initial fair value of $4.1 million, which was recorded as: (i) $4.1 million loss upon extinguishment of debt, (ii) $2.4 million additional paid in capital and (iii) $1.7 million derivative liability. The Warrant Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Warrants was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Warrant Shares derivative liability portion was $1.5 million, and the Company recorded a $0.2 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to remove the stock ownership limitations. As a result, the Company is able to physically deliver shares under the Warrants without the potential for cash settlement. In the three months ended June 30, 2020, the Company recorded a $1.3 million final mark-to-market loss on change in derivative liability, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and derecognized the $2.8 million derivative liability balance relate to this portion of the Warrant Shares into additional paid in capital.

In connection with the January 31, 2020 private placement transaction with Foris Ventures LLC (an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock discussed in Note 6, “Stockholders’ Deficit”), the Company issued a right (the Right) to purchase up to an aggregate of 5.2 million shares of common stock (the Right Shares). Due to certain contractual provisions in the Right, the Company concluded that a portion of the Right Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Right Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Right had an initial fair value of $5.3 million, of which $2.3 million was recorded as additional paid in capital and $3.0 million was recorded as a derivative liability. The Right Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Right Shares derivative liability portion was $2.0 million, and the Company recorded a $1.0 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to increase its authorized share count from 255 million to 355 million. As a result, the portion of the Right Shares initially accounting for as a derivative liability was no longer precluded from the derivative scope exception and met the criteria for equity classification. In the three months ended June 30, 2020, the Company recorded a $1.8 million final mark-to-market loss on change in fair value of derivative instruments using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the

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valuation methodology section below, and derecognized the $3.7 million derivative liability balance into additional paid in capital.

In connection with the January 31, 2020 Debt Equitization transaction with Foris, which was accounted for as a debt extinguishment as discussed in Note 4, “Debt” and Note 6, “Stockholders’ Deficit”, the Company issued rights (the Right) to purchase up to of 8.8 million shares of common stock at $2.87 per share for twelve months from the issuance date. The Company concluded that the Right met the derivative scope exception and criteria to be accounted for in equity. The Right had a fair value of $8.9 million which was recorded as additional paid in capital and a charge to loss upon extinguishment of debt. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below.

During the second half of 2019, the Company issued five freestanding liability warrants related to the September 2019 and November 2019 Schottenfeld Notes (the Schottenfeld Notes), which the Company recorded at fair value as a derivative liability and debt discount on the respective issuance dates (see Note 4, “Debt” for further information). These freestanding liability warrants had a collective fair value of $7.0 million at December 31, 2019. As a result of the Foris Debt Equitization transaction on January 31, 2020, the variability causing these instruments to be recorded as a derivative liability was eliminated and upon derecognition of this liability into equity, the Company recorded a $1.8 million gain on change in fair value of derivative instruments in the three months ended March 31, 2020, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and reclassified the derivative liability balance of $5.2 million to additional paid in capital.

On February 28, 2020, the Company entered into forbearance agreements with certain affiliates of the Schottenfeld Group LLC (the Lenders) related to certain defaults under the Schottenfeld Notes. The transaction was accounted for as a debt extinguishment. See Note 4, “Debt” for further information. In connection with entering into the forbearance agreements, the Company committed to issuing new warrants (the New Warrants) to the Lenders under certain contingent events for 1.9 million shares of common stock at a $2.87 purchase price and a two-year term. The contingent obligation to issue the New Warrants did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The contingently issuable New Warrants derivative liability had an initial fair value of $3.2 million and was recorded as a derivative liability with a $3.2 million charge to loss upon extinguishment of debt. The New Warrants derivative liability will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the New Warrants derivative liability was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At June 30, 2020, the fair value of the New Warrants derivative liability was $5.2 million, and the Company recorded a $2.1 million loss on change in fair value derivative instruments during the six months ended June 30, 2020.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price from $56.16 to $2.87 per share. See Note 4, “Debt” for further information. Historically, the embedded conversion option was bifurcated and accounted for as a derivative liability, and at December 31, 2019 and March 31, 2020 had a $0 fair value due to the Note’s short maturity and the significant conversion price differential when compared to the Company’s current stock price. As a result of the conversion price reduction, the Company remeasured the fair value of the conversion option using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and recorded a $6.5 million loss on change in fair value of derivative instruments in the three and six months ended June 30, 2020. On June 2, 2020, Total elected to convert all the outstanding principal and interest under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $6.5 million liability was derecognized into additional paid in capital, along with the debt principal and interest balance.

Bifurcated Embedded Features in Debt Instruments

During the second half of 2019, the Company issued four debt instruments with embedded mandatory redemption features which were bifurcated from the debt host instruments and recorded at fair value as a derivative liability and debt discount. The collective fair value of the four bifurcated derivatives totaled $2.8 million at December 31, 2019. In January and February 2020, the Company again modified certain key terms in three of the four underlying debt instruments, resulting in a debt extinguishment of the three modified debt instruments. Consequently, in the three months ended March 31, 2020, the collective fair value of the three extinguished bifurcated derivatives totaling $2.3 million was recorded as a loss upon extinguishment of debt and the $0.9 million collective fair value of the new bifurcated embedded mandatory redemption features was recorded as a derivative liability and new debt discount at the modification date. The fair value of the bifurcated derivative liability was determined using a probability weighted discounted cash flow analysis which is discussed in the valuation methodology and approach section below. As of and for the six months ended June 30, 2020, the fair value of the bifurcated embedded mandatory redemption features was $0.6 million, and the Company recorded a $0.5 million gain on

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change in fair value derivative instruments. Also, one of the bifurcated features was embedded in the Foris LSA, which was modified and accounted for as an extinguishment in the three months ended June 30, 2020. As a result, the $0.7 million derivative liability balance was derecognized and recorded into the initial fair value of the new Foris Convertible Note (see “Fair Value of Debt – Foris Convertible Note (LSA Amendment)” above).

Valuation Methodology and Approach to Measuring the Derivative Liabilities

The liabilities associated with the Company’s freestanding and embedded derivatives outstanding at June 30, 2020 and December 31, 2019 represent the fair value of freestanding equity instruments and mandatory redemption features embedded in certain debt instruments. See Note 4, "Debt", and Note 6, "Stockholders' Deficit" for further information regarding these host instruments. There is no current observable market for these types of derivatives and, as such, the Company determined the fair value of the freestanding instrument or embedded derivatives using the Black-Scholes-Merton option pricing model or a probability weighted discounted cash flow analysis measuring the fair value of the debt instrument both with and without the embedded feature, both of which are discussed in more detail below.

The Company used the Black-Scholes-Merton option pricing model to determine the fair value of its liability classified warrants as of June 30, 2020 and December 31, 2019. Input assumptions for these freestanding instruments are as follows:

	Range for the Period
Input assumptions for liability classified warrants:	June 30, 2020		December 31, 2019
Fair value of common stock on issue date	$2.56 – $4.27		$3.09 – $4.76
Exercise price of warrants	$2.87 – $3.25		$3.87 – $3.90
Expected volatility	111% – 214%		94% – 105%
Risk-free interest rate	0.09% – 0.20%		1.58% – 1.67%
Expected term in years	0.07 – 2.51		1.51 – 2.00
Dividend yield	0.0	%	0.0 %

The Company uses a probability weighted discounted cash flow model to measure the fair value of the mandatory redemption features embedded in the debt instruments modified in the first quarter of 2020. The model is designed to measure and determine if the debt instruments would be called or held at each decision point. Within the model, the following assumption is made: the underlying debt instrument will be called early if the change in control redemption value is greater than the holding value. If the underlying debt instrument is called, the holder will maximize their value by finding the optimal decision between (i) redeeming at the redemption price and (ii) holding the instrument until maturity. Using this assumption, the Company valued the embedded derivatives on a "with-and-without method", where the fair value of each underlying debt instrument including the embedded derivative is defined as the "with," and the fair value of each underlying debt instrument excluding the embedded derivatives is defined as the "without." This method estimates the fair value of the embedded derivatives by comparing the fair value differential between the with and without mandatory redemption feature. The model incorporates the mandatory redemption price, time to maturity, risk-free interest rate, estimated credit spread and estimated probability of a change in control default event.

The market-based assumptions and estimates used in valuing the embedded derivative liabilities include amounts in the following ranges/amounts:

	June 30, 2020	December 31, 2019
Risk-free interest rate	0.09% - 0.17%	1.6% - 1.7%
Risk-adjusted discount yield	25.0% - 26.0%	20.0% - 27.0%
Probability of change in control	5.0%	5.0%
Credit spread	24.7% - 36.8%	18.4% - 25.4%
Estimated conversion dates	2022 - 2023	2022 - 2023

Changes in valuation assumptions can have a significant impact on the valuation of the embedded and freestanding derivative liabilities and debt that the Company elects to account for at fair value. For example, all other things being equal, generally, an increase in the Company’s stock price, change of control probability, risk-adjusted yields term to maturity/conversion or stock price volatility increases the value of the derivative liability.

Assets and Liabilities Recorded at Carrying Value

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Financial Assets and Liabilities

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable and other current accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. Loans payable and credit facilities are recorded at carrying value, which is representative of fair value at the date of acquisition. The Company estimates the fair value of these instruments using observable market-based inputs (Level 2). The carrying amount (the total amount of net debt presented on the balance sheet) of the Company's debt at June 30, 2020 and at December 31, 2019, excluding the debt instruments recorded at fair value, was $87.7 million and $195.8 million, respectively. The fair value of such debt at June 30, 2020 and at December 31, 2019 was $77.8 million and $194.8 million, respectively, and was determined by (i) discounting expected cash flows using current market discount rates estimated for certain of the debt instruments and (ii) using third-party fair value estimates for the remaining debt instruments.

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4. Debt

Net carrying amounts of debt are as follows:

	June 30, 2020								December 31, 2019
(In thousands)	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Convertible notes payable
Senior convertible notes	$	30,020	$	—	$	6,604	$	36,624	$	66,000	$	—	$	(15,376)	$	50,624
	30,020		—		6,604		36,624		66,000		—		(15,376)		50,624
Related party convertible notes payable
Foris convertible note	50,041		—		31,510		81,551		—		—		—		—
2014 Rule 144A convertible notes	—		—		—		—		10,178		—		—		10,178
	50,041		—		31,510		81,551		10,178		—		—		10,178
Loans payable and credit facilities
Schottenfeld notes	12,500		(299)		—		12,201		20,350		(1,315)		—		19,035
Nikko notes	8,632		(830)		—		7,802		14,318		(901)		—		13,417
Ginkgo note	12,000		(2,648)		—		9,352		12,000		(3,139)		—		8,861
Other loans payable	1,034		—		—		1,034		1,828		—		—		1,828
	34,166		(3,777)		—		30,389		48,496		(5,355)		—		43,141
Related party loans payable
Foris notes	5,000		—		—		5,000		115,351		(9,516)		—		105,835
DSM notes	33,000		(3,557)		—		29,443		33,000		(4,621)		—		28,379
Naxyris note	23,559		(655)		—		22,904		24,437		(822)		—		23,615
	61,559		(4,212)		—		57,347		172,788		(14,959)		—		157,829
Total debt	$	175,786	$	(7,989)	$	38,114	205,911		$	297,462	$	(20,314)	$	(15,376)	261,772
Less: current portion							(43,482)								(63,805)
Long-term debt, net of current portion							$	162,429							$	197,967

Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (ii) an aggregate of 2,742,160 shares of common stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of common stock (the Rights Shares), (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of common stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, (v) accrued and unpaid interest on the Senior Convertible Notes (payable on or prior to January 31, 2020) and (vi) cash fees in an aggregate amount of $1.0 million (payable on or prior to January 31, 2020). The Exchange Shares and Warrants were issued on January 14, 2020. The unpaid interest and cash fees were paid in accordance with the Exchange Agreements. The Rights were exercised by the Holder and common stock shares issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020.

The New Notes have substantially similar terms as the Prior Notes, except under the New Notes (i) the requirement to redeem an aggregate principal amount of $10 million on December 31, 2019 was eliminated, (ii) the Company would be required to redeem the New Notes in an aggregate amount of $10 million following the receipt by the Company of at least $80 million of aggregate net cash proceeds from one or more financing transactions, and at a price of 107% of the amount being redeemed, (iii) the financing activity requirement was reduced such that the Company would be required to raise aggregate net cash proceeds of $50 million from one or more financing transactions by January 31, 2020, (iv) the Company would have until January 31, 2020 to comply with certain covenants related to the repayment, conversion or exchange into equity or amendment of certain outstanding indebtedness of the Company, and (v) the deadline for the Company to seek stockholder approval for the Holders to exceed a 19.99% stock exchange ownership limitation (the Stockholder Approval) would be extended from January 31, 2020 to March 15, 2020.

Due to multiple changes in key provisions of the Prior Notes, the Company analyzed the before and after cash flows between the (i) fair value of the New Notes and (ii) reacquisition price of the Prior Notes resulting from the (A) decreased principal from $66 million to $51 million, (B) fair value of the Exchange Shares, (C) fair value of the Rights, (D) fair value of

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the Warrants and (E) cash fees to be paid prior to January 31, 2020 to determine whether these changes resulted in a modification or extinguishment of the Prior Notes. Based on the before and after cash flows of each note, the change was significantly different. Consequently, the Exchange Agreements were accounted for as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt in the three months ended March 31, 2020, which was comprised of the $4.1 million fair value of the Warrants (considered a non-cash fee paid to the lender), the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and the Rights Shares over the contractual value. See Note 6, “Stockholders’ Deficit” for further information on the accounting treatment of the Exchange Shares and the Rights Shares upon issuance of the New Notes. Also, see Note 3, “Fair Value Measurement” for more information regarding the valuation methodology used to determine the fair value of the Warrants.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the New Notes. For the three months ended March 31, 2020, the Company recorded a loss of $1.1 million, which is shown as Fair Value Adjustment in the table at the beginning of this Note 4. See Note 3, "Fair Value Measurement" for information about the assumptions that the Company used to measure the fair value of the Senior Convertible Notes.

On February 18, 2020, the Company and the Holders entered into separate waiver and forbearance agreements, (the W&F Agreements), pursuant to which the Holders agreed to, for 60 days following the date of the W&F Agreement, except in case of early termination of the W&F Agreement or, solely with respect to the Stockholder Approval if the other defaults described below have been cured on or prior to the date that is 60 days following the date of the W&F Agreement, until May 31, 2020 (the W&F Period), and in each case subject to certain conditions to effectiveness contained in the W&F Agreement, (i) forbear from exercising certain of their rights and remedies with respect to certain defaults by the Company, including, but not limited to, the Company's failure, on or before January 31, 2020, (A) to receive aggregated net cash proceeds of not less than $50 million from one or more financing transactions, (B) to repay in full or convert into equity the $20.4 million of indebtedness outstanding under the Schottenfeld Credit Agreements (discussed under the Schottenfeld Forbearance Agreement below) or amend all such indebtedness outstanding to fit within the definition of permitted indebtedness of the New Notes, and certain other events of default, and (ii) waive any event of default for (A) violations of the minimum liquidity covenant since December 31, 2019 and (B) failure to obtain the Stockholder Approval prior to March 15, 2020.

In addition, pursuant to the W&F Agreements, the Company and the Holders agreed that (i) the New Note amortization payment due on March 1, 2020 would be in the aggregate amount of $10.0 million (the Amortization Payment), split proportionally among the Holders, and that the Company would elect to pay such amortization payment in shares of Common Stock in accordance with the terms of the New Notes, provided however, that: (A) the Amortization Stock Payment Price (as defined in the New Notes) would be $3.00, (B) the Amortization Share Payment Period (as defined in the New Notes) with respect to the Amortization Payment would end on April 30, 2020 rather than March 31, 2020; and (C) in the event that Holder did not elect to receive the full Amortization Share Amount (as defined in the New Notes) during such Amortization Share Payment Period, then the Amortization Payment would be automatically reduced by the portion of such Amortization Payment not received by the Holder, (ii) there would be no amortization payment due on April 1, 2020, and (iii) the amortization payment due on May 1, 2020 would be in the aggregate amount of $8.9 million split proportionally among the Holders. The W&F Agreements were accounted for as a debt modification, as the before and after cash flows were not significantly different.

Amendment to Senior Convertible Notes Due 2022

On May 1, 2020, the Company and the holders of the New Senior Convertible Notes Due 2022 entered into separate amendments to the New Notes and the W&F Agreements (Note Amendment), pursuant to which the Company and the Holders agreed: (i) to amend the maturity date of the New Notes from September 30, 2022 to June 1, 2021 (Maturity Date); (ii) to remove from the New Notes all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances other than events of default; (iii) that the Company would no longer be required to redeem the New Notes in an aggregate amount of $10 million following the receipt by the Company of at least $80 million of aggregate net cash proceeds from one or more financing transactions; (iv) that interest payments would be due quarterly (as opposed to monthly), starting on August 1, 2020; (v) that an aggregate amortization payment of approximately $16.4 million (split proportionally among the Holders) would be due on or before the earlier of May 31, 2020 and the date on which the Company receives at least $50 million of aggregate net proceeds in an offering of securities (Amended May Amortization), an amortization payment of $5 million (to the largest Holder) would be due on December 1, 2020 unless the Company receives at least $50 million of aggregate net cash proceeds from one or more financing transactions after May 1, 2020, and no other amortization payment would be due prior to the Maturity Date; (vi) to reduce the conversion price of the New Notes from $5.00 to $3.50; (vii) to reduce the redemption price with respect to optional redemptions by the Company prior to October 1, 2020 to 100%, prior to December 31, 2020 to 105% and to 110% thereafter (as opposed to 115%), of the amount being redeemed; and (viii) that an aggregate of 2,836,364 shares of Common Stock held by the Holders would not be considered as Pre-Delivery

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Shares (issued in connection with the November 15, 2019 Senior Convertible Notes Due 2022 and as defined in the New Notes) and would be subject to certain selling restrictions until June 15, 2020, and that an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders would be promptly returned to the Company. These Pre-Delivery Shares were returned to the Company on May 5, 2020 and May 6, 2020. The Company paid $16.4 million on June 1, 2020 to satisfy the required amortization payment and is no longer required to make the $5.0 million amortization payment on December 1, 2020. On June 4, 2020, the Company released an additional 700,000 Pre-Delivery Shares to the largest Holder in connection with the Second Amendment to New Notes and the W&F Agreements. The Company recorded $10.5 million of additional interest expense, representing the fair value of the 3,536,364 Pre-Delivery Shares released to the Holders.

Further, in connection with the Note Amendment, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share, from $3.25, with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s Common Stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share, from $5.02, and the exercise term of such warrant was extended to January 31, 2022, from May 10, 2021; and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s Common Stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022, from January 31, 2021. See Note 6, “Stockholders’ Deficit” for more information regarding the accounting treatment of these warrant modifications.

Debt Equitization – Foris, Related Party

As of December 31, 2019, the Company had two loans payable to Foris Ventures, LLC (Foris) with a total principal balance of $110.0 million, excluding capitalized interest of $5.3 million. Foris is an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and an owner of greater than five percent of the Company’s outstanding common stock. The first loan (Foris $19 million Note) was a $19 million unsecured borrowing that accrued interest at 12% per annum and matures on January 1, 2023. The second loan (Foris LSA) is a $91.0 million secured borrowing that accrues interest at 12.5% per annum and matured on March 1, 2023. The Foris LSA required quarterly principal payments and monthly interest payments. See Amendment No. 1 to Amended and Restated LSA — Foris, Related Party below for more information on the maturity date and payment terms of the Foris LSA.

On January 31, 2020, the Company completed a series of equity transactions with Foris that resulted in the Company (i) reducing its aggregate debt principal with Foris by $60.0 million and accrued interest and fees due to Foris by $9.9 million (including $5.4 million of capitalized interest), (ii) issuing an aggregate of 19,287,780 shares of common stock as a result of the exercise of outstanding warrants at a weighted average exercise price of approximately $2.84 per share for an aggregate of $54.8 million, (iii) issuing an aggregate of 5,279,171 shares of common stock at $2.87 per share for an aggregate of $15.1 million in a private placement, and (iv) issuing rights (the Rights) to purchase an aggregate of 8,778,230 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months. The exercise price of the outstanding warrants and the purchase price of the private placement common stock was paid through the cancellation of principal and accrued interest and fees totaling $69.9 million. See Note 6, “Stockholders’ Deficit” for information on the accounting treatment of the various equity related instruments.

As a result of the transaction described above, on January 31, 2020, the principal balance of the Foris $19 million Note and accrued but unpaid interest was fully settled through the exercise price of certain of outstanding warrants. Upon settlement of the Foris $19 million Note, the Company recorded a $5.7 million loss upon extinguishment debt, which was comprised of $6.1 million of unaccreted discount, less the $0.4 million fair value of the extinguished bifurcated derivative liability.

In addition, this series of equity transactions directly impacted the cash flows of the Foris LSA and, as a result, the Company analyzed the before and after cash flows resulting from the significant decrease in principal, the warrant exercise price modifications and the issuance rights to purchase additional shares of common stock at $2.87, to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was significantly different. Consequently, the accelerated paydown of the Foris LSA loan balance through the exercise price of the remaining outstanding warrants and the purchase price of the private placement common stock was accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $10.4 million loss upon extinguishment of debt, which was comprised of $8.9 million fair value of the Rights and $3.1 million of unaccreted discount, less the $1.6 million fair value of the extinguished bifurcated derivative liability. See Note 6, “Stockholders’ Deficit” for further information on the valuation methodology and related accounting treatment of the Rights. In recording the new debt issuance, the Company capitalized $0.7 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

Amendment No. 1 to Foris LSA — Foris, Related Party

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On June 1, 2020, the Company and Foris entered into Amendment No. 1 to the Foris LSA (LSA Amendment), pursuant to which: (i) the interest rate applicable to the then outstanding secured indebtedness (Secured Indebtedness) was amended from and after June 1, 2020 to a per annum rate of interest equal to 6.00% (previously 12.5%), (ii) the Company shall not be required to make any interest payments outstanding as of May 31, 2020 or accruing thereafter prior to July 1, 2022 (previously due monthly), (iii) the quarterly principal amortization payments were eliminated and all outstanding principal under the LSA Amendment became due on July 1, 2022, and (iv) Foris shall have the option, in its sole discretion, to convert all or portion of the Secured Indebtedness, including accrued interest, into shares of common stock at a $3.00 conversion price (Conversion Option), subject to the Company’s stockholder approval to issue shares of common stock upon exercise of the Conversion Option in accordance with applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d); provided that, if the stockholder approval is obtained before August 15, 2020, Foris would exercise its Conversion Option with respect to no less than $15 million of the Secured Indebtedness within 30 days of such stockholder approval.

The Company analyzed the before and after cash flows resulting from the LSA Amendment to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was significant. Consequently, the LSA Amendment was accounted for as a debt extinguishment and a new debt issuance. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). Management believes the fair value option best reflects the underlying economics of the LSA Amendment, which contains embedded derivatives, a conversion option requiring bifurcation and a beneficial conversion feature. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the LSA Amendment. The Company also recorded a loss of $9.5 million for the three months ended June 30, 2020 related to the change in fair value of the LSA Amendment after the June 1, 2020 issuance date, which is shown as Fair Value Adjustment in the table at the beginning of this Note 4. See Note 3, "Fair Value Measurement" for information about the assumptions that the Company used to measure the fair value of the LSA Amendment.

Schottenfeld Forbearance Agreement

The Company, Schottenfeld Group LLC (Schottenfeld) and certain of its affiliates (collectively, the Lenders) are parties (i) to certain Credit Agreements, each dated September 10, 2019 (collectively, the September Credit Agreements) and (ii) to a Credit and Security Agreement, dated November 14, 2019 (the CSA, and collectively with the September Credit Agreements, the Credit Agreements), pursuant to which the Company issued to the Lenders certain notes (the September Notes and the November Notes, respectively, and collectively, the Schottenfeld Notes) and warrants (the September Warrants and the November Warrants, respectively, and collectively, the Schottenfeld Warrants) to purchase shares (the Warrant Shares) of the Company’s common stock. See Note 6, “Stockholders’ Deficit” for further information. Indebtedness under the September Notes totals $12.5 million, accrues interest at 12% per annum and matures on January 1, 2023. Indebtedness under the November Notes total $7.9 million, accrued interest at 12% per annum and originally matured on January 15, 2020. The Company failed to repay the $7.9 million November Notes by January 15, 2020.

On February 28, 2020, the Company entered into a forbearance agreement with the Lenders (Forbearance Agreement), pursuant to which the Lenders would forbear, for 60 days from the date of the Forbearance Agreement, unless terminated earlier (the Forbearance Period), to exercise certain rights as a result of the Company’s defaults under the Credit Agreements and related Schottenfeld Notes, including the failure of the Company to (i) to pay all principal and accrued interest on the November Notes at the maturity date, (ii) the failure to pay on or before December 31, 2019, all accrued and unpaid interest through December 31, 2019 on the September Notes, and (iii) the failure, on or before December 15, 2019, to convert or exchange at least $60 million, but not less than 100%, of certain junior outstanding indebtedness into equity in the Company, and certain other events of default. Under the Forbearance Agreement, the Company agreed to (i) pay a late fee of 5% on any obligations under the November Notes not paid in full on or before the last day of the Forbearance Period; (ii) pay on or prior to the earliest to occur of April 19, 2020 or the last day of the Forbearance Period, (A) all interest due pursuant to the November Notes and the September Notes, plus all interest accruing on such unpaid interest, plus all interest accrued on account of the November Notes and the September Notes from the date of the Forbearance Agreement through the date of such payment, and (B) a forbearance fee in the amount of $150,000; (iii) pay, upon signature of the Forbearance Agreement, $150,000 as a partial payment of the interest that has accrued pursuant to the November Notes and the September Notes as of the date of the Forbearance Agreement; (iv) issue new warrants upon the occurrence of certain contingent events and (v) amend the Schottenfeld Warrants to (A) reduce the exercise price of each Schottenfeld Warrant to $2.87 per share, and (B) with respect to the November Warrants, extend the deadline to register the Warrant Shares for resale by the Holders.

Due to multiple changes in key provisions of Schottenfeld Credit Agreements, the Company analyzed the before and after cash flows resulting from the warrant modification and forbearance fee to determine whether these changes result in a

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modification or extinguishment of the original Schottenfeld and Phase Five notes. Based on the combined before and after cash flows of each note, the change was significantly different. Consequently, the modifications resulting from the Forbearance Agreement were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $5.6 million loss upon extinguishment of debt, which was comprised of the $3.2 million fair value of contingent warrant issuance obligation, the $1.3 million incremental fair value of the modified warrants, $1.1 million of unaccreted discount and the forbearance fee, less the balance of the extinguished bifurcated derivative liability. In recording the new debt issuance, the Company capitalized $0.2 million of legal fees and $0.2 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

On April 19, 2020, the Company failed to pay the amounts due under the Forbearance Agreement, including the past due interest on the September Notes, and was unable to obtain a waiver or extension for the past due amounts. As a result, $20.4 million of principal outstanding under the Schottenfeld Notes was classified as a current liability on the condensed consolidated balance sheet as of March 31, 2020. On June 5, 2020, the Company repaid the past due November 2019 Notes totaling $7.9 million. Consequently, the September 2019 Notes due January 1, 2023 totaling $12.5 million were reclassified to a non-current liability as of June 30, 2020.

2014 Rule 144A Note Exchange and Extensions – Total, Related Party

On March 11, 2020, the Company and Total Raffinage Chimie (Total) entered into a Senior Convertible Note Maturity Extension Agreement (the Extension Agreement) due to the Company’s failure to pay the $10.2 million principal amount due under the December 20, 2019 reissued 2014 Rule 144A Convertible Notes that matured on January 31, 2020. The Extension Agreement resulted in the reissuance and extension of the December 20, 2019 promissory note to March 31, 2020. Under the terms of the extension agreement, the Company paid Total $1.5 million to satisfy all accrued but unpaid interest and to reduce the principal balance of the reissued note by $1.1 million. The reissued note: (i) had a maturity date of March 31, 2020, (ii) had a $9.1 million principal amount due, (iii) accrued interest at a rate of 12.0% per annum, and (iv) had terms substantially identical to the December 20, 2019 promissory note. The Extension Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note to $2.87 per share. Effective April 30, 2020, the Company and Total entered into a subsequent Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The 2014 Rule 144A Convertible Note was reissued as a result of such extensions with terms substantially identical to the previously issued promissory notes. On June 2, 2020, Total elected to convert all the outstanding principal and interest due under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the fair value of the conversion option was derecognized into additional paid in capital. See Note 3, “Fair Value Measurement” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

Ginkgo Waiver Agreement

On March 11, 2020, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a Waiver Agreement and Amendment to Partnership Agreement (the Ginkgo Waiver), pursuant to the terms of (i) the Ginkgo promissory note dated October 20, 2017, issued by the Company to Ginkgo (as amended, the Ginkgo Note), (ii) the Ginkgo Partnership Agreement, dated October 20, 2017, by and between the Company and Ginkgo, and (iii) the Waiver Agreement and Amendment to Ginkgo Note, dated September 29, 2019, by and between the Company and Ginkgo, pursuant to which Ginkgo agreed to (a) waive the Company’s failure to pay past due interest and partnership payments, including interest thereon of $6.7 million by December 15, 2019, and to comply with a reporting covenant prior to March 31, 2020, (b) to make a prior waiver fee payment of $0.5 million on December 15, 2019, (c) waive any cross defaults due to events of default under other debt obligations by the Company, (d) amend payments on the Ginkgo Partnership Agreement beginning on March 31, 2020 to a monthly payment of $0.5 million through and including October 31, 2021, and (e) to defer all past due payments totaling $7.2 million until April 30, 2020. The Ginkgo Waiver was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On May 6, 2020, the Company entered into a waiver agreement under which the maturity date for all past due amounts to Ginkgo was extended to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The Company paid all past-due amounts to Ginkgo and on August 10, 2020 amended the Ginkgo Note to reflect a reduced interest rate and a change from monthly to quarterly interest payments and

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amended the Ginkgo Partnership Agreement to reflect changes to the frequency and amount of the periodic payments due under the agreement. See Note 12, “Subsequent Events” for further information.

Nikko Secured Loan Agreement Amendment

On March 12, 2020, the Company and Nikko Chemicals Co. Ltd. (Nikko), entered into an amendment to the secured loan agreement (Loan Agreement) under which the Company paid Nikko $0.5 million to reduce the principal balance of the Loan Agreement to $4.0 million, extended the maturity date of the loan from January 31, 2020 to March 31, 2020 and increased the interest rate to 8.0% per annum. The loan (i) matured on March 31, 2020, (ii) accrued interest at a rate of 2.75% per annum, and (iii) was secured by a first-priority lien on 27.2% of the Aprinnova JV interests owned by the Company. The Loan Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 3, 2020, the Company entered into a second amendment to the Loan Agreement under which the maturity date of the loan was extended to April 30, 2020. Subsequently, on May 7, 2020, the Company entered into a third amendment to the Loan Agreement under which the maturity date of the loan was extended to May 31, 2020. The Company fully repaid the $4.0 million loan on June 5, 2020.

Paycheck Protection Plan Loan

On April 7, 2020, the Company applied for a Paycheck Protection Plan loan (PPP Loan) established by the Coronavirus Aid, Relief, and Economic Security Act (CARES Act). On May 7, 2020, the Company received a $10 million loan pursuant to a promissory note issued by the Company. The PPP Loan accrued interest at an annual fixed rate of 1% and had a term of 2 years with no payments due in the first six months of such term; however, interest still accrued during this six-month period. Upon receipt of the PPP Loan, the Company applied the funds to payroll and building rent expenses. Following the completion of the private placement of its securities in early June 2020, the Company repaid the PPP Loan in full, including applicable interest, on June 12, 2020.

Foris $5 Million Note – Foris, Related Party

On April 29, 2020, the Company borrowed $5.0 million from Foris Ventures, LLC, an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock. The note is unsecured and accrues interest at 12% per annum. Principal and interest will be payable at maturity, on December 31, 2022.

Future Minimum Payments

Future minimum payments under the Company's debt agreements as of June 30, 2020 are as follows:

(In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020 (remaining six months)	$	814	$	10,132	$	—	$	3,084	$	14,030
2021	33,898		4,255		—		31,777		69,930
2022	—		15,058		59,578		40,558		115,194
2023	—		12,899		—		—		12,899
2024	—		398		—		—		398
Thereafter	—		1,869		—		—		1,869
Total future minimum payments	34,712		44,611		59,578		75,419		214,320
Less: amount representing interest	(4,692)		(10,445)		(9,537)		(13,860)		(38,534)
Present value of minimum debt payments	30,020		34,166		50,041		61,559		175,786
Less: current portion of debt principal	(30,020)		(6,996)		—		—		(37,016)
Noncurrent portion of debt principal	$	—	$	27,170	$	50,041	$	61,559	$	138,770

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5. Mezzanine Equity

Mezzanine equity at June 30, 2020 and December 31, 2019 is comprised of proceeds from shares of common stock sold on May 10, 2016 to the Bill & Melinda Gates Foundation (Gates Foundation). In connection with the stock sale, the Company and the Gates Foundation entered into an agreement under which the Company agreed to expend an aggregate amount not less than the proceeds from the stock sale to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria. If the Company defaults in its obligation to use the proceeds from the stock sale as set forth above or defaults under certain other commitments in the agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party, the shares then held by the Gates Foundation at a price per share equal to the greater of (i) the closing price of the Company’s common stock on the trading day prior to the redemption or purchase, as applicable, or (ii) an amount equal to $17.10 plus a compounded annual return of 10%.

As of June 30, 2020, the Company's remaining research and development obligation under this arrangement was $0.3 million.

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6. Stockholders' Deficit

Foris Warrant Exercises for Cash

On January 13, 2020, Foris Ventures, LLC (Foris), an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock, delivered to the Company an irrevocable notice of cash exercise with respect to a warrant to purchase 4,877,386 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to a warrant issued by the Company on August 17, 2018. The Company received approximately $14.0 million from Foris in connection with the warrant exercise representing 4,877,386 shares of common stock issued and recorded $14.0 million as additional paid-in capital.

On March 11, 2020, Foris provided to the Company a notice of cash exercise to purchase 5,226,481 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to the PIPE Rights (discussed in the January 2020 Private Placement section below) issued by the Company on January 31, 2020. On March 12, 2020, the Company received approximately $15.0 million from Foris in connection with the PIPE Rights exercise. The Company and Foris agreed to defer the issuance of the shares until such time as stockholder approval has been obtained to increase the Company’s authorized share count. At March 31, 2020, the PIPE Rights exercise proceeds were recorded as additional paid-in capital as there is no contractual obligation to return the consideration if stockholder approval is not obtained. Stockholder approval was obtained on May 29, 2020 and the 5,226,481 shares of common stock were issued to Foris on June 2, 2020.

January 2020 Warrant Amendments and Exercises, Foris Debt Equitization and Private Placement

As described below in further detail, on January 31, 2020, the Company completed a series of equity transactions that resulted in the Company (i) receiving $28.3 million in cash, (ii) reducing its aggregate debt principal by $60.0 million and accrued interest by approximately $9.9 million, (iii) issuing an aggregate of (A) 25,326,095 shares of common stock as a result of the exercise of outstanding warrants, and (B) 13,989,973 new shares of common stock in private placements, and (iv) issuing rights to purchase an aggregate of 18,649,961 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months. See Note 4, “Debt,” for more information regarding the accounting treatment of the $60.0 million debt reduction.

Warrant Amendments and Exercises by Certain Holders

On January 31, 2020, the Company entered into separate warrant amendment agreements (the Warrant Amendments) with certain holders (the Warrant Holders) of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of certain warrants (the Amended Warrants) held by the Warrant Holders totaling 1.2 million shares was reduced to $2.87 per share. In connection with the entry into the Warrant Amendments, on January 31, 2020, the Warrant Holders exercised their Amended Warrants, representing an aggregate of 1,160,929 shares of common stock (the Warrant Amendment Shares), and the Company issued the Warrant Amendment Shares to the Holders along with a right to purchase an aggregate of 1,160,929 shares of Common Stock, at an exercise price of $2.87 per share, for an exercise term of twelve months from the January 31, 2020 issuance (the Rights). The Company received net proceeds of $3.3 million from the exercise of the Amended Warrants and recorded the $3.3 million as additional paid in capital. The Company also measured the before and after fair value of the Amended Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Rights warrants met the derivative scope exception and equity classification criteria to be accounted for in equity.

Warrant Amendments and Exercises, Common Stock Purchase and Debt Equitization by Foris – Related Party

On January 31, 2020, the Company and Foris entered into certain warrant amendment agreements (the Foris Warrant Amendments) totaling 10.2 million shares of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of these certain warrants (the Amended Foris Warrants) was reduced to $2.87 per share. In connection with the Foris Warrant Amendments, on January 31, 2020 (i) Foris exercised all of its then outstanding common stock purchase warrants, including the Amended Foris Warrants, totaling 19,287,780 shares of common stock, at a weighted average exercise price of approximately $2.84 per share for an aggregate exercise price of $54.8 million (the Exercise Price), and purchased 5,279,171 shares of common stock (the Foris Shares) at $2.87 per share for a total purchase price of $15.1 million (Purchase Price), (ii) Foris paid the Exercise Price and the Purchase Price through the cancellation of $60 million of principal and $9.9 million of accrued interest and fees owed by the Company to Foris under the Foris $19 million Note and the Foris LSA (which was treated as a debt extinguishment as discussed in Note 4, "Debt") and (iii) the Company issued to Foris the Foris Shares and an additional right (the Additional Right) to purchase 8,778,230 shares of Common Stock at a purchase price of $2.87 per share, for a period of 12 months from the execution of the warrant exercise agreement.

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Upon exercise of the Amended Foris Warrants and issuance of the Foris Shares, the Company recorded a $69.9 million increase to additional paid-in capital. The Company also measured the before and after fair value of the Amended Foris Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Company concluded the Additional Rights met the derivative scope exception and criteria to be accounted for in equity and recorded the $8.9 million fair value of the Additional Rights to additional paid-in capital and loss upon extinguishment of debt. The fair value was determined using a Black-Scholes-Merton option pricing model based on the following input assumptions: (i) $2.56 stock price, (ii) 112% volatility, (iii) 1.45% risk free rate and (iv) 0% dividend.

January 2020 Private Placement

On January 31, 2020, the Company entered into separate Security Purchase Agreements with certain accredited investors and Foris, for the issuance and sale of an aggregate of 8,710,802 shares of common stock and rights to purchase an aggregate of 8,710,802 shares of common stock (PIPE Rights) at a purchase price of $2.87 per share, for a period of 12 months, for an aggregate purchase price of $25 million. The $25 million in proceeds was recorded as additional paid-in capital. See Note 3, “Fair Value Measurement,” for information regarding the valuation methodology used to determine fair value and the related accounting treatment of the PIPE rights.

Principal Conversion into Common Stock and New Warrants Issued in Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (ii) an aggregate of 2,742,160 shares of common stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of common stock (the Rights Shares), and (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of common stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, The New Notes, Exchange Shares, Rights and Warrants were issued on January 14, 2020. The Rights were exercised by the Holder and the Rights Shares were issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020. The contractual value of the Exchange Shares and the Rights Shares was $2.87 per share. Upon issuance of the New Notes, Exchange Shares and Rights, the $15.0 million of debt principal was extinguished and the $15.2 million fair value of the Exchange Shares and the Rights Shares was recorded as additional paid in capital. See Note 3, “Fair Value Measurement,” for more information regarding the valuation methodology used to determine the fair value and the related accounting treatment of the Warrants, and see Note 4, “Debt,” for further information on the accounting treatment and the terms of the note exchange.

Release of Pre-Delivery Shares and Amendment to Warrants Issued to Holders of Senior Convertible Notes Due 2022

Under the terms of the November 15, 2019 Senior Convertible Notes Due 2022 and the January 14, 2020 New Senior Convertible Notes, the Company was required to pre-deliver 7.5 million shares of common stock (the Pre-Delivery Shares) to the Holders, which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the Holders to sell, trade or hold, subject to certain limitations, for as long as the Senior Convertible Notes Due 2022 are outstanding. However, the Company may elect or be required to apply the value of the pre-delivered shares to satisfy periodic principal and interest payments or other repayment events. Within ten business days following redemption or repayment of in full the Senior Convertible Notes Due 2022 and the satisfaction or discharge by the Company of all outstanding Company obligations under the Senior Convertible Notes Due 2022, the Holders shall deliver 7.5 million shares of the Company’s common stock to the Company, less any shares used to satisfy any accrued interest or principal amortization payments under such notes. The Company concluded the Pre-Delivery Shares provision meets the criteria of freestanding instrument that is legally detachable and separately exercisable from the Senior Convertible Notes Due 2022 and should be classified in equity as the common shares issued are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company accounted for the fair value of the Pre-Delivery Shares within equity.

On May 1, 2020, in connection with the amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”, the Company and the Holders of the New Senior Convertible Notes Due 2022 agreed, among other provisions described in Note 4, “Debt”: (i) to remove all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances; (ii) to reduce the conversion price of the New Notes from $5.00 to $3.50; (iii) to release to the Holders an aggregate of 2,836,364 shares of common stock originally required to be returned under the Pre-Delivery Share arrangement, and (iv) return an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders to the Company. Further, on June 4, 2020, the Company agreed to release an additional 700,000 Pre-Delivery Shares to one of the Holders, in connection with the second amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”. After the release and return of the Pre-Delivery Shares on May 1, 2020 and June 4, 2020, the total number of Pre-Delivery

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Shares subject to the arrangement is 2,600,000 and must be returned to the Company following full redemption or repayment of the New Senior Convertible Notes Due 2022. As a result of releasing the 3,536,364 Pre-Delivery Shares to the Holders, the Company recorded $10.5 million of additional interest expense, representing the fair value of the released share.

Further, in connection with the May 1, 2020 amendment to the Senior Convertible Notes Due 2022, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share (from $3.25) with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s common stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share (from $5.02), and the exercise term of such warrant was extended to January 31, 2022 (from May 10, 2021); and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s common stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022 (from January 31, 2021). Each of these warrant instruments were previously accounted for in equity. As a result of the warrant amendments, the Company performed a before and after remeasurement of the warrants using the Black-Scholes-Merton option pricing model and recorded $1.1 million of incremental interest expense and a corresponding increase to additional paid in capital.

Increase in Authorized Common Stock

On May 29, 2020, through a proxy vote at the Company’s Annual Stockholder meeting, the Company’s stockholders approved an increase in the Company’s authorized common stock share count from 250 million to 350 million.

Total Conversion Price Reduction and Subsequent Conversion into Common Stock

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note from $56.16 to $2.87 per share. See Note 4, “Debt” for further information related to this debt instrument. On June 2, 2020, Total elected to convert all the outstanding principal and interest totaling $9.3 million due under the 2014 Rule 144A Convertible Note into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the conversion option was derecognized into additional paid-in capital. See Note 3, “Fair Value Measurement,” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

June 2020 PIPE

On June 1, 2020 and June 4, 2020, the Company entered into separate security purchase agreements (Purchase Agreements) with certain accredited investors (Investors), including Foris Ventures, LLC and Vivo Capital LLC, stockholders that beneficially own more than five percent of the Company’s outstanding common stock and are, respectively, owned by or affiliated with individuals serving on the Company’s Board of Directors, for the issuance and sale of an aggregate of 32,614,573 shares of the Company’s common stock, $0.0001 par value per share and 102,156 shares of the Company’s Series E Convertible Preferred Stock, $0.0001 par value per share, convertible into 34,052,070 shares of common stock, at a price of $3.00 per common share and $1,000 per preferred share, resulting in an aggregate purchase price of $200 million (Offering). The transaction closed on June 5, 2020, following the satisfaction of customary closing conditions. Upon closing, the Company received aggregate net proceeds of approximately $190 million after payment of the Offering expenses and placement agent fees. The Company used the proceeds from the Offering for the repayment of certain outstanding indebtedness and the remainder for general corporate purposes.

The Purchase Agreements included customary representations, warranties and covenants of the parties. In addition, the Company executed a letter agreement pursuant to which, subject to certain exceptions, the Company, the members of the Company’s Board of Directors, and the Company’s named executive officers agreed not to issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of Common Stock or securities convertible into or exercisable or exchangeable for common stock until September 2, 2020. The securities issued pursuant to the Purchase Agreements were sold in private placements pursuant to an exemption from registration under Section 4(a)(2) of the Securities Act of 1933, as amended (Securities Act) and Rule 506(b) of Regulation D promulgated under the Securities Act, without general solicitation, made only to and with accredited investors as defined in Regulation D.

Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws

On June 5, 2020, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series E Convertible Preferred Stock (Preferred Stock) with the Secretary of State of Delaware. Each share of Series E Preferred Stock issued in the June 2020 PIPE has a stated value of $1,000 and is convertible into 333.33 shares of common stock. All preferred shares will automatically convert into common stock without any further action by the holders on the first trading day after the

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Company obtains stockholder approval (as described below). Unless and until converted into common stock in accordance with its terms, the Preferred Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the Preferred Stock.

The Company shall obtain stockholder approval for the issuance of common stock upon conversion of the Preferred Stock as is required by the applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d), and including the issuance of common stock upon conversion of the Preferred Shares in excess of 19.99% of the issued and outstanding common stock on the date of the Purchase Agreements. Pursuant to the Purchase Agreements, the Company is required to hold a special meeting of stockholders within 75 calendar days of the date of the Purchase Agreements for the purpose of obtaining stockholder approval. This special meeting is scheduled to occur on August 14, 2020.

The Company analyzed the automatic conversion provision related to the Series E Preferred Stock and determined the holders received a contingent beneficial conversion feature (BCF) equal to $67.2 million. This amount represents the difference between the Company’s closing stock price at the June 1, 2020 and June 4, 2020 commitment dates ($5.35 and $4.88, respectively) and the $3.00 conversion price. As the automatic conversion provision is contingent on stockholder approval, the BCF will not be recognized until the contingency is resolved. Upon obtaining stockholder approval, the $67.2 million BCF will be recognized in additional paid-in capital and reflected as a deemed dividend in the consolidated statement of operations, increasing the net loss attributable to common stockholders and increasing basic net loss per share.

Warrants and Rights Activity Summary

In connection with various debt and equity transactions (see Note 4, “Debt” above and Note 4, "Debt" and Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 2019 Form 10-K), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrants activity for the six months ended June 30, 2020:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2019	Additional Warrants Issued	Exercises	Expired	Exercise Price per Share of Warrants Exercised		Number Outstanding as of June 30, 2020	Exercise Price per Share as of June 30, 2020
High Trail/Silverback warrants	2020	January 14, 2022	—	3,000,000	—	—	$	—	3,000,000	$2.87/$3.25
2020 PIPE right shares	2020	February 4, 2021	—	8,710,802	(5,226,481)	—	$	2.87	3,484,321	$	2.87
January 2020 warrant exercise right shares	2020	January 31, 2021 and January 31, 2022	—	9,939,159	—	—	$	—	9,939,159	$	2.87
Foris LSA warrants	2019	August 14, 2021	3,438,829	—	(3,438,829)	—	$	2.87	—	$	—
November 2019 Foris warrant	2019	November 27, 2021	1,000,000	—	(1,000,000)	—	$	2.87	—	$	—
August 2019 Foris warrant	2019	August 28, 2021	4,871,795	—	(4,871,795)	—	$	2.87	—	$	—
April 2019 PIPE warrants	2019	April 26, 2021, April 29, 2021 and May 3, 2021	8,084,770	—	(4,712,781)	—	$	2.87	3,371,989	$4.76/$5.02
April 2019 Foris warrant	2019	April 16, 2021	5,424,804	—	(5,424,804)	—	$	2.87	—	$	—
September and November 2019 Investor Credit Agreement warrants	2019	September 10, 2021 and November 14, 2021	5,233,551	—	—	—	$	—	5,233,551	$	2.87
Naxyris LSA warrants	2019	August 14, 2021	2,000,000	—	—	—	$	—	2,000,000	$	2.87
October 2019 Naxyris warrant	2019	October 28, 2021	2,000,000	—	—	—	$	—	2,000,000	$	3.87
May-June 2019 6% Note Exchange warrants	2019	May 15, 2021 and June 24, 2021	2,181,818	—	—	—	$	—	2,181,818	$2.87/$5.12
May 2019 6.50% Note Exchange warrants	2019	May 14, 2021 and January 31, 2022	1,744,241	—	(784,016)	—	$	2.87	960,225	$	2.87
July 2019 Wolverine warrant	2019	July 8, 2021	1,080,000	—	—	—	$	—	1,080,000	$	2.87
August 2018 warrant exercise agreements	2018	May 17, 2020 and May 20, 2020	12,097,164	—	(4,877,386)	(7,219,778)	$	2.87	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,078,156	—	—	—	$	—	6,078,156	$	2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	—	3,968,116	$	2.87
May 2017 dilution warrants	2017	July 10, 2022	3,085,893	—	—	—	$	—	3,085,893	$	—
August 2017 dilution warrants	2017	May 23, 2023	3,028,983	—	—	—	$	—	3,028,983	$	—
February 2016 related party private placement	2016	February 12, 2021	171,429	—	(152,381)	—	$	0.15	19,048	$	0.15
July 2015 related party debt exchange	2015	July 29, 2020 and July 29, 2025	133,334	—	(133,334)	—	$	0.15	—	$	—
July 2015 private placement	2015	July 29, 2020	72,650	—	(72,650)	—	$	0.15	—	$	—
July 2015 related party debt exchange	2015	July 29, 2020	58,690	—	—	—	$	—	58,690	$	0.15
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$	160.05
			65,755,629	21,649,961	(30,694,457)	(7,219,778)			49,491,355

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7. Loss per Share

For the three and six months ended June 30, 2020 and June 30, 2019, basic loss per share was the same as diluted loss per share, because the inclusion of all potentially dilutive securities outstanding was antidilutive.

The Company follows the two-class method when computing net loss per common share when shares are issued that meet the definition of participating securities. The two-class method requires income available to common stockholders for the period to be allocated between common stock and participating securities based upon their respective rights to receive dividends as if all income for the period had been distributed. The two-class method also requires losses for the period to be allocated between common stock and participating securities based on their respective rights if the participating security contractually participates in losses. The Company’s convertible preferred stock are participating securities as they contractually entitle the holders of such shares to participate in dividends and contractually require the holders of such shares to participate in the Company’s losses.

The following table presents the calculation of basic and diluted loss per share:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Numerator:
Net loss attributable to Amyris, Inc.	$	(110,422)	$	(38,088)	$	(198,266)	$	(104,331)
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D	—		(34,964)		—		(34,964)
Add: losses allocated to participating securities	6,361		2,255		7,435		4,690
Net loss attributable to Amyris, Inc. common stockholders	$	(104,061)	$	(70,797)	$	(190,831)	$	(134,605)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	184,827,330		92,785,752		169,946,482		84,831,269
Loss per share attributable to common stockholders, basic and diluted	$	(0.56)	$	(0.76)	$	(1.12)	$	(1.59)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted loss per share of common stock because including them would have been antidilutive:

	Three Months Ended June 30,		Six Months Ended June 30,
	2020	2019	2020	2019
Period-end common stock warrants	43,298,741	5,535,538	43,298,741	5,535,538
Convertible promissory notes(1)	8,574,399	11,007,316	8,574,399	11,007,316
Period-end stock options to purchase common stock	5,479,334	49,747,628	5,479,334	49,747,628
Period-end restricted stock units	4,468,266	5,284,742	4,468,266	5,284,742
Period-end preferred stock(2)	1,943,661	2,955,732	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted loss per share	63,764,401	74,530,956	63,764,401	74,530,956

______________

⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

⁽²⁾ The 102,156 shares of Series E Preferred Stock, which is convertible into 34,052,070 common shares, is not included in this share count. The automatic conversion of the Series E Preferred Stock is contingent upon stockholder approval, and is therefore, not considered a potentially dilutive security until the contingency is resolved.

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8. Commitments and Contingencies

Contingencies

The Company has levied indirect taxes on sugarcane-based biodiesel sales that took place several years ago by Amyris Brasil Ltda. (see Note 12, “Divestiture” in Part II, Item 8 of the 2019 Form 10-K) to customers in Brazil, based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate the Company levied.

On April 3, 2019, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and former CFO (and current Chief Business Officer), Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all persons and entities that purchased or otherwise acquired our securities between March 15, 2018 and March 19, 2019. The complaint, which was amended by the lead plaintiff on September 13, 2019, alleges securities law violations based on statements and omissions made by the Company during such period. On October 25, 2019, the defendants filed a motion to dismiss the securities class action complaint. The hearing on such motion to dismiss was held on February 18, 2020 and we are awaiting a ruling from the Court. Subsequent to the filing of the securities class action complaint described above, on June 21, 2019 and October 1, 2019, respectively, two separate purported shareholder derivative complaints were filed in the U.S. District Court for the Northern District of California (Bonner v. Doerr, et al., and Carlson v. Doerr, et al.) based on similar allegations to those made in the securities class action complaint described above and named the Company and certain of the Company’s current and former officers and directors as defendants. The derivative lawsuits sought to recover, on the Company’s behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and omissions made in connection with the Company’s securities filings. The derivative lawsuits were dismissed on October 18, 2019 (Bonner) and December 10, 2019 (Carlson), without prejudice. We believe the securities class action complaint lacks merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

On July 24, 2020, a securities class action complaint was filed against Amyris and the members of our Board in the Court of Chancery of the State of Delaware (Flatischler v. Melo, et. al.). The complaint alleged a breach of fiduciary obligation to disclose material information to stockholders in the proxy statement filed with the Securities and Exchange Commission on July 6, 2020 (Proxy), with respect to the Company’s special stockholders’ meeting to be held on August 14, 2020 (Special Meeting), at which stockholders will vote to approve the conversion of all outstanding indebtedness under the Foris Convertible Note and of our Series E Preferred Stock issued in the June 2020 PIPE into shares of common stock, in accordance with Nasdaq Listing Standard Rule 5635(d). See Note 4, “Debt,” “Amendment No. 1 to Foris LSA — Foris, Related Party,” and Note 6, “Stockholders’ Deficit,” “June 2020 PIPE,” and “Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws” in Part I, Item 1 of this Quarterly Report on Form 10-Q for more information. The plaintiffs sought to enjoin the Special Meeting. On August 6, 2020, the plaintiffs withdrew their complaint as moot following the Company’s filing of a supplement to the Proxy on August 5, 2020. The Proxy supplement provided additional information regarding the approval process of the LSA Amendment and the June 2020 PIPE, and the relationships between the Company and its financial advisors to the June 2020 PIPE. The plaintiffs currently seek attorney’s fees and reimbursement of certain legal expenses related to filing the complaint. Three substantially similar complaints were filed: one on July 28, 2020, in the United States District Court of Delaware (Sabatini v. Amyris, Inc.); one on July 31, 2020, in the Northern District of California (Nair v. Amyris); and another on August 4, 2020, in the Southern District of New York (Chamorro v. Amyris). We believe that these complaints lack merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes that are not predictable with reasonable assurance, and therefore, an estimate of all the reasonably possible losses cannot be determined at this time. If one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management's expectations, the Company's consolidated financial statements for the relevant reporting period could be materially adversely affected.

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Other Matters

Certain conditions may exist as of the date the condensed consolidated financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgement. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be reasonably estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

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9. Revenue Recognition and Contract Assets and Liabilities

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

	Three Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	16,866	$	—	$	—	$	16,866	$	5,806	$	—	$	6,408	$	12,214
Europe	3,106		990		1,798		5,894		2,102		40,964		3,197		46,263
Asia	4,341		—		2,029		6,370		3,899		—		—		3,899
Brazil	670		—		—		670		295		—		5		300
Other	205		—		—		205		18		—		—		18
	$	25,188	$	990	$	3,827	$	30,005	$	12,120	$	40,964	$	9,610	$	62,694
	Six Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	28,809	$	—	$	—	$	28,809	$	12,879	$	—	$	6,901	$	19,780
Europe	6,349		6,151		5,154		17,654		4,956		41,082		4,826		50,864
Asia	6,359		—		4,788		11,147		5,617		—		250		5,867
Brazil	1,247		—		—		1,247		515		—		5		520
Other	278		—		—		278		37		—		—		37
	$	43,042	$	6,151	$	9,942	$	59,135	$	24,004	$	41,082	$	11,982	$	77,068

Significant Revenue Agreements During the Six Months Ended June 30, 2020

Cannabinoid Agreement

On May 2, 2019, the Company consummated a research, collaboration and license agreement (the Cannabinoid Agreement) with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids, subject to certain closing conditions. The Company is performing research and development activities, and Lavvan is responsible for manufacturing and commercialization, related to the cannabinoids developed in accordance with the Cannabinoid Agreement. The Cannabinoid Agreement principally funds milestones that include both technical R&D targets and completion of production campaigns, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. Additionally, the Cannabinoid Agreement provides for profit share to the Company on Lavvan's gross profit margin once the cannabinoid products are commercialized; such payments will be due for the following 20 years. The Company could receive aggregate funding of up to $300 million over the term of the Cannabinoid Agreement if all of the milestones are achieved. On May 2, 2019, the parties formed a special purpose entity to hold certain intellectual property created during the collaboration (the Cannabinoid Collaboration IP), the licensing of certain Company intellectual property to Lavvan, the licensing of the Cannabinoid Collaboration IP to the Company and Lavvan, and the granting by the Company to Lavvan of a lien on the Company background intellectual property being licensed to Lavvan under the Cannabinoid Agreement, which lien would be subordinated to the lien on such intellectual property under the Foris Convertible Note (see Note 4, “Debt”). On March 11, 2020, the parties revised the agreement to reflect product specifications and cost assumptions.

The Cannabinoid Agreement is accounted for as a revenue contract under ASC 606, with the total transaction price estimated and updated on a quarterly basis, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligation. The Company concluded the agreement contained a single performance obligation of research and development services provided continuously over time. The Company estimated the total unconstrained transaction price to be $145 million, based on a high probability of achieving certain underlying milestones. As of June 30, 2020, the Company has constrained $155 million of variable consideration related to milestones that have not met the criteria necessary under ASC 606 to be included in the

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transaction price. The Company concluded the performance obligation is delivered over time and that revenue recognition is based on an input measure of progress of hours incurred compared to total estimated hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, with cumulative adjustments to revenue recorded as necessary. The Company recognized no collaboration revenue for the three and six months ended June 30, 2020, and $18.3 million of cumulative revenue to date. At June 30, 2020 has recorded an $8.3 million contract asset in connection with the Cannabinoid Agreement.

DSM Ingredients Collaboration

In September 2017, the Company entered into a collaboration agreement with DSM (DSM Collaboration Agreement) to jointly develop a new molecule in the Clean Health market using the Company’s technology (DSM Ingredient), which the Company would have the sole right to manufacture, and DSM would commercialize. Pursuant to the DSM Collaboration Agreement, DSM provides funding for the development of the DSM Ingredients in the form of milestone-based payments and, upon commercialization, the parties would enter into supply agreements whereby DSM would purchase the applicable DSM Ingredient from the Company at prices agreed by the parties. The development services are directed by a joint steering committee with equal representation by DSM and the Company and are governed by a milestone project plan. The timing of milestone achievements is subject to review and revision as agreed by the joint steering committee. In addition, the parties will share profit margin from DSM’s sales of products that incorporate the DSM Ingredient subject to the DSM Collaboration Agreement.

The DSM Collaboration Agreement is accounted for as a revenue contract under ASC 606, and has a total transaction price of $14.1 million, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligations. The Company concluded the agreement contained three performance obligations of research and development services that are delivered over time and that revenue recognition is based on an input measure of progress as labor hours are expended in the achievement of each milestone. The Company recognized $1.3 million and $4.3 million of collaboration revenue for the three and six months, respectively, ended June 30, 2020, and $9.1 million of cumulative-to-date collaboration revenues.

Yifan Collaborations

From September 2018 to December 2019, the Company entered into a series of license and collaboration agreements, culminating in a master services agreement for research and development services, with a subsidiary of Yifan Pharmaceutical Co., Ltd. (Yifan), a leading Chinese pharmaceutical company. Upon execution of the master services agreement in December 2019 (the Collaboration Agreement), the Company evaluated and concluded that the series of agreements should be combined and accounted for as a single revenue contract under ASC 606.

The Yifan Collaboration Agreement has a total transaction price of $21.0 million, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligation. The Company concluded the Collaboration Agreement contained a single performance obligation of research and development services provided continuously over time. The Collaboration Agreement provides for upfront and periodic payments based on project milestones. The Company concluded the performance obligation is delivered over time and that revenue recognition is based on an input measure of progress of hours incurred compared to total estimated hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, with cumulative adjustments to revenue recorded as necessary. The Company recognized $2.0 million and $4.7 million of collaboration revenue in the three and six months, respectively, ended June 30, 2020, and $10.8 million of cumulative-to-date collaboration revenue. At June 30, 2020, the Company also recorded a $2.9 million contract asset in connection with the Collaboration Agreement.

DSM Value Sharing Agreement

The original December 2017 DSM Value Sharing Agreement was accounted for as a single performance obligation in connection with a license with fixed and determinable consideration and variable consideration that was accounted for pursuant to the sales-based royalty scope exception. The April 16, 2019 assignment of the December 2017 DSM Value Sharing Agreement was accounted for as a contract modification under ASC 606, resulting in additional fixed and determinable consideration of $37.1 million and variable consideration of $12.5 million in the form of a stand-ready obligation to refund some or all of the $12.5 million consideration if certain criteria outlined in the assignment agreement are not met by December 2021. The Company periodically updates its estimate of amounts to be refunded and reduces the refund liability by recording additional license and royalty revenue as the Company’s estimate of the refund obligation decreases. The Company recorded $8.8 million of license and royalty revenue in the fourth quarter of 2019 related to a change in the estimated refund liability and

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recorded the remaining $3.8 million in the three months ended March 31, 2020 related to a change in the Company’s estimate of the refund liability.

In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K), the Company recognized the following revenues for the three and six months ended June 30, 2020 and 2019:

	Three Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	16	$	—	$	1,251	$	1,267	$	—	$	40,682	$	2,646	$	43,328
Sephora	2,442		—		—		2,442		2,397		—		—		2,397
Firmenich	933		990		339		2,262		—		282		277		559
Givaudan	1,161		—		—		1,161		1,240		—		—		1,240
Subtotal revenue from significant revenue agreements	4,552		990		1,590		7,132		3,637		40,964		2,923		47,524
Revenue from all other customers	20,636		—		2,237		22,873		8,483		—		6,687		15,170
Total revenue from all customers	$	25,188	$	990	$	3,827	$	30,005	$	12,120	$	40,964	$	9,610	$	62,694
	Six Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	65	$	3,750	$	4,269	$	8,084	$	2	$	40,302	$	3,042	$	43,346
Sephora	6,888		—		—		6,888		3,744		—		—		3,744
Firmenich	2,162		2,401		500		5,063		1,891		780		1,005		3,676
Givaudan	3,269		—		—		3,269		2,815		—		—		2,815
Subtotal revenue from significant revenue agreements	12,384		6,151		4,769		23,304		8,452		41,082		4,047		53,581
Revenue from all other customers	30,658		—		5,173		35,831		15,552		—		7,935		23,487
Total revenue from all customers	$	43,042	$	6,151	$	9,942	$	59,135	$	24,004	$	41,082	$	11,982	$	77,068

Contract Assets and Liabilities

When a contract results in revenue being recognized in excess of the amount the Company has invoiced or has the right to invoice to the customer, a contract asset is recognized. Contract assets are transferred to accounts receivable, net when the rights to the consideration become unconditional.

Contract liabilities consist of payments received from customers, or such consideration that is contractually due, in advance of providing the product or performing services such that control has not passed to the customer.

Trade receivables related to revenue from contracts with customers are included in accounts receivable on the condensed consolidated balance sheets, net of the allowance for doubtful accounts. Trade receivables are recorded for the sale of goods or the performance of services at the point of renewable product sale or in accordance with the contractual payment terms for licenses and royalties, and grants and collaborative research and development services for the amount payable by the customer to the Company.

Contract Balances

The following table provides information about accounts receivable, contract liabilities and refund liability from contracts with customers:

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(In thousands)	June 30, 2020		December 31, 2019
Accounts receivable, net	$	22,029	$	16,322
Accounts receivable - related party, net	$	94	$	3,868
Contract assets	$	11,724	$	8,485
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Contract liabilities	$	5,180	$	1,353
Contract liabilities, noncurrent(1)	$	245	$	1,449

⁽¹⁾As of June 30, 2020 and December 31, 2019, contract liabilities, noncurrent is presented in Other noncurrent liabilities in the condensed consolidated balance sheets.

Remaining Performance Obligations

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of June 30, 2020.

(In thousands)	As of June 30, 2020
Remaining 2020	$	4,849
2021	112,357
2022	20,750
2023 and thereafter	571
Total from all customers	$	138,527

In accordance with the disclosure provisions of ASC 606, the table above excludes estimated future revenues for performance obligations that are part of a contract that has an original expected duration of one year or less or a performance obligation with variable consideration that is recognized using the sales-based royalty exception for licenses of intellectual property. Additionally, approximately $175.4 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

10. Related Party Transactions

Related Party Debt

See Note 4, "Debt," for details of these related party debt transactions during the six months ended June 30, 2020:

•Debt equitization – Foris

•$5 million unsecured loan - Foris

•2014 Rule 144A Note exchange, extensions and conversion – Total

•LSA Amendment - Foris

Related party debt was as follows:

	June 30, 2020								December 31, 2019
In thousands	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Foris notes	$	55,041	$	—	$	31,510	$	86,551	$	115,351	$	(9,516)	$	—	$	105,835
DSM notes	33,000		(3,557)		—		29,443		33,000		(4,621)		—		28,379
Naxyris note	23,559		(655)		—		22,904		24,437		(822)		—		23,615
Total 2014 Rule 144A convertible note	—		—		—		—		10,178		—		—		10,178
	$	111,600	$	(4,212)	$	31,510	$	138,898	$	182,966	$	(14,959)	$	—	$	168,007

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Related Party Equity

See Note 6, "Stockholders' Deficit," for details of these related party equity transactions during the six months ended June 30, 2020:

•Foris warrant exercises for cash

•Foris warrant exercise, common stock purchase and debt equitization

•January 2020 private placement, in which Foris purchased 5,226,481 shares of common stock

•June 2020 private placement, in which Foris and affiliated entities purchased 30,000 shares of Series E preferred stock

•June 2020 private placement, in which Vivo Capital LLC and affiliated entities purchased 3,689,225 shares of common stock and 8,932.32 shares of Series E preferred stock

Related Party Accounts Receivable, Unbilled Receivables and Accounts Payable

Related party accounts receivable, unbilled receivables and accounts payable were as follows:

(In thousands)	June 30, 2020		December 31, 2019
Accounts receivable - related party	$	94	$	3,868
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Accounts payable	$	5,677	$	13,957

11. Stock-based Compensation

The Company’s stock option activity and related information for the six months ended June 30, 2020 was as follows:

	Quantity of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years	Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Granted	80,507	$	2.85
Exercised	(5,227)	$	2.99
Forfeited or expired	(216,365)	$	43.33
Outstanding - June 30, 2020	5,479,334	$	8.86	7.5	$	542
Vested or expected to vest after June 30, 2020	4,904,654	$	9.31	7.5	$	518
Exercisable at June 30, 2020	1,445,710	$	19.65	6.2	$	278

The Company’s restricted stock units (RSUs) activity and related information for the six months ended June 30, 2020 was as follows:

	Quantity of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Awarded	410,899	$	2.89
Released	(1,249,075)	$	4.83
Forfeited	(476,209)	$	4.39
Outstanding - June 30, 2020	4,468,266	$	4.61	1.4
Vested or expected to vest after June 30, 2020	4,089,810	$	4.63	1.3

Stock-based compensation expense related to employee and non-employee options, RSUs and ESPP during the three and six months ended June 30, 2020 and 2019 was allocated to research and development expense and sales, general and administrative expense as follows:

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	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Research and development	$	781	$	676	$	1,846	$	1,339
Sales, general and administrative	2,150		2,699		4,589		5,488
Total stock-based compensation expense	$	2,931	$	3,375	$	6,435	$	6,827

As of June 30, 2020, there was unrecognized compensation expense of $20.1 million related to stock options and RSUs. The Company expects to recognize this expense over a weighted-average period of 2.1 years.

Evergreen Shares for 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan

In February 2020, the Board approved increases to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (the Equity Plan) and 2010 Employee Stock Purchase Plan (the Purchase Plan). These shares in connection with the Equity Plan represented an automatic annual increase in the number of shares available for grant and issuance under the Equity Plan of 5,887,133 shares (Evergreen Shares). This increase is equal to approximately 5.0% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020. These shares in connection with the Purchase Plan represented an automatic annual increase in the number of shares reserved for issuance under the Purchase Plan of 588,713 shares. This increase is equal to approximately 0.5% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020.

In May 2020, the Company’s stockholders approved the Company’s 2020 Equity Incentive Plan (the New Plan) to replace the Equity Plan that expired in June 2020. The shares available for grant and issuance under the New Plan represent 9,896,751 shares of common stock previously reserved but unissued under the Equity Plan, including the Evergreen Shares. No additional stock awards will be granted under the Equity Plan, and, (a) shares that are subject to stock options or other awards granted under the Equity Plan that cease to be subject to such stock options or other awards by forfeiture or otherwise, (b) shares issued under the Equity Plan pursuant to the exercise of stock options that are forfeited, (c) shares issued under the Equity Plan that are repurchased by the Company at the original issue price and (d) shares that are subject to stock options or other awards under the Equity Plan that are used to pay the exercise price of an option or withheld to satisfy the tax withholding obligations related to any award will be available for future grant and issuance under the New Plan.

12. Subsequent Events

Second Amendment to Ginkgo Note and Partnership Agreement

On August 10, 2020, the Company and Ginkgo entered into a Second Amendment to Promissory Note and Partnership Agreement (Second Amendment) to, among other things, (i) with respect to the Promissory Note, amend the interest payment frequency from monthly to quarterly beginning September 30, 2020 and reduce the interest rate from 12% to 9% beginning January 1, 2021, conditioned to the timely payment of interest on September 30 and December 31, 2020; and (ii) with respect to the Partnership Agreement, reduce the partnership payments frequency from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022 (the “End of Term Payment”), provided that, if the Promissory Note is not fully repaid by April 19, 2022, the End of Term Payment shall be of $10.4 million. See Note 4, “Debt” for further information regarding the Ginkgo Promissory Note and Partnership Agreement.

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ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion and analysis should be read in conjunction with our condensed consolidated financial statements and the related notes that appear elsewhere in this Quarterly Report on Form 10-Q. These discussions contain forward-looking statements reflecting our current expectations that involve risks and uncertainties which are subject to safe harbors under the Securities Act of 1933, as amended (the Securities Act), and the Securities Exchange Act of 1934 (the Exchange Act). These forward-looking statements include, but are not limited to, statements concerning our strategy of achieving a significant reduction in net cash outflows in 2020 and 2021, aspects of our future operations, our future financial position, including obtaining project financing for a new manufacturing facility, expectations for our future revenues, margins and projected costs, expectations regarding demand and acceptance for our technologies and products, introductions of new products, growth opportunities and trends in the market in which we operate, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward-looking statements. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part II, Item 1A, “Risk Factors” in this Quarterly Report on Form 10-Q, in Part I, Item 1A, “Risk Factors” in our Annual Report on Form 10-K for the fiscal year ended December 31, 2019 (the 2019 Form 10-K) and in our other filings with the Securities and Exchange Commission. We do not assume any obligation to update any forward-looking statements.

Overview

As a leading synthetic biotechnology company, we apply our technology platform to engineer, manufacture and sell high performance, natural, sustainably sourced products into the Clean Health & Beauty, and Flavor & Fragrance markets. Our proven technology platform enables us to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. Our platform, combined with our proprietary fermentation process, replaces existing complex and oftentimes expensive manufacturing processes. We have successfully used our technology to develop and produce nine distinct molecules at commercial volumes, leading to more than 17 commercial ingredients used by thousands of leading global brands.

We believe that synthetic biology represents a third industrial revolution, bringing together biology and engineering to generate new, more sustainable materials to meet the growing global demand for bio-based replacements for petroleum-based and traditional animal- or plant-derived ingredients. We continue to build demand for our current portfolio of products through an extensive sales network provided by our collaboration partners that represent leading companies for our target market sectors. We also have a small group of direct sales and distributors who support our Clean Beauty market and proprietary sweetener product, Purecane^TM. Via our partnership model, our partners invest in the development of each molecule to bring it from the lab to commercial-scale and use their extensive sales force to sell our ingredients and formulations to their customers as part of their core business. We capture long-term revenue both through the production and sale of the molecule to our partners and through royalty revenues from our partners' product sales to their customers.

We were founded in 2003 in the San Francisco Bay area by a group of scientists from the University of California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda Gates Foundation, we developed technology capable of creating microbial strains that produce artemisinic acid, a precursor of artemisinin, an effective anti-malarial drug. Building on our success with artemisinic acid, in 2007 we began applying our technology platform to develop, manufacture and sell sustainable alternatives to a broad range of markets. We focused our initial development efforts primarily on the production of Biofene®, our brand of renewable farnesene, a long-chain, branched hydrocarbon molecule that we manufacture through fermentation using engineered microbes. The commercialization of farnesene pushed us to create a more cost efficient, faster and accurate development process in the lab and to drive manufacturing costs down. This investment has enabled our technology platform to rapidly develop microbial strains and commercialize target molecules. In 2014, we began manufacturing additional molecules for the Flavor & Fragrance industry; in 2015 we began investing to expand our capabilities to other small molecule chemical classes beyond terpenes via our collaboration with the Defense Advanced Research Projects Agency (DARPA); and in 2016 we expanded into proteins.

Several years ago, we made the strategic decision to transition our business model from collaborating and commercializing molecules in low margin commodity markets to higher margin specialty markets. We began the transition by first commercializing and supplying farnesene-derived squalane as a cosmetic ingredient sold to formulators and distributors. We also entered into collaboration and supply agreements for the development and commercialization of molecules within the

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Flavor & Fragrance and Clean Beauty markets where we utilize our strain generation technology to develop molecules that meet the customer’s rigorous specifications. During this transition, we solidified the business model of partnering with our customers to create sustainable, high performing, low-cost molecules that replace an ingredient in their supply chain, commercially scale and manufacture those molecules, and share in the profits earned by our customers once our customer sells its product into these specialty markets. These three steps constitute our grants and collaborations revenues, renewable product revenues, and royalty revenues.

During 2017, we completed several development agreements with DSM and others for new products such as Vitamin A, a human nutrition molecule and others, and in late 2018 we began commercial production and shipment of an alternative sweetener product developed from the Reb M molecule, Purecane^TM, which is a superior sweetener and sugar replacement. We monetized the use of one of our lower margin molecules, farnesene, in the Vitamin E and Lubricants specialty markets while retaining any associated royalties, and licensed farnesene to DSM for use in the Vitamin E field. We also sold our subsidiary Amyris Brasil Ltda. (Amyris Brasil), which operated our purpose-built, large-scale manufacturing facility located in Brotas, Brazil, to DSM in December 2017. The Brotas facility was built to batch manufacture one commodity product at a time (originally for high-volume production of biofuels, a business Amyris had exited), which is an inefficient manufacturing process that is not suited for the high-margin specialty markets in which we operate today. The inefficiencies we experienced included having to idle the facility for two weeks at a time to prepare for the next product batch manufacture, causing significantly higher costs of products sold. As a result, we are building a new large-scale plant focused solely on specialty ingredients in Brazil, which we anticipate will allow for the manufacture of five products concurrently, including our alternative sweetener product, and over 10 different products annually. In September 2019, we obtained the necessary permits and broke ground on our new specialty ingredients plant and expect the facility to become fully operational by the end of 2021. During construction, we are manufacturing our products at four contract manufacturing sites in Brazil, the U.S. and Spain. Finally, as part of the December 2017 sale of Brotas, we contracted with DSM for the use of Brotas to manufacture products for us to fulfill our product supply commitments to our customers until the new production facility is built and becomes operational; in November 2018, we amended the supply agreement with DSM to secure capacity at the Brotas facility for production of our alternative sweetener product through 2022.

In May 2019, we entered into an agreement with Raizen Energia S.A. (Raizen) for the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products whereby the parties would construct a manufacturing facility exclusively for sweetener molecules on land owned by Raizen and leased to the joint venture.

Also, in May 2019, we consummated a research, collaboration and license agreement with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids. Under the Cannabinoid Agreement, we perform research and development activities and Lavvan is responsible for the commercialization of the cannabinoids developed. The Cannabinoid Agreement is being principally funded on a milestone basis, with Amyris also entitled to receive certain supplementary research and development funding from Lavvan. We could receive aggregate funding of up to $300 million over the term of the Cannabinoid Agreement if all of the milestones are achieved. Additionally, the Cannabinoid Agreement provides for profit share to Amyris on Lavvan's gross profit margin once products are commercialized; these payments will be due for the 20 years following such commercialization.

On April 24, 2020, the Food and Drug Administration (FDA) granted us full Over-the-Counter approval for product listing in the U.S. of our alcohol-based hand sanitizer. Sold through our Pipette^TM brand, this hand sanitizer addresses critical public and institutional health needs during the current COVID-19 pandemic. We also became authorized to sell this hand sanitizer in Portugal and are currently pursuing additional authorizations in other European markets. The Company’s Reb M sweetener, Purecane^TM, achieved national approvals by the Columbian INVIMA Food Safety, Brazilian ANVISA and Health Canada Authorities on January 29, April 15, and April 17, 2020. Additionally, the product was authorized in Costa Rica on July 20, 2020. Each of these approvals allows for immediate distribution of Amyris’s sweetener product in these markets. On April 28, 2020, Amyris’s Aprinnova joint venture received new chemical approval for its hemisqualane ingredient by China's Ministry of Environment; this approval authorizes unlimited quantity importation to supply China's cosmetic manufacturing industry. Finally, on May 5, 2020, our infant nutritional ingredient (known as HMO (2'-FL)), received validation by a medical Panel of Experts as Generally Recognized As Safe (“GRAS”), and we have submitted a petition for FDA GRAS approval of this ingredient.

We have invested over $700 million in infrastructure and technology to create microbes that produce molecules from sugar or other feedstocks at commercial scale. We have focused on accessing Brazilian sugarcane for our large-scale production because of its renewability, low cost and relative price stability. Our time to market for molecules has decreased from seven years to less than a year for our most recent molecules, mainly due to our ability to leverage the technology platform we have built. The key performance characteristics of our platform that we believe differentiate us include our proprietary computational tools, strain construction tools, screening and analytics tools, and advanced lab automation and data integration. Our state-of-

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the-art infrastructure includes industry-leading strain engineering and lab automation located in Emeryville, California, pilot-scale production facilities in Emeryville, California and Campinas, Brazil, a demonstration-scale facility in Campinas, Brazil and a commercial-scale production facility in Leland, North Carolina, which is owned and operated by our Aprinnova joint venture to convert our Biofene into squalane and other products.

Sales and Revenue

We recognize revenue from product sales, license fees and royalties, and grants and collaborations.

We have research and development collaboration arrangements for which we receive payments from our collaboration partners, which include DARPA, DSM, Firmenich SA (Firmenich), Givaudan International SA (Givaudan), Lavvan and others. Some of our collaboration arrangements provide for advance payments to us in consideration for grants of exclusivity or research efforts that we will perform. In 2017, we signed collaboration agreements for an infant nutrition ingredient, and through 2018 and 2019 we signed a collaboration agreement for four vitamins that we expect will contribute to our collaboration revenue and ultimately product sales. We also signed a collaboration agreement for up to $300 million to develop cannabinoids in 2019. Our collaboration agreements, which may require us to achieve milestones prior to receiving payments, are expected to contribute revenues from product sales and royalties if and when they are commercialized. See Note 9, “Revenue Recognition” in Part II, Item 8 of our 2019 Form 10-K for additional information.

All of our non-government partnerships include commercial terms for the supply of molecules we successfully upscale and produce at commercial volumes. The first molecule to generate revenue for us outside of farnesene was a fragrance molecule launched in 2015. Since the launch, the product has continued to grow in sales year over year. In 2016, we launched our second fragrance molecule and in 2017, we launched our third fragrance molecule as well as our first cosmetic active ingredient. Our partners for these molecules are indicating continued strong growth due to their cost advantaged position, high purity and sustainable production method. We are continuing to identify new opportunities to apply our technology and deliver sustainable access to key molecules. As a result, we have a pipeline that we believe can deliver two to three new molecules each year over the coming years with a flavor ingredient, a cosmetic active ingredient and a fragrance molecule. In 2019, we commercially produced and shipped our Reb M product that is a sweetener and sugar replacement for food and beverages.

Concurrent with the 2017 sale of Amyris Brasil and the Brotas facility, we entered into a series of commercial agreements with DSM that included (i) a license agreement to DSM of our farnesene product for DSM to use in the Vitamin E and lubricant specialty markets and (ii) a royalty agreement, pursuant to which DSM agreed to pay us specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene sold under a supply agreement with Nenter & Co., Inc. (Nenter) which was assigned to DSM. Under the terms of the royalty agreement, DSM was obligated to pay us minimum royalties totaling $18.1 million for 2019 and 2020. In June 2018, we received the 2019 non-refundable minimum royalty payment totaling $9.3 million (net of a $0.7 million early payment discount) and in March 2019, we received the 2020 non-refundable payment totaling $7.4 million (net of a $0.7 million early payment discount). In April 2019, we assigned the right to receive such royalty payments under the Vitamin E royalty agreement to DSM for total consideration of $57 million, of which approximately $40.3 million was recognized as royalty revenue in 2019 and $3.8 million was recognized as royalty revenue in 2020. See Note 9, “Revenue Recognition,” and Note 10, "Related Party Transactions" in Part I, Item 1 of this Quarterly Report on Form 10-Q and Part II, Item 8 of our 2019 Form 10-K for information regarding the accounting treatment of the assignment of Vitamin E royalty agreement and for a full listing of our agreements with DSM.

We have several other collaboration molecules in our development pipeline with partners including DSM, Givaudan, Firmenich and Lavvan that we expect will contribute revenues from product sales and royalties if and when they are commercialized.

Critical Accounting Policies and Estimates

Management's discussion and analysis of results of operations and financial condition are based on our consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the U.S. (U.S. GAAP). We believe that the critical accounting policies described in this section are those that significantly impact our financial condition and results of operations and require the most difficult, subjective or complex judgements, often as a result of the need to make estimates about the effects of matters that are inherently uncertain. Because of this uncertainty, actual results may vary from these estimates.

Our most critical accounting estimates include:

•Recognition of revenue for arrangements with service delivery over time and multiple performance obligations;

•Valuation and allocation of fair value to various elements of complex related party transactions;

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•The valuation of freestanding and embedded derivatives, which impacts gains or losses on such derivatives, the carrying value of debt, interest expense and deemed dividends; and

•The valuation of debt for which we have elected fair value accounting.

For more information about our critical accounting estimates and policies, see Note 1, "Basis of Presentation and Summary of Significant Accounting Policies" in Part I, Item 1 of this Quarterly Report on Form 10-Q and in Part II, Item 8 of our 2019 Form 10-K.

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Results of Operations

Revenue

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Revenue
Renewable products	$	25,188	$	12,120	$	43,042	$	24,004
Licenses and royalties	990		40,964		6,151		41,082
Grants and collaborations	3,827		9,610		9,942		11,982
Total revenue	$	30,005	$	62,694	$	59,135	$	77,068

Three months ended June 30, 2020

Total revenue decreased by 52% to $30.0 million for the three months ended June 30, 2020 compared to the same period in 2019. The decrease was comprised of a $40.0 million decrease in licenses and royalties revenue and a $5.8 million decrease in grants and collaborations revenue, partially offset by a $13.1 million increase in renewable products revenue. The three months ended June 30, 2019 included one-off revenue for Vitamin E of $40.7 million. Excluding this item, revenue increased by 36% from $22.0 million in 2019 to $30.0 million in 2020.

Renewable products revenue increased by 108% to $25.2 million for the three months ended June 30, 2020 compared to the same period in 2019, primarily driven by our consumer product lines.

Licenses and royalties revenue decreased by 98% to $1.0 million for the three months ended June 30, 2020 compared to the same period in 2019, primarily due to $40.7 million of one-off royalty revenue in 2019 from DSM related to the assignment of a value sharing agreement.

Grants and collaborations revenue decreased by 60% to $3.8 million for the three months ended June 30, 2020 compared to the same period in 2019, due to no collaboration revenue in 2020 from Lavvan and DARPA.

Six months ended June 30, 2020

Total revenue decreased by 23% to $59.1 million for the six months ended June 30, 2020 compared to the same period in 2019. The decrease was comprised of a $34.9 million decrease in licenses and royalties revenue and a $2.0 million decrease in grants and collaborations revenue, partially offset by a $19.0 million increase in renewable products revenue. The six months ended June 30, 2019 included one-off revenue for Vitamin E of $40.7 million, and the six months ended June 30, 2020 included one-off revenue for Vitamin E of $3.8 million. Excluding these items, revenue increased by 51% from $36.8 million in 2019 to $55.4 million in 2020.

Renewable products revenue increased by 79% to $43.0 million for the six months ended June 30, 2020 compared to the same period in 2019, primarily driven by our consumer product lines.

Licenses and royalties revenue decreased by 85% to $6.2 million for the six months ended June 30, 2020 compared to the same period in 2019, primarily due to $40.7 million of royalty revenue in 2019 from DSM related to the assignment of a value sharing agreement.

Grants and collaborations revenue decreased by 17% to $9.9 million for the six months ended June 30, 2020 compared to the same period in 2019, primarily due to no collaboration revenue in 2020 from Lavvan and DARPA.

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Costs and Operating Expenses

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Cost and operating expenses
Cost of products sold	$	23,098	$	15,121	$	34,888	$	32,828
Research and development	16,965		19,222		34,091		37,061
Sales, general and administrative	30,503		30,862		62,517		59,115
Total cost and operating expenses	$	70,566	$	65,205	$	131,496	$	129,004

Cost of Products Sold

Cost of products sold includes raw materials, labor and overhead, amounts paid to contract manufacturers, inventory write-downs, and costs related to production scale-up. Because of our diverse consumer and business-to-business product mix and the timing and quantities of product sales, our overall cost of products sold can, but sometimes does not change in proportion to or directionally with changes in our renewable product revenues.

Three months ended June 30, 2020

Cost of products sold increased by 53% to $23.1 million for the three months ended June 30, 2020 compared to the same period in 2019, primarily due to a 108% increase in product revenue, partly offset by improved manufacturing efficiencies.

Six months ended June 30, 2020

Cost of products sold increased by 6% to $34.9 million for the six months ended June 30, 2020 compared to the same period in 2019, primarily due to a 79% increase in product revenue. The disproportionate increase in product revenue over cost of products sold was due mostly to improved manufacturing efficiencies.

Research and Development Expenses

Three months ended June 30, 2020

Research and development expenses decreased by 12% to $17.0 million for the three months ended June 30, 2020 compared to the same period in 2019, primarily due to decreases in laboratory equipment and supplies expenses.

Six months ended June 30, 2020

Research and development expenses decreased by 8% to $34.1 million for the six months ended June 30, 2020 compared to the same period in 2019, primarily due to decreases in laboratory equipment and supplies expenses.

Sales, General and Administrative Expenses

Three months ended June 30, 2020

Sales, general and administrative expenses decreased by 1% to $30.5 million for the three months ended June 30, 2020 compared to the same period in 2019, primarily due to reduced audit and legal fees, partly offset by increases in marketing expense and employee compensation costs related to our consumer product lines.

Six months ended June 30, 2020

Sales, general and administrative expenses increased by 6% to $62.5 million for the six months ended June 30, 2020 compared to the same period in 2019, primarily due to increases in marketing expense and employee compensation costs related to our consumer product lines, partly offset by reduced audit and legal fees.

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Other Expense, Net

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Other income (expense):
Interest expense	(20,118)		(15,217)		(35,120)		(27,751)
Loss from change in fair value of derivative instruments	(11,779)		—		(8,497)		(2,039)
Loss from change in fair value of debt	(14,949)		(14,444)		(31,452)		(16,574)
Loss upon extinguishment of debt	(22,029)		(5,875)		(49,348)		(5,875)
Other income (expense), net	1,497		(41)		1,501		(156)
Total other expense, net	$	(67,378)	$	(35,577)	$	(122,916)	$	(52,395)

Three months ended June 30, 2020

Total other expense, net was $67.4 million for the three months ended June 30, 2020, compared to $35.6 million for the same period in 2019. The $31.8 million increase was primarily due to a $16.2 million increase in loss upon extinguishment of debt, an $11.8 million loss from change in fair value of derivative instruments in 2020, and a $4.9 million increase in interest expense. See Note 3, “Fair value Measurements” and Note 4, “Debt” in Part 1, Item 1 of this Form 10-Q for more information on the individual transactions giving rise to these charges in the three months ended June 30. 2020.

Six months ended June 30, 2020

Total other expense, net was $122.9 million for the six months ended June 30, 2020, compared to $52.4 million for the same period in 2019. The $70.5 million increase was primarily due to a $43.5 million increase in loss upon extinguishment of debt, a $14.9 million increase in loss from change in fair value of derivative instruments, and a $7.4 million increase in interest expense. See Note 3, “Fair value Measurements” and Note 4, “Debt” in Part 1, Item 1 of this Form 10-Q for more information on the individual transactions giving rise to these charges in the six months ended June 30. 2020.

Provision for Income Taxes

Three and six months ended June 30, 2020

For the three and six months ended June 30, 2020, we recorded provisions of $0.1 million and $0.2 million for income taxes related to accrued interest on uncertain tax positions. For the three and six months ended June 30, 2019, the provision for income taxes was zero.

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Liquidity and Capital Resources

(In thousands)	June 30, 2020		December 31, 2019
Working capital (working capital deficit)	$	61,660	$	(87,526)
Cash and cash equivalents	$	99,998	$	270
Debt and lease obligations	$	229,172	$	289,065
Accumulated deficit	$	(1,953,919)	$	(1,755,653)

	Six Months Ended June 30,
(In thousands)	2020		2019
Net cash (used in) provided by:
Operating activities	$	(110,332)	$	(58,257)
Investing activities	$	(5,494)	$	(5,951)
Financing activities	$	215,287	$	20,054

Liquidity. We have incurred significant operating losses since our inception, and we expect to continue to incur losses and negative cash flows from operations for at least the next 12 months following the filing of this Quarterly Report on Form 10-Q. As of June 30, 2020, we had working capital of $61.7 million (compared to negative working capital of $87.5 million as of December 31, 2019), and an accumulated deficit of $2.0 billion.

As of June 30, 2020, our outstanding debt principal (including related party debt) totaled $175.8 million, of which $37.0 million is classified as current. Our debt agreements contain various covenants, including certain restrictions on our business that could cause us to be at risk of defaults, such as restrictions on additional indebtedness, material adverse effect and cross default provisions. A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of a substantial portion of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under our other outstanding indebtedness, permitting acceleration of a substantial portion of such other outstanding indebtedness. At December 31, 2019, we failed to meet certain covenants under several credit arrangements, including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. Further, at March 31, 2020, we failed to meet certain covenants and provisions under several credit arrangements, including those associated with cross-default provisions (as discussed below). In March 2020 and again in May 2020, these lenders (except Schottenfeld) provided permanent waivers to us for breaches of all past covenant violations and cross-default payment failures through May 8, 2020 under the respective credit agreements (discussed below). We cured these defaults with the closing of the $200 million equity offering described below and the repayment of these past due amounts. As of June 30, 2020, we failed to achieve the minimum revenue thresholds under the Foris Convertible Note, Naxyris LSA and Senior Convertible Notes Due 2022, which are described in more detail in Note 4, “Debt”, Part 1, Item 1 of this Form 10-Q, and obtained a waiver from each of these lenders to cure the June 30, 2020 minimum revenue covenant violations.

Between March 31, 2020 and April 30, 2020, we failed to pay (i) Total Raffinage Chimie (Total), Nikko Chemicals Co. Ltd (Nikko) and certain affiliates of the Schottenfeld Group LLC (Schottenfeld) an aggregate of $17.6 million of maturing promissory notes, (ii) failed to pay Ginkgo $7.2 million of past due interest, waiver fees and partnership payments and (iii) failed to make interest payments to all of our lenders totaling $2.8 million. These payment failures resulted in an event of default under the respective agreements and triggered cross-defaults under other debt instruments that permitted each of the affected debt holders (the Cross-Default Lenders) to accelerate the amounts owing under such cross-defaulted instruments. In May 2020, we obtained waivers from the lenders, except Schottenfeld, to extend the due date for all payments due under the respective agreements to the earlier of the day we receive cash proceeds from any private placement of our equity and/or equity-linked securities, and May 31, 2020; and amended the credit arrangements with Total and Nikko to extend the maturity dates of the original respective promissory notes to the earlier of the day we receive cash proceeds from any private placement of our equity and/or equity-linked securities, and May 31, 2020. Also, we received waivers from each of the affected Cross-Default Lenders to waive the right to accelerate due to the event-specific cross-defaults.

Beginning in May 2020 and continuing through June 2020, we executed a series of financial transactions to minimize cash outflows related to debt service payments and to increase operating cash. On May 1, 2020, we amended the Senior Convertible Notes Due 2022 to eliminate the monthly amortization payments and change the interest payment frequency from monthly to quarterly. On May 7, 2020, we received a $10 million Paycheck Protection Plan loan (PPP Loan). On June 1, 2020, we amended the Foris LSA to eliminate the quarterly principal payments and defer all interest payments until maturity on July

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1, 2022, and to provide for the conversion of all outstanding indebtedness under the LSA at a $3.00 per share conversion price, which conversion is subject to stockholder approval. Further, on June 1, 2020 and June 4, 2020, we entered into securities purchase agreements with investors for the private placement of an aggregate of $200 million of common and preferred stock, resulting in our receiving approximately $190 million of net proceeds. A portion of the proceeds from the offering was used to pay down approximately $37.1 million of debt principal (which included $10 million to repay the PPP Loan) and $6.1 million of accrued interest. Also, on June 2, 2020, Total converted approximately $9.1 million of debt principal into common stock under the terms of the 2014 Rule 144A Convertible Note, further reducing our outstanding indebtedness. As a result of closing the equity offering, making all past due payments, converting the $9.1 million 2014 Rule 144A Convertible Note principal into equity, and executing amendments to the Foris LSA and the Senior Convertible Notes Due 2022, we cured all payment defaults and other events of default, including cross-defaults under our various debt instruments as of June 30, 2020. Although we have been able to obtain waivers in the past for substantially all of our prior defaults to date and were able to cure the existing payment defaults, it may not be able to cure or obtain a waiver for any defaults in the future.

Further, our cash and cash equivalents of $100.0 million as of June 30, 2020 may not be sufficient to fund expected future negative cash flows from operations and cash debt service obligations through August 2021. These factors raise substantial doubt about our ability to continue as a going concern within one year after the date these condensed consolidated financial statements are issued. The condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. Our ability to continue as a going concern will depend, in large part, on our ability to eliminate or minimize the anticipated negative cash flows from operations during the 12 months from the date of this filing, and to either raise additional cash proceeds through financings or refinance the debt maturities occurring in June 2021, all of which are uncertain and outside our control. Further, our operating plan for the remainder of 2020 contemplates (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) reduced spending in general and administrative areas, and (iv) continued cash inflows from collaborations and grants. If we are unable to complete these actions, we expect to be unable to meet our operating cash flow needs and our obligations under our existing debt facilities over the next 12 months. This could result in an acceleration of our obligation to repay all amounts outstanding under those facilities, and we may be forced to obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all, and/or liquidate assets. In such a scenario, the value received for assets in liquidation or dissolution could be significantly lower than the value reflected in these financial statements.

If we do not achieve our planned operating results, our ability to continue as a going concern would be jeopardized and we may need to take the following actions to support our liquidity needs during the next 12 months:

•Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts;

•Reduce expenditures for employees and third-party contractors, including consultants, professional advisors and other vendors;

•Reduce or delay uncommitted capital expenditures, including expenditures related to the construction and commissioning of the new production facility in Brazil, non-essential facility and lab equipment, and information technology projects; and

•Closely monitor our working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

•Achieve planned production levels;

•Develop and commercialize products within planned timelines or at planned scales; and

•Continue other core activities.

We expect to fund operations for the foreseeable future with cash and investments currently on hand and cash inflows from collaborations, grants, product sales, licenses and royalties. All of our research and development collaboration milestone payments are subject to risks that we may not meet milestones. Our planned working capital and capital expenditure needs for the remainder of 2020 and into the first half of 2021 are dependent on significant inflows of cash from renewable product sales, license and royalties and existing and new collaborations, as well as additional debt financing for the construction of our new specialty ingredients fermentation facility in Brazil.

Cash Flows during the Six Months Ended June 30, 2020 and 2019

Cash Flows from Operating Activities

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Our primary uses of cash from operating activities are costs related to the production and sale of our products and personnel-related expenditures, offset by cash received from renewable product sales, licenses and royalties, and grants and collaborations.

For the six months ended June 30, 2020, net cash used in operating activities was $110.3 million, consisting primarily of a $196.2 million net loss, partially offset by $115.6 million of non-cash adjustments that were primarily comprised of a $49.3 million loss upon extinguishment of debt, a $31.5 million loss from change in fair value of debt, $11.6 million of non-cash interest expense, an $8.5 million loss from change in fair value of derivative instruments, and $6.4 million of stock-based compensation. Additionally, there was a $29.7 million net decrease in working capital balances.

For the six months ended June 30, 2019, net cash used in operating activities was $58.3 million, consisting of a $104.3 million net loss, $51.0 million of favorable non-cash adjustments and a $4.9 million net decrease in working capital. The non-cash adjustments were primarily comprised of $7.3 million of debt discount accretion, $6.8 million of stock-based compensation, and $5.8 million of amortization of right-of-use assets under operating leases.

Cash Flows from Investing Activities

For the six months ended June 30, 2020 and June 30, 2019, net cash used in investing activities was $5.5 million, and $6.0 million, respectively, comprised of property, plant and equipment purchases.

Cash Flows from Financing Activities

For the six months ended June 30, 2020, net cash provided by financing activities was $215.3 million, primarily comprised of $247.7 million of net proceeds from common and preferred stock issuances and deemed issuance, plus $15.3 million of net proceeds from debt issuance, partly offset by $45.9 million of debt principal payments.

For the six months ended June 30, 2019, net cash provided by financing activities was $20.1 million, primarily comprised of $53.8 million of net proceeds from common stock issuances, plus $18.6 million of net proceeds from debt issuance, mostly offset by $52.1 million of debt principal payments.

Off-Balance Sheet Arrangements

At June 30, 2020, we did not have any material off-balance sheet arrangements, as defined in Item 303(a)(4)(ii) of Regulation S-K.

Contractual Obligations

The following is a summary of our contractual obligations as of June 30, 2020:

Payable by year ending December 31,(In thousands)	Total		2020		2021		2022		2023		2024		Thereafter
Principal payments on debt	$	175,786	$	5,950	$	56,201	$	98,881	$	12,793	$	307	$	1,654
Interest payments on debt(1)	38,534		8,080		13,729		16,313		106		91		215
Financing leases	6,751		2,185		4,566		—		—		—		—
Operating leases	22,520		3,918		7,478		7,654		3,318		152		—
Partnership payment obligation	11,112		7,381		3,731		—		—		—		—
Contract termination fee	3,670		3,670		—		—		—		—		—
Total	$	258,373	$	31,184	$	85,705	$	122,848	$	16,217	$	550	$	1,869

____________________

⁽¹⁾Fixed and variable interest rates are described in Note 4, "Debt" in Part II, Item 8 of the 2019 Form 10-K. Future interest payments shown above for variable-rate debt instruments are measured on the basis of interest rates for such instruments as of June 30, 2020. The fixed interest rates are more fully described in Note 4, "Debt" in Part II, Item 8 of the 2019 Form 10-K.

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ITEM 4. CONTROLS AND PROCEDURES

Evaluation of Disclosure Controls and Procedures

We maintain disclosure controls and procedures, as such term is defined under Rule 13a-15(e) promulgated under the Exchange Act. In designing and evaluating the disclosure controls and procedures, management recognizes that any disclosure controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and management necessarily is required to apply its judgment in evaluating the cost-benefit of possible controls and procedures.

Under the supervision and with the participation of management, including our principal executive officer and principal financial officer, we conducted an evaluation of the effectiveness of our disclosure controls and procedures as of the end of the period covered by this report. Based on this evaluation, our principal executive officer and principal financial officer have concluded that our disclosure controls and procedures were not effective at the reasonable assurance level as of June 30, 2020. This conclusion was based on the material weaknesses in our internal control over financial reporting described in Part II, Item 9A, “Controls and Procedures” of our 2019 Form 10-K. The material weaknesses have not been remediated as of June 30, 2020.

A material weakness is a deficiency, or combination of deficiencies, in internal control over financial reporting such that there is a reasonable possibility that a material misstatement of the Company’s annual or interim consolidated financial statements will not be prevented or detected on a timely basis. If not remediated, the material weaknesses in our internal control over financial reporting described in the 2019 Form 10-K could result in a material misstatement of our annual or interim consolidated financial statements that would not be prevented or detected on a timely basis.

Changes in Internal Control over Financial Reporting

During the fiscal quarter ended June 30, 2020, there were no changes in our internal control over financial reporting that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Inherent Limitations on Effectiveness of Controls

Our management, including our principal executive officer and principal financial officer, does not expect that our disclosure controls and procedures or our internal control over financial reporting will prevent or detect all errors and all fraud. A control system, no matter how well-designed and operated, can provide only reasonable, not absolute, assurance that the control system’s objectives will be met. The design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. Further, because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that misstatements due to error or fraud will not occur or that all control issues and instances of fraud, if any, have been detected. The design of any system of controls is based in part on certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Projections of any evaluation of the effectiveness of controls to future periods are subject to risks. Over time, controls may become inadequate because of changes in conditions or deterioration in the degree of compliance with policies or procedures.

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PART II

ITEM 1. LEGAL PROCEEDINGS

On April 3, 2019, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and former CFO (and current Chief Business Officer), Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all persons and entities that purchased or otherwise acquired our securities between March 15, 2018 and March 19, 2019. The complaint, which was amended by the lead plaintiff on September 13, 2019, alleges securities law violations based on statements and omissions made by the Company during such period. On October 25, 2019, the defendants filed a motion to dismiss the securities class action complaint. The hearing on such motion to dismiss was held on February 18, 2020 and we are awaiting a ruling from the Court. Subsequent to the filing of the securities class action complaint described above, on June 21, 2019 and October 1, 2019, respectively, two separate purported shareholder derivative complaints were filed in the U.S. District Court for the Northern District of California (Bonner v. Doerr, et al., and Carlson v. Doerr, et al.) based on similar allegations to those made in the securities class action complaint described above and named the Company and certain of the Company’s current and former officers and directors as defendants. The derivative lawsuits sought to recover, on the Company’s behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and omissions made in connection with the Company’s securities filings. The derivative lawsuits were dismissed on October 18, 2019 (Bonner) and December 10, 2019 (Carlson), without prejudice. We believe the securities class action complaint lacks merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

On July 24, 2020, a securities class action complaint was filed against Amyris and the members of our Board in the Court of Chancery of the State of Delaware (Flatischler v. Melo, et. al.). The complaint alleged a breach of fiduciary obligation to disclose material information to stockholders in the proxy statement filed with the Securities and Exchange Commission on July 6, 2020 (Proxy), with respect to the Company’s special stockholders’ meeting to be held on August 14, 2020 (Special Meeting), at which stockholders will vote to approve the conversion of all outstanding indebtedness under the Foris Convertible Note and of our Series E Preferred Stock issued in the June 2020 PIPE into shares of common stock, in accordance with Nasdaq Listing Standard Rule 5635(d). See Note 4, “Debt,” “Amendment No. 1 to Foris LSA — Foris, Related Party,” and Note 6, “Stockholders’ Deficit,” “June 2020 PIPE,” and “Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws” in Part I, Item 1 of this Quarterly Report on Form 10-Q for more information. The plaintiffs sought to enjoin the Special Meeting. On August 6, 2020, the plaintiffs withdrew their complaint as moot following the Company’s filing of a supplement to the Proxy on August 5, 2020. The Proxy supplement provided additional information regarding the approval process of the LSA Amendment and the June 2020 PIPE, and the relationships between the Company and its financial advisors to the June 2020 PIPE. The plaintiffs currently seek attorney’s fees and reimbursement of certain legal expenses related to filing the complaint. Three substantially similar complaints were filed: one on July 28, 2020, in the United States District Court of Delaware (Sabatini v. Amyris, Inc.); one on July 31, 2020, in the Northern District of California (Nair v. Amyris); and another on August 4, 2020, in the Southern District of New York (Chamorro v. Amyris). We believe that these complaints lack merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

We may be involved, from time to time, in legal proceedings and claims arising in the ordinary course of our business. Such matters are subject to many uncertainties and there can be no assurance that legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on our business, results of operations, financial position or cash flows.

ITEM 1A. RISK FACTORS

In addition to the risk described below, the risks described in Part I, Item 1A, "Risk Factors" in our 2019 Form 10-K could materially and adversely affect our business, financial condition and results of operations, and the trading price of our common stock could decline. These risk factors do not identify all risks that we face; our operations could also be affected by factors that are not presently known to us or that we currently consider to be immaterial to our operations. Due to risks and uncertainties, known and unknown, our past financial results may not be a reliable indicator of future performance, and historical trends should not be used to anticipate results or trends in future periods. The “Risk Factors” section of the 2019 Form 10-K remains current in all material respects.

Our operations and financial results could be adversely impacted by the COVID-19 pandemic, and governmental measures taken in relation thereto, in the United States and the rest of the world.

On May 18, 2020, the health department of Alameda County, California (the County) revised its March 17, 2020 shelter-in-place order covering our corporate headquarters, primary research and development laboratories and employees. The order is

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in effect indefinitely, and has been amended in its scope on personal and business activities numerous times through July 19, 2020. In order to maintain our facilities, support on-going critical production campaigns, and provide information to facilitate our employees working from home, we are currently operating under applicable minimum business operations guidelines. Accordingly, we have instituted policies for those of our employees working on-site such as limiting the number of staff in our laboratories, temperature and symptom confirmations, mandatory wearing of masks, and social distancing. As the COVID-19 pandemic continues to evolve, we may experience disruptions that could severely impact our business operations, research and development processes, manufacturing, commercialization and other activities, including:

•delays or disruptions in our supply chain due to staffing shortages, production slowdowns or stoppages and disruptions in delivery systems;

•delays or disruptions in the manufacture and/or shipment of our products, including facilities we rely upon in Brazil;

•delays or disruptions with respect to our activities in China;

•a decline in demand for our consumer goods products (including our Clean Beauty products) due to any measures put in place in response to the pandemic or any related economic downturn;

•store closings of our retail partners as mandated or recommended by federal, state or city governments;

•interruption of key research and development activities due to restricted or limited operations at our facilities and/or limitations on travel imposed or recommended by federal or state governments, employers and others;

•delays in receiving the supplies and materials needed to conduct our research and development and interruption in global shipping that may affect the transport of materials;

•interruption or delays to our development pipeline; limitations on employee resources that would otherwise be focused on the conduct of our business, including because of sickness of employees or their families or the responsibility of employees to manage family obligations while working from home;

•interruptions or delays in the operations of regulatory authorities, which may impact review or approval timelines;

•delays in necessary interactions with other agencies and contractors due to limitations in employee resources or forced furlough of government employees;

•termination of, or difficulties in procuring or maintaining, arrangements with third parties upon whom we depend such as manufacturers, including contract manufacturing organizations, suppliers and other strategic partners;

•delays in, or limited access to, the capital markets or other sources of funding; and

•disruptions or restrictions on our ability to travel, pursue partnerships and other business transactions.

The COVID-19 pandemic and the resulting mitigation measures may have an adverse impact on global economic conditions which could have an adverse effect on our business and financial condition. In addition, the COVID-19 pandemic has impacted, and may continue to impact, the trading price of shares of our common stock and could further impact our ability to raise additional capital on a timely basis or at all.

The full extent to which the COVID-19 pandemic impacts our business, financial condition or results of operations will depend on future developments, which are highly uncertain and cannot be accurately predicted. New information may emerge concerning the severity of the COVID-19 pandemic and the actions to contain the pandemic or treat COVID-19, such as the ultimate geographic spread of the disease, the duration of the pandemic, continued travel restrictions and social distancing, business closures or disruptions as well as the effectiveness of actions taken to contain or treat COVID-19, in the United States and other countries. The COVID-19 pandemic could also result in social, political, economic, and labor instability in the countries in which we, or third parties with whom we engage, operate.

To the extent the COVID-19 pandemic adversely affects our business and financial results, it may also have the effect of impacting other risks described in Part I, Item 1A, "Risk Factors" in our 2019 Form 10-K.

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

See Note 4, “Debt” and Note 6, “Stockholders’ Deficit,” in Part I, Item 1 of this Quarterly Report on Form 10-Q for information regarding unregistered sales of equity securities during the six months ended June 30, 2020.

No underwriters or agents were involved in the issuance or sale of such securities, except that each of Jefferies LLC and Cowen and Company, LLC served as joint lead placement agents and Oppenheimer & Co. Inc. served as a co-placement agent with respect to the June 2020 PIPE offering of shares of common stock and Series E Preferred Stock, and we paid an aggregate of $9 million in fees in connection therewith. The securities were issued in private placements pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act, or in private exchanges pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The investors participating in the offerings or exchanges acquired the applicable securities for investment purposes only and without intent to resell, were able to fend for themselves in these transactions, and are accredited investors as defined in Rule 501 of Regulation D promulgated under the Securities Act. These purchasers had adequate access, through their relationships with us, to information about us.

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ITEM 3. DEFAULTS UPON SENIOR SECURITIES

During the three months ended June 30, 2020, we failed to make required interest and/or principal payments under the Schottenfeld Notes (in the 2019 Form 10-K, Part II, Item 8, see Note 4, “Debt” and Note 15, “Subsequent Events”, and in this Quarterly Report on form 10-Q, Part I, Item 1, see Note 4, “Debt”). The total amounts of such defaults were, (a) in respect of interest and principal under the Schottenfeld November Notes, aggregate $8.4 million due April 19, and (b) in respect of interest under the Schottenfeld September Notes, $0.4 million due April 19. These payment failures resulted in an event of default under the respective agreements and also triggered cross-defaults under those and other debt instruments that permitted each of the affected debt holders to accelerate the amounts owing under such cross-defaulted instruments. In May 2020, the Company received waivers from each of the affected cross-default debt holders to waive their right to accelerate due to certain event-specific cross-defaults. On June 5, 2020, the Company repaid the past due principal and interest under the Schottenfeld November Notes and the past due interest under the Schottenfeld September Notes.

ITEM 5. OTHER INFORMATION

None.

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ITEM 6. EXHIBITS

Exhibit No.	Description	Incorporation by Reference
		Form	File No.	Exhibit	Filing Date	Filed Herewith
2.01	Amendment No. 4, dated as of March 30, 2020, to the Quota Purchase Agreement, dated November 17, 2017, among registrant, AB Technologies LLC and DSM Produtos Nutricionais Brasil S.A.					x
2.02	Amendment No. 5, dated May 22, 2020, to the Quota Purchase Agreement, dated November 17, 2017, among registrant, AB Technologies LLC and DSM Produtos Nutricionais Brasil S.A.					x
3.01	Certificate of Amendment of the Restated Certificate of Incorporation dated May 29, 2020	S-1	333-239823	3.12	07-10-2020
3.02	Form of Certificate of Designation of Preferences, Rights and Limitations of Series E Convertible Preferred Stock	8-K	001-34885	3.1	06-04-2020
4.01	Senior Convertible Note Maturity Extension, dated April 6, 2020, between registrant and Total Raffinage Chimie					x
4.02	Form of Senior Convertible Note Amendment, dated May 1, 2020, between registrant and certain accredited investors	8-K	001-34885	10.1	05-05-2020
4.03	Warrant Amendment Agreement, dated May 1, 2020, between registrant and LMAP Kappa Limited					x
4.04	Warrant Amendment Agreement, dated May 1, 2020, between registrant and HT Investments MA LLC					x
4.05	Rights Amendment Agreement, dated May 1, 2020, between registrant and Silverback Opportunistic Credit Master Fund Limited					x
4.06	Senior Convertible Note Maturity Extension, dated May 7, 2020, between registrant and Total Raffinage Chimie					x
4.07	Amendment n. 1 to Amended and Restated Loan And Security Agreement, dated June 1, 2022, between registrant and Foris Ventures, LLC	8-K	001-34885	10.2	06-04-2020
4.08	Form of Security Purchase Agreement, dated June 1, 2020 or June 4, 2020, between registrant and certain accredited investors	8-K	001-34885	10.1	06-04-2020
4.09	Second Amendment to the Senior Convertible Notes and Waiver and Forbearance Agreement, dated June 4, 2020, between the registrant and HT Investments MA LLC	S-8	333-239820	4.17	07-10-2020	x
10.01	Waiver Agreement and Amendment to Partnership Agreement, dated May 6, 2020 by and between registrant and Ginkgo Bioworks, Inc.					x
10.02	Second Amendment to Loan Agreement, dated April 3, 2020, between registrant and Nikko Chemicals Co., Ltd.					x
10.03	Credit Agreement, dated April 29, 2020, between registrant and Foris Ventures, LLC					x
10.04	Waiver Agreement and Amendment to Partnership Agreement, dated May 6, 2020 by and between registrant and Ginkgo Bioworks, Inc.					x
10.05	Third Amendment to Loan Agreement, dated May 7, 2020, between registrant and Nikko Chemicals Co., Ltd.					x
10.06	Promissory Note dated May 7, 2020, between registrant and Bank of the West					x
10.07	2020 Equity Incentive Plan	S-8	333-239820	4.17	07-10-2020
10.08	Form of Restricted Stock Unit Agreement for 2020 Equity Incentive Plan	S-8	333-239820	4.18	07-10-2020
10.09	Form of Stock Option Agreement for 2020 Equity Incentive Plan	S-8	333-239820	4.19	07-10-2020
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					x
31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					x

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Exhibit No.	Description	Incorporation by Reference
32.01a	Certification of Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002		x
32.02a	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002		x
101.INS	XBRL Instance Document
101.SCH	XBRL Taxonomy Extension Schema Document
101.CAL	XBRL Taxonomy Extension Calculation Linkbase Document
101.DEF	XBRL Taxonomy Extension Definition Linkbase Document
101.LAB	XBRL Taxonomy Extension Label Linkbase Document
101.PRE	XBRL Taxonomy Extension Presentation Linkbase Document

a This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this Quarterly Report on Form 10-Q to be signed on its behalf by the undersigned, thereunto duly authorized.

	AMYRIS, INC.
By:	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer (Principal Executive Officer)
	August 10, 2020
By:	/s/ Han Kieftenbeld
	Han Kieftenbeld
	Chief Financial Officer (Principal Financial Officer)
	August 10, 2020

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EX-4.01

Exhibit 4.01

Senior Convertible Note Maturity Extension

April 6, 2020

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, California 94608

Attention: Kathleen Valiasek

Re: Extension of Senior Convertible Note due March 31, 2020

Ladies and Gentlemen:

WHEREAS, Total Raffinage Chimie (the “Investor”) is the holder of that certain Senior Convertible Note due initially June 14, 2019, which has been extended to mature on July 18, 2019, then further extended to mature on August 28, 2019, then further extended to mature on October 28, 2019, then further extended to mature on December 16, 2019, then further extended to mature on January 31, 2020, and then further extended to mature on March 31, 2020 issued by Amyris, Inc. (the “Company”) in the principal amount of $9,075,414 (the “Note”; capitalized terms used but not defined herein shall have the meanings ascribed thereto in the Note), which Note is convertible into shares (the “Conversion Shares”, and, together with the Note, the “Securities”) of the Company’s common stock, par value $0.0001 per share (the “Common Stock”), in accordance with the terms of the Note, pursuant and subject to the terms and conditions set forth in that certain Exchange Agreement, dated May 15, 2019, between the Company and the Investor, the Senior Convertible Note Maturity Extensions, dated June 20, 2019; July 24, 2019; September 4, 2019; October 31, 2019; December 20, 2019; March 11, 2020, and this agreement (this “Agreement”); and

WHEREAS, the Company and the Investor desire to again extend the maturity date of the Note and to make certain other changes to the Note as set forth herein.

NOW, THEREFORE, in consideration of the promises, undertakings and obligations set forth herein, the sufficiency of which consideration is hereby acknowledged, each of the undersigned parties agree with each other as follows:

1. Extension of Maturity Date. Subject to the terms and conditions of this Agreement, effective March 31, 2020, (i) the maturity date of the Note shall be extended to April 30, 2020 and (ii) the Note shall continue to provide that the Company shall not effect any conversion thereof, and the Investor shall not have the right to convert any portion thereof, to the extent that the Investor (together with the Investor’s Affiliates, and any Persons acting as a group together with the Investor or any of the Investor’s Affiliates) would beneficially own in excess of 4.9% of the issued and outstanding shares of Common Stock after giving effect to such conversion, unless 61 days’ prior notice to waive such provision is given in writing by the Investor. In connection therewith, the Company shall re-issue the Note in the form set forth in Exhibit A attached hereto, and the Investor shall return the existing Note, each in accordance with the provisions of Section 3 below. Subject to the issuance by the Company of a new Note in accordance with Section 3 below, the Investor waives any failure by the Company to pay the principal of, and accrued and unpaid interest on, the Note on or prior to March 31, 2020.

2. Reduction in Conversion Price. The Conversion Price of the Notes shall be reduced to $2.87 per share of Common Stock.

3. Mechanics of Note Issuance and Cancellation. Within three (3) business days from the date hereof, (i) the Company shall re-issue the Note, in the form set forth in Exhibit A attached hereto, by delivering an

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originally executed re-issued Note to Investor’s counsel at the offices of Dentons US LLP at 1221 Avenue of the Americas, New York, NY 10020, Attn: Brian Lee, and (ii) the Investor shall return the originally executed existing Note to the Company at its headquarters, for cancellation, it being acknowledged by the Company that the existing Note shall not be cancelled until and unless an attorney at Dentons US LLP acknowledges receipt of the re-issued Note on behalf of Investor. For the avoidance of doubt, the parties agree that the re-issuance of the Note reflecting the terms of this Agreement is solely for the convenience of Investor and shall not be deemed the issuance of a new security distinct from the Note.

4. Representations and Warranties of the Company. The Company represents and warrants to the Investor that, as of the date hereof:

(a)  Organization and Standing. The Company and each of its Significant Subsidiaries (as defined in Regulation S-X of the Securities Act) is duly incorporated, validly existing, and in good standing under the laws of the jurisdiction of its incorporation or organization. The Company and each of its Significant Subsidiaries has all requisite power and authority to own and operate its properties and assets and to carry on its business as presently conducted and as proposed to be conducted. The Company and each of its Significant Subsidiaries is qualified to do business as a foreign entity in every jurisdiction in which the failure to be so qualified would have, or would reasonably be expected to have, a material adverse effect, individually or in the aggregate, upon the business, properties, tangible and intangible assets, liabilities, operations, prospects, financial condition or results of operation of the Company or the ability of the Company to perform its obligations under this Agreement or the Note.

(b)  Power. The Company has all requisite power to execute and deliver this Agreement and to carry out and perform its obligations under the terms of this Agreement.

(c)  Authorization. The execution, delivery, and performance of this Agreement by the Company has been duly authorized by all requisite action on the part of the Company and its officers, directors and stockholders, and this Agreement constitutes the legal, valid, and binding obligation of the Company enforceable in accordance with its terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium, and other laws of general application affecting enforcement of creditors’ rights generally, and (b) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies.

(d) Capitalization. The capitalization of the Company, on a fully diluted basis, is as set forth herein as Schedule 4(d), which information is true, complete and accurate.  

(e) Validity of Note and Waiver of Defenses. The Company acknowledges the validity, priority and enforceability of the Note as a debt instrument and any of the obligations thereunder and waives (on behalf of itself, and any other person, entity or other party in interest that may claim by, through, or on the Company’s behalf) any right, claim, or defense to the Note or any of the obligations thereunder on the grounds that they should be recharacterized as or subordinated to the level of equity.

(f) No Events of Default. After giving effect to this Agreement, there has not been any, and there is not any continuing, Event of Default that has not otherwise been cured or waived.

(g) Other Loan Agreements. The Company has entered into valid and enforceable waivers or extension agreements (“Waivers”) with each of Foris Ventures, LLC; Naxyris S.A.; Schottenfeld Opportunities Fund II, L.P.; Koyote Trading, LLC; Phase Five Partners, LP; DSM Finance B.V., Ginkgo Bioworks, Inc. and Nikko Chemicals Co. (collectively, the “Waiving Lenders”) with regards to payments due on or about March 31, 2020.

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(h) Indebtedness. Since November 15, 2019, the Company has not made any cash payment on or with respect to the principal amount of, or purchase, redeem, defease or otherwise settle in whole or in part any Indebtedness (as defined below) of the Company, except for any cash payment expressly permitted under Section 5(a) of that certain Note Extension Agreement entered into between the Company and Investor, dated October 31, 2019 and the cash payments described on Schedule 4(h) hereto.

5. Representations and Warranties of the Investor. The Investor hereby represents and warrants to and covenants with the Company that, as of the date hereof:

(a) Organization and Good Standing. The Investor is a corporation, limited partnership, limited liability company or other entity, as the case may be, duly formed, validly existing and in good standing under the laws of the jurisdiction of its formation.

(b) Due Authorization. The Investor has the requisite power and authority to enter into and perform its obligations under this Agreement.

6. Covenants and Negative Covenants of the Company.

(a) Indebtedness. Until such time as the Note is paid in full or converted into Conversion Shares, the Company shall not, without the prior written consent of the Investor, make any cash payment on or with respect to the principal amount of, or purchase, redeem, defease or otherwise settle in whole or in part any Indebtedness of the Company. For purposes of this Agreement, “Indebtedness” shall mean any amount, excluding trade payables occurring in the ordinary course of business, that (i) is owed by the Company resulting from borrowed money, or (ii) is evidenced by bonds, notes, debentures or similar instruments or letters of credit (or reimbursement agreements in respect thereof).

(b) Financing. At any time prior to the Maturity Date, if the Company raises funds equal to or greater than $20 million, the Company will repay the outstanding principal amount and all accrued and unpaid interest on the Note in full upon the close of such financing.

(c) Exercise of Warrants. At such time as the Investor exercises some or all of its warrants to purchase shares of common stock of the Company pursuant to the cashless exercise mechanism provided for under such warrants, the Company shall cause the Company’s stock transfer agent to issue the number of shares of common stock of the Company in accordance with the provisions of the warrants, free of any restrictive legend relating to the Securities Act. The Company agrees that the shares of common stock of the Company issuable to Investor from a cashless exercise of such warrants would be, for purposes of Rule 144, acquired from the Company (or from an Affiliate of the Company) more than one year prior to the relevant date of determination and therefore, are eligible for resale under Rule 144(b).

(d) Validity of Waivers. Each of the Waivers shall be valid and enforceable at all times from the date of its execution through April 30, 2020, and all of the Waiving Lenders shall continue through April 30, 2020 to waive from exercising their respective rights and remedies. Furthermore, no person at any time shall exercise for any reason any of rights or remedies against the Company under any instrument evidencing Indebtedness, or against the Company’s properties or assets, in each case, of the type that would constitute an Event of Default under the Note.

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(e) Payment of Legal Expenses. Within ten (10) business days of the Company’s receipt from Investor of an invoice of Dentons US LLP, counsel to the Investor, relating to reasonable legal fees incurred by Investor in connection with the transaction contemplated by this Agreement, the Company shall reimburse Investor the amount set forth in such invoice.

7. Disclosure. At or prior to 9:00 a.m., New York City time, on the second business day after the date hereof, the Company shall file a press release or Current Report on Form 8-K announcing the execution of this Agreement, which press release or Current Report on Form 8-K the Company acknowledges and agrees will disclose all material non-public information, if any, with respect to the terms of this Agreement.

8. Waiver and Amendment. Neither this Agreement, the Note nor any provisions hereof or thereof shall be modified, changed, discharged, waived or terminated except by an instrument in writing signed by the Company and the Investor.

9. Waiver of Jury Trial. EACH OF THE COMPANY AND THE INVESTOR IRREVOCABLY WAIVES ANY AND ALL RIGHT TO TRIAL BY JURY WITH RESPECT TO ANY LEGAL PROCEEDING ARISING OUT OF THE TRANSACTIONS CONTEMPLATED BY THIS AGREEMENT.

10. Governing Law/Venue. THIS AGREEMENT SHALL BE GOVERNED BY THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO CONFLICT OF LAW PRINCIPLES THAT WOULD RESULT IN THE APPLICATION OF ANY LAW OTHER THAN THE LAW OF THE STATE OF NEW YORK. Each of the Company and the Investor (a) agrees that any legal suit, action or proceeding arising out of or relating to this agreement or the transactions contemplated hereby shall be instituted exclusively in the courts of the State of New York located in the City and County of New York or in the United States District Court for the Southern District of New York; (b) waives any objection that it may now or hereafter have to the venue of any such suit, action or proceeding; and (c) irrevocably consents to the jurisdiction of the aforesaid courts in any such suit, action or proceeding.

11. Section and Other Headings. The section and other headings contained in this Agreement are for reference purposes only and shall not affect the meaning or interpretation of this Agreement.

12. Counterparts. This Agreement may be executed by one or more of the parties hereto in any number of separate counterparts (including by facsimile or other electronic means, including telecopy, email or otherwise), and all of said counterparts taken together shall be deemed to constitute one and the same instrument. Delivery of an executed signature page of this Agreement by facsimile or other transmission (e.g., “pdf” or “tif” format) shall be effective as delivery of a manually executed counterpart hereof.

13. Notices. All notices and other communications provided for herein shall be in writing and shall be deemed to have been duly given if delivered personally or sent by prepaid overnight courier or registered or certified mail, return receipt requested, postage prepaid to, in the case of the Company, the following address and, in the case of the Investor, the address provided on the signature page of the Investor hereto (or such other address as any party shall have specified by notice in writing to the other):

If to the Company: Amyris, Inc. 5885 Hollis Street, Suite 100 Emeryville, California 94608 Fax: Attention: General Counsel

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14. Binding Effect. The provisions of this Agreement shall be binding upon and accrue to the benefit of the parties hereto and their respective heirs, legal representatives, successors and permitted assigns.

15. Severability. If any term or provision (in whole or in part) of this Agreement is determined to be invalid, illegal or unenforceable in any jurisdiction, such invalidity, illegality or unenforceability shall not affect any other term or provision of this Agreement or invalidate or render unenforceable such term or provision in any other jurisdiction.

16. Release. In consideration of the agreements of the Investor set forth in this Agreement, the Company, its affiliates and subsidiaries, and all of their respective directors, officers, agents, heirs, personal representatives, predecessors, successors and assigns (individually and collectively, the “Releasors”), hereby fully, finally, and forever release and discharge the Investor, its affiliates and subsidiaries, and its any of their successors, assigns, directors, officers, employees, agents, and representatives (including those on the board of Company or any of its subsidiaries or affiliates) from any and all actions, causes of action, claims, debts, demands, liabilities, obligations, and suits of whatever kind or nature, in law or equity, the Releasors or any of them have, whether known or unknown, in respect of, relating to, or concerning this Agreement, the Securities, any other potential agreement or transaction relating to the Securities, or any open market transactions in the Company effectuated by the Investor arising from events occurring prior to the date hereof.

[SIGNATURE PAGES FOLLOW]

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IN WITNESS WHEREOF, the undersigned has executed this Agreement as of the date first written above.

AMYRIS, INC.

By: /s/ Kathleen Valiasek

Name: Kathleen Valiasek

Title: Chief Business Officer

IN WITNESS WHEREOF, the undersigned has executed this Agreement as of the date first written above.

INVESTOR:

TOTAL RAFFINAGE CHIMIE

By: /s/ Philippe Orts

Name: Philippe Orts

Title: Senior VP Corporate Affairs

Address for Notices:

TOTAL RAFFINAGE CHIMIE

Attention:

EX-4.03

Exhibit 4.03

EXECUTION VERSION

WARRANT AMENDMENT AGREEMENT

This Warrant Amendment Agreement (this “Amendment”) is made as of May 1, 2020 by and between Amyris, Inc., a Delaware corporation (the “Company”), and LMAP KAPPA LIMITED (the “Holder”).

RECITALS

WHEREAS, on May 10, 2019, the Company issued to the Holder a common stock purchase warrant (the “Warrant”), pursuant to the terms of that certain Exchange Agreement, dated as of the same date, between the Company and the Holder.

WHEREAS, the Company and the Holder hereby agree to amend the Warrant to extend the termination date and reduce its exercise price as provided herein; and

WHEREAS, pursuant to Section 5(l) of the Warrant, the Warrant may be amended with the written consent of the Company and the Holder.

AGREEMENT

NOW, THEREFORE, in consideration of the premises and mutual covenants contained herein and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, and intending to be legally bound hereby, the parties hereto agree as follows:

1.Warrant Amendments.

(a) The definition of “Termination Date” shall be amended to January 31, 2022.

(b) The definition of “Exercise Price” on Section 2.b) shall be amended and restated in its entirety as follows:

“b) Exercise Price. The exercise price per share of the Common Stock under this Warrant shall be $2.87, subject to adjustment hereunder (the “Exercise Price”).”

2.No Other Amendments. Except as expressly set forth above, all of the terms and conditions of the Warrant shall remain in full force and effect.

3.Effectiveness of Amendment. This Amendment shall be effective as of the date hereof.

4.Miscellaneous.

(a) Governing Law. This Amendment and all acts and transactions pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with the laws of the State of California, without giving effect to principles of conflicts of law.

(b) Counterparts. This Amendment may be executed in two counterparts, each of which shall be deemed an original and all of which together shall constitute one instrument.

[SIGNATURE PAGES FOLLOW]

The undersigned has executed this Warrant Amendment Agreement as of the date first set forth above.

THE COMPANY:

AMYRIS, INC.

By: _/s/ Han Kieftenbeld

(Signature)

Name: Han Kieftenbeld

Title: Chief Financial Officer

The undersigned has executed this Warrant Amendment Agreement as of the date first set forth above.

HOLDER:

LMAP KAPPA LIMITED

/s/ Robert Barron

     (Signature)

Name: Robert Barron

Title: Portfolio Manager

EX-4.04

Exhibit 4.04

Execution Copy

AMENDMENT TO WARRANTS TO PURCHASE SHARES OF COMMON STOCK

This AMENDMENT TO COMMON STOCK PURCHASE WARRANT (this “Amendment”) is made and entered into as of May 1, 2020, by and among Amyris, Inc., a Delaware corporation (the “Company”) and HT Investments MA LLC (the “Holder”).

RECITALS

Whereas, the Company has issued that certain Common Stock Purchase Warrant (the “Warrant”), to the Holder pursuant to that certain Exchange Agreement (as the same may be amended from time to time) (the “Exchange Agreement”), dated as of December 30, 2019, by and among the Company and the Holder (as the same may be amended from time to time);

Whereas, the Company and the Holder desire to amend the Warrant in order to adjust the Exercise Price (as defined therein); and

Whereas, pursuant to Section 5(l) of the Warrant, the Warrant may be amended with the written consent of the Company and the Holder.

Now, Therefore, in consideration of the mutual covenants and agreements set forth herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto, intending to be legally bound, agree as follows:

ARTICLE I

AMENDMENT OF WARRANTS

1.1. Section 2(b) of the Warrant. Section 2(b) of the Warrant is hereby amended and restated in its entirety to read as follows:

“b) Exercise Price. The exercise price per share of the Common Stock under this Warrant shall be $2.87, subject to adjustment hereunder (the “Exercise Price”):

ARTICLE II

MISCELLANEOUS

2.1. Rule 144 Holding Period. The Company and the Holder acknowledge and agree that, as set forth in the Exchange Agreement, the Warrant will continue to have a holding period under Rule 144 promulgated under the Securities Act of 1933, as amended, that will be deemed to have commenced as of December 10, 2018.

2.2. Disclosure of Amendment. On or before 4:30 p.m., New York time, on May 4, 2020, the Company shall file a Current Report on Form 8-K describing all the material terms of the transactions contemplated by this Amendment in the form required by the U.S. Securities

Exchange Act of 1934, as amended, and attaching the form of this Amendment (including all attachments, the “8-K Filing”). From and after the filing of the 8-K Filing, the Company shall have disclosed all material, nonpublic information (if any) provided to the Holder by the Company or any of its subsidiaries or any of their respective officers, directors, employees or agents in connection with the transactions contemplated by the Exchange Agreement, this Amendment or the Transaction Documents (as defined in the Exchange Agreement).

2.3. Captions. The headings contained in this Amendment are for reference purposes only and shall not affect in any way the meaning or interpretation of this Amendment. Except as otherwise indicated, all references in this Amendment to “Sections” are intended to refer to the Sections of each Warrant.

2.4.  Jurisdiction. All questions concerning the construction, validity, enforcement and interpretation of this Amendment shall be determined in accordance with the provisions of the Exchange Agreement.

2.5. No Other Amendment. Except for the matters expressly set forth in this Amendment, all other terms of the Warrant are hereby ratified and shall remain unchanged and in full force and effect.

2.6. Counterparts. This Amendment may be executed in counterparts, each of which shall be deemed to be an original, and all of which together shall be deemed to be one and the same instrument.

2.7. Electronic and Facsimile Signatures. Any signature page delivered electronically or by facsimile (including without limitation transmission by .pdf) shall be binding to the same extent as an original signature page, with regard to any agreement subject to the terms hereof or any amendment thereto. Any party who delivers such a signature page agrees to later deliver an original counterpart to the other party if so requested.

[Signature Pages Follow]

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The parties hereto have executed this Amendment to Common Stock Purchase Warrant as of the date first written above.

company:

Amyris, inc.

By: /s/ Han Kieftenbeld

        Name: Han Kieftenbeld

        Title: Chief Financial Officer

[Signature Page to Amendment to Common Stock Purchase Warrant]

The parties hereto have executed this Amendment To Common Stock Purchase Warrant as of the date first written above.

HOLDER:

HT INVESTMENTS MA LLC

By: /s/ Eric Helenek

        Name: Eric Helenek

        Title: Authorized Signatory

[Signature Page to Amendment to Common Stock Purchase Warrant]

EX-4.05

Exhibit 4.05

EXECUTION VERSION

RIGHTS AMENDMENT AGREEMENT

This Rights Amendment Agreement (this “Amendment”) is made as of May 1, 2020 by and between Amyris, Inc., a Delaware corporation (the “Company”), and SILVERBACK OPPORTUNISTIC CREDIT MASTER FUND LIMITED (the “Holder”).

RECITALS

WHEREAS, on January 31, 2020, the Company issued to the Holder rights (the “Rights”) to purchase additional shares of the Company’s Common Stock, pursuant to the terms of that certain Warrant Amendment Agreement, dated as of the same date, between the Company and the Holder; and

WHEREAS, the Company and the Holder hereby agree to amend the Rights to extend the termination date as provided herein.

AGREEMENT

NOW, THEREFORE, in consideration of the premises and mutual covenants contained herein and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, and intending to be legally bound hereby, the parties hereto agree as follows:

1.Rights Amendment. The definition of “Termination Date” shall be amended and restated in its entirety as follows:

1.“Termination Date. The Right shall terminate upon the twenty-four (24) month anniversary of the Issue Date (the “Right Termination Date”).”

2.No Other Amendments. Except as expressly set forth above, all of the terms and conditions of the Rights shall remain in full force and effect.

3.Effectiveness of Amendment. This Amendment shall be effective as of the date hereof.

4.Miscellaneous.

(a) Governing Law. This Amendment and all acts and transactions pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with the laws of the State of California, without giving effect to principles of conflicts of law.

(b) Counterparts. This Amendment may be executed in two counterparts, each of which shall be deemed an original and all of which together shall constitute one instrument.

[SIGNATURE PAGES FOLLOW]

The undersigned has executed this Rights Amendment Agreement as of the date first set forth above.

THE COMPANY:

AMYRIS, INC.

By: _/s/ Han Kieftenbeld

(Signature)

Name: Han Kieftenbeld

Title: Chief Financial Officer

The undersigned has executed this Rights Amendment Agreement as of the date first set forth above.

HOLDER:

SILVERBACK OPPORTUNISTIC CREDIT MASTER FUND LIMITED

/s/ Robert Barron

     (Signature)

Name: Robert Barron

Title: Portfolio Manager

EX-4.06

Exhibit 4.06

Senior Convertible Note Maturity Extension

May 7, 2020

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, California 94608

Attention: Kathleen Valiasek

Re: Extension of Senior Convertible Note due April 30, 2020

Ladies and Gentlemen:

WHEREAS, Total Raffinage Chimie (the “Investor”) is the holder of that certain Senior Convertible Note due initially June 14, 2019, which has been extended to mature on July 18, 2019, then further extended to mature on August 28, 2019, then further extended to mature on October 28, 2019, then further extended to mature on December 16, 2019, then further extended to mature on January 31, 2020, and then further extended to mature on March 31, 2020 issued by Amyris, Inc. (the “Company”) in the principal amount of $9,075,414 (the “Note”; capitalized terms used but not defined herein shall have the meanings ascribed thereto in the Note), and further extended to mature on April 30, 2020, which Note is convertible into shares (the “Conversion Shares”, and, together with the Note, the “Securities”) of the Company’s common stock, par value $0.0001 per share (the “Common Stock”), in accordance with the terms of the Note, pursuant and subject to the terms and conditions set forth in that certain Exchange Agreement, dated May 15, 2019, between the Company and the Investor, the Senior Convertible Note Maturity Extensions, dated June 20, 2019; July 24, 2019; September 4, 2019; October 31, 2019; December 20, 2019; March 11, 2020, April 6, 2020 and this agreement (this “Agreement”); and

WHEREAS, the Company and the Investor desire to again extend the maturity date of the Note and to make certain other changes to the Note as set forth herein.

NOW, THEREFORE, in consideration of the promises, undertakings and obligations set forth herein, the sufficiency of which consideration is hereby acknowledged, each of the undersigned parties agree with each other as follows:

1. Extension of Maturity Date. Subject to the terms and conditions of this Agreement, effective April 30, 2020, (i) the maturity date (the “Maturity Date”) of the Note shall be extended to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020, and (ii) the Note shall continue to provide that the Company shall not effect any conversion thereof, and the Investor shall not have the right to convert any portion thereof, to the extent that the Investor (together with the Investor’s Affiliates, and any Persons acting as a group together with the Investor or any of the Investor’s Affiliates) would beneficially own in excess of 4.99% of the issued and outstanding shares of Common Stock after giving effect to such conversion, unless 61 days’ prior notice to waive such provision is given in writing by the Investor. In connection therewith, the Company shall re-issue the Note in the form set forth in Exhibit A attached hereto, and the Investor shall return the existing Note, each in accordance with the provisions of Section 3 below. Subject to the issuance by the Company of a new Note in accordance with Section 3 below, the Investor waives any failure by the Company to pay the principal of, and accrued and unpaid interest on, the Note on or prior to April 30, 2020.

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2. Mechanics of Note Issuance and Cancellation. Within three (3) business days from the date hereof, (i) the Company shall re-issue the Note, in the form set forth in Exhibit A attached hereto, by delivering an originally executed re-issued Note to Investor’s counsel at the offices of Dentons US LLP at 1221 Avenue of the Americas, New York, NY 10020, Attn: Brian Lee, and (ii) the Investor shall return the originally executed existing Note to the Company at its headquarters, for cancellation, it being acknowledged by the Company that the existing Note shall not be cancelled until and unless an attorney at Dentons US LLP acknowledges receipt of the re-issued Note on behalf of Investor. For the avoidance of doubt, the parties agree that the re-issuance of the Note reflecting the terms of this Agreement is solely for the convenience of Investor and shall not be deemed the issuance of a new security distinct from the Note.

3. Representations and Warranties of the Company. The Company represents and warrants to the Investor that, as of the date hereof:

(a)  Organization and Standing. The Company and each of its Significant Subsidiaries (as defined in Regulation S-X of the Securities Act) is duly incorporated, validly existing, and in good standing under the laws of the jurisdiction of its incorporation or organization. The Company and each of its Significant Subsidiaries has all requisite power and authority to own and operate its properties and assets and to carry on its business as presently conducted and as proposed to be conducted. The Company and each of its Significant Subsidiaries is qualified to do business as a foreign entity in every jurisdiction in which the failure to be so qualified would have, or would reasonably be expected to have, a material adverse effect, individually or in the aggregate, upon the business, properties, tangible and intangible assets, liabilities, operations, prospects, financial condition or results of operation of the Company or the ability of the Company to perform its obligations under this Agreement or the Note.

(b)  Power. The Company has all requisite power to execute and deliver this Agreement and to carry out and perform its obligations under the terms of this Agreement.

(c)  Authorization. The execution, delivery, and performance of this Agreement by the Company has been duly authorized by all requisite action on the part of the Company and its officers, directors and stockholders, and this Agreement constitutes the legal, valid, and binding obligation of the Company enforceable in accordance with its terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium, and other laws of general application affecting enforcement of creditors’ rights generally, and (b) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies.

(d) Capitalization. The capitalization of the Company, on a fully diluted basis, is as set forth herein as Schedule 4(d), which information is true, complete and accurate.  

(e) Validity of Note and Waiver of Defenses. The Company acknowledges the validity, priority and enforceability of the Note as a debt instrument and any of the obligations thereunder and waives (on behalf of itself, and any other person, entity or other party in interest that may claim by, through, or on the Company’s behalf) any right, claim, or defense to the Note or any of the obligations thereunder on the grounds that they should be recharacterized as or subordinated to the level of equity.

(f) No Events of Default. After giving effect to this Agreement, there has not been any, and there is not any continuing, Event of Default that has not otherwise been cured or waived.

(g) Other Loan Agreements. The Company has entered into valid and enforceable waivers, forbearances or extension agreements (“Waivers”) with each of Foris Ventures, LLC; Naxyris S.A.; Schottenfeld Opportunities Fund II, L.P.; Koyote Trading, LLC; Phase Five Partners, LP; DSM Finance

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B.V., Ginkgo Bioworks, Inc. and Nikko Chemicals Co. (collectively, the “Waiving Lenders”) with regards to payments due on or about April 30, 2020.

(h) Indebtedness. Since March 31, 2020, the Company has not made any cash payment on or with respect to the principal amount of, or purchase, redeem, defease or otherwise settle in whole or in part any Indebtedness (as defined below) of the Company, except for any cash payment expressly permitted under Section 5(a) of that certain Note Extension Agreement entered into between the Company and Investor, dated October 31, 2019.

4. Representations and Warranties of the Investor. The Investor hereby represents and warrants to and covenants with the Company that, as of the date hereof:

(a) Organization and Good Standing. The Investor is a corporation, limited partnership, limited liability company or other entity, as the case may be, duly formed, validly existing and in good standing under the laws of the jurisdiction of its formation.

(b) Due Authorization. The Investor has the requisite power and authority to enter into and perform its obligations under this Agreement.

5. Covenants and Negative Covenants of the Company.

(a) Indebtedness. Until such time as the Note is paid in full or converted into Conversion Shares, the Company shall not, without the prior written consent of the Investor, make any cash payment on or with respect to the principal amount of, or purchase, redeem, defease or otherwise settle in whole or in part any Indebtedness of the Company. For purposes of this Agreement, “Indebtedness” shall mean any amount, excluding trade payables occurring in the ordinary course of business, that (i) is owed by the Company resulting from borrowed money, or (ii) is evidenced by bonds, notes, debentures or similar instruments or letters of credit (or reimbursement agreements in respect thereof).

(b) Financing. At any time prior to the Maturity Date, if the Company raises funds equal to or greater than $20 million, the Company will repay the outstanding principal amount and all accrued and unpaid interest on the Note in full upon the close of such financing.

(c) Exercise of Warrants. At such time as the Investor exercises some or all of its warrants to purchase shares of common stock of the Company pursuant to the cashless exercise mechanism provided for under such warrants, the Company shall cause the Company’s stock transfer agent to issue the number of shares of common stock of the Company in accordance with the provisions of the warrants, free of any restrictive legend relating to the Securities Act. The Company agrees that the shares of common stock of the Company issuable to Investor from a cashless exercise of such warrants would be, for purposes of Rule 144, acquired from the Company (or from an Affiliate of the Company) more than one year prior to the relevant date of determination and therefore, are eligible for resale under Rule 144(b).

(d) Validity of Waivers. Each of the Waivers shall be valid and enforceable at all times from the date of its execution through the Maturity Date, and all of the Waiving Lenders shall continue through the Maturity Date to waive from exercising their respective rights and remedies. Furthermore, no person at any time shall exercise for any reason any of rights or remedies against the Company under any instrument evidencing Indebtedness, or against the Company’s properties or assets, in each case, of the type that would constitute an Event of Default under the Note.

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(e) Payment of Legal Expenses. Within ten (10) business days of the Company’s receipt from Investor of an invoice of Dentons US LLP, counsel to the Investor, relating to reasonable legal fees incurred by Investor in connection with the transaction contemplated by this Agreement, the Company shall reimburse Investor the amount set forth in such invoice.

6. Waiver and Amendment. Neither this Agreement, the Note nor any provisions hereof or thereof shall be modified, changed, discharged, waived or terminated except by an instrument in writing signed by the Company and the Investor.

7. Waiver of Jury Trial. EACH OF THE COMPANY AND THE INVESTOR IRREVOCABLY WAIVES ANY AND ALL RIGHT TO TRIAL BY JURY WITH RESPECT TO ANY LEGAL PROCEEDING ARISING OUT OF THE TRANSACTIONS CONTEMPLATED BY THIS AGREEMENT.

8. Governing Law/Venue. THIS AGREEMENT SHALL BE GOVERNED BY THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO CONFLICT OF LAW PRINCIPLES THAT WOULD RESULT IN THE APPLICATION OF ANY LAW OTHER THAN THE LAW OF THE STATE OF NEW YORK. Each of the Company and the Investor (a) agrees that any legal suit, action or proceeding arising out of or relating to this agreement or the transactions contemplated hereby shall be instituted exclusively in the courts of the State of New York located in the City and County of New York or in the United States District Court for the Southern District of New York; (b) waives any objection that it may now or hereafter have to the venue of any such suit, action or proceeding; and (c) irrevocably consents to the jurisdiction of the aforesaid courts in any such suit, action or proceeding.

9. Section and Other Headings. The section and other headings contained in this Agreement are for reference purposes only and shall not affect the meaning or interpretation of this Agreement.

10. Counterparts. This Agreement may be executed by one or more of the parties hereto in any number of separate counterparts (including by facsimile or other electronic means, including telecopy, email or otherwise), and all of said counterparts taken together shall be deemed to constitute one and the same instrument. Delivery of an executed signature page of this Agreement by facsimile or other transmission (e.g., “pdf” or “tif” format) shall be effective as delivery of a manually executed counterpart hereof.

11. Notices. All notices and other communications provided for herein shall be in writing and shall be deemed to have been duly given if delivered personally or sent by prepaid overnight courier or registered or certified mail, return receipt requested, postage prepaid to, in the case of the Company, the following address and, in the case of the Investor, the address provided on the signature page of the Investor hereto (or such other address as any party shall have specified by notice in writing to the other):

If to the Company: Amyris, Inc. 5885 Hollis Street, Suite 100 Emeryville, California 94608 Fax: Attention: General Counsel

12. Binding Effect. The provisions of this Agreement shall be binding upon and accrue to the benefit of the parties hereto and their respective heirs, legal representatives, successors and permitted assigns.

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13. Severability. If any term or provision (in whole or in part) of this Agreement is determined to be invalid, illegal or unenforceable in any jurisdiction, such invalidity, illegality or unenforceability shall not affect any other term or provision of this Agreement or invalidate or render unenforceable such term or provision in any other jurisdiction.

14. Release. In consideration of the agreements of the Investor set forth in this Agreement, the Company, its affiliates and subsidiaries, and all of their respective directors, officers, agents, heirs, personal representatives, predecessors, successors and assigns (individually and collectively, the “Releasors”), hereby fully, finally, and forever release and discharge the Investor, its affiliates and subsidiaries, and its any of their successors, assigns, directors, officers, employees, agents, and representatives (including those on the board of Company or any of its subsidiaries or affiliates) from any and all actions, causes of action, claims, debts, demands, liabilities, obligations, and suits of whatever kind or nature, in law or equity, the Releasors or any of them have, whether known or unknown, in respect of, relating to, or concerning this Agreement, the Securities, any other potential agreement or transaction relating to the Securities, or any open market transactions in the Company effectuated by the Investor arising from events occurring prior to the date hereof.

[SIGNATURE PAGES FOLLOW]

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IN WITNESS WHEREOF, the undersigned has executed this Agreement as of the date first written above.

AMYRIS, INC.

By: /s/ Kathleen Valiasek

Name: Kathleen Valiasek

Title: Chief Business Officer

IN WITNESS WHEREOF, the undersigned has executed this Agreement as of the date first written above.

INVESTOR:

TOTAL RAFFINAGE CHIMIE

By: /s/ Philippe Orts

Name: Philippe Orts

Title: Senior VP Corporate Affairs

Address for Notices:

TOTAL RAFFINAGE CHIMIE

Attention:

EX-4.09

Exhibit 4.09

Execution Copy

SECOND AMENDMENT TO SENIOR CONVERTIBLE NOTE DUE 2022 AND WAIVER AND FORBEARANCE AGREEMENT

This SECOND AMENDMENT TO SENIOR CONVERTIBLE NOTE DUE 2022 AND WAIVER AND FORBEARANCE AGREEMENT (this “Second Amendment”) is made and entered into as of June 4, 2020, by and among Amyris, Inc., a Delaware corporation (the “Company”) and HT Investments MA LLC (the “Holder”).

RECITALS

WHEREAS, the Company has issued that certain Senior Convertible Note due 2022 (the “Note”), to the Holder pursuant to exchanges for prior convertible notes of the Company in reliance upon the exemption from registration provided by Section 3(a)(9) of the Securities Act of 1933, as amended (the “Securities Act”), as set forth in (i) that certain Exchange Agreement, dated as of November 8, 2019, by and among the Company and the investors on the Schedule of Buyers attached thereto (the “Original Exchange Agreement”) (as the same may be amended from time to time) and (ii) that certain Exchange Agreement, dated as of December 30, 2019, by and among the Company and the Buyer (the “Subsequent Exchange Agreement”) (as the same may be amended from time to time);

WHEREAS, the Company and Holder previously entered into that certain Amendment to Senior Convertible Note Due 2022 and Waiver and Forbearance Agreement as of May 1, 2020 (the First Amendment”); and

WHEREAS, the Company and the Holder desire to further amend certain provisions of the Note;

WHEREAS, pursuant to Section 18 of the Note, the Note may be amended with the written consent of the Company and the Required Holders (as defined in the Original Exchange Agreement);

WHEREAS, as of the date hereof, the Holder constitutes the Required Holders (as defined in the Original Exchange Agreement); and

WHEREAS, the Company and Holder have entered into that certain Waiver and Forbearance Agreement, dated as of February 18, 2020 (the “Forbearance Agreement”) and desire to further amend certain provisions of the Forbearance Agreement.

NOW, THEREFORE, in consideration of the mutual covenants and agreements set forth herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto, intending to be legally bound, agree as follows:

ARTICLE I

AMENDMENT OF NOTES

1.1. Section 5(G)(iii) of the Note. Section 5(G)(iii) of the Note is hereby amended and restated in its entirety to read as follows:

(iii)Pre-Delivery Share Reduction. Notwithstanding anything to the contrary contained herein, (A) from and after May 1, 2020, one million seven hundred

thousand (1,700,000) shares of Common Stock that were previously Pre-Delivery Shares hereunder shall no longer constitute Pre-Delivery Shares and, subject to that certain letter agreement between the Company and the Holder dated as of May 1, 2020, shall be Freely Tradable shares of Common Stock owned by the Holder, free from all preemptive or similar rights or Liens with respect thereto and (B) from and after June 4, 2020, an additional seven hundred thousand (700,000) shares of Common Stock that were previously Pre-Delivery Shares hereunder shall no longer constitute Pre-Delivery Shares, subject to that certain letter agreement between the Company and the Holder dated as of June 4, 2020, and shall be Freely Tradable shares of Common Stock owned by the Holder, free from all preemptive or similar rights or Liens with respect thereto. For the avoidance of doubt, as of June 4, 2020, the total number of Pre-Delivery Shares outstanding shall be deemed to be two million six hundred thousand (2,600,000) shares.

1.2. Section 5(G)(iv) of the Note. Section 5(G)(iv) of the Note is hereby amended and restated in its entirety to read as follows:

(ii) Delivery of Pre-Delivery Shares by the Holder. Within ten (10) Business Days following redemption or repayment of this Note in full and the satisfaction or discharge by the Company of all outstanding Company obligations hereunder, the Holder shall deliver two million six hundred thousand (2,600,000) shares (subject to proportionate adjustments for events of the type set forth in Section 8(F)(i)(1)) of the Company’s Common Stock to the Company, free from all preemptive or similar rights or Liens with respect to the delivery thereof; provided, that, to the extent the Company fails to deliver any fully paid and nonassessable Freely Tradable shares of Common Stock to the Holder as required under Section 5(G)(i) or Section 5(G)(ii), the number of shares of the Company’s Common Stock to be delivered under this Section 5(G)(iv) shall be reduced by the number of such shares of Common Stock the Company failed to deliver. For the avoidance of doubt, this Section 5(G)(iv) shall not apply to the transactions contemplated by the Exchange Agreement.

ARTICLE II

AMENDMENT OF FORBEARANCE AGREEMENT

2.1. The definition of “Forbearance Period” as set forth in the Forbearance Agreement is hereby amended and restated in its entirety to read as follows:

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(a) “Forbearance Period” means the period commencing on the date hereof and ending on the date which is the earliest of (i) with respect to the Specified Existing Defaults, the earlier of (X) the day the Company has received aggregate cash proceeds from any public offerings or private placements of its securities occurring on or after May 1, 2020 of not less than fifty million dollars ($50,000,000) and (Y) June 30, 2020, and with respect to the Specified Anticipated Default, May 29, 2020, (ii) the occurrence or existence of any Event of Default, other than the Specified

Defaults and any Event of Default giving rise to a Termination Event, or (iii) the occurrence of any Termination Event.

2.2. The definition of “Specified Existing Defaults” as set forth in the Forbearance Agreement is hereby amended and restated in its entirety to read as follows:

(d) “Specified Existing Defaults” means each of: (1) Company's failure, on or before January 31, 2020, to receive aggregated net cash proceeds of not less than fifty million dollars ($50,000,000) from one or more issuances of Capital Stock or incurrences of Permitted Indebtedness (as defined in the Note) by the Company, or any combination thereof, and before giving effect to transaction expenses; (2) Company’s failure, on or before January 31, 2020, to (i) repay in full or convert into equity all Indebtedness outstanding under its Credit and Security Agreement, dated November 14, 2019 by and among the Company, certain of the Company’s subsidiaries, Schottenfeld Opportunities Fund II, L.P. (“SOP”) and Phase Five Partners, LP (“Phase Five”) (the “November Credit Agreement”), or (ii) amend all such Indebtedness to fit within clause (E) of the definition of Permitted Indebtedness so it does not have a final maturity date, amortization payment, sinking fund, mandatory redemption or other repurchase obligation or put right at the option of the lender or holder of such Indebtedness earlier than ninety one (91) days following the Maturity Date, or any combination of the foregoing with respect to all such Indebtedness; (3) Company’s entry into a secured loan agreement on December 19, 2019 with an initial maturity date of January 31, 2020 with Nikko Chemicals Co., Ltd., in violation of Section 9(D) of the Note; and (4) the occurrence of an Event of Default under clause 11(A)(xi) of the Note, solely to the extent arising from defaults (I) in existence on the date hereof with respect to the notes issued under (A) those certain credit agreements dated September 10, 2019 by and among the Company, certain of the Company’s subsidiaries and each of SOP, Koyote Trading, LLC, and Phase Five (the “September Credit Agreements”) or (B) the November Credit Agreement and (II) for which the holder of such notes has not declared any portion of such indebtedness due and payable or taken any other steps to enforce such indebtedness.

ARTICLE III

MISCELLANEOUS

3.1. Rule 144 Holding Period. The Company and the Holder acknowledge and agree that, as set forth in the Original Exchange Agreement and the Subsequent Exchange

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Agreement, the Note will continue to have a holding period under Rule 144 promulgated under the Securities Act that will be deemed to have commenced as of December 10, 2018.

3.2. Material Non-Public Information. The Company represents to Holder that neither this Second Amendment, nor the further amendment of the Note and/or the Warrant pursuant to the terms of this Second Amendment constitutes material, nonpublic information (if any) provided to the Holder by the Company.

3.3 Captions. The headings contained in this Amendment are for reference purposes only and shall not affect in any way the meaning or interpretation of this Amendment. Except as otherwise indicated, all references in this Amendment to “Sections” are intended to refer to the Sections or Articles of the Note, as applicable.

3.4. Governing Law. The internal law of the State of New York will govern and be used to construe this Amendment. The Company and the Holder irrevocably waive, to the fullest extent permitted by applicable law, any and all right to trial by jury in any legal proceeding arising out of or relating to this Amendment.

3.5. Principal Amount; No Other Amendment. The Company and the Holder acknowledge and agree that the Principal Amount outstanding under the Note as of the date hereof is twenty million dollars ($20,000,000). Except for the matters expressly set forth in this Second Amendment, all other terms of the Note and Warrant, as amended by the First Amendment, are hereby ratified and shall remain unchanged and in full force and effect.

3.6. Counterparts. This Amendment may be executed in counterparts, each of which shall be deemed to be an original, and all of which together shall be deemed to be one and the same instrument.

3.7. Electronic and Facsimile Signatures. Any signature page delivered electronically or by facsimile (including without limitation transmission by .pdf) shall be binding to the same extent as an original signature page, with regard to any agreement subject to the terms hereof or any amendment thereto. Any party who delivers such a signature page agrees to later deliver an original counterpart to the other party if so requested.

[Signature Pages Follow]

The parties hereto have executed this Second Amendment to Senior Convertible Note due 2022 and Waiver and Forbearance Agreementas of the date first written above.

COMPANY:

AMYRIS, INC.

By: /s/ Han Kieftenbeld

        Name: Han Kieftenbeld

        Title: Chief Financial Officer

The parties hereto have executed this Second Amendment to Senior Convertible Note due 2022and Waiver and Forbearance Agreement as of the date first written above.

REQUISITE HOLDER:

HT INVESTMENTS MA LLC

By: /s/ Eric Helenek

        Name: Eric Helenek

        Title: Authorized Signatory

EX-10.01

Exhibit 10.01

EXECUTION VERSION

WAIVER AGREEMENT

This Waiver Agreement (this “Third Waiver Agreement”) is made as of May 6, 2020 by and between Amyris, Inc., a Delaware corporation (the “Company”), and Ginkgo Bioworks, Inc., a Delaware corporation (“Ginkgo”), pursuant to the terms of (i) that certain Promissory Note, dated October 20, 2017 (as amended, the “Note”), issued by the Company to Ginkgo, (ii) that certain Partnership Agreement, dated October 20, 2017 (the “Partnership Agreement”), by and between the Company and Ginkgo, (iii) that certain Waiver Agreement and Amendment to Promissory Note Issued October 20, 2017, dated September 29, 2019 (the “First Waiver Agreement”), by and between the Company and Ginkgo, and (iv) that certain Waiver Agreement and Amendment, dated March 11, 2020 (the “Second Waiver Agreement”), by and between the Company and Ginkgo. Capitalized terms used but not otherwise defined herein shall have the meanings given to such terms in the Note or the Partnership Agreement, as applicable.

RECITALS

A. Pursuant to Section 2.1(b) of the Note, the Company is required to make monthly interest payments to Ginkgo beginning on November 30, 2017 and continuing on the last day of each month thereafter, through and including the Maturity Date (each, an “Interest Payment”).

B. Pursuant to Section 4.3(a) of the Partnership Agreement, as amended by the Second Waiver Agreement, the Company is required to pay Ginkgo monthly fees beginning on March 31, 2020 and continuing on the last day of each month thereafter, through and including October 31, 2021 (each, a “Partnership Payment”).

C. Pursuant to Section 6.3 of the Note, the Company is required to notify Ginkgo in writing in the event that the consolidated cash balance of the Company is less than $10,000,000 at monthly close (the “Reporting Covenant”).

D. Pursuant to Section 4(d) of the Note, certain cross defaults by the Company are considered an Event of Default (the “Cross Default”).

E. Pursuant to Section 6 of the Second Waiver Agreement, the Company was required to pay Ginkgo on or before April 30, 2020, an aggregate of $7,153,770 (the “April 2020 Payment”), which represents all the payments due on or before April 30, 2020 pursuant to the Note, the Partnership Agreement, the First Waiver Agreement, and the Second Waiver Agreement.

F. The Company has requested and Ginkgo has agreed, in consideration of and subject to the terms and conditions contained herein, to (i) waive any failure by the Company to make the April 2020 Payment prior to April 30, 2020, (ii) waive any failure by the Company to comply with the Reporting Covenant prior to the date hereof, and (iii) waive any Cross Default by the Company occurring or existing during the period beginning on March 31, 2020 and ending on the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020.

G. Pursuant to Section 10.7 of the Note, provisions of the Note may be amended or waived only by written agreement of the Company and Ginkgo.

H. Pursuant to Section 9.4 of the Partnership Agreement, any modification to the Partnership Agreement shall only be effective if made in a writing signed by the Company and Ginkgo.

AGREEMENT

For good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Company and Ginkgo agree as follows:

1. Reporting Covenant Waiver. In accordance with Section 10.7 of the Note, Ginkgo hereby waives any failure by the Company to comply with the Reporting Covenant prior to the date hereof, including any default or Event of Default resulting therefrom under the Note or the Partnership Agreement, including without limitation with respect to acceleration of any Partnership Payments pursuant to Section 4.3(d) of the Partnership Agreement.

2. Cross Default Waiver. In accordance with Section 10.7 of the Note, Ginkgo hereby waives any Cross Default by the Company occurring or existing during the period beginning on March 31, 2020 and ending on the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020 (inclusive), including any default or Event of Default resulting therefrom under the Note or the Partnership Agreement, including without limitation with respect to acceleration of any Partnership Payments pursuant to Section 4.3(d) of the Partnership Agreement.

3. May 2020 Payment. Ginkgo hereby waives timely payment of the April 2020 Payment until the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020 (the “Payment Deadline”), and agrees that, notwithstanding anything to the contrary in this Third Waiver Agreement, the Second Waiver Agreement remains in full force and effect with respect to the waivers and amendment set forth therein. Moreover, the Company agrees that in addition to the April 2020 Payment, it will pay to Ginkgo the additional sum of $774,011, for a total payment of $7,927,781 (the “May 2020 Payment”), which represents all the payments due on or before May 31, 2020 pursuant to the Note, the Partnership Agreement, the First Waiver Agreement, the Second Waiver Agreement, and this Third Waiver Agreement. The May 2020 Payment will be paid by the Company by wire transfer of immediately available funds in accordance with the wire instructions delivered to the Company by Ginkgo no later than two (2) Business Days prior to the applicable payment date. Any failure by the Company to make any payment set forth in this Section 3 on or prior to the applicable payment deadline shall (a) constitute an Event of Default under the Note and the Partnership Agreement; and (b) render all waivers set forth in Sections 1-5 of the Second Waiver Agreement and Sections 1-2 of this Third Waiver Agreement null and void.

4. Full Force and Effect.Except as expressly modified by this Third Waiver Agreement, the terms of the Note (as amended by the First Waiver Agreement), the Partnership Agreement (as amended by the Second Waiver Agreement), and the First and Second Waiver Agreements shall remain in full force and effect.

5. Release.In consideration of the agreements contained in this Third Waiver Agreement and other good and valuable consideration, the Company unconditionally and irrevocably releases, waives, and forever discharges Ginkgo, together with its respective predecessors, successors, assigns, subsidiaries, affiliates, agents, employees, directors, officers, attorneys, and attorneys’ consultants (collectively, the “Released Parties”), from (x) any and all liabilities, obligations, duties, promises, or

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indebtedness of any kind (if any) of the Released Parties to the Company or any of its affiliates, which existed, arose, or occurred at any time from the beginning of the world to the date of this Third Waiver Agreement; and (y) all claims, offsets, causes of action, suits, or defenses of any kind whatsoever (if any), which the Company or any of its affiliates might otherwise have against the Released Parties, or any of them; in either case of (x) or (y) on account of any condition, act, omission, event, contract, liability, obligation, indebtedness, claim, cause of action, defense, circumstance, or matter of any kind, which existed, arose, or occurred at any time from the beginning of the world to the date of this Third Waiver Agreement, whether at law or in equity, whether based upon statute, common law or otherwise, whether matured, contingent or non-contingent, whether direct or indirect, whether known or unknown, whether suspected or unsuspected, which the Company ever had, now has, or may claim to have against, arising out of, based on, asserted in, or in connection with any agreement or event.

6. Section 1542 Waiver. In consideration of the agreements contained in this Third Waiver Agreement and other good and valuable consideration, the Company unconditionally and irrevocably waives any rights it has or may have pursuant to California Civil Code Section 1542, which provides as follows:

A general release does not extend to claims that the creditor or releasing party does not know or suspect to exist in his or her favor at the time of executing the release and that, if known by him or her, would have materially affected his or her settlement with the debtor or released party.

7. Attorneys’ Fees. The Company promises to pay to Ginkgo immediately upon receipt of an invoice any and all reasonable attorneys’ and other professionals’ fees and expenses incurred by Ginkgo between March 12, 2020 and the date hereof, inclusive, in connection with the Note, the Partnership Agreement, the First and Second Waiver Agreements, and/or this Third Waiver Agreement, including, without limitation, with respect to the administration, collection, enforcement, amendment or modification of any of them; and with respect to any waiver, consent, release, termination, litigation, administrative proceeding, arbitration, bankruptcy proceeding, or dispute resolution. Any failure by the Company to make timely payment as set forth in this Section 7 shall render all waivers set forth in Sections 1-5 of the Second Waiver Agreement and Sections 1-2 of this Third Waiver Agreement null and void.

8. Integration.This Third Waiver Agreement, the Note (as amended by the First Waiver Agreement), the Partnership Agreement (as amended by the Second Waiver Agreement), and the First and Second Waiver Agreements constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between the parties hereto with respect to the specific subject matter hereof.

9. Counterparts.This Third Waiver Agreement may be executed in one (1) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Third Waiver Agreement may be executed and delivered by facsimile, or by email in portable document format (.pdf) or other electronic format, and delivery of any signature page by any such method will be deemed to have the same effect as if the original signature page had been delivered to the other party.

[Signature pages follow]

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IN WITNESS WHEREOF, the parties hereto have executed this Third Waiver Agreement as of the date first above written.

AMYRIS, INC.

By: /s/ Kathleen Valiasek

Name: Kathleen Valiasek

Title: Chief Business Officer

[Waiver Signature Page]

IN WITNESS WHEREOF, the parties hereto have executed this Third Waiver Agreement as of the date first above written.

GINKGO BIOWORKS, INC.

By: /s/ Jason Kelly

Name: Jason Kelly

Title: CEO

[Waiver Signature Page]

EX-10.02

Exhibit 10.02

SECOND AMENDMENT

TO LOAN AGREEMENT

THIS AMENDMENT TO AMENDMENT TO LOAN AGREEMENT (the “Second Amendment Agreement”), is made and entered into, as of April 3, 2020 (the “Effective Date”) by and between Nikko Chemicals Co., Ltd. (“Lender”) and Amyris, Inc. (“Borrower”). Except as otherwise defined herein, all capitalized terms in this Amendment have the same meaning as set forth in the Loan Agreement as amended by the First Amendment Agreement (as defined below).

WHEREAS, the parties hereto entered into a Loan Agreement dated December 19, 2019 (the “Loan Agreement”);

WHEREAS, the parties hereto entered into an Amendment to Loan Agreement dated March 12, 2020 (the “First Amendment Agreement”); and

WHEREAS, the parties hereto desire to confirm and amend certain terms of the Loan Agreement and the First Amendment Agreement.

NOW, THEREFORE, in consideration of the agreements and obligations set forth herein and for other good and valuable consideration, the receipt and sufficiency of which are here acknowledged, the parties hereto hereby agree and confirm as follows:

1.  Payment. The repayment date of the Principal under Section 3(1) of the Loan Agreement shall be “April 30, 2020” (the “Maturity Date”), rather than March 31, 2020. Upon the execution of this Amendment, Borrower shall make an outstanding payment of all of the Interest under the Loan Agreement and the First Amendment Agreement which shall be US$55,718.74. Any Interest on the Second Amendment Agreement shall be payable on the Maturity Date. Notwithstanding above, all outstanding Loan and Interest shall be prepaid upon closing of the Borrower’s fundraising in the amount of $70,000,000.00 or more.

2.  Effective Date. This Agreement shall be effective as of the Effective Date (subject to Borrower’s full payment under Paragraph 4 to Lender). Except as expressly amended in this Agreement, any other terms and conditions shall remain unchanged and continue to be in full force and effect.

IN WITNESS WHEREOF, the parties hereto have executed and delivered this Agreement as of the date first above written.

NIKKO CHEMICALS CO., LTD.
By: /s/ Shizuo Ukaji___________________
Name: Shizuo Ukaji
Title: President & Chief Executive Officer
AMYRIS, INC.
By:	_/s/ John Melo_________________
Name:	John Melo
Title:	President & Chief Executive Officer

EX-10.03

Exhibit 10.03

EXECUTION VERSION

CREDIT AGREEMENT

This CREDIT AGREEMENT, dated as of April 29, 2020 (as amended, modified or supplemented from time to time, this “Agreement”), is entered into by and between AMYRIS, INC., a Delaware corporation (the “Company”), and Foris Ventures, LLC, a Delaware limited liability company (the “Lender”).

RECITALS

    A.  Subject to the terms and conditions hereof, the Lender has agreed to purchase from the Company, and the Company has agreed to sell to the Lender, an unsecured promissory note (the “Note”) in the form attached hereto as Exhibit Ahaving an aggregate principal amount of Five Million Dollars ($5,000,000).

AGREEMENT

NOW THEREFORE, in consideration of the representations, warranties, and conditions set forth below, the parties hereto, intending to be legally bound, hereby agree as follows:

    1.  Purchase and Sale of the Note.  The sale and purchase of the Note shall take place at such place and time as the Company and the Lender may determine, but in no event later than April 29, 2020 (the “Closing”). At the Closing, the Company will deliver to the Lender the Note, against receipt by the Company of Five Million Dollars ($5,000,000) in immediately available funds. The Note will be registered in the Lender’s name in the Company’s records.

   2.  Representations and Warranties of the Company.  The Company represents and warrants to the Lender as of the date hereof and as of the Closing that:

(a)Due Incorporation, Qualification, etc.  The Company (i) is a corporation duly organized, validly existing and in good standing under the laws of Delaware; (ii) has the power and authority to own, lease and operate its properties and carry on its business as now conducted; and (iii) is duly qualified, licensed to do business and in good standing as a foreign corporation in each jurisdiction where the failure to be so qualified or licensed could reasonably be expected to have a Material Adverse Effect.

(b)Authority.  The execution, delivery and performance by the Company of this Agreement and the Note and the consummation by the Company of the transactions contemplated hereby and thereby have been duly authorized by all necessary corporate actions on the part of the Company.

(c)Enforceability.  This Agreement and the Note have been duly executed and delivered by the Company and constitute a legal, valid and binding obligation of the Company, enforceable against the Company in accordance with its respective terms, except in each case as may be limited by bankruptcy, insolvency or other laws of general application relating to or affecting the enforcement of creditors’ rights generally and general principles of equity.

(d)Non-Contravention.  The execution and delivery by the Company of this Agreement and the Note and the performance and consummation by the Company of the transactions contemplated hereby and thereby do not and will not (i) violate the certificate of incorporation or bylaws of the Company or any judgment, order, writ, decree, statute, rule or

regulation applicable to the Company; (ii) violate any provision of, or result in the breach or the acceleration of, or entitle any other Person to accelerate (whether after the giving of notice or lapse of time or both), any mortgage, indenture, agreement, instrument or contract to which the Company is a party or by which it is bound except to the extent such violation, breach or acceleration could not reasonably be expected to result in a Material Adverse Effect; or (iii) result in the creation or imposition of any lien upon any property, asset or revenue of the Company or the suspension, revocation, impairment, forfeiture, or nonrenewal of any permit, license, authorization or approval applicable to the Company, its business or operations, or any of its assets or properties except to the extent such suspension, revocation, impairment, forfeiture or nonrenewal could not reasonably be expected to have a Material Adverse Effect. The Company is not in breach of any mortgage, indenture, agreement, instrument or contract to which the Company is a party or by which it is bound except to the extent such breach could not reasonably be expected to result in a Material Adverse Effect.

(e)Approvals.  No consent, approval, order or authorization of, or registration, declaration or filing with, any governmental authority or other Person is required in connection with the execution and delivery by the Company of this Agreement and the Note and the performance and consummation by the Company of the transactions contemplated hereby and thereby, except for those already obtained or those that will be obtained prior to the Closing.

(f)Tax Returns and Payments. The Company has timely filed all required tax returns and reports, and the Company has timely paid all foreign, federal, state and local taxes, assessments, deposits and contributions owed by the Company except to the extent such taxes are being contested in good faith by appropriate proceedings promptly instituted and diligently conducted, so long as such reserve or other appropriate provision, if any, as shall be required in conformity with GAAP shall have been made therefor.

(g)Litigation. There are no actions or proceedings pending or threatened in writing by or against the Company except for such actions or proceedings that, individually or in the aggregate, would not reasonably be expected to result in a Material Adverse Effect.

(h)Full Disclosure. No written representation, warranty or other statement of the Company in any certificate or written statement given to Lender by the Company in connection with this Agreement or the Note, as of the date such representation, warranty, or other statement was made, contains any untrue statement of a material fact or omits to state a material fact necessary to make the statements contained in the certificates or written statements not misleading in light of the circumstances under which they were made.

   3.  Representations and Warranties of the Lender.  The Lender represents and warrants to the Company as of the date hereof and as of the Closing that:

(a)Due Incorporation, Qualification, etc.  The Lender (i) is a limited liability company duly organized, validly existing and in good standing under the laws of Delaware; and (ii) has all requisite power to execute and deliver this Agreement and to carry out and perform its obligations under the terms of this Agreement.

(b)Authority.  The execution, delivery and performance by the Lender of this Agreement and the consummation by the Company of the transactions contemplated hereby have been duly authorized by all necessary corporate actions on the part of the Lender.

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(c)Enforceability.  The Lender has full legal capacity, power and authority to execute and deliver this Agreement and to perform its obligations hereunder. This Agreement is a valid and binding obligation of the Lender, enforceable in accordance with its terms, except as limited by bankruptcy, insolvency or other laws of general application relating to or affecting the enforcement of creditors’ rights generally and general principles of equity.

(d)Securities Law Compliance.   The Lender is purchasing the Note for its own account for investment, not as a nominee or agent, and not with a view to, or for resale in connection with, the distribution thereof. Lender has received or has had full access to all of the information necessary and appropriate to make an informed investment decision. The Lender is an accredited investor as such term is defined in Rule 501 of Regulation D under the Securities Act of 1933, as amended. The Lender acknowledges that it can bear the economic risk of the investment the Note.

(e)Approvals. No consent, approval, order or authorization of, or registration, declaration or filing with, any governmental authority or other Person is required in connection with the execution and delivery by the Lender of this Agreement and the performance and consummation by the Lender of the transactions contemplated hereby, except for those already obtained.

(f)Non-Contravention.  The execution and delivery by the Lender of this Agreement and the performance and consummation by the Lender of the transactions contemplated hereby do not and will not (i) violate the organizational documents of the Lender or any judgment, order, writ, decree, statute, rule or regulation applicable to the Lender; or (ii) violate any agreement to which the Lender is a party or by which it is bound.

    4.  Conditions to Obligations of the Lender.  The Lender’s obligations hereunder are subject to the fulfillment, on or prior to the Closing, of all of the following conditions, any of which may be waived in whole or in part by the Lender:

(a)Representations and Warranties.  The representations and warranties made by the Company in Section 2 hereof shall have been true and correct when made, and shall be true and correct as of the Closing.

(b)Governmental Approvals and Filings.  The Company shall have obtained all governmental approvals required in connection with the sale and issuance of the Note.

(c)Legal Requirements.  At the Closing, the sale and issuance by the Company, and the purchase by the Lender, of the Note shall be legally permitted by all laws and regulations to which the Lender or the Company is subject.

(d)Transaction Documents.  The Company shall have duly executed and delivered to the Lender this Agreement and the Note.

(e)Material Adverse Effect. No event shall have occurred that could reasonably be expected to result in a Material Adverse Effect.

    5.  Conditions to Obligations of the Company.  The Company’s obligations hereunder are subject to the fulfillment, on or prior to the Closing, of all of the following conditions, any of which may be waived in whole or in part by the Company:

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(a)Representations and Warranties.  The representations and warranties made by the Lender in Section 3 hereof shall be true and correct when made, and shall be true and correct as of the Closing.

(b)Governmental Approvals and Filings.  The Lender shall have obtained all governmental approvals required in connection with the sale and issuance of the Note.

(c)Legal Requirements.  At the Closing, the sale and issuance by the Company, and the purchase by the Lender, of the Note shall be legally permitted by all laws and regulations to which the Lender or the Company are subject.

(d)Purchase Price.  The Lender shall have delivered to the Company, in immediately available funds, an amount equal to the principal amount of the Note being issued at the Closing.

    6.   Definitions.  As used in this Agreement, the following capitalized terms have the following meanings:

“Material Adverse Effect” means a material adverse effect, individually or in the aggregate, upon the business, properties, tangible and intangible assets, liabilities, operations, prospects, financial condition or results of operation of the Company or the ability of the Company to perform its obligations under this Agreement.

“Obligations” means all loans, advances, debts, liabilities and obligations, howsoever arising, owed by the Company to the Lender under the Note of every kind and description (whether or not evidenced by any note or instrument and whether or not for the payment of money), now existing or hereafter arising under or pursuant to the terms of the Note, including all principal, interest, fees, charges, expenses, attorneys’ fees and costs and accountants’ fees and costs chargeable to and payable by the Company thereunder, in each case, whether direct or indirect, absolute or contingent, due or to become due, and whether or not arising after the commencement of a proceeding under Title 11 of the United States Code (11 U.S.C. Section 101 et seq.), as amended from time to time (including post-petition interest) and whether or not allowed or allowable as a claim in any such proceeding.

“Person” means and includes an individual, a partnership, a corporation (including a business trust), a joint stock company, a limited liability company, an unincorporated association, a joint venture or other entity or a governmental authority.

    7.  Miscellaneous.

(a)Waivers and Amendments.  Any provision of this Agreement may be amended, waived or modified only upon the written consent of the Company and the Lender.

(b)Governing Law.  This Agreement and all actions arising out of or in connection with this Agreement shall be governed by and construed in accordance with the laws of the State of California, without regard to the conflicts of law provisions of the State of California.

(c)Survival.  The representations, warranties, covenants and agreements made herein shall survive the execution and delivery of this Agreement.

(d)Successors and Assigns.  Subject to the restrictions on transfer described in Section 7(e) below, the rights and obligations of the Company and the Lender hereunder and under

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the Note shall be binding upon and inure to the benefit of the successors, assigns, heirs, administrators and transferees of the parties.

(e)Assignment by the Company; Assignment by the Lender.  Neither this Agreement nor the Note nor any of the rights, interests or obligations hereunder or thereunder may be assigned, by operation of law or otherwise, in whole or in part, by the Company without the prior written consent of the Lender. The Lender will not assign, by operation of law or otherwise, this Agreement or the Note or any of its rights, interests or obligations hereunder or thereunder without the prior written consent of the Company.

(f)Entire Agreement.  This Agreement and the Note constitute the full and entire understanding and agreement between the parties relating to the subject matter hereof and thereof and supersede any previous written or verbal agreements between the parties with regard to the subject matter hereof and thereof.

(g)Notices.  Any notice, request or other communication required or permitted hereunder shall be in writing and shall be deemed to have been duly given if delivered personally or by commercial delivery service, or sent via telecopy (receipt confirmed) to the parties at the following addresses or telecopy numbers (or at such other address or telecopy numbers for a party as shall be specified by like notice):

If to the Company, to:

Amyris, Inc.

5885 Hollis St., Ste. 100

Emeryville, CA 94608

Attention: 

If to the Lender, to:

Foris Ventures, LLC

Attention:

(h)Severability of this Agreement.  If any provision of this Agreement shall be judicially determined to be invalid, illegal or unenforceable, the validity, legality and enforceability of the remaining provisions shall not in any way be affected or impaired thereby.

(i)Counterparts.  This Agreement may be executed in any number of counterparts, each of which shall be an original, but all of which together shall be deemed to constitute one instrument.

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Exhibit 10.03

IN WITNESS WHEREOF, the parties have caused this Agreement to be duly executed and delivered by their proper and duly authorized officers as of the date and year first written above.

COMPANY:
AMYRIS, INC.
By:	/s/ Kathleen Valiasek
Name:	Kathleen Valiasek
Title:	Chief Business Officer
LENDER:
FORIS VENTURES, LLC
By:	/s/ Barbara Hager
Name:	Barbara Hager
Title:	Manager

EXHIBIT A

FORM OF NOTE

AMYRIS, INC.

PROMISSORY NOTE 

$5,000,000 Issuance date: April 29, 2020

Amyris, Inc., a Delaware corporation (the “Company”), for value received, hereby promises to pay to FORIS VENTURES, LLC, or registered assigns (the “Holder”), the principal sum of Five Million Dollars ($5,000,000), or such lesser amount as shall then equal the outstanding principal amount hereunder, on December 31, 2022 (the “Maturity Date”) and to pay interest thereon, from the date of this Note, or from the most recent date to which interest has been paid on this Note, at the rate of twelve percent (12.0%) per annum (calculated on a simple interest basis) until the Maturity Date or the earlier repayment or other satisfaction of this Note.

    Payment of the principal of this Note shall be made upon the surrender of this Note to the Company at its chief executive office (or such other office within the United States as shall be designated by the Company to the holder hereof) (the “Designated Office”) on the Maturity Date or such earlier date in accordance with the terms of this Note. All amounts payable in cash with respect to this Note shall be made by wire transfer to the holder, provided that if the holder shall not have furnished wire instructions in writing to the Company no later than the business day immediately prior to the date on which the Company makes such payment, such payment may be made by U.S. dollar check mailed to the address of the holder as such address shall appear in the Company register.

  This Note was issued pursuant to the Credit Agreement, dated as of April 29, 2020 (as amended from time to time, the “Agreement”), by and between the Company and the original holder of this Note and is subject to provisions of the Agreement. Capitalized terms used but not otherwise defined herein shall have the meaning given to such terms in the Agreement.

1.  Redemption.  This Note is subject to redemption, in whole or from time to time in part (in any amount that is an integral multiple of $1,000), upon not less than five (5) days’ prior written notice in the manner provided in Section 4(b) hereof, at the election of the Company, at a redemption price of 100% of the amount hereof, together with accrued and unpaid interest to, but excluding, the redemption date.

2.  Certain Covenants. Until the Obligations hereunder are paid or otherwise satisfied in full:

(a)The Company will maintain or cause to be maintained its corporate or other organizational existence and good standing in its jurisdiction of incorporation and maintain its qualification in each jurisdiction where the failure to so qualify would reasonably be expected to have a Material Adverse Effect.

(b)The Company will comply with all applicable statutes, regulation and orders of, and all applicable restrictions imposed by, all governmental bodies, domestic or foreign, in respect of the conduct of its business and the ownership of its property, other than those the noncompliance with which would not have, and which would not reasonably be expected to have, a Material Adverse Effect.

(c)The Company will cause the proceeds of the loans evidenced under this Note to be used solely (a) as working capital and (b) to fund the Company’s general business requirements, and not for personal, family or household purposes.

(d)The Company will execute any further instruments and take any further action as the Holder reasonably requests to effect the purposes of this Note or the Agreement.

    3.  Events of Default.

(a)“Event of Default”, wherever used herein, means any one of the following events (whatever the reason for such Event of Default and whether it shall be voluntary or involuntary or be effected by operation of law or pursuant to any judgment, decree or order of any court or any order, rule or regulation of any administrative or governmental body):

(i)default in the payment of any amount upon this Note when it becomes due and payable;

(ii)default in the performance, or breach, of any covenant of the Company herein (other than a default in the performance or breach of which is specifically dealt with elsewhere in this Section 3(a)) and continuance of such default or breach for a period of 10 days;

(iii)the commencement against the Company of an involuntary case or proceeding under any applicable federal or state bankruptcy, insolvency, reorganization or other similar law or of any other case or proceeding to be adjudicated bankrupt or insolvent and such case or proceeding is not dismissed or stayed within 45 days;

(iv)the commencement by the Company of a voluntary case or proceeding under any applicable federal or state bankruptcy, insolvency, reorganization or other similar law or of any other case or proceeding to be adjudicated a bankrupt or insolvent, or the consent by the Company to the entry of a decree or order for relief in respect of the Company in an involuntary case or proceeding under any applicable federal or state bankruptcy, insolvency, reorganization or other similar law or to the commencement of any bankruptcy or insolvency case or proceeding against either the Company, or the filing by either the Company of a petition or answer or consent seeking reorganization or similar relief under any applicable Federal or state law, or the consent by it to the filing of such petition or to the appointment of or taking possession by a custodian, receiver, liquidator, assignee, trustee, sequestrator or other similar official of the Company or of any substantial part of its property, or the making by either the Company of an assignment for the benefit of creditors, or the admission by either the Company in writing of its inability to pay its debts generally as they become due, or the taking of corporate action by the Company in furtherance of any such action;

(v)the Company or any Person acting for the Company makes any representation, warranty, or other statement now or later in this Note or the Agreement or in any writing delivered to the Holder or to induce the Holder in connection with this Note, the Agreement or any other document entered into in connection with this Note or the Agreement or to enter this Note, the Agreement or any other document entered into in connection with this Note or the Agreement, and such representation, warranty, or other statement is incorrect in any material respect when made;or

(vi)at any time, any “person” or “group” (as such terms are used in Sections 13(d) and 14(d) of the Securities Exchange Act of 1934 (the “Exchange Act”)), shall become, or obtain rights (whether by means of warrants, options or otherwise) to become, the “beneficial owner” (as defined in Rules 13(d)-3 and 13(d)-5 under the Exchange Act), directly or indirectly, of fifty percent (50.0%) or more of the ordinary voting power for the election of directors of the Company (determined on a fully diluted basis).

(b)Upon the occurrence and during the continuance of an Event of Default, the Holder may (a) declare all Obligations hereunder immediately due and payable (but if an Event of Default described in Section 3(a)(iii) or 3(a)(iv) occurs all Obligations hereunder are immediately due and payable without any action by the Holder) and (b) exercise all rights and remedies available to the Holder under this Note, the Agreement or at law or equity. The Company will give the Holder notice, within five (5) business days of the occurrence thereof, of any Event of Default of which it is or becomes aware. Such notice shall be given in the manner provided in Section 4(b).

4.  Other.

(a)No provision of this Note shall alter or impair the obligation of the Company, which is absolute and unconditional, to pay the principal of and interest on this Note at the times and places herein prescribed or to repay or otherwise satisfy this Note as herein provided.

(b)The Company will give prompt written notice to the Holder of any change in the location of the Designated Office. Any notice to the Company or to the Holder shall be given in the manner set forth in the Agreement.

(c)The transfer of this Note is registrable on the register maintained by the Company upon surrender of this Note for registration of transfer at the Designated Office, duly endorsed by, or accompanied by a written instrument of transfer in form satisfactory to the Company duly executed by, the holder hereof or such holder’s attorney duly authorized in writing, and thereupon one or more new notes, of authorized denominations and for the same aggregate principal amount, will be issued to the designated transferee or transferees. Such securities are issuable only in registered form without coupons in denominations of $1,000 and any integral multiple thereof. No service charge shall be made for any such registration of transfer, but the Company may require payment of a sum sufficient to recover any tax or other governmental charge payable in connection therewith. Prior to due presentation of this Note for registration of transfer, the Company and any agent of the Company may treat the Person in whose name this Note is registered as the owner thereof for all purposes, whether or not this Note be overdue, and neither the Company nor any such agent shall be affected by notice to the contrary.

(d)This Note shall be governed by and construed in accordance with the internal laws of the State of California, without regard to the conflicts of law provisions of the State of California.

[The remainder of this page is intentionally left blank]

IN WITNESS WHEREOF, the Company has caused this Note to be duly executed.

Dated: April 29, 2020

Amyris, Inc.
By:	/s/ Kathleen Valiasek
Name:	Kathleen Valiasek
Title:	Chief Business Officer

EX-10.04

Exhibit 10.04

EXECUTION VERSION

WAIVER AGREEMENT

This Waiver Agreement (this “Third Waiver Agreement”) is made as of May 6, 2020 by and between Amyris, Inc., a Delaware corporation (the “Company”), and Ginkgo Bioworks, Inc., a Delaware corporation (“Ginkgo”), pursuant to the terms of (i) that certain Promissory Note, dated October 20, 2017 (as amended, the “Note”), issued by the Company to Ginkgo, (ii) that certain Partnership Agreement, dated October 20, 2017 (the “Partnership Agreement”), by and between the Company and Ginkgo, (iii) that certain Waiver Agreement and Amendment to Promissory Note Issued October 20, 2017, dated September 29, 2019 (the “First Waiver Agreement”), by and between the Company and Ginkgo, and (iv) that certain Waiver Agreement and Amendment, dated March 11, 2020 (the “Second Waiver Agreement”), by and between the Company and Ginkgo. Capitalized terms used but not otherwise defined herein shall have the meanings given to such terms in the Note or the Partnership Agreement, as applicable.

RECITALS

A. Pursuant to Section 2.1(b) of the Note, the Company is required to make monthly interest payments to Ginkgo beginning on November 30, 2017 and continuing on the last day of each month thereafter, through and including the Maturity Date (each, an “Interest Payment”).

B. Pursuant to Section 4.3(a) of the Partnership Agreement, as amended by the Second Waiver Agreement, the Company is required to pay Ginkgo monthly fees beginning on March 31, 2020 and continuing on the last day of each month thereafter, through and including October 31, 2021 (each, a “Partnership Payment”).

C. Pursuant to Section 6.3 of the Note, the Company is required to notify Ginkgo in writing in the event that the consolidated cash balance of the Company is less than $10,000,000 at monthly close (the “Reporting Covenant”).

D. Pursuant to Section 4(d) of the Note, certain cross defaults by the Company are considered an Event of Default (the “Cross Default”).

E. Pursuant to Section 6 of the Second Waiver Agreement, the Company was required to pay Ginkgo on or before April 30, 2020, an aggregate of $7,153,770 (the “April 2020 Payment”), which represents all the payments due on or before April 30, 2020 pursuant to the Note, the Partnership Agreement, the First Waiver Agreement, and the Second Waiver Agreement.

F. The Company has requested and Ginkgo has agreed, in consideration of and subject to the terms and conditions contained herein, to (i) waive any failure by the Company to make the April 2020 Payment prior to April 30, 2020, (ii) waive any failure by the Company to comply with the Reporting Covenant prior to the date hereof, and (iii) waive any Cross Default by the Company occurring or existing during the period beginning on March 31, 2020 and ending on the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020.

G. Pursuant to Section 10.7 of the Note, provisions of the Note may be amended or waived only by written agreement of the Company and Ginkgo.

H. Pursuant to Section 9.4 of the Partnership Agreement, any modification to the Partnership Agreement shall only be effective if made in a writing signed by the Company and Ginkgo.

AGREEMENT

For good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Company and Ginkgo agree as follows:

1. Reporting Covenant Waiver. In accordance with Section 10.7 of the Note, Ginkgo hereby waives any failure by the Company to comply with the Reporting Covenant prior to the date hereof, including any default or Event of Default resulting therefrom under the Note or the Partnership Agreement, including without limitation with respect to acceleration of any Partnership Payments pursuant to Section 4.3(d) of the Partnership Agreement.

2. Cross Default Waiver. In accordance with Section 10.7 of the Note, Ginkgo hereby waives any Cross Default by the Company occurring or existing during the period beginning on March 31, 2020 and ending on the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020 (inclusive), including any default or Event of Default resulting therefrom under the Note or the Partnership Agreement, including without limitation with respect to acceleration of any Partnership Payments pursuant to Section 4.3(d) of the Partnership Agreement.

3. May 2020 Payment. Ginkgo hereby waives timely payment of the April 2020 Payment until the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020 (the “Payment Deadline”), and agrees that, notwithstanding anything to the contrary in this Third Waiver Agreement, the Second Waiver Agreement remains in full force and effect with respect to the waivers and amendment set forth therein. Moreover, the Company agrees that in addition to the April 2020 Payment, it will pay to Ginkgo the additional sum of $774,011, for a total payment of $7,927,781 (the “May 2020 Payment”), which represents all the payments due on or before May 31, 2020 pursuant to the Note, the Partnership Agreement, the First Waiver Agreement, the Second Waiver Agreement, and this Third Waiver Agreement. The May 2020 Payment will be paid by the Company by wire transfer of immediately available funds in accordance with the wire instructions delivered to the Company by Ginkgo no later than two (2) Business Days prior to the applicable payment date. Any failure by the Company to make any payment set forth in this Section 3 on or prior to the applicable payment deadline shall (a) constitute an Event of Default under the Note and the Partnership Agreement; and (b) render all waivers set forth in Sections 1-5 of the Second Waiver Agreement and Sections 1-2 of this Third Waiver Agreement null and void.

4. Full Force and Effect.Except as expressly modified by this Third Waiver Agreement, the terms of the Note (as amended by the First Waiver Agreement), the Partnership Agreement (as amended by the Second Waiver Agreement), and the First and Second Waiver Agreements shall remain in full force and effect.

5. Release.In consideration of the agreements contained in this Third Waiver Agreement and other good and valuable consideration, the Company unconditionally and irrevocably releases, waives, and forever discharges Ginkgo, together with its respective predecessors, successors, assigns, subsidiaries, affiliates, agents, employees, directors, officers, attorneys, and attorneys’ consultants (collectively, the “Released Parties”), from (x) any and all liabilities, obligations, duties, promises, or

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indebtedness of any kind (if any) of the Released Parties to the Company or any of its affiliates, which existed, arose, or occurred at any time from the beginning of the world to the date of this Third Waiver Agreement; and (y) all claims, offsets, causes of action, suits, or defenses of any kind whatsoever (if any), which the Company or any of its affiliates might otherwise have against the Released Parties, or any of them; in either case of (x) or (y) on account of any condition, act, omission, event, contract, liability, obligation, indebtedness, claim, cause of action, defense, circumstance, or matter of any kind, which existed, arose, or occurred at any time from the beginning of the world to the date of this Third Waiver Agreement, whether at law or in equity, whether based upon statute, common law or otherwise, whether matured, contingent or non-contingent, whether direct or indirect, whether known or unknown, whether suspected or unsuspected, which the Company ever had, now has, or may claim to have against, arising out of, based on, asserted in, or in connection with any agreement or event.

6. Section 1542 Waiver. In consideration of the agreements contained in this Third Waiver Agreement and other good and valuable consideration, the Company unconditionally and irrevocably waives any rights it has or may have pursuant to California Civil Code Section 1542, which provides as follows:

A general release does not extend to claims that the creditor or releasing party does not know or suspect to exist in his or her favor at the time of executing the release and that, if known by him or her, would have materially affected his or her settlement with the debtor or released party.

7. Attorneys’ Fees. The Company promises to pay to Ginkgo immediately upon receipt of an invoice any and all reasonable attorneys’ and other professionals’ fees and expenses incurred by Ginkgo between March 12, 2020 and the date hereof, inclusive, in connection with the Note, the Partnership Agreement, the First and Second Waiver Agreements, and/or this Third Waiver Agreement, including, without limitation, with respect to the administration, collection, enforcement, amendment or modification of any of them; and with respect to any waiver, consent, release, termination, litigation, administrative proceeding, arbitration, bankruptcy proceeding, or dispute resolution. Any failure by the Company to make timely payment as set forth in this Section 7 shall render all waivers set forth in Sections 1-5 of the Second Waiver Agreement and Sections 1-2 of this Third Waiver Agreement null and void.

8. Integration.This Third Waiver Agreement, the Note (as amended by the First Waiver Agreement), the Partnership Agreement (as amended by the Second Waiver Agreement), and the First and Second Waiver Agreements constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between the parties hereto with respect to the specific subject matter hereof.

9. Counterparts.This Third Waiver Agreement may be executed in one (1) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Third Waiver Agreement may be executed and delivered by facsimile, or by email in portable document format (.pdf) or other electronic format, and delivery of any signature page by any such method will be deemed to have the same effect as if the original signature page had been delivered to the other party.

[Signature pages follow]

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IN WITNESS WHEREOF, the parties hereto have executed this Third Waiver Agreement as of the date first above written.

AMYRIS, INC.

By: _/s/ Kathleen Valiasek

Name: Kathleen Valiasek

Title: Chief Business Officer

[Waiver Signature Page]

IN WITNESS WHEREOF, the parties hereto have executed this Third Waiver Agreement as of the date first above written.

GINKGO BIOWORKS, INC.

By: /s/ Jason Kelly

Name: Jason Kelly

Title: CEO

[Waiver Signature Page]

EX-10.05

Exhibit 10.05

THIRD AMENDMENT

TO LOAN AGREEMENT

THIS AMENDMENT TO THE SECOND AMENDMENT TO LOAN AGREEMENT (the “Third Amendment Agreement”), is made and entered into, as of May 7, 2020 (the “Effective Date”) by and between Nikko Chemicals Co., Ltd. (“Lender”) and Amyris, Inc. (“Borrower”). Except as otherwise defined herein, all capitalized terms in this Amendment have the same meaning as set forth in the Loan Agreement as amended by the First Amendment Agreement and Second Amendment Agreement (as defined below).

WHEREAS, the parties hereto entered into a Loan Agreement dated December 19, 2019 (the “Loan Agreement”);

WHEREAS, the parties hereto entered into an Amendment to Loan Agreement dated March 12, 2020 (the “First Amendment Agreement”);

WHEREAS, the parties hereto entered into an Amendment to the First Amendment Agreement dated April 2, 2020 (the “Second Amendment Agreement”); and

WHEREAS, the parties hereto desire to confirm and amend certain terms of the Loan Agreement, the First Amendment Agreement, and the Second Amendment Agreement.

NOW, THEREFORE, in consideration of the agreements and obligations set forth herein and for other good and valuable consideration, the receipt and sufficiency of which are here acknowledged, the parties hereto hereby agree and confirm as follows:

1.  Payment. The repayment date of the Principal under Section 3(1) of the Loan Agreement shall be “May 31, 2020 or the date of the closing of the Borrower’s fundraising in the amount of $70,000,000.00 or more, whichever comes earlier” (the “Maturity Date”), rather than April 30, 2020. Upon the execution of this Amendment, Borrower shall make an outstanding payment of all of the Interest under the Loan Agreement and the Second Amendment Agreement which shall be US$26,666.67 if Borrower hasn’t done so already.

2.  Interest. Section 2(1) of the Loan Agreement shall read as follows: “Borrower shall pay to Lender interest on the principal amount of the Loan (the “Principal”) at the rate of 12.50 percent per annum from and including the Effective Date (the “Interest”).

3.  Default Interest. Default Interest defined in Section 2(2) of the Loan Agreement shall be “the Interest plus 5.00 percent per annum” rather than 15.00 percent per annum.

2.  Effective Date. This Agreement shall be effective as of the Effective Date (subject to Borrower’s full payment under Paragraph 1 to Lender). Except as expressly amended in this Agreement, any other terms and conditions shall remain unchanged and continue to be in full force and effect.

IN WITNESS WHEREOF, the parties hereto have executed and delivered this Agreement as of the date first above written.

NIKKO CHEMICALS CO., LTD.
By: /s/ Shizuo Ukaji___________________
Name: Shizuo Ukaji
Title: President & Chief Executive Officer
AMYRIS, INC.
By:	_/s/ John Melo_________________
Name:	John Melo
Title:	President & Chief Executive Officer

EX-10.06

Exhibit 10.06

PROMISSORY NOTE

PAYCHECK PROTECTION PROGRAM

U.S. SMALL BUSINESS ADMINISTRATION

SBA Loan #	81081173-06
Date	5/7/2020
Loan Amount	$9,999,995
Interest Rate	1.00%
Operating Company
SBA Loan Name	Amyris, Inc.
Borrower	Amyris, Inc.
Lender	Bank of the West

1.  PROMISE TO PAY:

In return for the Loan, Borrower promises to pay to the order of Lender the amount of

$9,999,995______________________________________and no/100 Dollars, interest on the unpaid principal balance, and all other amounts required by this Note.

2.  DEFINITIONS:

“Amortization Commencement Date” means the date that is the six (6) month anniversary of the date of initial disbursement on this Note.

“Deferral Period” means a period of six (6) months commencing with the date of initial disbursement on this Note and ending on the day immediately preceding the six (6) month anniversary of such date.

“Loan” means the loan evidenced by this Note.

“Loan Documents” means the documents related to this loan signed by Borrower.

“Maturity Date” shall mean the date that is the two year anniversary of the date of initial disbursement on this Note.

“SBA” means the Small Business Administration, an Agency of the United States of America.

Exhibit 10.06

3. PAYMENT TERMS:

Borrower must make all payments at the place Lender designates. The payment terms for this Note

are:

The interest rate is 1.00% per annum, fixed for the term of the Note.

Principal and interest payments are deferred during the first six (6) months of the term of this Note

(the “Deferral Period”). Interest will continue to accrue on the outstanding principal balance during

the Deferral Period.

After proceeds of this Note have been expended by Borrower, but not sooner than eight weeks

after the date of initial disbursement on this Note, Borrower may submit to Lender a request for

forgiveness of the Loan. Borrower must submit all documentation required by Lender to verify

number of full-time equivalent employees and pay rates, as well as the payments on eligible

mortgage, lease, and utility obligations, certifying that the documents are true and that Borrower

used the forgiveness amount to keep employees and make eligible mortgage interest, rent, and

utility payments. Lender will notify Borrower within 60 days whether all or part of the requested

forgiveness of the Loan has been approved.

If the entire principal balance of this Note and accrued interest is not forgiven before the end of the

Deferral Period, then the principal balance together with and all accrued and unpaid interest

outstanding on the Amortization Commencement Date shall be paid in eighteen (18) monthly

payments, commencing in the month immediately following the Amortization Commencement Date

and continuing each month thereafter until the Maturity Date; provided, however, that the last

monthly installment shall be on the Maturity Date and shall be in an amount equal to all principal

and accrued interest outstanding on the Maturity Date. Monthly payments will be in an amount

determined by the Lender to be the amount necessary to fully amortize the principal and interest

outstanding on the Amortization Commencement Date over the remaining term of this Note.

Payment must be made on the fifth calendar day in the month it is due.

Lender will apply each installment payment first to pay interest accrued to the day Lender receives

payment, then bring principal current, then to pay any late fees, and will apply any remaining

balance to reduce principal.

Borrower may prepay this Note at any time without penalty. Borrower must:

a. Give Lender written notice; and

b. Pay all accrued interest.

All remaining principal and accrued interest is due and payable two (2) years from the date of initial

disbursement.

Late Charge: If a payment on this Note is more than 10 days late, Lender may charge Borrower a

late fee of up to 5.00% of the unpaid portion of the regularly scheduled payment.

4. DEFAULT:

Borrower is in default under this Note if Borrower does not make a payment when due under this

Note, or if Borrower or Operating Company:

A.  Fails to do anything required by this Note and other Loan Documents;

B.  Defaults on any other loan with Lender;

C.  Does not disclose, or anyone acting on their behalf does not disclose, any material fact to

Exhibit 10.06

Lender or SBA;

D.  Makes, or anyone acting on their behalf makes, a materially false or misleading representation

to Lender or SBA;

E.  Defaults on any loan or agreement with another creditor, if Lender believes the default may

materially affect Borrower’s ability to pay this Note;

H.  Becomes the subject of a proceeding under any bankruptcy or insolvency law;

I.  Has a receiver or liquidator appointed for any part of their business or property;

J.  Makes an assignment for the benefit of creditors;

K.  Has any adverse change in financial condition or business operation that Lender believes may

materially affect Borrower’s ability to pay this Note;

L.  Reorganizes, merges, consolidates, or otherwise changes ownership or business structure

without Lender’s prior written consent; or

M.  Becomes the subject of a civil or criminal action that Lender believes may materially affect

Borrower’s ability to pay this Note.

5. LENDER’S RIGHTS IF THERE IS A DEFAULT:

Without notice or demand and without giving up any of its rights, Lender may:

A.  Require immediate payment of all amounts owing under this Note;

B.  Collect all amounts owing from Borrower; and

C.  File suit and obtain judgment.

6. LENDER’S GENERAL POWERS:

Without notice and without Borrower’s consent, Lender may:

A.  Incur expenses to collect amounts due under this Note, enforce the terms of this Note or any

other Loan Document. Among other things, the expenses may include payments for reasonable

attorney’s fees and costs. If Lender incurs such expenses, it may demand immediate repayment

from Borrower or add the expenses to the principal balance;

B.  Release anyone obligated to pay this Note;

C.  Take any action necessary to collect amounts owing on this Note.

7. WHEN FEDERAL LAW APPLIES:

When SBA is the holder, this Note will be interpreted and enforced under federal law, including SBA regulations, Lender or SBA may use state or local procedures for filing papers, recording documents, giving notice, foreclosing liens, and other purposes. By using such procedures, SBA does not waive

any federal immunity from state or local control, penalty, tax, or liability. As to this Note, Borrower may

not claim or assert against SBA any local or state law to deny any obligation, defeat any claim of

SBA, or preempt federal law.

8. SUCCESSORS AND ASSIGNS

Under this Note, Borrower and Operating Company include the successors of each, and Lender

includes its successors and assigns.

9. GENERAL PROVISIONS:

A.  All individuals and entities signing this Note are jointly and severally liable.

B.  Borrower waives all suretyship defenses.

Exhibit 10.06

C.  Borrower must sign all documents necessary at any time to comply with the Loan Documents and to enable Lender to acquire, perfect, or maintain Lender’s liens on Collateral.

D.  Lender may exercise any of its rights separately or together, as many times and in any order it chooses. Lender may delay or forgo enforcing any of its rights without giving up any of them.

E.  Borrower may not use an oral statement of Lender or SBA to contradict or alter the written terms of this Note.

F.  If any part of this Note is unenforceable, all other parts remain in effect.

G.  To the extent allowed by law, Borrower waives all demands and notices in connection with  this Note, including presentment, demand, protest, and notice of dishonor. Borrower also waives any

defenses based upon any claim that Lender did not obtain any guarantee; did not obtain, perfect,

or maintain a lien upon Collateral; impaired Collateral; or did not obtain the fair market

value of Collateral at a sale.

10. STATE-SPECIFIC PROVISIONS: If Borrower is located in any of the following states, the clause

indicated for such state is incorporated herein:

MISSOURI.

Oral or unexecuted agreements or commitments to loan money, extend credit or to forbear from

enforcing repayment of a debt including promises to extend or renew such debt are not enforceable,

regardless of the legal theory upon which it is based that is in any way related to the credit

agreement. To protect you (Borrowers(s)) and us (Creditor) from misunderstanding or

disappointment, any agreements we reach covering such matters are contained in this writing, which

is the complete and exclusive statement of the agreement between us, except as we may later agree

in writing to modify it.

OREGON.

UNDER OREGON LAW, MOST AGREEMENTS, PROMISES AND COMMITMENTS MADE BY

LENDER CONCERNING LOANS AND OTHER CREDIT EXTENSIONS WHICH ARE NOT FOR

PERSONAL, FAMILY, OR HOUSEHOLD PURPOSES OR SECURED SOLELY BY BORROWER'S

RESIDENCE MUST BE IN WRITING, EXPRESS CONSIDERATION AND BE SIGNED BY AN

AUTHORIZED REPRESENTATIVE OF LENDER TO BE ENFORCEABLE.

WASHINGTON.

Oral agreements or oral commitments to loan money, extend credit or to forbear from enforcing

Repayment of a debt are not enforceable under Washington law.

WISCONSIN.

Each Borrower who is married represents that this obligation is incurred in the interest of his or her marriage or family.

11. BORROWER’S NAME(S) AND SIGNATURE(S):

        By signing below, each individual or entity becomes obligated under this Note as Borrower.

/s/ John Melo      5/7/2020 

Signature of Authorized Representative of Applicant    Date

John Melo      President & CEO

Print Name         Title

EX-20.1

Secret

Exhibit 2.01

AMENDMENT NO. 4 TO

QUOTA PURCHASE AGREEMENT

This Amendment No. 4 to the Quota Purchase Agreement (the “Agreement”), dated as of November 17, 2017, between Amyris, Inc., a Delaware corporation, AB Technologies LLC, a Delaware limited liability company (collectively, the “Seller”), and DSM Produtos Nutricionais Brasil S.A., a Brazilian corporation (the “Purchaser” and together with the Seller, the “Parties”) is made between the Seller and the Purchaser as of March 30, 2020 (this “Amendment No. 4”). Capitalized terms used herein but not defined shall have the meanings ascribed to them in the Agreement.

WHEREAS, the Agreement was amended by Amendment No. 1 to the Agreement, dated as of December 28, 2017, Amendment No. 2 to the Agreement, dated April 16, 2019, and Amendment No. 3, dated February 24, 2020;

WHEREAS, the Parties desire to further amend the Agreement as set forth in this Amendment No. 4.

NOW, THEREFORE, in consideration of the mutual promises contained herein, and for other good and valuable consideration the receipt and sufficiency of which are hereby acknowledged, the Parties agree as follows:

1.Amendments. Section 2.07 of the Agreement is hereby amended to read in its entirety as follows:

“SECTION 2.07 Payment of Tax Attribute Benefit Amounts.

For the taxable year including the Closing Date and through the end of the taxable year ending eight (8) years following the end of the taxable year that includes the Closing Date, the Purchaser shall deliver or cause to be delivered to the Seller an amount equal to the sum of (i) the Dollar value of (A) fifty seven and one-half percent (57.5%) multiplied by (B) the Tax savings from the utilization or monetization of Closing Date ICMS/IPI Tax Credits and the Closing Date Net Operating Loss Carryovers following the Closing Date plus (ii) the Dollar value of (C) eighty percent (80%) multiplied by (D) the excess, if any, of (x) the Tax savings from the utilization or monetization of any Closing Date PIS/COFINS Tax Credits following the Closing Date over(y) the Tax Benefit Threshold Amount. For purposes of this Section 2.07, the Tax savings described in the immediately preceding sentence shall be determined at the time actually realized by the Company; provided, that at the time any such Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits or Closing Date Net Operating Loss Carryovers are actually realized by the Company, if any Affiliate of the Company that is a Brazilian taxpayer also has ICMS, PIS/COFINS, IPI or Net Operating Loss Carryovers of the same nature and character (including the same taxing jurisdiction) (the “Affiliate Tax Attributes”) available to be used by the Company at such time, the Tax savings amount deemed to be realized from the Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax

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Credits and Closing Date Net Operating Loss Carryovers shall be deemed to be equal to (a) the total Tax savings amount (taking into account both the

Affiliate Tax Attributes and the Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits or Closing Date Net Operating Loss Carryovers) realized at such time, in each case of the same nature and character (including the same taxing jurisdiction) (the “Aggregate Tax Savings”) minus (b) the lesser of (x) the actual Affiliate Tax Attributes of the same nature and character (including the same taxing jurisdiction) or (y) the product of 50% multiplied by the Aggregate Tax Savings, provided, however, that the total Tax savings amount deemed to be realized from the Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits and Closing Date Net Operating Loss Carryovers shall not exceed the amount of Tax savings amount that would be realized if there were no Affiliate Tax Attributes available as of such time. An example of the intention of the parties with respect to such calculation is set forth in Exhibit 2.07. Any amount required to be paid by the Purchaser shall be paid to the Seller within ten (10) days of realization of such reduction in Tax. A reduction in Tax will be considered to be realized for purposes of this Section 2.07 at the time that the applicable Tax Return is filed on which such Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits or Closing Date Net Operating Loss Carryover is taken into account and the amount of the reduction shall equal 100% of any Closing Date ICMS/IPI Tax Credits and Closing Date PIS/COFINS utilized and 34% of any Closing Date Net Operating Loss Carryovers recognized, as applicable. Any such amount payable under this Section 2.07 shall be converted from Reals into Dollars based on the PTAX selling rate as published by Banco Central do Brasil (BACEN) on the date such reduction of Tax is considered to be realized. The Purchaser shall provide to Seller a statement of the amount of any Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits and Closing Date Net Operating Loss Carryovers realized, together with supporting calculations and details, on an annual basis (or, in the case of Closing Date ICMS/IPI Tax Credits or Closing Date PIS/COFINS Tax Credits if requested by the Seller, on a quarterly basis). This clause shall not apply in relation to any Tax savings from the utilization or monetization of Closing Date ICMS/IPI Tax Credits, Closing Date Net Operating Loss Carryovers or Closing Date PIS/COFINS Tax Credits to the extent that such Tax savings would not have been realized following the Closing Date but for (i) the occurrence of the Post-Closing Registrations following the Closing Date or (ii) the conduct or operation of the Retained Businesses by the Company following the Closing Date.”

2.Second Advance Credit of ICMS/IPI Tax Credits Payment. In addition to the advance credit of ICMS/IPI Tax Credits payment that is set forth in Amendment No. 3, and subject to the terms of this Section 2, Purchaser has agreed to pay to Seller, as an advance of any future payments that may become payable pursuant to Section 2.07 of the Agreement in respect of Closing Date ICMS/IPI Tax Credits, 2,800,000 Reals (the “Second ICMS Advance Amount”). The Parties agree that the aggregate amount payable by Purchaser pursuant to Section 2.07 of the Agreement in respect of Closing Date ICMS/IPI Tax Credits shall be reduced by the amount of the ICMS Advance Amount and the Second ICMS Advance Amount, and no payments shall be made by Purchaser to

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Seller pursuant to Section 2.07 of the Agreement in respect of Closing Date ICMS/IPI Tax Credits unless and until any amount payable thereunder exceeds 8,200,000 Reals (and thereafter, only to the extent of such excess). Purchaser and Seller hereby agree that

in lieu of a cash payment, the Second ICMS Advance Amount shall be delivered in the form of a credit equal to the Second ICMS Advance Amount to be applied to future invoices issued by Purchaser to Seller or its affiliates to off-set amounts that would otherwise be payable by Seller or its affiliates to Purchaser or its affiliates. For the avoidance of doubt, nothing in this Amendment No. 4 is intended to modify the agreement of the Parties regarding the ICMS Advance Amount payment of 5,400,000 Reals that is set forth in Amendment No. 3.

3.No Other Amendments. Except as provided above, the Agreement shall remain in full force and effect, and the execution of this Amendment No. 4 is not a waiver by either Party of any of the terms or provisions of the Agreement.

4.Counterparts. This Amendment No. 4 may be executed in one or more counterparts, each of which shall be deemed and original, but all of which together shall constitute one and the same document.

[Remainder of Page Intentionally Left Blank.]

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IN WITNESS WHEREOF, the Seller and the Purchaser have caused this Amendment No. 4 to be executed as of the date first written above by their respective officers thereunto duly authorized.

AMYRIS, INC.

By: /s/ John Melo

Name:

Title:

AB TECHNOLOGIES LLC

By: /s/ John Melo

Name:

Title:

DSM PRODUTOS NUTRICIONAIS BRASIL S.A.

By: /s/ Mauricio Adade

Name: Mauricio Adade – Presidente DSM Latam

Title:

By: 

Name:

Title:

EX-20.2

Exhibit 2.02

Secret

Execution version 05/22/2020

AMENDMENT NO. 5 TO

QUOTA PURCHASE AGREEMENT

This Amendment No. 5 to the Quota Purchase Agreement (the “Agreement”), dated as of November 17, 2017, between Amyris, Inc., a Delaware corporation, AB Technologies LLC, a Delaware limited liability company (collectively, the “Seller”), and DSM Produtos Nutricionais Brasil S.A., a Brazilian corporation (the “Purchaser” and together with the Seller, the “Parties”) is made between the Seller and the Purchaser as of May 22, 2020 (this “Amendment No. 5”). Capitalized terms used herein but not defined shall have the meanings ascribed to them in the Agreement.

WHEREAS, the Agreement was amended by Amendment No. 1 to the Agreement, dated as of December 28, 2017, Amendment No. 2 to the Agreement, dated April 16, 2019, Amendment No. 3, dated February 24, 2020 and Amendment No. 4, dated March 30, 2020;

WHEREAS, the Parties desire to further amend the Agreement as set forth in this Amendment No. 5.

NOW, THEREFORE, in consideration of the mutual promises contained herein, and for other good and valuable consideration the receipt and sufficiency of which are hereby acknowledged, the Parties agree as follows:

1.Amendments. Section 2.07 of the Agreement is hereby amended to read in its entirety as follows:

“SECTION 2.07 Payment of Tax Attribute Benefit Amounts.

For the taxable year including the Closing Date and through the end of the taxable year ending eight (8) years following the end of the taxable year that includes the Closing Date, the Purchaser shall deliver or cause to be delivered to the Seller an amount equal to the sum of (i) the Dollar value of (A) forty percent (40.0%) multiplied by (B) the Tax savings from the utilization or monetization of Closing Date ICMS/IPI Tax Credits and the Closing Date Net Operating Loss Carryovers following the Closing Date plus (ii) the Dollar value of (C) eighty percent (80%) multiplied by (D) the excess, if any, of (x) the Tax savings from the utilization or monetization of any Closing Date PIS/COFINS Tax Credits following the Closing Date over(y) the Tax Benefit Threshold Amount. For purposes of this Section 2.07, the Tax savings described in the immediately preceding sentence shall be determined at the time actually realized by the Company; provided, that at the time any such Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits or Closing Date Net Operating Loss Carryovers are actually realized by the Company, if any Affiliate of the Company that is a Brazilian taxpayer also has ICMS, PIS/COFINS, IPI or Net Operating Loss Carryovers of the same nature and character (including the same taxing jurisdiction) (the “Affiliate Tax Attributes”) available to be used by the Company at such time, the Tax savings amount deemed to be realized from the Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits and Closing Date Net Operating Loss Carryovers shall be deemed to be equal to

Secret

(a) the total Tax savings amount (taking into account both the Affiliate Tax Attributes and the Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits or Closing Date Net Operating Loss Carryovers) realized at such time, in each case of the same nature and character (including the same taxing jurisdiction) (the “Aggregate Tax Savings”) minus (b) the lesser of (x) the actual Affiliate Tax Attributes of the same nature and character (including the same taxing jurisdiction) or (y) the product of 50% multiplied by the Aggregate Tax Savings, provided, however, that the total Tax savings amount deemed to be realized from the Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits and Closing Date Net Operating Loss Carryovers shall not exceed the amount of Tax savings amount that would be realized if there were no Affiliate Tax Attributes available as of such time. An example of the intention of the parties with respect to such calculation is set forth in Exhibit 2.07. Any amount required to be paid by the Purchaser shall be paid to the Seller within ten (10) days of realization of such reduction in Tax. A reduction in Tax will be considered to be realized for purposes of this Section 2.07 at the time that the applicable Tax Return is filed on which such Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits or Closing Date Net Operating Loss Carryover is taken into account and the amount of the reduction shall equal 100% of any Closing Date ICMS/IPI Tax Credits and Closing Date PIS/COFINS utilized and 34% of any Closing Date Net Operating Loss Carryovers recognized, as applicable. Any such amount payable under this Section 2.07 shall be converted from Reals into Dollars based on the PTAX selling rate as published by Banco Central do Brasil (BACEN) on the date such reduction of Tax is considered to be realized. The Purchaser shall provide to Seller a statement of the amount of any Closing Date ICMS/IPI Tax Credits, Closing Date PIS/COFINS Tax Credits and Closing Date Net Operating Loss Carryovers realized, together with supporting calculations and details, on an annual basis (or, in the case of Closing Date ICMS/IPI Tax Credits or Closing Date PIS/COFINS Tax Credits if requested by the Seller, on a quarterly basis). This clause shall not apply in relation to any Tax savings from the utilization or monetization of Closing Date ICMS/IPI Tax Credits, Closing Date Net Operating Loss Carryovers or Closing Date PIS/COFINS Tax Credits to the extent that such Tax savings would not have been realized following the Closing Date but for (i) the occurrence of the Post-Closing Registrations following the Closing Date or (ii) the conduct or operation of the Retained Businesses by the Company following the Closing Date.”

2.Third Advance Credit of ICMS/IPI Tax Credits Payment. In addition to the advance credit of ICMS/IPI Tax Credits payment that is set forth in Amendment No. 3 and the advance credit of ICMS/IPI Tax Credits payment that is set forth in Amendment No. 4, and subject to the terms of this Section 2, Purchaser has agreed to pay to Seller, as an advance of any future payments that may become payable pursuant to Section 2.07 of the Agreement in respect of Closing Date ICMS/IPI Tax Credits, 6,750,000 Reals (the “Third ICMS Advance Amount”). The Parties agree that the aggregate amount payable by Purchaser pursuant to Section 2.07 of the Agreement in respect of Closing Date ICMS/IPI Tax Credits has been reduced by the amount of the ICMS Advance Amount, the Second ICMS Advance Amount and the Third ICMS Advance Amount, and that there will be no future payments made by Purchaser to Seller pursuant to Section 2.07 of the

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Agreement in respect of Closing Date ICMS/IPI Tax Credits as all such future potential payments have been advanced in full. Purchaser and Seller hereby agree that in lieu of a cash payment, the Third ICMS Advance Amount shall be delivered in the form of a credit equal to the Third ICMS Advance Amount to be applied to past due and currently outstanding invoices issued by Purchaser to Seller or its affiliates to off-set amounts that would otherwise be payable by Seller or its affiliates to Purchaser or its affiliates. For the avoidance of doubt, nothing in this Amendment No. 5 is intended to modify the agreement of the Parties regarding the ICMS Advance Amount payment of 5,400,000 Reals that is set forth in Amendment No. 3 or the ICMS Advance Amount payment of 2,800,000 Reals that is set forth in Amendment No. 4.

3.No Other Amendments. Except as provided above, the Agreement shall remain in full force and effect, and the execution of this Amendment No. 5 is not a waiver by either Party of any of the terms or provisions of the Agreement.

4.Counterparts. This Amendment No. 5 may be executed in one or more counterparts, each of which shall be deemed and original, but all of which together shall constitute one and the same document.

[Remainder of Page Intentionally Left Blank.]

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IN WITNESS WHEREOF, the Seller and the Purchaser have caused this Amendment No. 5 to be executed as of the date first written above by their respective officers thereunto duly authorized.

AMYRIS, INC.

By: /s/ John Melo

Name:

Title:

AB TECHNOLOGIES LLC

By: /s/ John Melo

Name:

Title:

DSM PRODUTOS NUTRICIONAIS BRASIL S.A.

By: /s/ Mauricio Adade

Name:

Title:

By: 

Name:

Title:

EX-31.01

Exhibit 31.01

CERTIFICATION OF CHIEF EXECUTIVE OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, John G. Melo, certify that:

        1. I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

        2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

        3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

        4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

        a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

        b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

        c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

        d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

        5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

        a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

        b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: August 10, 2020	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer

1

EX-31.02

Exhibit 31.02

CERTIFICATION OF CHIEF FINANCIAL OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, Han Kieftenbeld, certify that:

        1. I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

        2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

        3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

        4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

        a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

        b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

        c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

        d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

        5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

        a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

        b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: August 10, 2020	/s/ Han Kieftenbeld
	Han Kieftenbeld
	Chief Financial Officer

1

EX-32.01

Exhibit 32.01

Certification of CEO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended June 30, 2020, as filed with the Securities and Exchange Commission on the date hereof, I, John G. Melo, Chief Executive Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended June 30, 2020 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: August 10, 2020	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

1

EX-32.02

Exhibit 32.02

Certification of CFO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended June 30, 2020, as filed with the Securities and Exchange Commission on the date hereof, I, Han Kieftenbeld, Chief Financial Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended June 30, 2020 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: August 10, 2020	/s/ Han Kieftenbeld
	Han Kieftenbeld
	Chief Financial Officer
	(Principal Financial Officer)

1

XML

Cover Page - shares	6 Months Ended
	Jun. 30, 2020	Aug. 04, 2020
Cover [Abstract]
Entity Registrant Name	AMYRIS, INC.
Entity Central Index Key	0001365916
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Current Reporting Status	Yes
Entity Emerging Growth Company	false
Entity Small Business	true
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		204,730,979
Document Type	10-Q
Document Period End Date	Jun. 30, 2020
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q2
Amendment Flag	false
Document Quarterly Report	true
Document Transition Report	false
Entity File Number	001-34885
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	55-0856151
Entity Address, Address Line One	5885 Hollis Street
Entity Address, Address Line Two	Suite 100
Entity Address, City or Town	Emeryville
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	94608
Title of 12(b) Security	Common Stock, $0.0001 par value per share
Trading Symbol	AMRS
Security Exchange Name	NASDAQ
City Area Code	510
Local Phone Number	450-0761
Entity Interactive Data Current	Yes

XML

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 99,998	$ 270
Restricted cash	362	469
Accounts receivable, net of allowance of $102 and $45, respectively	22,029	16,322
Accounts receivable - related party, net of allowance of $0 and $0, respectively	94	3,868
Contract assets	11,724	8,485
Contract assets - related party	1,203	0
Inventories	33,059	27,770
Deferred cost of products sold - related party	7,709	3,677
Prepaid expenses and other current assets	14,531	12,750
Total current assets	190,709	73,611
Property, plant and equipment, net	27,394	28,930
Contract assets, noncurrent - related party	0	1,203
Deferred cost of products sold, noncurrent - related party	14,260	12,815
Restricted cash, noncurrent	960	960
Recoverable taxes from Brazilian government entities	5,725	7,676
Right-of-use assets under financing leases, net	11,422	12,863
Right-of-use assets under operating leases	11,662	13,203
Other assets	5,557	9,705
Total assets	267,689	160,966
Current liabilities:
Accounts payable	22,779	51,234
Accrued and other current liabilities	49,110	36,655
Financing lease liabilities	3,605	3,465
Operating lease liabilities	4,893	4,625
Contract liabilities	5,180	1,353
Debt, current portion (includes instrument measured at fair value $36,624 and $24,392, respectively)	43,482	45,313
Due to related parties, current	0	18,492
Total current liabilities	129,049	161,137
Long-term debt, net of current portion (includes instrument measured at fair value of $0 and $26,232, respectively)	23,532	48,452
Related party debt, net of current portion (includes instrument measured at fair value of $81,551 and $0, respectively)	138,898	149,515
Financing lease liabilities, net of current portion	2,305	4,166
Operating lease liabilities, net of current portion	12,457	15,037
Derivative liabilities	5,833	9,803
Other noncurrent liabilities	15,254	23,024
Total liabilities	327,328	411,134
Commitments and contingencies
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of June 30, 2020 and December 31, 2019; 110,436 and 8,280 shares issued and outstanding as of June 30, 2020 and December 31, 2019, respectively	0	0
Common stock - $0.0001 par value, 350,000,000 and 250,000,000 shares authorized as of June 30, 2020 and December 31, 2019, respectively; 204,618,423 and 117,742,677 shares issued and outstanding as of June 30, 2020 and December 31, 2019, respectively	20	12
Additional paid-in capital	1,935,252	1,543,668
Accumulated other comprehensive loss	(48,708)	(43,804)
Accumulated deficit	(1,953,919)	(1,755,653)
Total Amyris, Inc. stockholders’ deficit	(67,355)	(255,777)
Noncontrolling interest	2,716	609
Total stockholders' deficit	(64,639)	(255,168)
Total liabilities, mezzanine equity and stockholders' deficit	267,689	160,966
Contingently redeemable common stock
Current liabilities:
Contingently redeemable common stock	$ 5,000	$ 5,000

XML

Condensed Consolidated Balance Sheets (Parentheticals) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Statement of Financial Position [Abstract]
Accounts receivable, allowance	$ 102	$ 45
Accounts receivable, allowance, related parties	0	0
Fair value of debt	36,624	24,392
Fair value of long-term debt	0	26,232
Related party debt, net, fair value	$ 81,551	$ 0
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, shares authorized (in shares)	5,000,000	5,000,000
Preferred stock, shares issued (in shares)	110,436	8,280
Preferred stock, shares outstanding (in shares)	110,436	8,280
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (in shares)	350,000,000	250,000,000
Common stock, shares issued (in shares)	204,618,423	117,742,677
Common stock, shares outstanding (in shares)	204,618,423	117,742,677

XML

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Revenues [Abstract]
Revenue	$ 30,005	$ 62,694	$ 59,135	$ 77,068
Cost and operating expenses:
Cost of products sold	23,098	15,121	34,888	32,828
Research and development	16,965	19,222	34,091	37,061
Sales, general and administrative	30,503	30,862	62,517	59,115
Total cost and operating expenses	70,566	65,205	131,496	129,004
Loss from operations	(40,561)	(2,511)	(72,361)	(51,936)
Other income (expense):
Interest expense	(20,118)	(15,217)	(35,120)	(27,751)
Loss from change in fair value of derivative instruments	(11,779)	0	(8,497)	(2,039)
Loss from change in fair value of debt	(14,949)	(14,444)	(31,452)	(16,574)
Loss upon extinguishment of debt	(22,029)	(5,875)	(49,348)	(5,875)
Other income (expense), net	1,497	(41)	1,501	(156)
Total other expense, net	(67,378)	(35,577)	(122,916)	(52,395)
Loss before income taxes and loss from investment in affiliate	(107,939)	(38,088)	(195,277)	(104,331)
Provision for income taxes	(99)	0	(190)	0
Loss from investment in affiliate	(277)	0	(692)	0
Net loss	(108,315)	(38,088)	(196,159)	(104,331)
Less: income attributable to noncontrolling interest in Aprinnova	(2,107)	0	(2,107)	0
Net loss	(110,422)	(38,088)	(198,266)	(104,331)
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D	0	(34,964)	0	(34,964)
Add: losses allocated to participating securities	6,361	2,255	7,435	4,690
Net loss attributable to Amyris, Inc. common stockholders	$ (104,061)	$ (70,797)	$ (190,831)	$ (134,605)
Loss per share attributable to common stockholders, basic and diluted (in dollars per share)	$ (0.56)	$ (0.76)	$ (1.12)	$ (1.59)
Weighted-average shares of common stock outstanding used in computing loss per share of common stock, basic and diluted (in shares)	184,827,330	92,785,752	169,946,482	84,831,269
Cost, Product and Service [Extensible List]			us-gaap:ProductMember
Product
Revenues [Abstract]
Revenue	$ 25,188	$ 12,120	$ 43,042	$ 24,004
Licenses and Royalties
Revenues [Abstract]
Revenue	990	40,964	6,151	41,082
Grants and Collaborations
Revenues [Abstract]
Revenue	$ 3,827	$ 9,610	$ 9,942	$ 11,982

XML

Condensed Consolidated Statements of Operations (Parentheticals) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Revenues, related party	$ 1,307	$ 43,328	$ 8,124	$ 43,346
Product
Revenues, related party	56	0	105	2
Licenses and Royalties
Revenues, related party	0	40,682	3,750	40,302
Grants and Collaborations
Revenues, related party	$ 1,251	$ 2,646	$ 4,269	$ 3,042

XML

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Comprehensive loss:
Net loss	$ (108,315)	$ (38,088)	$ (196,159)	$ (104,331)
Foreign currency translation adjustment	(2,355)	(1,100)	(4,904)	(136)
Total comprehensive loss	(110,670)	(39,188)	(201,063)	(104,467)
Less: income attributable to noncontrolling interest in Aprinnova	(2,107)	0	(2,107)	0
Comprehensive loss attributable to Amyris, Inc.	$ (112,777)	$ (39,188)	$ (203,170)	$ (104,467)

XML

Consolidated Statements of Stockholders' Deficit and Mezzanine Equity - USD ($) $ in Thousands	Total	Preferred Stock	Common Stock	Additional Paid-in Capital	Additional Paid-in Capital Cumulative Effect, Period of Adoption, Adjustment	Accumulated Other Comprehensive Loss	Accumulated Deficit	Accumulated Deficit Cumulative Effect, Period of Adoption, Adjustment	Noncontrolling Interest	Total Stockholders' Deficit	Total Stockholders' Deficit Cumulative Effect, Period of Adoption, Adjustment	Mezzanine Equity - Common Stock
Balance (in shares) at Dec. 31, 2018		14,656	76,564,829
Balance at Dec. 31, 2018		$ 0	$ 8	$ 1,346,996	$ 32,512	$ (43,343)	$ (1,521,417)	$ 8,531	$ 937	$ (216,819)	$ 41,043	$ 5,000
Issuance of common stock upon exercise of warrants (in shares)			450,568
Issuance of common stock upon exercise of warrants				1						1
Issuance of common stock upon restricted stock settlement (in shares)			191,672
Issuance of common stock upon restricted stock settlement				(9)						(9)
Issuance of common stock upon exercise of stock options (in shares)			3,612
Issuance of common stock upon exercise of stock options				13						13
Fair value of bifurcated embedded conversion feature in connection with debt modification				398						398
Stock-based compensation				3,452						3,452
Foreign currency translation adjustment						964				964
Net loss							(66,243)			(66,243)
Balance (in shares) at Mar. 31, 2019		14,656	77,210,681
Balance at Mar. 31, 2019		$ 0	$ 8	1,383,363		(42,379)	(1,579,129)		937	(237,200)		5,000
Balance (in shares) at Dec. 31, 2018		14,656	76,564,829
Balance at Dec. 31, 2018		$ 0	$ 8	1,346,996	$ 32,512	(43,343)	(1,521,417)	$ 8,531	937	(216,819)	$ 41,043	5,000
Net loss	$ (104,331)
Net loss	(104,331)
Balance (in shares) at Jun. 30, 2019		14,656	101,186,738
Balance at Jun. 30, 2019		$ 0	$ 10	1,479,415		(43,479)	(1,617,217)		937	(180,334)		5,000
Balance (in shares) at Mar. 31, 2019		14,656	77,210,681
Balance at Mar. 31, 2019		$ 0	$ 8	1,383,363		(42,379)	(1,579,129)		937	(237,200)		5,000
Issuance of common stock in private placement (in shares)			3,610,944
Issuance of common stock in private placement			$ 1	14,221						14,222
Issuance of common stock in private placement - related party (in shares)			10,478,338
Issuance of common stock in private placement - related party				39,499						39,499
Issuance of common stock upon exercise of warrants (in shares)			2,064,606
Issuance of common stock upon exercise of warrants				0						0
Issuance of common stock upon restricted stock settlement (in shares)			589,241
Issuance of common stock upon restricted stock settlement				(347)						(347)
Issuance of common stock upon ESPP purchase (in shares)			131,460
Issuance of common stock upon ESPP purchase				464						464
Issuance of common stock upon conversion of debt (in shares)			7,101,468
Issuance of common stock upon conversion of debt			$ 1	34,650						34,651
Issuance of warrants in connection with debt accounted for at fair value				4,428						4,428
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock				34,964						34,964
Deemed dividend on preferred stock discounts upon conversion of Series D preferred stock				(34,964)						(34,964)
Stock-based compensation				3,375						3,375
Other				(238)						(238)
Foreign currency translation adjustment						(1,100)				(1,100)
Net loss	(38,088)						(38,088)			(38,088)
Net loss	$ (38,088)
Balance (in shares) at Jun. 30, 2019		14,656	101,186,738
Balance at Jun. 30, 2019		$ 0	$ 10	1,479,415		(43,479)	(1,617,217)		937	(180,334)		5,000
Balance (in shares) at Dec. 31, 2019	117,742,677	8,280	117,742,677
Balance at Dec. 31, 2019	$ (255,168)	$ 0	$ 12	1,543,668		(43,804)	(1,755,653)		609	(255,168)		5,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest (in shares)			6,337,594
Issuance of common stock and warrants upon conversion of debt principal and accrued interest			$ 1	21,259						21,260
Issuance of common stock in private placement (in shares)			3,484,321
Issuance of common stock in private placement				10,000						10,000
Issuance of common stock in private placement - related party (in shares)			10,505,652
Issuance of common stock in private placement - related party			$ 1	27,188						27,189
Issuance of common stock upon exercise of warrants (in shares)			1,160,929
Issuance of common stock upon exercise of warrants				3,332						3,332
Issuance of common stock upon exercise of warrants - related party (in shares)			24,165,166
Issuance of common stock upon exercise of warrants - related party			$ 2	68,763						68,765
Exercise of common stock rights warrant - related party				15,000						15,000
Issuance of common stock right warrant - related party				8,904						8,904
Modification of previously issued common stock warrants				1,286						1,286
Derecognition of liability warrants to equity				5,200						5,200
Issuance of common stock upon restricted stock settlement (in shares)			495,581
Issuance of common stock upon restricted stock settlement				(8)						(8)
Stock-based compensation				3,504						3,504
Foreign currency translation adjustment						(2,549)				(2,549)
Net loss							(87,844)			(87,844)
Balance (in shares) at Mar. 31, 2020		8,280	163,891,920
Balance at Mar. 31, 2020		$ 0	$ 16	1,708,096		(46,353)	(1,843,497)		609	(181,129)		5,000
Balance (in shares) at Dec. 31, 2019	117,742,677	8,280	117,742,677
Balance at Dec. 31, 2019	$ (255,168)	$ 0	$ 12	1,543,668		(43,804)	(1,755,653)		609	(255,168)		5,000
Issuance of common stock upon exercise of warrants (in shares)	30,694,457
Issuance of common stock upon exercise of stock options (in shares)	5,227
Net loss	$ (198,266)
Net loss	(196,159)
Balance (in shares) at Jun. 30, 2020		110,436	204,618,423
Balance at Jun. 30, 2020	$ (64,639)	$ 0	$ 20	1,935,252		(48,708)	(1,953,919)		2,716	(64,639)		5,000
Balance (in shares) at Mar. 31, 2020		8,280	163,891,920
Balance at Mar. 31, 2020		$ 0	$ 16	1,708,096		(46,353)	(1,843,497)		609	(181,129)		5,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest (in shares)		30,000
Issuance of common stock and warrants upon conversion of debt principal and accrued interest				30,000						30,000
Issuance of common stock upon exercise of warrants (in shares)			132,746
Issuance of common stock upon exercise of warrants				0						0
Derecognition of liability warrants to equity				6,550						6,550
Fair value of modification to previously issued common stock warrants				1,067						1,067
Issuance of common stock upon restricted stock settlement (in shares)			720,100
Issuance of common stock upon restricted stock settlement				(98)						(98)
Issuance of common stock upon exercise of stock options (in shares)			5,227
Issuance of common stock upon exercise of stock options				16						16
Issuance of common stock upon ESPP purchase (in shares)			144,523
Issuance of common stock upon ESPP purchase				421						421
Issuance of preferred and common stock in private placement, net of issuance costs (in shares)	72,156		32,614,573
Issuance of preferred and common stock in private placement, net of issuance costs			$ 3	160,014						160,017
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)			5,226,481
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party			$ 1	(1)						0
Fair value of pre-delivery shares released to holder in connection with debt amendment				10,478						10,478
Return of pre-delivery shares previously issued in connection with debt agreement (in shares)			(1,363,636)
Return of pre-delivery shares previously issued in connection with debt agreement										0
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity (in shares)			3,246,489
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity				15,778						15,778
Stock-based compensation				2,931						2,931
Foreign currency translation adjustment						(2,355)				(2,355)
Net loss	$ (110,422)						(110,422)		2,107	(108,315)
Net loss	(108,315)
Balance (in shares) at Jun. 30, 2020		110,436	204,618,423
Balance at Jun. 30, 2020	$ (64,639)	$ 0	$ 20	$ 1,935,252		$ (48,708)	$ (1,953,919)		$ 2,716	$ (64,639)		$ 5,000

XML

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019
Operating activities
Net loss	$ (196,159)	$ (104,331)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss upon extinguishment of debt	49,348	5,875
Loss from change in fair value of debt	31,452	16,574
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	10,478	0
Stock-based compensation	6,435	6,827
Amortization of right-of-use assets under operating leases	1,336	5,846
Non-cash interest expense in connection with modification of warrants	1,066	0
Depreciation and amortization	4,115	1,722
Accretion of debt discount	2,308	7,260
Loss in equity-method investee	692	0
Non-cash interest expense added to debt principal	100	0
Loss (gain) on disposal of property, plant and equipment	42	(4)
Impairment of property, plant and equipment	13	438
Expense for warrants issued for debt covenant waivers	0	4,428
Gain on foreign currency exchange rates	(327)	(36)
Loss from change in fair value of derivative instruments	8,497	2,039
Changes in assets and liabilities:
Accounts receivable	(1,971)	(2,147)
Contract assets	(3,239)	0
Accounts receivable, unbilled - related party	0	8,021
Inventories	(6,229)	(4,310)
Deferred cost of products sold - related party	(5,477)	(14,066)
Prepaid expenses and other assets	868	(1,000)
Accounts payable	(27,934)	4,532
Accrued and other liabilities	12,580	7,659
Lease liabilities	(2,153)	(8,096)
Contract liabilities	3,827	4,512
Net cash used in operating activities	(110,332)	(58,257)
Investing activities
Purchases of property, plant and equipment	(5,494)	(5,951)
Net cash used in investing activities	(5,494)	(5,951)
Financing activities
Proceeds from exercise of common stock rights warrant - related party	15,000	0
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs - related party	45,000	39,500
Proceeds from exercises of warrants - related party	13,998	0
Proceeds from issuance of common and preferred stock in private placements, net of issuance costs	170,017	14,221
Proceeds from exercises of warrants	3,332	1
Proceeds from issuance of debt, net of issuance costs	15,279	18,614
Proceeds from issuance of common stock upon ESPP purchase	421	464
Proceeds from exercises of common stock options	16	13
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(106)	(356)
Principal payments on financing leases	(1,721)	(258)
Principal payments on debt	(45,949)	(52,145)
Net cash provided by financing activities	215,287	20,054
Effect of exchange rate changes on cash, cash equivalents and restricted cash	160	(507)
Net increase (decrease) in cash, cash equivalents and restricted cash	99,621	(44,661)
Cash, cash equivalents and restricted cash at beginning of period	1,699	47,054
Cash, cash equivalents and restricted cash at end of the period	101,320	2,393
Cash and cash equivalents	99,998	940
Restricted cash, current	362	493
Restricted cash, noncurrent	960	960
Total cash, cash equivalents and restricted cash	101,320	2,393
Supplemental disclosures of cash flow information:
Cash paid for interest	8,281	7,986
Supplemental disclosures of non-cash investing and financing activities:
Accrued interest added to debt principal	1,702	448
Unpaid property, plant and equipment balances in accounts payable and accrued liabilities at end of period	708	1,026
Acquisition of right-of-use assets under operating leases	0	1,675
Cumulative effect of change in accounting principle	0	41,043
Derecognition of derivative liabilities to equity upon extinguishment of debt	6,461	0
Derecognition of derivative liabilities upon authorization of shares	6,550	0
Derecognition of derivative liabilities upon exercise of warrants	5,200	0
Exercise of common stock warrants in exchange for debt principal and accrued interest reduction	69,918	0
Fair value of embedded features in connection with private placement	2,962	0
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances	188	0
Fair value of warrants and embedded features recorded as debt discount in connection with debt issuances - related party	747	0
Fair value of warrants recorded as debt discount in connection with debt modification	0	398
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	27,650	34,650
Lease liabilities recorded upon adoption of ASC 842	0	33,552
Right-of-use assets under operating leases recorded upon adoption of ASC 842	$ 0	$ 29,713

XML

Basis of Presentation and Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Presentation and Summary of Significant Accounting Policies

Basis of Presentation and Summary of Significant Accounting Policies

Amyris, Inc. (Amyris or the Company) is a leading synthetic biotechnology company in Clean Health and Beauty markets through its consumer brands, and is a supplier of sustainable and natural ingredients. Amyris applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably sourced products into the Health, Beauty, and Flavor & Fragrance end-markets. The Company's technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume ingredients. This platform, combined with our proprietary fermentation process, replaces existing complex and oftentimes expensive manufacturing processes, resulting in our successful development and production of many distinct molecules at commercial volumes.

The accompanying unaudited condensed consolidated financial statements of Amyris, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2019 (the 2019 Form 10-K), from which the condensed consolidated balance sheet as of December 31, 2019 is derived. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP) for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the accompanying interim condensed consolidated financial statements do not include all of the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are not necessarily indicative of results for a full year.

Raizen Joint Venture Agreement

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into a joint venture agreement relating to the formation and operation of a joint venture relating to the production, sale and commercialization of alternative sweetener products. In connection with the formation of the joint venture, among other things, (i) the joint venture will construct a manufacturing facility on land owned by Raizen and leased to the joint venture (the Sweetener Plant), (ii) the Company will grant to the joint venture an exclusive, royalty-free, worldwide, license to certain technology owned by the Company relevant to the joint venture’s business, and (iii) the Company and Raizen will enter into a shareholders agreement setting forth the rights and obligations of the parties with respect to, and for the management of, the joint venture. The formation of the joint venture is subject to certain conditions, including certain regulatory approvals, and the achievement of certain technological and economic milestones relating to the Company’s existing production of its alternative sweetener product. The COVID-19 pandemic caused a disruption in the production campaign of the Company’s alternative sweetener product. The disruption delayed the generation of the requisite data required to complete technological and economic analysis underpinning the joint venture agreement between the parties. Therefore, the parties have agreed to extend the previous July 2020 deadline to conduct the relevant analysis of the sweetener production data in order to determine potential next steps for the joint venture. In addition, notwithstanding the satisfaction of the closing conditions, Raizen may elect not to consummate the formation and operation of the joint venture, in which event, the Company will retain the right to construct and operate the Sweetener Plant. The Company is evaluating the accounting treatment for its future interest in the joint venture under ASC 810, Consolidations and ASC 323, Equity Method and Joint Ventures and will conclude once the corporate governance and economic participation structure is finalized and the formation of the joint venture is consummated.

Potential Impact of COVID-19 on the Company's Business

With the global spread of the COVID-19 pandemic beginning in the first quarter of 2020 and anticipated continuation throughout 2020, and the resulting shelter-in-place orders covering the Company’s corporate headquarters, primary research and development laboratories, and employees, the Company has implemented policies and procedures to continue its operations under applicable minimum business operations guidelines. The extent to which the COVID-19 pandemic impacts the Company’s business, financial condition or results of operations will depend on future developments, which are highly uncertain and cannot be accurately predicted. New information may emerge concerning the severity of the COVID-19 pandemic and the actions to contain the pandemic or treat COVID-19, such as the ultimate geographic spread of the disease, the duration of the pandemic, continued travel restrictions, social distancing, business closures or disruptions, and the effectiveness of actions taken to contain or treat COVID-19 in the United States and in other countries. As the COVID-19 pandemic continues to evolve, to the extent it adversely affects our business and financial results, it may also impact other risks to which the Company is subject as set forth in the “Risk Factors” section (Part I, Item 1A) of the 2019 Form 10-K.

Going Concern

The Company has incurred significant operating losses since its inception and expects to continue to incur losses and negative cash flows from operations over the course of at least the next 12 months following the issuance of these condensed consolidated financial statements. As of June 30, 2020, the Company had working capital of $61.7 million (compared to negative working capital of $87.5 million as of December 31, 2019), and an accumulated deficit of $2.0 billion.

As of June 30, 2020, the Company's outstanding debt principal (including related party debt) totaled $175.8 million, of which $37.0 million is classified as current. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as restrictions on additional indebtedness, material adverse effect and cross default provisions. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of a substantial portion of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of such other outstanding indebtedness. At December 31, 2019, the Company failed to meet certain covenants under several credit arrangements, including those associated with cross-default provisions, minimum liquidity and minimum asset coverage requirements. Further, at March 31, 2020, the Company failed to meet certain covenants and provisions under several credit arrangements, including those associated with cross-default provisions (as discussed below). In March 2020 and again in May 2020, these lenders (except Schottenfeld Group LLC and certain of its affiliates (Schottenfeld)) provided waivers to the Company for breaches of all past covenant violations and cross-default payment failures, under the respective credit agreements (discussed in the paragraph below) through the earlier of the closing of a significant equity offering or May 31, 2020. The Company cured these defaults with the closing of the $200 million equity offering described below and the repayment of these past due amounts. As of June 30, 2020, the Company failed to achieve the minimum revenue thresholds under the Foris LSA, Naxyris LSA and Senior Convertible Notes Due 2022, which are described in more detail in Note 4, “Debt”, and obtained a waiver from each of these lenders to cure the June 30, 2020 minimum revenue covenant violation.

Between March 31, 2020 and April 30, 2020, the Company failed to pay (i) Total Raffinage Chimie (Total), Nikko Chemicals Co. Ltd (Nikko) and certain affiliates of Schottenfeld an aggregate of $17.6 million of maturing promissory notes, (ii) failed to pay Ginkgo $7.2 million of past due interest, waiver fees and partnership payments and (iii) failed to make interest payments to all of its lenders totaling $2.8 million. These payment failures resulted in an event of default under the respective agreements and triggered cross-defaults under other debt instruments that permitted each of the affected debt holders (the Cross-Default Lenders) to accelerate the amounts owing under such cross-defaulted instruments. In May 2020, the Company obtained waivers from the lenders, except Schottenfeld, to extend the due date for all payments due under the respective agreements to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020; and amended the credit arrangements with Total and Nikko to extend the maturity dates of the original respective promissory notes to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. Also, the Company received waivers from each of the affected Cross-Default Lenders to waive the right to accelerate due to the event-specific cross-defaults.

Beginning in May 2020 and continuing through June 2020, the Company executed a series of financial transactions to minimize cash outflows related to debt service payments and to increase operating cash. On May 1, 2020, the Company amended the Senior Convertible Notes Due 2022 to eliminate the monthly amortization payments and change the interest payment frequency from monthly to quarterly. On May 7, 2020, the Company received a $10 million Paycheck Protection Plan loan (PPP Loan). On June 1, 2020, the Company amended the Foris LSA to eliminate the quarterly principal payments and defer all interest payments until maturity on July 1, 2022, and to provide for the conversion of all outstanding indebtedness under the LSA at a $3.00 per share conversion price, which conversion is subject to stockholder approval. Further, on June 1, 2020 and June 4, 2020, the Company entered into securities purchase agreements with investors for the private placement of an aggregate of $200 million of common and preferred stock, resulting in the Company receiving approximately $190 million of net proceeds. A portion of the proceeds from the offering was used to pay down approximately $37.1 million of debt principal (which included $10 million to repay the PPP Loan) and $6.1 million of accrued interest. Also, on June 2, 2020, Total converted approximately $9.3 million of debt principal and accrued interest into common stock under the terms of the 2014 Rule 144A Convertible Note, further reducing the Company’s outstanding indebtedness. As a result of closing the equity offering, making all past due payments, converting the $9.1 million 2014 Rule 144A Convertible Note principal into equity, and executing amendments to the Foris LSA and the Senior Convertible Notes Due 2022, the Company cured all payment defaults and other events of default, including cross-defaults under the Company’s various debt instruments as of June 30, 2020. Although the Company has been able to obtain waivers in the past for substantially all of its prior defaults to date and was able to cure the existing payment defaults, it may not be able to cure or obtain a waiver for any defaults in the future.

Further, the Company's cash and cash equivalents of $100.0 million as of June 30, 2020 may not be sufficient to fund expected cash flows requirements from operations and cash debt service obligations through August 2021. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date these condensed consolidated financial statements are issued. The condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty. The Company's ability to continue as a going concern will depend, in large part, on its ability to eliminate or minimize the anticipated negative cash flows from operations during the 12 months from the date of this filing and to either raise additional cash proceeds through financings or refinance the debt maturities occurring in June 2021, all of which are uncertain and outside the control of the Company. Further, the Company's operating plan for the remainder of 2020 contemplates (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) reduced spending in general and administrative areas, and (iv) continued cash inflows from collaborations and grants. If the Company is unable to complete these actions, it may be unable to meet its operating cash flow needs and its obligations under its existing debt facilities over the next 12 months. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and the Company may be forced to obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all, and/or liquidate its assets. In such a scenario, the value received for assets in liquidation or dissolution could be significantly lower than the value reflected in these financial statements.

Significant Accounting Policies

Note 1, "Basis of Presentation and Summary of Significant Accounting Policies", to the audited consolidated financial statements in the 2019 Form 10-K includes a discussion of the significant accounting policies and estimates used in the preparation of the Company’s consolidated financial statements. There have been no material changes to the Company's significant accounting policies and estimates during the six months ended June 30, 2020.

Accounting Standards or Updates Recently Adopted

In the six months ended June 30, 2020, the Company adopted these accounting standards or updates:

Fair Value Measurement In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement, which amends ASC 820, Fair Value Measurement. ASU 2018-13 modifies the disclosure requirements for fair value measurements by removing, modifying or adding certain disclosures. ASU 2018-13 became effective in the first quarter of fiscal 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The adoption of this standard did not have a material impact on the Company’s condensed consolidated financial statements.

Collaborative Revenue Arrangements In November 2018, the FASB issued ASU 2018-18, Clarifying the Interaction between Topic 808 and Topic 606, that clarifies the interaction between the guidance for certain collaborative arrangements and Topic 606, the new revenue recognition standard. A collaborative arrangement is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. The ASU provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. ASU 2018-18 became effective in the first quarter of fiscal year 2020 retrospectively. The adoption of this standard did not have any impact on the Company’s condensed consolidated financial statements.

Accounting Standards or Updates Not Yet Adopted

Credit Losses In June 2016, the FASB issued ASU 2016-13, Financial Instruments—Credit Losses (Topic 326), Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires entities to measure all expected credit losses for most financial assets held at the reporting date based on an expected loss model which includes historical experience, current conditions, and reasonable and supportable forecasts. Entities will now use forward-looking information to better form their credit loss estimates. ASU 2016-13 also requires enhanced disclosures to help financial statement users better understand significant estimates and judgments used in estimating credit losses, as well as the credit quality and underwriting standards of an entity's portfolio. ASU 2016-13 is effective for the Company in the first quarter of 2021. The Company is currently evaluating the impact this standard will have on its condensed consolidated financial statements.

Accounting for Income Taxes In December 2019, the FASB issued ASU 2019-12, “Simplifying the Accounting for Income Taxes” (“ASU 2019-12”). The amendments in ASU 2019-12 simplify the accounting for income taxes by removing certain exceptions to the general principles in ASC Topic 740, Income Taxes. The amendments also improve consistent application of and simplify U.S. GAAP for other areas of ASC Topic 740 by clarifying and amending existing guidance. ASU

2019-12 will be effective for the Company commencing in the first quarter of fiscal year 2021. The transition requirements are dependent upon each amendment within this update and will be applied either prospectively or retrospectively. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Convertible Debt, and Derivatives and Hedging On August 5, 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity, to improve financial reporting associated with accounting for convertible instruments and contracts in an entity’s own equity. ASU 2020-06 is effective for the Company in the first quarter of 2022. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Use of Estimates and Judgements

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates, judgements and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates, and such differences may be material to the condensed consolidated financial statements.

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Balance Sheet Details

6 Months Ended

Jun. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Balance Sheet Details

Balance Sheet Details

Allowance for Doubtful Accounts

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Period
Six months ended June 30, 2020	$	45	$	57	$	—	$	102
Year ended December 31, 2019	$	642	$	110	$	(707)	$	45

Inventories

(In thousands)	June 30, 2020		December 31, 2019
Raw materials	$	4,487	$	3,255
Work-in-process	8,204		7,204
Finished goods	20,368		17,311
Inventories	$	33,059	$	27,770

Deferred cost of products sold - related party

(In thousands)	June 30, 2020		December 31, 2019
Deferred cost of products sold - related party	$	7,709	$	3,677
Deferred cost of products sold, noncurrent - related party	14,260		12,815
Total	$	21,969	$	16,492

In November 2018, the Company amended the supply agreement with DSM to secure capacity at the Brotas 1 facility for sweetener production through December 2022. See Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K for information regarding the November 2018 Supply Agreement Amendment. As part of the amendment, the Company made a series of manufacturing capacity fee payments from November 2018 to March 31, 2020. Of these payments $17.4 million was recorded as deferred cost of products sold. In June 2020, the Company paid an additional $6.9 million manufacturing capacity fee, which represents the final payment under the amendment. The capitalized deferred cost of products sold asset is expensed to cost of products sold on a units of production basis as the Company's sweetener product is produced and sold over the five-year term of the supply agreement. Each quarter, the Company evaluates its estimated future production volumes through the end of the agreement and adjusts the unit cost to be expensed over the remaining estimated production volume. During the three and six months ended June 30, 2020, the Company expensed $1.1 million and $1.3 million, respectively, of the deferred cost of products sold asset to cost of products sold. Inception to date amortization through June 30, 2020 totaled $2.3 million.

Prepaid expenses and other current assets

(In thousands)	June 30, 2020		December 31, 2019
Non-inventory production supplies	$	4,687	$	5,376
Prepayments, advances and deposits	6,423		4,726
Other	3,421		2,648
Total prepaid expenses and other current assets	$	14,531	$	12,750

Property, Plant and Equipment, Net

(In thousands)	June 30, 2020		December 31, 2019
Machinery and equipment	$	46,568	$	48,041
Leasehold improvements	41,479		41,478
Computers and software	9,700		9,822
Furniture and office equipment, vehicles and land	3,496		3,510
Construction in progress	8,985		9,752
	110,228		112,603
Less: accumulated depreciation and amortization	(82,834)		(83,673)
Property, plant and equipment, net	$	27,394	$	28,930

During the three and six months ended June 30, 2020 and 2019, depreciation and amortization expense was as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Depreciation and amortization expense	$	1,675	$	873	$	3,395	$	1,722

Leases

Operating Leases

The Company has operating leases primarily for administrative offices, laboratory equipment and other facilities. The operating leases have remaining terms that range from 1 to 5 years, and often include one or more options to renew. These renewal terms can extend the lease term from 1 to 5 years and are included in the lease term when it is reasonably certain that the Company will exercise the option. The operating leases are classified as ROU assets under operating leases on the Company's condensed consolidated balance sheets and represent the Company’s right to use the underlying asset for the lease term. The Company’s obligation to make operating lease payments is included in "Lease liabilities" and "Lease liabilities, net of current portion" on the Company's condensed consolidated balance sheets. Operating lease right-of-use assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. The Company had $11.7 million and $13.2 million of right-of-use assets as of June 30, 2020 and December 31, 2019, respectively. Operating lease liabilities were $17.4 million and $19.7 million as of June 30, 2020 and December 31, 2019, respectively. During the three and six months ended June 30, 2020 and 2019, respectively, the Company recorded $1.5 million, $3.0 million, $3.0 million and $5.8 million of operating lease amortization that was charged to expense, of which $0.3 million, $0.6 million, $0.2 million and $0.4 million was recorded to cost of products sold.

Because the rate implicit in each lease is not readily determinable, the Company uses its incremental borrowing rate to determine the present value of the lease payments. The Company has certain contracts for real estate and marketing which may contain lease and non-lease components which it has elected to treat as a single lease component.

Information related to the Company's right-of-use assets and related lease liabilities were as follows:

	Six Months Ended June 30,
	2020	2019
Cash paid for operating lease liabilities, in thousands	$3,807	$10,660
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$—	$31,293
Weighted-average remaining lease term	2.9	2.6
Weighted-average discount rate	18.0%	18.0%

(1) 2019 amount includes $29.7 million for operating leases existing on January 1, 2019 and $1.7 million for operating leases that commenced during the six months ended June 30, 2019.

Financing Leases

The Company has financing leases primarily for laboratory and computer equipment. Assets purchased under financing leases are included in "Right-of-use assets under financing leases, net" on the condensed consolidated balance sheets. For financing leases, the associated assets are depreciated or amortized over the shorter of the relevant useful life of each asset or the lease term. Accumulated amortization of assets under financing leases totaled $3.1 million and $1.7 million as of June 30, 2020 and December 31, 2019, respectively.

Maturities of Financing and Operating Leases

Maturities of lease liabilities as of June 30, 2020 were as follows:

Years ending December 31: (In thousands)	Financing Leases		Operating Leases		Total Leases
2020 (remaining six months)	$	2,185	$	3,918	$	6,103
2021	4,566		7,478		12,044
2022	—		7,654		7,654
2023	—		3,318		3,318
2024	—		152		152
Total lease payments	6,751		22,520		29,271
Less: amount representing interest	(841)		(5,170)		(6,011)
Total lease liability	$	5,910	$	17,350	$	23,260
Current lease liability	$	3,605	$	4,893	$	8,498
Noncurrent lease liability	2,305		12,457		14,762
Total lease liability	$	5,910	$	17,350	$	23,260

Other Assets

(In thousands)	June 30, 2020		December 31, 2019
Equity-method investment	$	4,043	$	4,734
Deposits	277		295
Contingent consideration	—		3,303
Other	1,237		1,373
Total other assets	$	5,557	$	9,705

In connection with the December 2017 sale of its subsidiary Amyris Brasil Ltda. (Amyris Brasil), the Company recorded a long-term receivable related to certain contingent consideration to be received from DSM upon DSM’s realization of certain Brazilian value-added tax benefits it acquired with its purchase of Amyris Brasil. In the three months ended June 30, 2020, the Company received the $3.3 million remaining balance of contingent consideration due to the Company under the 2017 asset purchase agreement.

Accrued and Other Current Liabilities

(In thousands)	June 30, 2020		December 31, 2019
Accrued interest	$	10,810	$	8,209
Ginkgo partnership payments obligation	10,134		4,319
Equity issuance costs	9,983		—
Payroll and related expenses	6,718		7,296
Contract termination fees	5,490		5,347
Asset retirement obligation	2,447		3,184
Professional services	1,595		2,968
Tax-related liabilities	—		1,685
Other	1,933		3,647
Total accrued and other current liabilities	$	49,110	$	36,655

Other noncurrent liabilities

(In thousands)	June 30, 2020		December 31, 2019
Liability for unrecognized tax benefit	$	7,384	$	7,204
Liability in connection with acquisition of equity-method investment	5,962		5,249
Ginkgo partnership payments, net of current portion	725		4,492
Contract liabilities, net of current portion	245		1,449
Refund liability(1)	—		3,750
Other	938		880
Total other noncurrent liabilities	$	15,254	$	23,024

(1) In April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" in Part II, Item 8 of the 2019 Form 10-K for further information. The assignment was accounted for as a contract modification under ASC 606 that resulted in $12.5 million of prepaid variable consideration to the Company. The $12.5 million was recorded as a refund liability. During the three months ended March 31, 2020, the Company concluded that it would not be required to return any portion of the remaining refund liability to DSM, and recorded $3.8 million of royalty revenue related to this change in estimate and reduction of the refund liability.

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Fair Value Measurement

6 Months Ended

Jun. 30, 2020

Fair Value Disclosures [Abstract]

Fair Value Measurement

Fair Value Measurement

Liabilities Measured and Recorded at Fair Value on a Recurring Basis

The following tables summarize liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

(In thousands)	June 30, 2020								December 31, 2019
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Foris Convertible Note (LSA Amendment)	$	—	$	—	$	81,551	$	81,551	$	—	$	—	$	—	$	—
Senior Convertible Notes	—		—		36,624		36,624		—		—		50,624		50,624
Embedded derivatives bifurcated from debt instruments	—		—		5,833		5,833		—		—		2,832		2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		—		—		—		—		6,971		6,971
Total liabilities measured and recorded at fair value	$	—	$	—	$	124,008	$	124,008	$	—	$	—	$	60,427	$	60,427

The Company did not hold any financial assets to be measured and recorded at fair value on a recurring basis as of June 30, 2020 and December 31, 2019. Also, there were no transfers between the levels during the three months ended June 30, 2020 or the year ended December 31, 2019.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgements and consider factors specific to the asset or liability. The method of determining the fair value of embedded derivative liabilities is described subsequently in this note. Market risk associated with embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

Changes in fair value of derivative liabilities are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of derivative instruments".

Changes in the fair value of debt that is accounted for at fair value are presented as gains or losses in the consolidated statements of operations in the line captioned "Gain (loss) from change in fair value of debt".

Fair Value of Debt — Foris Convertible Note (LSA Amendment)

On June 1, 2020, the Company and Foris entered into an Amendment No. 1 to the Amended and Restated Foris LSA (LSA Amendment), pursuant to which, among other provisions, Foris will have the option in its sole discretion to convert all or a portion of the secured indebtedness, including accrued interest, into shares of Common Stock at a $3.00 conversion price (Conversion Option), which Conversion Option is subject to stockholder approval. See Note 4, “Debt” for further information regarding the LSA Amendment and related extinguishment accounting treatment. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). The LSA Amendment also contains certain change in control embedded derivatives and a contingent beneficial conversion feature and management believes the fair value option best reflects the underlying economics of new convertible note. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the LSA Amendment.

At June 1, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $72.1 million. The Company measured the initial fair value of the LSA Amendment using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $3.73 stock price, (ii) 26% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year. At June 30, 2020, the contractual outstanding principal of the LSA Amendment was $50.0 million and the fair value was $81.6 million. The Company remeasured the fair value of the LSA Amendment using the following inputs: (i) $4.27 stock price, (ii) 25% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility and (v) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year. The Company recorded a $9.5 million loss related to the change in fair value of the LSA Amendment for the three months ended June 30, 2020.

Fair Value of Debt — Senior Convertible Notes

On January 14, 2020, the Company exchanged the $66 million Senior Convertible Notes (or the Prior Notes) for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (ii) an aggregate of 2,742,160 shares of common stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of common stock, (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of common stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, (v) accrued and unpaid interest on the Senior Convertible Notes (payable on or prior to January 31, 2020) and (vi) cash fees in an aggregate amount of $1.0 million (payable on or prior to January 31, 2020). Due to the legal extinguishment and exchange of the Prior Notes and significantly different cash flows contained in the New Notes, the Company accounted for the exchange as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt, which was comprised of the $4.1 million fair value of the Warrants, the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and Rights over the $2.87 per share contractual value. See Note 4, "Debt” for further information regarding the transaction.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported as "Gain (loss) from change in fair value of debt" in the consolidated statements of operations in each reporting period subsequent to the issuance of the New Notes.

At January 14, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $51.0 million and the fair value was $35.8 million. The Company measured the fair value at January 14, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $2.90 stock price, (ii) 226% discount yield, (iii) 1.59% risk free interest rate (iv) 45% equity volatility, (v) 25% / 75% probability of principal repayment in cash or stock, respectively and (vi) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year.

At June 30, 2020, the contractual outstanding principal of the New Senior Convertible Notes was $30.0 million and the fair value was $36.6 million. The Company measured the fair value at June 30, 2020 using a binomial lattice model (which is discussed in further detail below) using the following inputs: (i) $4.27 stock price, (ii) 232% discount yield, (iii) 0.16% risk free interest rate (iv) 45% equity volatility, and (v) 5% probability of change in control. The Company assumed that if a change of control event were to occur, it would occur at the end of the calendar year.

For the three and six months ended June 30, 2020, the Company recorded a $5.5 million loss and a $22.0 million loss from change in fair value of debt, respectively, in connection with the fair value remeasurement of the Prior Notes and the New Senior Convertible Notes, as follows:

In thousands
Fair value at December 31, 2019	$	50,624
Less: principal paid	(35,980)
Loss from change in fair value	21,980
Fair value at June 30, 2020	$	36,624

A binomial lattice model was used to determine whether the LSA Amendment and the Senior Convertible Notes (Debt Instruments) would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible note will be converted early if the conversion value is greater than the holding value and (ii) the convertible note will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible note is called, the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible note. Using this lattice method, the Company valued the Debt Instruments using the "with-and-without method", where the fair value of the Debt Instruments including the embedded and freestanding features is defined as the "with," and the fair value of the Debt Instruments excluding the embedded and freestanding features is defined as the "without." This method estimates the fair value of the Debt Instruments by looking at the difference in the values of the Debt Instruments with the embedded and freestanding derivatives and the fair value of the Debt Instruments without the embedded and freestanding features. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility, estimated credit spread and other instrument-specific

assumptions. The Company remeasures the fair value of the Debt Instruments and records the change as a gain or loss from change in fair value of debt in the statement of operations for each reporting period.

Derivative Liabilities Recognized in Connection with the Issuance of Debt Instruments

The following table provides a reconciliation of the beginning and ending balances for the Company's derivative liabilities recognized in connection with the issuance of debt instruments, either freestanding or embedded, measured at fair value using significant unobservable inputs (Level 3):

(In thousands)	Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2019	$	9,803	$	9,803
Fair value of derivative liabilities issued during the period	8,752		8,752
Change in fair value of derivative instruments	8,496		8,496
Derecognition on settlement or extinguishment	(21,218)		(21,218)
Balance at June 30, 2020	$	5,833	$	5,833

Freestanding Derivative Instruments

In connection with the January 14, 2020 issuance of the New Senior Convertible Notes as discussed above and in Note 4, “Debt” (which was accounted for as an extinguishment of the original $66 million Senior Convertible Notes), the Company issued warrants (the Warrants) to purchase up to an aggregate of 3.0 million shares of common stock (the Warrant Shares). Due to stock exchange ownership limitations, which if exceeded would require stockholder approval and possibly require cash settlement for failure to deliver shares upon exercise, the Company concluded that a portion of the Warrant Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Warrant Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Warrants had an initial fair value of $4.1 million, which was recorded as: (i) $4.1 million loss upon extinguishment of debt, (ii) $2.4 million additional paid in capital and (iii) $1.7 million derivative liability. The Warrant Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Warrants was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Warrant Shares derivative liability portion was $1.5 million, and the Company recorded a $0.2 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to remove the stock ownership limitations. As a result, the Company is able to physically deliver shares under the Warrants without the potential for cash settlement. In the three months ended June 30, 2020, the Company recorded a $1.3 million final mark-to-market loss on change in derivative liability, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and derecognized the $2.8 million derivative liability balance relate to this portion of the Warrant Shares into additional paid in capital.

In connection with the January 31, 2020 private placement transaction with Foris Ventures LLC (an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock discussed in Note 6, “Stockholders’ Deficit”), the Company issued a right (the Right) to purchase up to an aggregate of 5.2 million shares of common stock (the Right Shares). Due to certain contractual provisions in the Right, the Company concluded that a portion of the Right Shares met the derivative scope exception and equity classification criteria and were accounted for as additional paid in capital, and a portion of the Right Shares did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The Right had an initial fair value of $5.3 million, of which $2.3 million was recorded as additional paid in capital and $3.0 million was recorded as a derivative liability. The Right Shares derivative liability portion will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At March 31, 2020, the fair value of the Right Shares derivative liability portion was $2.0 million, and the Company recorded a $1.0 million gain on change in fair value of derivative instruments during the three months ended March 31, 2020. On May 29, 2020, the Company obtained stockholder approval to increase its authorized share count from 255 million to 355 million. As a result, the portion of the Right Shares initially accounting for as a derivative liability was no longer precluded from the derivative scope exception and met the criteria for equity classification. In the three months ended June 30, 2020, the Company recorded a $1.8 million final mark-to-market loss on change in fair value of derivative instruments using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the

valuation methodology section below, and derecognized the $3.7 million derivative liability balance into additional paid in capital.

In connection with the January 31, 2020 Debt Equitization transaction with Foris, which was accounted for as a debt extinguishment as discussed in Note 4, “Debt” and Note 6, “Stockholders’ Deficit”, the Company issued rights (the Right) to purchase up to of 8.8 million shares of common stock at $2.87 per share for twelve months from the issuance date. The Company concluded that the Right met the derivative scope exception and criteria to be accounted for in equity. The Right had a fair value of $8.9 million which was recorded as additional paid in capital and a charge to loss upon extinguishment of debt. The fair value of the Right was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below.

During the second half of 2019, the Company issued five freestanding liability warrants related to the September 2019 and November 2019 Schottenfeld Notes (the Schottenfeld Notes), which the Company recorded at fair value as a derivative liability and debt discount on the respective issuance dates (see Note 4, “Debt” for further information). These freestanding liability warrants had a collective fair value of $7.0 million at December 31, 2019. As a result of the Foris Debt Equitization transaction on January 31, 2020, the variability causing these instruments to be recorded as a derivative liability was eliminated and upon derecognition of this liability into equity, the Company recorded a $1.8 million gain on change in fair value of derivative instruments in the three months ended March 31, 2020, using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and reclassified the derivative liability balance of $5.2 million to additional paid in capital.

On February 28, 2020, the Company entered into forbearance agreements with certain affiliates of the Schottenfeld Group LLC (the Lenders) related to certain defaults under the Schottenfeld Notes. The transaction was accounted for as a debt extinguishment. See Note 4, “Debt” for further information. In connection with entering into the forbearance agreements, the Company committed to issuing new warrants (the New Warrants) to the Lenders under certain contingent events for 1.9 million shares of common stock at a $2.87 purchase price and a two-year term. The contingent obligation to issue the New Warrants did not meet the derivative scope exception or equity classification criteria and were accounted for as a derivative liability. The contingently issuable New Warrants derivative liability had an initial fair value of $3.2 million and was recorded as a derivative liability with a $3.2 million charge to loss upon extinguishment of debt. The New Warrants derivative liability will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations. The fair value of the New Warrants derivative liability was determined using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below. At June 30, 2020, the fair value of the New Warrants derivative liability was $5.2 million, and the Company recorded a $2.1 million loss on change in fair value derivative instruments during the six months ended June 30, 2020.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price from $56.16 to $2.87 per share. See Note 4, “Debt” for further information. Historically, the embedded conversion option was bifurcated and accounted for as a derivative liability, and at December 31, 2019 and March 31, 2020 had a $0 fair value due to the Note’s short maturity and the significant conversion price differential when compared to the Company’s current stock price. As a result of the conversion price reduction, the Company remeasured the fair value of the conversion option using a Black-Scholes-Merton option pricing model based on the input assumptions for liability classified warrants table in the valuation methodology section below, and recorded a $6.5 million loss on change in fair value of derivative instruments in the three and six months ended June 30, 2020. On June 2, 2020, Total elected to convert all the outstanding principal and interest under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $6.5 million liability was derecognized into additional paid in capital, along with the debt principal and interest balance.

Bifurcated Embedded Features in Debt Instruments

During the second half of 2019, the Company issued four debt instruments with embedded mandatory redemption features which were bifurcated from the debt host instruments and recorded at fair value as a derivative liability and debt discount. The collective fair value of the four bifurcated derivatives totaled $2.8 million at December 31, 2019. In January and February 2020, the Company again modified certain key terms in three of the four underlying debt instruments, resulting in a debt extinguishment of the three modified debt instruments. Consequently, in the three months ended March 31, 2020, the collective fair value of the three extinguished bifurcated derivatives totaling $2.3 million was recorded as a loss upon extinguishment of debt and the $0.9 million collective fair value of the new bifurcated embedded mandatory redemption features was recorded as a derivative liability and new debt discount at the modification date. The fair value of the bifurcated derivative liability was determined using a probability weighted discounted cash flow analysis which is discussed in the valuation methodology and approach section below. As of and for the six months ended June 30, 2020, the fair value of the bifurcated embedded mandatory redemption features was $0.6 million, and the Company recorded a $0.5 million gain on

change in fair value derivative instruments. Also, one of the bifurcated features was embedded in the Foris LSA, which was modified and accounted for as an extinguishment in the three months ended June 30, 2020. As a result, the $0.7 million derivative liability balance was derecognized and recorded into the initial fair value of the new Foris Convertible Note (see “Fair Value of Debt – Foris Convertible Note (LSA Amendment)” above).

Valuation Methodology and Approach to Measuring the Derivative Liabilities

The liabilities associated with the Company’s freestanding and embedded derivatives outstanding at June 30, 2020 and December 31, 2019 represent the fair value of freestanding equity instruments and mandatory redemption features embedded in certain debt instruments. See Note 4, "Debt", and Note 6, "Stockholders' Deficit" for further information regarding these host instruments. There is no current observable market for these types of derivatives and, as such, the Company determined the fair value of the freestanding instrument or embedded derivatives using the Black-Scholes-Merton option pricing model or a probability weighted discounted cash flow analysis measuring the fair value of the debt instrument both with and without the embedded feature, both of which are discussed in more detail below.

The Company used the Black-Scholes-Merton option pricing model to determine the fair value of its liability classified warrants as of June 30, 2020 and December 31, 2019. Input assumptions for these freestanding instruments are as follows:

	Range for the Period
Input assumptions for liability classified warrants:	June 30, 2020		December 31, 2019
Fair value of common stock on issue date	$2.56 – $4.27		$3.09 – $4.76
Exercise price of warrants	$2.87 – $3.25		$3.87 – $3.90
Expected volatility	111% – 214%		94% – 105%
Risk-free interest rate	0.09% – 0.20%		1.58% – 1.67%
Expected term in years	0.07 – 2.51		1.51 – 2.00
Dividend yield	0.0	%	0.0 %

The Company uses a probability weighted discounted cash flow model to measure the fair value of the mandatory redemption features embedded in the debt instruments modified in the first quarter of 2020. The model is designed to measure and determine if the debt instruments would be called or held at each decision point. Within the model, the following assumption is made: the underlying debt instrument will be called early if the change in control redemption value is greater than the holding value. If the underlying debt instrument is called, the holder will maximize their value by finding the optimal decision between (i) redeeming at the redemption price and (ii) holding the instrument until maturity. Using this assumption, the Company valued the embedded derivatives on a "with-and-without method", where the fair value of each underlying debt instrument including the embedded derivative is defined as the "with," and the fair value of each underlying debt instrument excluding the embedded derivatives is defined as the "without." This method estimates the fair value of the embedded derivatives by comparing the fair value differential between the with and without mandatory redemption feature. The model incorporates the mandatory redemption price, time to maturity, risk-free interest rate, estimated credit spread and estimated probability of a change in control default event.

The market-based assumptions and estimates used in valuing the embedded derivative liabilities include amounts in the following ranges/amounts:

	June 30, 2020	December 31, 2019
Risk-free interest rate	0.09% - 0.17%	1.6% - 1.7%
Risk-adjusted discount yield	25.0% - 26.0%	20.0% - 27.0%
Probability of change in control	5.0%	5.0%
Credit spread	24.7% - 36.8%	18.4% - 25.4%
Estimated conversion dates	2022 - 2023	2022 - 2023

Changes in valuation assumptions can have a significant impact on the valuation of the embedded and freestanding derivative liabilities and debt that the Company elects to account for at fair value. For example, all other things being equal, generally, an increase in the Company’s stock price, change of control probability, risk-adjusted yields term to maturity/conversion or stock price volatility increases the value of the derivative liability.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable and other current accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. Loans payable and credit facilities are recorded at carrying value, which is representative of fair value at the date of acquisition. The Company estimates the fair value of these instruments using observable market-based inputs (Level 2). The carrying amount (the total amount of net debt presented on the balance sheet) of the Company's debt at June 30, 2020 and at December 31, 2019, excluding the debt instruments recorded at fair value, was $87.7 million and $195.8 million, respectively. The fair value of such debt at June 30, 2020 and at December 31, 2019 was $77.8 million and $194.8 million, respectively, and was determined by (i) discounting expected cash flows using current market discount rates estimated for certain of the debt instruments and (ii) using third-party fair value estimates for the remaining debt instruments.

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Debt

6 Months Ended

Jun. 30, 2020

Debt Disclosure [Abstract]

Debt

Debt

Net carrying amounts of debt are as follows:

	June 30, 2020								December 31, 2019
(In thousands)	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Convertible notes payable
Senior convertible notes	$	30,020	$	—	$	6,604	$	36,624	$	66,000	$	—	$	(15,376)	$	50,624
	30,020		—		6,604		36,624		66,000		—		(15,376)		50,624
Related party convertible notes payable
Foris convertible note	50,041		—		31,510		81,551		—		—		—		—
2014 Rule 144A convertible notes	—		—		—		—		10,178		—		—		10,178
	50,041		—		31,510		81,551		10,178		—		—		10,178
Loans payable and credit facilities
Schottenfeld notes	12,500		(299)		—		12,201		20,350		(1,315)		—		19,035
Nikko notes	8,632		(830)		—		7,802		14,318		(901)		—		13,417
Ginkgo note	12,000		(2,648)		—		9,352		12,000		(3,139)		—		8,861
Other loans payable	1,034		—		—		1,034		1,828		—		—		1,828
	34,166		(3,777)		—		30,389		48,496		(5,355)		—		43,141
Related party loans payable
Foris notes	5,000		—		—		5,000		115,351		(9,516)		—		105,835
DSM notes	33,000		(3,557)		—		29,443		33,000		(4,621)		—		28,379
Naxyris note	23,559		(655)		—		22,904		24,437		(822)		—		23,615
	61,559		(4,212)		—		57,347		172,788		(14,959)		—		157,829
Total debt	$	175,786	$	(7,989)	$	38,114	205,911		$	297,462	$	(20,314)	$	(15,376)	261,772
Less: current portion							(43,482)								(63,805)
Long-term debt, net of current portion							$	162,429							$	197,967

Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (ii) an aggregate of 2,742,160 shares of common stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of common stock (the Rights Shares), (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of common stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, (v) accrued and unpaid interest on the Senior Convertible Notes (payable on or prior to January 31, 2020) and (vi) cash fees in an aggregate amount of $1.0 million (payable on or prior to January 31, 2020). The Exchange Shares and Warrants were issued on January 14, 2020. The unpaid interest and cash fees were paid in accordance with the Exchange Agreements. The Rights were exercised by the Holder and common stock shares issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020.

The New Notes have substantially similar terms as the Prior Notes, except under the New Notes (i) the requirement to redeem an aggregate principal amount of $10 million on December 31, 2019 was eliminated, (ii) the Company would be required to redeem the New Notes in an aggregate amount of $10 million following the receipt by the Company of at least $80 million of aggregate net cash proceeds from one or more financing transactions, and at a price of 107% of the amount being redeemed, (iii) the financing activity requirement was reduced such that the Company would be required to raise aggregate net cash proceeds of $50 million from one or more financing transactions by January 31, 2020, (iv) the Company would have until January 31, 2020 to comply with certain covenants related to the repayment, conversion or exchange into equity or amendment of certain outstanding indebtedness of the Company, and (v) the deadline for the Company to seek stockholder approval for the Holders to exceed a 19.99% stock exchange ownership limitation (the Stockholder Approval) would be extended from January 31, 2020 to March 15, 2020.

Due to multiple changes in key provisions of the Prior Notes, the Company analyzed the before and after cash flows between the (i) fair value of the New Notes and (ii) reacquisition price of the Prior Notes resulting from the (A) decreased principal from $66 million to $51 million, (B) fair value of the Exchange Shares, (C) fair value of the Rights, (D) fair value of

the Warrants and (E) cash fees to be paid prior to January 31, 2020 to determine whether these changes resulted in a modification or extinguishment of the Prior Notes. Based on the before and after cash flows of each note, the change was significantly different. Consequently, the Exchange Agreements were accounted for as a debt extinguishment of the Prior Notes and a new debt issuance of the New Notes. The Company recorded a $5.3 million loss upon extinguishment of debt in the three months ended March 31, 2020, which was comprised of the $4.1 million fair value of the Warrants (considered a non-cash fee paid to the lender), the $1.0 million cash fee and $0.2 million excess fair value of the Exchange Shares and the Rights Shares over the contractual value. See Note 6, “Stockholders’ Deficit” for further information on the accounting treatment of the Exchange Shares and the Rights Shares upon issuance of the New Notes. Also, see Note 3, “Fair Value Measurement” for more information regarding the valuation methodology used to determine the fair value of the Warrants.

The Company elected to account for the New Notes at fair value, as of the January 14, 2020 issuance date. Management believes that the fair value option better reflects the underlying economics of the New Senior Convertible Notes, which contain multiple embedded derivatives. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the New Notes. For the three months ended March 31, 2020, the Company recorded a loss of $1.1 million, which is shown as Fair Value Adjustment in the table at the beginning of this Note 4. See Note 3, "Fair Value Measurement" for information about the assumptions that the Company used to measure the fair value of the Senior Convertible Notes.

On February 18, 2020, the Company and the Holders entered into separate waiver and forbearance agreements, (the W&F Agreements), pursuant to which the Holders agreed to, for 60 days following the date of the W&F Agreement, except in case of early termination of the W&F Agreement or, solely with respect to the Stockholder Approval if the other defaults described below have been cured on or prior to the date that is 60 days following the date of the W&F Agreement, until May 31, 2020 (the W&F Period), and in each case subject to certain conditions to effectiveness contained in the W&F Agreement, (i) forbear from exercising certain of their rights and remedies with respect to certain defaults by the Company, including, but not limited to, the Company's failure, on or before January 31, 2020, (A) to receive aggregated net cash proceeds of not less than $50 million from one or more financing transactions, (B) to repay in full or convert into equity the $20.4 million of indebtedness outstanding under the Schottenfeld Credit Agreements (discussed under the Schottenfeld Forbearance Agreement below) or amend all such indebtedness outstanding to fit within the definition of permitted indebtedness of the New Notes, and certain other events of default, and (ii) waive any event of default for (A) violations of the minimum liquidity covenant since December 31, 2019 and (B) failure to obtain the Stockholder Approval prior to March 15, 2020.

In addition, pursuant to the W&F Agreements, the Company and the Holders agreed that (i) the New Note amortization payment due on March 1, 2020 would be in the aggregate amount of $10.0 million (the Amortization Payment), split proportionally among the Holders, and that the Company would elect to pay such amortization payment in shares of Common Stock in accordance with the terms of the New Notes, provided however, that: (A) the Amortization Stock Payment Price (as defined in the New Notes) would be $3.00, (B) the Amortization Share Payment Period (as defined in the New Notes) with respect to the Amortization Payment would end on April 30, 2020 rather than March 31, 2020; and (C) in the event that Holder did not elect to receive the full Amortization Share Amount (as defined in the New Notes) during such Amortization Share Payment Period, then the Amortization Payment would be automatically reduced by the portion of such Amortization Payment not received by the Holder, (ii) there would be no amortization payment due on April 1, 2020, and (iii) the amortization payment due on May 1, 2020 would be in the aggregate amount of $8.9 million split proportionally among the Holders. The W&F Agreements were accounted for as a debt modification, as the before and after cash flows were not significantly different.

Amendment to Senior Convertible Notes Due 2022

On May 1, 2020, the Company and the holders of the New Senior Convertible Notes Due 2022 entered into separate amendments to the New Notes and the W&F Agreements (Note Amendment), pursuant to which the Company and the Holders agreed: (i) to amend the maturity date of the New Notes from September 30, 2022 to June 1, 2021 (Maturity Date); (ii) to remove from the New Notes all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances other than events of default; (iii) that the Company would no longer be required to redeem the New Notes in an aggregate amount of $10 million following the receipt by the Company of at least $80 million of aggregate net cash proceeds from one or more financing transactions; (iv) that interest payments would be due quarterly (as opposed to monthly), starting on August 1, 2020; (v) that an aggregate amortization payment of approximately $16.4 million (split proportionally among the Holders) would be due on or before the earlier of May 31, 2020 and the date on which the Company receives at least $50 million of aggregate net proceeds in an offering of securities (Amended May Amortization), an amortization payment of $5 million (to the largest Holder) would be due on December 1, 2020 unless the Company receives at least $50 million of aggregate net cash proceeds from one or more financing transactions after May 1, 2020, and no other amortization payment would be due prior to the Maturity Date; (vi) to reduce the conversion price of the New Notes from $5.00 to $3.50; (vii) to reduce the redemption price with respect to optional redemptions by the Company prior to October 1, 2020 to 100%, prior to December 31, 2020 to 105% and to 110% thereafter (as opposed to 115%), of the amount being redeemed; and (viii) that an aggregate of 2,836,364 shares of Common Stock held by the Holders would not be considered as Pre-Delivery

Shares (issued in connection with the November 15, 2019 Senior Convertible Notes Due 2022 and as defined in the New Notes) and would be subject to certain selling restrictions until June 15, 2020, and that an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders would be promptly returned to the Company. These Pre-Delivery Shares were returned to the Company on May 5, 2020 and May 6, 2020. The Company paid $16.4 million on June 1, 2020 to satisfy the required amortization payment and is no longer required to make the $5.0 million amortization payment on December 1, 2020. On June 4, 2020, the Company released an additional 700,000 Pre-Delivery Shares to the largest Holder in connection with the Second Amendment to New Notes and the W&F Agreements. The Company recorded $10.5 million of additional interest expense, representing the fair value of the 3,536,364 Pre-Delivery Shares released to the Holders.

Further, in connection with the Note Amendment, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share, from $3.25, with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s Common Stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share, from $5.02, and the exercise term of such warrant was extended to January 31, 2022, from May 10, 2021; and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s Common Stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022, from January 31, 2021. See Note 6, “Stockholders’ Deficit” for more information regarding the accounting treatment of these warrant modifications.

Debt Equitization – Foris, Related Party

As of December 31, 2019, the Company had two loans payable to Foris Ventures, LLC (Foris) with a total principal balance of $110.0 million, excluding capitalized interest of $5.3 million. Foris is an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and an owner of greater than five percent of the Company’s outstanding common stock. The first loan (Foris $19 million Note) was a $19 million unsecured borrowing that accrued interest at 12% per annum and matures on January 1, 2023. The second loan (Foris LSA) is a $91.0 million secured borrowing that accrues interest at 12.5% per annum and matured on March 1, 2023. The Foris LSA required quarterly principal payments and monthly interest payments. See Amendment No. 1 to Amended and Restated LSA — Foris, Related Party below for more information on the maturity date and payment terms of the Foris LSA.

On January 31, 2020, the Company completed a series of equity transactions with Foris that resulted in the Company (i) reducing its aggregate debt principal with Foris by $60.0 million and accrued interest and fees due to Foris by $9.9 million (including $5.4 million of capitalized interest), (ii) issuing an aggregate of 19,287,780 shares of common stock as a result of the exercise of outstanding warrants at a weighted average exercise price of approximately $2.84 per share for an aggregate of $54.8 million, (iii) issuing an aggregate of 5,279,171 shares of common stock at $2.87 per share for an aggregate of $15.1 million in a private placement, and (iv) issuing rights (the Rights) to purchase an aggregate of 8,778,230 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months. The exercise price of the outstanding warrants and the purchase price of the private placement common stock was paid through the cancellation of principal and accrued interest and fees totaling $69.9 million. See Note 6, “Stockholders’ Deficit” for information on the accounting treatment of the various equity related instruments.

As a result of the transaction described above, on January 31, 2020, the principal balance of the Foris $19 million Note and accrued but unpaid interest was fully settled through the exercise price of certain of outstanding warrants. Upon settlement of the Foris $19 million Note, the Company recorded a $5.7 million loss upon extinguishment debt, which was comprised of $6.1 million of unaccreted discount, less the $0.4 million fair value of the extinguished bifurcated derivative liability.

In addition, this series of equity transactions directly impacted the cash flows of the Foris LSA and, as a result, the Company analyzed the before and after cash flows resulting from the significant decrease in principal, the warrant exercise price modifications and the issuance rights to purchase additional shares of common stock at $2.87, to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was significantly different. Consequently, the accelerated paydown of the Foris LSA loan balance through the exercise price of the remaining outstanding warrants and the purchase price of the private placement common stock was accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $10.4 million loss upon extinguishment of debt, which was comprised of $8.9 million fair value of the Rights and $3.1 million of unaccreted discount, less the $1.6 million fair value of the extinguished bifurcated derivative liability. See Note 6, “Stockholders’ Deficit” for further information on the valuation methodology and related accounting treatment of the Rights. In recording the new debt issuance, the Company capitalized $0.7 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

Amendment No. 1 to Foris LSA — Foris, Related Party

On June 1, 2020, the Company and Foris entered into Amendment No. 1 to the Foris LSA (LSA Amendment), pursuant to which: (i) the interest rate applicable to the then outstanding secured indebtedness (Secured Indebtedness) was amended from and after June 1, 2020 to a per annum rate of interest equal to 6.00% (previously 12.5%), (ii) the Company shall not be required to make any interest payments outstanding as of May 31, 2020 or accruing thereafter prior to July 1, 2022 (previously due monthly), (iii) the quarterly principal amortization payments were eliminated and all outstanding principal under the LSA Amendment became due on July 1, 2022, and (iv) Foris shall have the option, in its sole discretion, to convert all or portion of the Secured Indebtedness, including accrued interest, into shares of common stock at a $3.00 conversion price (Conversion Option), subject to the Company’s stockholder approval to issue shares of common stock upon exercise of the Conversion Option in accordance with applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d); provided that, if the stockholder approval is obtained before August 15, 2020, Foris would exercise its Conversion Option with respect to no less than $15 million of the Secured Indebtedness within 30 days of such stockholder approval.

The Company analyzed the before and after cash flows resulting from the LSA Amendment to determine whether these changes result in a modification or extinguishment of the Foris LSA. Based on the before and after cash flows, the change was significant. Consequently, the LSA Amendment was accounted for as a debt extinguishment and a new debt issuance. The Company elected to account for the new debt issuance under the fair value option and recorded a $22.0 million loss upon extinguishment of the Foris LSA, representing the difference between the carrying value of the Foris LSA prior to the modification and the $72.1 million reacquisition price of the Foris LSA (which is the fair value of the LSA Amendment with the conversion option). Management believes the fair value option best reflects the underlying economics of the LSA Amendment, which contains embedded derivatives, a conversion option requiring bifurcation and a beneficial conversion feature. Under the fair value election, changes in fair value will be reported in the consolidated statements of operations as "Gain (loss) from change in fair value of debt" in each reporting period subsequent to the issuance of the LSA Amendment. The Company also recorded a loss of $9.5 million for the three months ended June 30, 2020 related to the change in fair value of the LSA Amendment after the June 1, 2020 issuance date, which is shown as Fair Value Adjustment in the table at the beginning of this Note 4. See Note 3, "Fair Value Measurement" for information about the assumptions that the Company used to measure the fair value of the LSA Amendment.

Schottenfeld Forbearance Agreement

The Company, Schottenfeld Group LLC (Schottenfeld) and certain of its affiliates (collectively, the Lenders) are parties (i) to certain Credit Agreements, each dated September 10, 2019 (collectively, the September Credit Agreements) and (ii) to a Credit and Security Agreement, dated November 14, 2019 (the CSA, and collectively with the September Credit Agreements, the Credit Agreements), pursuant to which the Company issued to the Lenders certain notes (the September Notes and the November Notes, respectively, and collectively, the Schottenfeld Notes) and warrants (the September Warrants and the November Warrants, respectively, and collectively, the Schottenfeld Warrants) to purchase shares (the Warrant Shares) of the Company’s common stock. See Note 6, “Stockholders’ Deficit” for further information. Indebtedness under the September Notes totals $12.5 million, accrues interest at 12% per annum and matures on January 1, 2023. Indebtedness under the November Notes total $7.9 million, accrued interest at 12% per annum and originally matured on January 15, 2020. The Company failed to repay the $7.9 million November Notes by January 15, 2020.

On February 28, 2020, the Company entered into a forbearance agreement with the Lenders (Forbearance Agreement), pursuant to which the Lenders would forbear, for 60 days from the date of the Forbearance Agreement, unless terminated earlier (the Forbearance Period), to exercise certain rights as a result of the Company’s defaults under the Credit Agreements and related Schottenfeld Notes, including the failure of the Company to (i) to pay all principal and accrued interest on the November Notes at the maturity date, (ii) the failure to pay on or before December 31, 2019, all accrued and unpaid interest through December 31, 2019 on the September Notes, and (iii) the failure, on or before December 15, 2019, to convert or exchange at least $60 million, but not less than 100%, of certain junior outstanding indebtedness into equity in the Company, and certain other events of default. Under the Forbearance Agreement, the Company agreed to (i) pay a late fee of 5% on any obligations under the November Notes not paid in full on or before the last day of the Forbearance Period; (ii) pay on or prior to the earliest to occur of April 19, 2020 or the last day of the Forbearance Period, (A) all interest due pursuant to the November Notes and the September Notes, plus all interest accruing on such unpaid interest, plus all interest accrued on account of the November Notes and the September Notes from the date of the Forbearance Agreement through the date of such payment, and (B) a forbearance fee in the amount of $150,000; (iii) pay, upon signature of the Forbearance Agreement, $150,000 as a partial payment of the interest that has accrued pursuant to the November Notes and the September Notes as of the date of the Forbearance Agreement; (iv) issue new warrants upon the occurrence of certain contingent events and (v) amend the Schottenfeld Warrants to (A) reduce the exercise price of each Schottenfeld Warrant to $2.87 per share, and (B) with respect to the November Warrants, extend the deadline to register the Warrant Shares for resale by the Holders.

Due to multiple changes in key provisions of Schottenfeld Credit Agreements, the Company analyzed the before and after cash flows resulting from the warrant modification and forbearance fee to determine whether these changes result in a

modification or extinguishment of the original Schottenfeld and Phase Five notes. Based on the combined before and after cash flows of each note, the change was significantly different. Consequently, the modifications resulting from the Forbearance Agreement were accounted for as a debt extinguishment and a new debt issuance. The Company recorded a $5.6 million loss upon extinguishment of debt, which was comprised of the $3.2 million fair value of contingent warrant issuance obligation, the $1.3 million incremental fair value of the modified warrants, $1.1 million of unaccreted discount and the forbearance fee, less the balance of the extinguished bifurcated derivative liability. In recording the new debt issuance, the Company capitalized $0.2 million of legal fees and $0.2 million for the initial fair value of the embedded mandatory redemption feature as a debt discount to be amortized to interest expense under the effective interest method over the term of the remaining term of the new debt issuance.

On April 19, 2020, the Company failed to pay the amounts due under the Forbearance Agreement, including the past due interest on the September Notes, and was unable to obtain a waiver or extension for the past due amounts. As a result, $20.4 million of principal outstanding under the Schottenfeld Notes was classified as a current liability on the condensed consolidated balance sheet as of March 31, 2020. On June 5, 2020, the Company repaid the past due November 2019 Notes totaling $7.9 million. Consequently, the September 2019 Notes due January 1, 2023 totaling $12.5 million were reclassified to a non-current liability as of June 30, 2020.

2014 Rule 144A Note Exchange and Extensions – Total, Related Party

On March 11, 2020, the Company and Total Raffinage Chimie (Total) entered into a Senior Convertible Note Maturity Extension Agreement (the Extension Agreement) due to the Company’s failure to pay the $10.2 million principal amount due under the December 20, 2019 reissued 2014 Rule 144A Convertible Notes that matured on January 31, 2020. The Extension Agreement resulted in the reissuance and extension of the December 20, 2019 promissory note to March 31, 2020. Under the terms of the extension agreement, the Company paid Total $1.5 million to satisfy all accrued but unpaid interest and to reduce the principal balance of the reissued note by $1.1 million. The reissued note: (i) had a maturity date of March 31, 2020, (ii) had a $9.1 million principal amount due, (iii) accrued interest at a rate of 12.0% per annum, and (iv) had terms substantially identical to the December 20, 2019 promissory note. The Extension Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note to $2.87 per share. Effective April 30, 2020, the Company and Total entered into a subsequent Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The 2014 Rule 144A Convertible Note was reissued as a result of such extensions with terms substantially identical to the previously issued promissory notes. On June 2, 2020, Total elected to convert all the outstanding principal and interest due under the 2014 Rule 144A Convertible Note totaling $9.3 million into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the fair value of the conversion option was derecognized into additional paid in capital. See Note 3, “Fair Value Measurement” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

Ginkgo Waiver Agreement

On March 11, 2020, the Company and Ginkgo Bioworks, Inc. (Ginkgo) entered into a Waiver Agreement and Amendment to Partnership Agreement (the Ginkgo Waiver), pursuant to the terms of (i) the Ginkgo promissory note dated October 20, 2017, issued by the Company to Ginkgo (as amended, the Ginkgo Note), (ii) the Ginkgo Partnership Agreement, dated October 20, 2017, by and between the Company and Ginkgo, and (iii) the Waiver Agreement and Amendment to Ginkgo Note, dated September 29, 2019, by and between the Company and Ginkgo, pursuant to which Ginkgo agreed to (a) waive the Company’s failure to pay past due interest and partnership payments, including interest thereon of $6.7 million by December 15, 2019, and to comply with a reporting covenant prior to March 31, 2020, (b) to make a prior waiver fee payment of $0.5 million on December 15, 2019, (c) waive any cross defaults due to events of default under other debt obligations by the Company, (d) amend payments on the Ginkgo Partnership Agreement beginning on March 31, 2020 to a monthly payment of $0.5 million through and including October 31, 2021, and (e) to defer all past due payments totaling $7.2 million until April 30, 2020. The Ginkgo Waiver was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On May 6, 2020, the Company entered into a waiver agreement under which the maturity date for all past due amounts to Ginkgo was extended to the earlier of the day the Company receives cash proceeds from any private placement of its equity and/or equity-linked securities, and May 31, 2020. The Company paid all past-due amounts to Ginkgo and on August 10, 2020 amended the Ginkgo Note to reflect a reduced interest rate and a change from monthly to quarterly interest payments and

amended the Ginkgo Partnership Agreement to reflect changes to the frequency and amount of the periodic payments due under the agreement. See Note 12, “Subsequent Events” for further information.

Nikko Secured Loan Agreement Amendment

On March 12, 2020, the Company and Nikko Chemicals Co. Ltd. (Nikko), entered into an amendment to the secured loan agreement (Loan Agreement) under which the Company paid Nikko $0.5 million to reduce the principal balance of the Loan Agreement to $4.0 million, extended the maturity date of the loan from January 31, 2020 to March 31, 2020 and increased the interest rate to 8.0% per annum. The loan (i) matured on March 31, 2020, (ii) accrued interest at a rate of 2.75% per annum, and (iii) was secured by a first-priority lien on 27.2% of the Aprinnova JV interests owned by the Company. The Loan Agreement was accounted for as a debt modification, as the before and after cash flows were not significantly different.

On April 3, 2020, the Company entered into a second amendment to the Loan Agreement under which the maturity date of the loan was extended to April 30, 2020. Subsequently, on May 7, 2020, the Company entered into a third amendment to the Loan Agreement under which the maturity date of the loan was extended to May 31, 2020. The Company fully repaid the $4.0 million loan on June 5, 2020.

Paycheck Protection Plan Loan

On April 7, 2020, the Company applied for a Paycheck Protection Plan loan (PPP Loan) established by the Coronavirus Aid, Relief, and Economic Security Act (CARES Act). On May 7, 2020, the Company received a $10 million loan pursuant to a promissory note issued by the Company. The PPP Loan accrued interest at an annual fixed rate of 1% and had a term of 2 years with no payments due in the first six months of such term; however, interest still accrued during this six-month period. Upon receipt of the PPP Loan, the Company applied the funds to payroll and building rent expenses. Following the completion of the private placement of its securities in early June 2020, the Company repaid the PPP Loan in full, including applicable interest, on June 12, 2020.

Foris $5 Million Note – Foris, Related Party

On April 29, 2020, the Company borrowed $5.0 million from Foris Ventures, LLC, an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock. The note is unsecured and accrues interest at 12% per annum. Principal and interest will be payable at maturity, on December 31, 2022.

Future Minimum Payments

Future minimum payments under the Company's debt agreements as of June 30, 2020 are as follows:

(In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020 (remaining six months)	$	814	$	10,132	$	—	$	3,084	$	14,030
2021	33,898		4,255		—		31,777		69,930
2022	—		15,058		59,578		40,558		115,194
2023	—		12,899		—		—		12,899
2024	—		398		—		—		398
Thereafter	—		1,869		—		—		1,869
Total future minimum payments	34,712		44,611		59,578		75,419		214,320
Less: amount representing interest	(4,692)		(10,445)		(9,537)		(13,860)		(38,534)
Present value of minimum debt payments	30,020		34,166		50,041		61,559		175,786
Less: current portion of debt principal	(30,020)		(6,996)		—		—		(37,016)
Noncurrent portion of debt principal	$	—	$	27,170	$	50,041	$	61,559	$	138,770

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Mezzanine Equity

6 Months Ended

Jun. 30, 2020

Temporary Equity Disclosure [Abstract]

Mezzanine Equity

Mezzanine Equity

Mezzanine equity at June 30, 2020 and December 31, 2019 is comprised of proceeds from shares of common stock sold on May 10, 2016 to the Bill & Melinda Gates Foundation (Gates Foundation). In connection with the stock sale, the Company and the Gates Foundation entered into an agreement under which the Company agreed to expend an aggregate amount not less than the proceeds from the stock sale to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria. If the Company defaults in its obligation to use the proceeds from the stock sale as set forth above or defaults under certain other commitments in the agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party, the shares then held by the Gates Foundation at a price per share equal to the greater of (i) the closing price of the Company’s common stock on the trading day prior to the redemption or purchase, as applicable, or (ii) an amount equal to $17.10 plus a compounded annual return of 10%.

As of June 30, 2020, the Company's remaining research and development obligation under this arrangement was $0.3 million.

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Stockholders' Deficit

6 Months Ended

Jun. 30, 2020

Equity [Abstract]

Stockholders' Deficit

Stockholders' Deficit

Foris Warrant Exercises for Cash

On January 13, 2020, Foris Ventures, LLC (Foris), an entity affiliated with director John Doerr and which beneficially owns greater than 5% of the Company’s outstanding common stock, delivered to the Company an irrevocable notice of cash exercise with respect to a warrant to purchase 4,877,386 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to a warrant issued by the Company on August 17, 2018. The Company received approximately $14.0 million from Foris in connection with the warrant exercise representing 4,877,386 shares of common stock issued and recorded $14.0 million as additional paid-in capital.

On March 11, 2020, Foris provided to the Company a notice of cash exercise to purchase 5,226,481 shares of the Company’s common stock at an exercise price of $2.87 per share, pursuant to the PIPE Rights (discussed in the January 2020 Private Placement section below) issued by the Company on January 31, 2020. On March 12, 2020, the Company received approximately $15.0 million from Foris in connection with the PIPE Rights exercise. The Company and Foris agreed to defer the issuance of the shares until such time as stockholder approval has been obtained to increase the Company’s authorized share count. At March 31, 2020, the PIPE Rights exercise proceeds were recorded as additional paid-in capital as there is no contractual obligation to return the consideration if stockholder approval is not obtained. Stockholder approval was obtained on May 29, 2020 and the 5,226,481 shares of common stock were issued to Foris on June 2, 2020.

January 2020 Warrant Amendments and Exercises, Foris Debt Equitization and Private Placement

As described below in further detail, on January 31, 2020, the Company completed a series of equity transactions that resulted in the Company (i) receiving $28.3 million in cash, (ii) reducing its aggregate debt principal by $60.0 million and accrued interest by approximately $9.9 million, (iii) issuing an aggregate of (A) 25,326,095 shares of common stock as a result of the exercise of outstanding warrants, and (B) 13,989,973 new shares of common stock in private placements, and (iv) issuing rights to purchase an aggregate of 18,649,961 shares of common stock, at an exercise price of $2.87 per share, for an exercise term of 12 months. See Note 4, “Debt,” for more information regarding the accounting treatment of the $60.0 million debt reduction.

Warrant Amendments and Exercises by Certain Holders

On January 31, 2020, the Company entered into separate warrant amendment agreements (the Warrant Amendments) with certain holders (the Warrant Holders) of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of certain warrants (the Amended Warrants) held by the Warrant Holders totaling 1.2 million shares was reduced to $2.87 per share. In connection with the entry into the Warrant Amendments, on January 31, 2020, the Warrant Holders exercised their Amended Warrants, representing an aggregate of 1,160,929 shares of common stock (the Warrant Amendment Shares), and the Company issued the Warrant Amendment Shares to the Holders along with a right to purchase an aggregate of 1,160,929 shares of Common Stock, at an exercise price of $2.87 per share, for an exercise term of twelve months from the January 31, 2020 issuance (the Rights). The Company received net proceeds of $3.3 million from the exercise of the Amended Warrants and recorded the $3.3 million as additional paid in capital. The Company also measured the before and after fair value of the Amended Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Rights warrants met the derivative scope exception and equity classification criteria to be accounted for in equity.

Warrant Amendments and Exercises, Common Stock Purchase and Debt Equitization by Foris – Related Party

On January 31, 2020, the Company and Foris entered into certain warrant amendment agreements (the Foris Warrant Amendments) totaling 10.2 million shares of the Company’s outstanding warrants to purchase shares of common stock, pursuant to which the exercise price of these certain warrants (the Amended Foris Warrants) was reduced to $2.87 per share. In connection with the Foris Warrant Amendments, on January 31, 2020 (i) Foris exercised all of its then outstanding common stock purchase warrants, including the Amended Foris Warrants, totaling 19,287,780 shares of common stock, at a weighted average exercise price of approximately $2.84 per share for an aggregate exercise price of $54.8 million (the Exercise Price), and purchased 5,279,171 shares of common stock (the Foris Shares) at $2.87 per share for a total purchase price of $15.1 million (Purchase Price), (ii) Foris paid the Exercise Price and the Purchase Price through the cancellation of $60 million of principal and $9.9 million of accrued interest and fees owed by the Company to Foris under the Foris $19 million Note and the Foris LSA (which was treated as a debt extinguishment as discussed in Note 4, "Debt") and (iii) the Company issued to Foris the Foris Shares and an additional right (the Additional Right) to purchase 8,778,230 shares of Common Stock at a purchase price of $2.87 per share, for a period of 12 months from the execution of the warrant exercise agreement.

Upon exercise of the Amended Foris Warrants and issuance of the Foris Shares, the Company recorded a $69.9 million increase to additional paid-in capital. The Company also measured the before and after fair value of the Amended Foris Warrants using the Black-Scholes-Merton option pricing model and determined there was no incremental value to record related to the purchase price reduction. Further, the Company concluded the Additional Rights met the derivative scope exception and criteria to be accounted for in equity and recorded the $8.9 million fair value of the Additional Rights to additional paid-in capital and loss upon extinguishment of debt. The fair value was determined using a Black-Scholes-Merton option pricing model based on the following input assumptions: (i) $2.56 stock price, (ii) 112% volatility, (iii) 1.45% risk free rate and (iv) 0% dividend.

January 2020 Private Placement

On January 31, 2020, the Company entered into separate Security Purchase Agreements with certain accredited investors and Foris, for the issuance and sale of an aggregate of 8,710,802 shares of common stock and rights to purchase an aggregate of 8,710,802 shares of common stock (PIPE Rights) at a purchase price of $2.87 per share, for a period of 12 months, for an aggregate purchase price of $25 million. The $25 million in proceeds was recorded as additional paid-in capital. See Note 3, “Fair Value Measurement,” for information regarding the valuation methodology used to determine fair value and the related accounting treatment of the PIPE rights.

Principal Conversion into Common Stock and New Warrants Issued in Exchange of Senior Convertible Notes

On January 14, 2020, the Company completed the exchange of the Company’s $66 million Senior Convertible Notes (or the Prior Notes), pursuant to separate exchange agreements (the Exchange Agreements) with certain private investors (the Holders), for (i) new senior convertible notes in an aggregate principal amount of $51 million (the New Notes or New Senior Convertible Notes), (ii) an aggregate of 2,742,160 shares of common stock (the Exchange Shares), (iii) rights (the Rights) to acquire up to an aggregate of 2,484,321 shares of common stock (the Rights Shares), and (iv) warrants (the Warrants) to purchase up to an aggregate of 3,000,000 shares of common stock (the Warrant Shares) at an exercise price of $3.25 per share, with an exercise term of two years from issuance, The New Notes, Exchange Shares, Rights and Warrants were issued on January 14, 2020. The Rights were exercised by the Holder and the Rights Shares were issued by the Company according to the terms of the New Senior Convertible Notes on February 24, 2020. The contractual value of the Exchange Shares and the Rights Shares was $2.87 per share. Upon issuance of the New Notes, Exchange Shares and Rights, the $15.0 million of debt principal was extinguished and the $15.2 million fair value of the Exchange Shares and the Rights Shares was recorded as additional paid in capital. See Note 3, “Fair Value Measurement,” for more information regarding the valuation methodology used to determine the fair value and the related accounting treatment of the Warrants, and see Note 4, “Debt,” for further information on the accounting treatment and the terms of the note exchange.

Release of Pre-Delivery Shares and Amendment to Warrants Issued to Holders of Senior Convertible Notes Due 2022

Under the terms of the November 15, 2019 Senior Convertible Notes Due 2022 and the January 14, 2020 New Senior Convertible Notes, the Company was required to pre-deliver 7.5 million shares of common stock (the Pre-Delivery Shares) to the Holders, which are freely tradeable, validly issued, fully paid, nonassessable and free from all preemptive or similar rights or liens, for the Holders to sell, trade or hold, subject to certain limitations, for as long as the Senior Convertible Notes Due 2022 are outstanding. However, the Company may elect or be required to apply the value of the pre-delivered shares to satisfy periodic principal and interest payments or other repayment events. Within ten business days following redemption or repayment of in full the Senior Convertible Notes Due 2022 and the satisfaction or discharge by the Company of all outstanding Company obligations under the Senior Convertible Notes Due 2022, the Holders shall deliver 7.5 million shares of the Company’s common stock to the Company, less any shares used to satisfy any accrued interest or principal amortization payments under such notes. The Company concluded the Pre-Delivery Shares provision meets the criteria of freestanding instrument that is legally detachable and separately exercisable from the Senior Convertible Notes Due 2022 and should be classified in equity as the common shares issued are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company accounted for the fair value of the Pre-Delivery Shares within equity.

On May 1, 2020, in connection with the amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”, the Company and the Holders of the New Senior Convertible Notes Due 2022 agreed, among other provisions described in Note 4, “Debt”: (i) to remove all equity triggering provisions that allowed the Holders to convert the notes at a reduced conversion price in certain circumstances; (ii) to reduce the conversion price of the New Notes from $5.00 to $3.50; (iii) to release to the Holders an aggregate of 2,836,364 shares of common stock originally required to be returned under the Pre-Delivery Share arrangement, and (iv) return an aggregate of 1,363,636 Pre-Delivery Shares held by certain Holders to the Company. Further, on June 4, 2020, the Company agreed to release an additional 700,000 Pre-Delivery Shares to one of the Holders, in connection with the second amendment to the Senior Convertible Notes Due 2022 described in Note 4, “Debt”. After the release and return of the Pre-Delivery Shares on May 1, 2020 and June 4, 2020, the total number of Pre-Delivery

Shares subject to the arrangement is 2,600,000 and must be returned to the Company following full redemption or repayment of the New Senior Convertible Notes Due 2022. As a result of releasing the 3,536,364 Pre-Delivery Shares to the Holders, the Company recorded $10.5 million of additional interest expense, representing the fair value of the released share.

Further, in connection with the May 1, 2020 amendment to the Senior Convertible Notes Due 2022, the Company and the Holders entered into certain warrant amendment agreements pursuant to which (i) the exercise price of the warrants issued on January 14, 2020 in connection with the Exchange of the Senior Convertible Notes due 2022 was reduced to $2.87 per share (from $3.25) with respect to an aggregate of 2,000,000 warrant shares; (ii) the exercise price of a warrant to purchase 960,225 shares of the Company’s common stock issued to one of the Holders on May 10, 2019 was reduced to $2.87 per share (from $5.02), and the exercise term of such warrant was extended to January 31, 2022 (from May 10, 2021); and (iii) the exercise term of a right to purchase 431,378 shares of the Company’s common stock issued to one of the Holders on January 31, 2020 was extended to January 31, 2022 (from January 31, 2021). Each of these warrant instruments were previously accounted for in equity. As a result of the warrant amendments, the Company performed a before and after remeasurement of the warrants using the Black-Scholes-Merton option pricing model and recorded $1.1 million of incremental interest expense and a corresponding increase to additional paid in capital.

Increase in Authorized Common Stock

On May 29, 2020, through a proxy vote at the Company’s Annual Stockholder meeting, the Company’s stockholders approved an increase in the Company’s authorized common stock share count from 250 million to 350 million.

Total Conversion Price Reduction and Subsequent Conversion into Common Stock

On April 6, 2020, the Company and Total entered into a Senior Convertible Note Maturity Extension Agreement to extend the maturity date of the 2014 Rule 144A Convertible Note to April 30, 2020 and reduce the conversion price of the 2014 Rule 144A Convertible Note from $56.16 to $2.87 per share. See Note 4, “Debt” for further information related to this debt instrument. On June 2, 2020, Total elected to convert all the outstanding principal and interest totaling $9.3 million due under the 2014 Rule 144A Convertible Note into 3,246,489 shares of common stock. Upon conversion, the $9.3 million debt principal and interest balance and the $6.5 million derivative liability balance related to the conversion option was derecognized into additional paid-in capital. See Note 3, “Fair Value Measurement,” for more information regarding the accounting treatment of the embedded conversion option and subsequent conversion price reduction.

June 2020 PIPE

On June 1, 2020 and June 4, 2020, the Company entered into separate security purchase agreements (Purchase Agreements) with certain accredited investors (Investors), including Foris Ventures, LLC and Vivo Capital LLC, stockholders that beneficially own more than five percent of the Company’s outstanding common stock and are, respectively, owned by or affiliated with individuals serving on the Company’s Board of Directors, for the issuance and sale of an aggregate of 32,614,573 shares of the Company’s common stock, $0.0001 par value per share and 102,156 shares of the Company’s Series E Convertible Preferred Stock, $0.0001 par value per share, convertible into 34,052,070 shares of common stock, at a price of $3.00 per common share and $1,000 per preferred share, resulting in an aggregate purchase price of $200 million (Offering). The transaction closed on June 5, 2020, following the satisfaction of customary closing conditions. Upon closing, the Company received aggregate net proceeds of approximately $190 million after payment of the Offering expenses and placement agent fees. The Company used the proceeds from the Offering for the repayment of certain outstanding indebtedness and the remainder for general corporate purposes.

The Purchase Agreements included customary representations, warranties and covenants of the parties. In addition, the Company executed a letter agreement pursuant to which, subject to certain exceptions, the Company, the members of the Company’s Board of Directors, and the Company’s named executive officers agreed not to issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of Common Stock or securities convertible into or exercisable or exchangeable for common stock until September 2, 2020. The securities issued pursuant to the Purchase Agreements were sold in private placements pursuant to an exemption from registration under Section 4(a)(2) of the Securities Act of 1933, as amended (Securities Act) and Rule 506(b) of Regulation D promulgated under the Securities Act, without general solicitation, made only to and with accredited investors as defined in Regulation D.

Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws

On June 5, 2020, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series E Convertible Preferred Stock (Preferred Stock) with the Secretary of State of Delaware. Each share of Series E Preferred Stock issued in the June 2020 PIPE has a stated value of $1,000 and is convertible into 333.33 shares of common stock. All preferred shares will automatically convert into common stock without any further action by the holders on the first trading day after the

Company obtains stockholder approval (as described below). Unless and until converted into common stock in accordance with its terms, the Preferred Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the Preferred Stock.

The Company shall obtain stockholder approval for the issuance of common stock upon conversion of the Preferred Stock as is required by the applicable rules and regulations of the Nasdaq Stock Market, including Nasdaq Listing Standard Rule 5635(d), and including the issuance of common stock upon conversion of the Preferred Shares in excess of 19.99% of the issued and outstanding common stock on the date of the Purchase Agreements. Pursuant to the Purchase Agreements, the Company is required to hold a special meeting of stockholders within 75 calendar days of the date of the Purchase Agreements for the purpose of obtaining stockholder approval. This special meeting is scheduled to occur on August 14, 2020.

The Company analyzed the automatic conversion provision related to the Series E Preferred Stock and determined the holders received a contingent beneficial conversion feature (BCF) equal to $67.2 million. This amount represents the difference between the Company’s closing stock price at the June 1, 2020 and June 4, 2020 commitment dates ($5.35 and $4.88, respectively) and the $3.00 conversion price. As the automatic conversion provision is contingent on stockholder approval, the BCF will not be recognized until the contingency is resolved. Upon obtaining stockholder approval, the $67.2 million BCF will be recognized in additional paid-in capital and reflected as a deemed dividend in the consolidated statement of operations, increasing the net loss attributable to common stockholders and increasing basic net loss per share.

Warrants and Rights Activity Summary

In connection with various debt and equity transactions (see Note 4, “Debt” above and Note 4, "Debt" and Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 2019 Form 10-K), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrants activity for the six months ended June 30, 2020:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2019	Additional Warrants Issued	Exercises	Expired	Exercise Price per Share of Warrants Exercised		Number Outstanding as of June 30, 2020	Exercise Price per Share as of June 30, 2020
High Trail/Silverback warrants	2020	January 14, 2022	—	3,000,000	—	—	$	—	3,000,000	$2.87/$3.25
2020 PIPE right shares	2020	February 4, 2021	—	8,710,802	(5,226,481)	—	$	2.87	3,484,321	$	2.87
January 2020 warrant exercise right shares	2020	January 31, 2021 and January 31, 2022	—	9,939,159	—	—	$	—	9,939,159	$	2.87
Foris LSA warrants	2019	August 14, 2021	3,438,829	—	(3,438,829)	—	$	2.87	—	$	—
November 2019 Foris warrant	2019	November 27, 2021	1,000,000	—	(1,000,000)	—	$	2.87	—	$	—
August 2019 Foris warrant	2019	August 28, 2021	4,871,795	—	(4,871,795)	—	$	2.87	—	$	—
April 2019 PIPE warrants	2019	April 26, 2021, April 29, 2021 and May 3, 2021	8,084,770	—	(4,712,781)	—	$	2.87	3,371,989	$4.76/$5.02
April 2019 Foris warrant	2019	April 16, 2021	5,424,804	—	(5,424,804)	—	$	2.87	—	$	—
September and November 2019 Investor Credit Agreement warrants	2019	September 10, 2021 and November 14, 2021	5,233,551	—	—	—	$	—	5,233,551	$	2.87
Naxyris LSA warrants	2019	August 14, 2021	2,000,000	—	—	—	$	—	2,000,000	$	2.87
October 2019 Naxyris warrant	2019	October 28, 2021	2,000,000	—	—	—	$	—	2,000,000	$	3.87
May-June 2019 6% Note Exchange warrants	2019	May 15, 2021 and June 24, 2021	2,181,818	—	—	—	$	—	2,181,818	$2.87/$5.12
May 2019 6.50% Note Exchange warrants	2019	May 14, 2021 and January 31, 2022	1,744,241	—	(784,016)	—	$	2.87	960,225	$	2.87
July 2019 Wolverine warrant	2019	July 8, 2021	1,080,000	—	—	—	$	—	1,080,000	$	2.87
August 2018 warrant exercise agreements	2018	May 17, 2020 and May 20, 2020	12,097,164	—	(4,877,386)	(7,219,778)	$	2.87	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,078,156	—	—	—	$	—	6,078,156	$	2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	—	3,968,116	$	2.87
May 2017 dilution warrants	2017	July 10, 2022	3,085,893	—	—	—	$	—	3,085,893	$	—
August 2017 dilution warrants	2017	May 23, 2023	3,028,983	—	—	—	$	—	3,028,983	$	—
February 2016 related party private placement	2016	February 12, 2021	171,429	—	(152,381)	—	$	0.15	19,048	$	0.15
July 2015 related party debt exchange	2015	July 29, 2020 and July 29, 2025	133,334	—	(133,334)	—	$	0.15	—	$	—
July 2015 private placement	2015	July 29, 2020	72,650	—	(72,650)	—	$	0.15	—	$	—
July 2015 related party debt exchange	2015	July 29, 2020	58,690	—	—	—	$	—	58,690	$	0.15
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$	160.05
			65,755,629	21,649,961	(30,694,457)	(7,219,778)			49,491,355

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Loss Per Share

6 Months Ended

Jun. 30, 2020

Earnings Per Share [Abstract]

Loss Per Share

Loss per Share

For the three and six months ended June 30, 2020 and June 30, 2019, basic loss per share was the same as diluted loss per share, because the inclusion of all potentially dilutive securities outstanding was antidilutive.

The Company follows the two-class method when computing net loss per common share when shares are issued that meet the definition of participating securities. The two-class method requires income available to common stockholders for the period to be allocated between common stock and participating securities based upon their respective rights to receive dividends as if all income for the period had been distributed. The two-class method also requires losses for the period to be allocated between common stock and participating securities based on their respective rights if the participating security contractually participates in losses. The Company’s convertible preferred stock are participating securities as they contractually entitle the holders of such shares to participate in dividends and contractually require the holders of such shares to participate in the Company’s losses.

The following table presents the calculation of basic and diluted loss per share:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Numerator:
Net loss attributable to Amyris, Inc.	$	(110,422)	$	(38,088)	$	(198,266)	$	(104,331)
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D	—		(34,964)		—		(34,964)
Add: losses allocated to participating securities	6,361		2,255		7,435		4,690
Net loss attributable to Amyris, Inc. common stockholders	$	(104,061)	$	(70,797)	$	(190,831)	$	(134,605)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	184,827,330		92,785,752		169,946,482		84,831,269
Loss per share attributable to common stockholders, basic and diluted	$	(0.56)	$	(0.76)	$	(1.12)	$	(1.59)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted loss per share of common stock because including them would have been antidilutive:

	Three Months Ended June 30,		Six Months Ended June 30,
	2020	2019	2020	2019
Period-end common stock warrants	43,298,741	5,535,538	43,298,741	5,535,538
Convertible promissory notes(1)	8,574,399	11,007,316	8,574,399	11,007,316
Period-end stock options to purchase common stock	5,479,334	49,747,628	5,479,334	49,747,628
Period-end restricted stock units	4,468,266	5,284,742	4,468,266	5,284,742
Period-end preferred stock(2)	1,943,661	2,955,732	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted loss per share	63,764,401	74,530,956	63,764,401	74,530,956

______________

⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

⁽²⁾ The 102,156 shares of Series E Preferred Stock, which is convertible into 34,052,070 common shares, is not included in this share count. The automatic conversion of the Series E Preferred Stock is contingent upon stockholder approval, and is therefore, not considered a potentially dilutive security until the contingency is resolved.

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Commitments and Contingencies

6 Months Ended

Jun. 30, 2020

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

Contingencies

The Company has levied indirect taxes on sugarcane-based biodiesel sales that took place several years ago by Amyris Brasil Ltda. (see Note 12, “Divestiture” in Part II, Item 8 of the 2019 Form 10-K) to customers in Brazil, based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate the Company levied.

On April 3, 2019, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and former CFO (and current Chief Business Officer), Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all persons and entities that purchased or otherwise acquired our securities between March 15, 2018 and March 19, 2019. The complaint, which was amended by the lead plaintiff on September 13, 2019, alleges securities law violations based on statements and omissions made by the Company during such period. On October 25, 2019, the defendants filed a motion to dismiss the securities class action complaint. The hearing on such motion to dismiss was held on February 18, 2020 and we are awaiting a ruling from the Court. Subsequent to the filing of the securities class action complaint described above, on June 21, 2019 and October 1, 2019, respectively, two separate purported shareholder derivative complaints were filed in the U.S. District Court for the Northern District of California (Bonner v. Doerr, et al., and Carlson v. Doerr, et al.) based on similar allegations to those made in the securities class action complaint described above and named the Company and certain of the Company’s current and former officers and directors as defendants. The derivative lawsuits sought to recover, on the Company’s behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and omissions made in connection with the Company’s securities filings. The derivative lawsuits were dismissed on October 18, 2019 (Bonner) and December 10, 2019 (Carlson), without prejudice. We believe the securities class action complaint lacks merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

On July 24, 2020, a securities class action complaint was filed against Amyris and the members of our Board in the Court of Chancery of the State of Delaware (Flatischler v. Melo, et. al.). The complaint alleged a breach of fiduciary obligation to disclose material information to stockholders in the proxy statement filed with the Securities and Exchange Commission on July 6, 2020 (Proxy), with respect to the Company’s special stockholders’ meeting to be held on August 14, 2020 (Special Meeting), at which stockholders will vote to approve the conversion of all outstanding indebtedness under the Foris Convertible Note and of our Series E Preferred Stock issued in the June 2020 PIPE into shares of common stock, in accordance with Nasdaq Listing Standard Rule 5635(d). See Note 4, “Debt,” “Amendment No. 1 to Foris LSA — Foris, Related Party,” and Note 6, “Stockholders’ Deficit,” “June 2020 PIPE,” and “Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws” in Part I, Item 1 of this Quarterly Report on Form 10-Q for more information. The plaintiffs sought to enjoin the Special Meeting. On August 6, 2020, the plaintiffs withdrew their complaint as moot following the Company’s filing of a supplement to the Proxy on August 5, 2020. The Proxy supplement provided additional information regarding the approval process of the LSA Amendment and the June 2020 PIPE, and the relationships between the Company and its financial advisors to the June 2020 PIPE. The plaintiffs currently seek attorney’s fees and reimbursement of certain legal expenses related to filing the complaint. Three substantially similar complaints were filed: one on July 28, 2020, in the United States District Court of Delaware (Sabatini v. Amyris, Inc.); one on July 31, 2020, in the Northern District of California (Nair v. Amyris); and another on August 4, 2020, in the Southern District of New York (Chamorro v. Amyris). We believe that these complaints lack merit, and intend to continue to defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from these matters.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes that are not predictable with reasonable assurance, and therefore, an estimate of all the reasonably possible losses cannot be determined at this time. If one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management's expectations, the Company's consolidated financial statements for the relevant reporting period could be materially adversely affected.

Other Matters

Certain conditions may exist as of the date the condensed consolidated financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgement. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be reasonably estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

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Revenue Recognition and Contract Assets and Liabilities

6 Months Ended

Jun. 30, 2020

Revenue from Contract with Customer [Abstract]

Revenue Recognition and Contract Assets and Liabilities

Revenue Recognition and Contract Assets and Liabilities

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

	Three Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	16,866	$	—	$	—	$	16,866	$	5,806	$	—	$	6,408	$	12,214
Europe	3,106		990		1,798		5,894		2,102		40,964		3,197		46,263
Asia	4,341		—		2,029		6,370		3,899		—		—		3,899
Brazil	670		—		—		670		295		—		5		300
Other	205		—		—		205		18		—		—		18
	$	25,188	$	990	$	3,827	$	30,005	$	12,120	$	40,964	$	9,610	$	62,694
	Six Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	28,809	$	—	$	—	$	28,809	$	12,879	$	—	$	6,901	$	19,780
Europe	6,349		6,151		5,154		17,654		4,956		41,082		4,826		50,864
Asia	6,359		—		4,788		11,147		5,617		—		250		5,867
Brazil	1,247		—		—		1,247		515		—		5		520
Other	278		—		—		278		37		—		—		37
	$	43,042	$	6,151	$	9,942	$	59,135	$	24,004	$	41,082	$	11,982	$	77,068

Significant Revenue Agreements During the Six Months Ended June 30, 2020

Cannabinoid Agreement

On May 2, 2019, the Company consummated a research, collaboration and license agreement (the Cannabinoid Agreement) with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for up to $300 million to develop, manufacture and commercialize cannabinoids, subject to certain closing conditions. The Company is performing research and development activities, and Lavvan is responsible for manufacturing and commercialization, related to the cannabinoids developed in accordance with the Cannabinoid Agreement. The Cannabinoid Agreement principally funds milestones that include both technical R&D targets and completion of production campaigns, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. Additionally, the Cannabinoid Agreement provides for profit share to the Company on Lavvan's gross profit margin once the cannabinoid products are commercialized; such payments will be due for the following 20 years. The Company could receive aggregate funding of up to $300 million over the term of the Cannabinoid Agreement if all of the milestones are achieved. On May 2, 2019, the parties formed a special purpose entity to hold certain intellectual property created during the collaboration (the Cannabinoid Collaboration IP), the licensing of certain Company intellectual property to Lavvan, the licensing of the Cannabinoid Collaboration IP to the Company and Lavvan, and the granting by the Company to Lavvan of a lien on the Company background intellectual property being licensed to Lavvan under the Cannabinoid Agreement, which lien would be subordinated to the lien on such intellectual property under the Foris Convertible Note (see Note 4, “Debt”). On March 11, 2020, the parties revised the agreement to reflect product specifications and cost assumptions.

The Cannabinoid Agreement is accounted for as a revenue contract under ASC 606, with the total transaction price estimated and updated on a quarterly basis, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligation. The Company concluded the agreement contained a single performance obligation of research and development services provided continuously over time. The Company estimated the total unconstrained transaction price to be $145 million, based on a high probability of achieving certain underlying milestones. As of June 30, 2020, the Company has constrained $155 million of variable consideration related to milestones that have not met the criteria necessary under ASC 606 to be included in the

transaction price. The Company concluded the performance obligation is delivered over time and that revenue recognition is based on an input measure of progress of hours incurred compared to total estimated hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, with cumulative adjustments to revenue recorded as necessary. The Company recognized no collaboration revenue for the three and six months ended June 30, 2020, and $18.3 million of cumulative revenue to date. At June 30, 2020 has recorded an $8.3 million contract asset in connection with the Cannabinoid Agreement.

DSM Ingredients Collaboration

In September 2017, the Company entered into a collaboration agreement with DSM (DSM Collaboration Agreement) to jointly develop a new molecule in the Clean Health market using the Company’s technology (DSM Ingredient), which the Company would have the sole right to manufacture, and DSM would commercialize. Pursuant to the DSM Collaboration Agreement, DSM provides funding for the development of the DSM Ingredients in the form of milestone-based payments and, upon commercialization, the parties would enter into supply agreements whereby DSM would purchase the applicable DSM Ingredient from the Company at prices agreed by the parties. The development services are directed by a joint steering committee with equal representation by DSM and the Company and are governed by a milestone project plan. The timing of milestone achievements is subject to review and revision as agreed by the joint steering committee. In addition, the parties will share profit margin from DSM’s sales of products that incorporate the DSM Ingredient subject to the DSM Collaboration Agreement.

The DSM Collaboration Agreement is accounted for as a revenue contract under ASC 606, and has a total transaction price of $14.1 million, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligations. The Company concluded the agreement contained three performance obligations of research and development services that are delivered over time and that revenue recognition is based on an input measure of progress as labor hours are expended in the achievement of each milestone. The Company recognized $1.3 million and $4.3 million of collaboration revenue for the three and six months, respectively, ended June 30, 2020, and $9.1 million of cumulative-to-date collaboration revenues.

Yifan Collaborations

From September 2018 to December 2019, the Company entered into a series of license and collaboration agreements, culminating in a master services agreement for research and development services, with a subsidiary of Yifan Pharmaceutical Co., Ltd. (Yifan), a leading Chinese pharmaceutical company. Upon execution of the master services agreement in December 2019 (the Collaboration Agreement), the Company evaluated and concluded that the series of agreements should be combined and accounted for as a single revenue contract under ASC 606.

The Yifan Collaboration Agreement has a total transaction price of $21.0 million, subject to the variable consideration constraint guidance in ASC 606 using the most likely outcome method to estimate the variable consideration associated with the identified performance obligation. The Company concluded the Collaboration Agreement contained a single performance obligation of research and development services provided continuously over time. The Collaboration Agreement provides for upfront and periodic payments based on project milestones. The Company concluded the performance obligation is delivered over time and that revenue recognition is based on an input measure of progress of hours incurred compared to total estimated hours to be incurred (i.e., proportional performance). Estimates of variable consideration are updated quarterly, with cumulative adjustments to revenue recorded as necessary. The Company recognized $2.0 million and $4.7 million of collaboration revenue in the three and six months, respectively, ended June 30, 2020, and $10.8 million of cumulative-to-date collaboration revenue. At June 30, 2020, the Company also recorded a $2.9 million contract asset in connection with the Collaboration Agreement.

DSM Value Sharing Agreement

The original December 2017 DSM Value Sharing Agreement was accounted for as a single performance obligation in connection with a license with fixed and determinable consideration and variable consideration that was accounted for pursuant to the sales-based royalty scope exception. The April 16, 2019 assignment of the December 2017 DSM Value Sharing Agreement was accounted for as a contract modification under ASC 606, resulting in additional fixed and determinable consideration of $37.1 million and variable consideration of $12.5 million in the form of a stand-ready obligation to refund some or all of the $12.5 million consideration if certain criteria outlined in the assignment agreement are not met by December 2021. The Company periodically updates its estimate of amounts to be refunded and reduces the refund liability by recording additional license and royalty revenue as the Company’s estimate of the refund obligation decreases. The Company recorded $8.8 million of license and royalty revenue in the fourth quarter of 2019 related to a change in the estimated refund liability and

recorded the remaining $3.8 million in the three months ended March 31, 2020 related to a change in the Company’s estimate of the refund liability.

In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K), the Company recognized the following revenues for the three and six months ended June 30, 2020 and 2019:

	Three Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	16	$	—	$	1,251	$	1,267	$	—	$	40,682	$	2,646	$	43,328
Sephora	2,442		—		—		2,442		2,397		—		—		2,397
Firmenich	933		990		339		2,262		—		282		277		559
Givaudan	1,161		—		—		1,161		1,240		—		—		1,240
Subtotal revenue from significant revenue agreements	4,552		990		1,590		7,132		3,637		40,964		2,923		47,524
Revenue from all other customers	20,636		—		2,237		22,873		8,483		—		6,687		15,170
Total revenue from all customers	$	25,188	$	990	$	3,827	$	30,005	$	12,120	$	40,964	$	9,610	$	62,694
	Six Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	65	$	3,750	$	4,269	$	8,084	$	2	$	40,302	$	3,042	$	43,346
Sephora	6,888		—		—		6,888		3,744		—		—		3,744
Firmenich	2,162		2,401		500		5,063		1,891		780		1,005		3,676
Givaudan	3,269		—		—		3,269		2,815		—		—		2,815
Subtotal revenue from significant revenue agreements	12,384		6,151		4,769		23,304		8,452		41,082		4,047		53,581
Revenue from all other customers	30,658		—		5,173		35,831		15,552		—		7,935		23,487
Total revenue from all customers	$	43,042	$	6,151	$	9,942	$	59,135	$	24,004	$	41,082	$	11,982	$	77,068

Contract Assets and Liabilities

When a contract results in revenue being recognized in excess of the amount the Company has invoiced or has the right to invoice to the customer, a contract asset is recognized. Contract assets are transferred to accounts receivable, net when the rights to the consideration become unconditional.

Contract liabilities consist of payments received from customers, or such consideration that is contractually due, in advance of providing the product or performing services such that control has not passed to the customer.

Trade receivables related to revenue from contracts with customers are included in accounts receivable on the condensed consolidated balance sheets, net of the allowance for doubtful accounts. Trade receivables are recorded for the sale of goods or the performance of services at the point of renewable product sale or in accordance with the contractual payment terms for licenses and royalties, and grants and collaborative research and development services for the amount payable by the customer to the Company.

Contract Balances

The following table provides information about accounts receivable, contract liabilities and refund liability from contracts with customers:

(In thousands)	June 30, 2020		December 31, 2019
Accounts receivable, net	$	22,029	$	16,322
Accounts receivable - related party, net	$	94	$	3,868
Contract assets	$	11,724	$	8,485
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Contract liabilities	$	5,180	$	1,353
Contract liabilities, noncurrent(1)	$	245	$	1,449

⁽¹⁾As of June 30, 2020 and December 31, 2019, contract liabilities, noncurrent is presented in Other noncurrent liabilities in the condensed consolidated balance sheets.

Remaining Performance Obligations

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of June 30, 2020.

(In thousands)	As of June 30, 2020
Remaining 2020	$	4,849
2021	112,357
2022	20,750
2023 and thereafter	571
Total from all customers	$	138,527

In accordance with the disclosure provisions of ASC 606, the table above excludes estimated future revenues for performance obligations that are part of a contract that has an original expected duration of one year or less or a performance obligation with variable consideration that is recognized using the sales-based royalty exception for licenses of intellectual property. Additionally, approximately $175.4 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

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Related Party Transactions

6 Months Ended

Jun. 30, 2020

Related Party Transactions [Abstract]

Related Party Transactions

Related Party Transactions

Related Party Debt

See Note 4, "Debt," for details of these related party debt transactions during the six months ended June 30, 2020:

•Debt equitization – Foris

•$5 million unsecured loan - Foris

•2014 Rule 144A Note exchange, extensions and conversion – Total

•LSA Amendment - Foris

Related party debt was as follows:

	June 30, 2020								December 31, 2019
In thousands	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Foris notes	$	55,041	$	—	$	31,510	$	86,551	$	115,351	$	(9,516)	$	—	$	105,835
DSM notes	33,000		(3,557)		—		29,443		33,000		(4,621)		—		28,379
Naxyris note	23,559		(655)		—		22,904		24,437		(822)		—		23,615
Total 2014 Rule 144A convertible note	—		—		—		—		10,178		—		—		10,178
	$	111,600	$	(4,212)	$	31,510	$	138,898	$	182,966	$	(14,959)	$	—	$	168,007

Related Party Equity

See Note 6, "Stockholders' Deficit," for details of these related party equity transactions during the six months ended June 30, 2020:

•Foris warrant exercises for cash

•Foris warrant exercise, common stock purchase and debt equitization

•January 2020 private placement, in which Foris purchased 5,226,481 shares of common stock

•June 2020 private placement, in which Foris and affiliated entities purchased 30,000 shares of Series E preferred stock

•June 2020 private placement, in which Vivo Capital LLC and affiliated entities purchased 3,689,225 shares of common stock and 8,932.32 shares of Series E preferred stock

Related Party Accounts Receivable, Unbilled Receivables and Accounts Payable

Related party accounts receivable, unbilled receivables and accounts payable were as follows:

(In thousands)	June 30, 2020		December 31, 2019
Accounts receivable - related party	$	94	$	3,868
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Accounts payable	$	5,677	$	13,957

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Stock-based Compensation

6 Months Ended

Jun. 30, 2020

Share-based Payment Arrangement [Abstract]

Stock-based Compensation

Stock-based Compensation

The Company’s stock option activity and related information for the six months ended June 30, 2020 was as follows:

	Quantity of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years	Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Granted	80,507	$	2.85
Exercised	(5,227)	$	2.99
Forfeited or expired	(216,365)	$	43.33
Outstanding - June 30, 2020	5,479,334	$	8.86	7.5	$	542
Vested or expected to vest after June 30, 2020	4,904,654	$	9.31	7.5	$	518
Exercisable at June 30, 2020	1,445,710	$	19.65	6.2	$	278

The Company’s restricted stock units (RSUs) activity and related information for the six months ended June 30, 2020 was as follows:

	Quantity of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Awarded	410,899	$	2.89
Released	(1,249,075)	$	4.83
Forfeited	(476,209)	$	4.39
Outstanding - June 30, 2020	4,468,266	$	4.61	1.4
Vested or expected to vest after June 30, 2020	4,089,810	$	4.63	1.3

Stock-based compensation expense related to employee and non-employee options, RSUs and ESPP during the three and six months ended June 30, 2020 and 2019 was allocated to research and development expense and sales, general and administrative expense as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Research and development	$	781	$	676	$	1,846	$	1,339
Sales, general and administrative	2,150		2,699		4,589		5,488
Total stock-based compensation expense	$	2,931	$	3,375	$	6,435	$	6,827

As of June 30, 2020, there was unrecognized compensation expense of $20.1 million related to stock options and RSUs. The Company expects to recognize this expense over a weighted-average period of 2.1 years.

Evergreen Shares for 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan

In February 2020, the Board approved increases to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (the Equity Plan) and 2010 Employee Stock Purchase Plan (the Purchase Plan). These shares in connection with the Equity Plan represented an automatic annual increase in the number of shares available for grant and issuance under the Equity Plan of 5,887,133 shares (Evergreen Shares). This increase is equal to approximately 5.0% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020. These shares in connection with the Purchase Plan represented an automatic annual increase in the number of shares reserved for issuance under the Purchase Plan of 588,713 shares. This increase is equal to approximately 0.5% of the 117,742,677 total outstanding shares of the Company’s common stock as of December 31, 2019. This automatic increase was effective as of January 1, 2020.

In May 2020, the Company’s stockholders approved the Company’s 2020 Equity Incentive Plan (the New Plan) to replace the Equity Plan that expired in June 2020. The shares available for grant and issuance under the New Plan represent 9,896,751 shares of common stock previously reserved but unissued under the Equity Plan, including the Evergreen Shares. No additional stock awards will be granted under the Equity Plan, and, (a) shares that are subject to stock options or other awards granted under the Equity Plan that cease to be subject to such stock options or other awards by forfeiture or otherwise, (b) shares issued under the Equity Plan pursuant to the exercise of stock options that are forfeited, (c) shares issued under the Equity Plan that are repurchased by the Company at the original issue price and (d) shares that are subject to stock options or other awards under the Equity Plan that are used to pay the exercise price of an option or withheld to satisfy the tax withholding obligations related to any award will be available for future grant and issuance under the New Plan.

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Subsequent Events

6 Months Ended

Jun. 30, 2020

Subsequent Events [Abstract]

Subsequent Events

Subsequent Events

Second Amendment to Ginkgo Note and Partnership Agreement

On August 10, 2020, the Company and Ginkgo entered into a Second Amendment to Promissory Note and Partnership Agreement (Second Amendment) to, among other things, (i) with respect to the Promissory Note, amend the interest payment frequency from monthly to quarterly beginning September 30, 2020 and reduce the interest rate from 12% to 9% beginning January 1, 2021, conditioned to the timely payment of interest on September 30 and December 31, 2020; and (ii) with respect to the Partnership Agreement, reduce the partnership payments frequency from monthly to quarterly, in an aggregate amount of $2.1 million, and to defer an aggregate of $9.8 million in partnership payments to the end of the agreement in October 2022 (the “End of Term Payment”), provided that, if the Promissory Note is not fully repaid by April 19, 2022, the End of Term Payment shall be of $10.4 million. See Note 4, “Debt” for further information regarding the Ginkgo Promissory Note and Partnership Agreement.

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Basis of Presentation and Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of accounting

The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP) for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the accompanying interim condensed consolidated financial statements do not include all of the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are not necessarily indicative of results for a full year.

Accounting Standards or Updates Recently Adopted and Recent Accounting Standards or Updates Not Yet Effective

Accounting Standards or Updates Recently Adopted

In the six months ended June 30, 2020, the Company adopted these accounting standards or updates:

Fair Value Measurement In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement, which amends ASC 820, Fair Value Measurement. ASU 2018-13 modifies the disclosure requirements for fair value measurements by removing, modifying or adding certain disclosures. ASU 2018-13 became effective in the first quarter of fiscal 2020, with removed and modified disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis. The adoption of this standard did not have a material impact on the Company’s condensed consolidated financial statements.

Collaborative Revenue Arrangements In November 2018, the FASB issued ASU 2018-18, Clarifying the Interaction between Topic 808 and Topic 606, that clarifies the interaction between the guidance for certain collaborative arrangements and Topic 606, the new revenue recognition standard. A collaborative arrangement is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. The ASU provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. ASU 2018-18 became effective in the first quarter of fiscal year 2020 retrospectively. The adoption of this standard did not have any impact on the Company’s condensed consolidated financial statements.

Accounting Standards or Updates Not Yet Adopted

Credit Losses In June 2016, the FASB issued ASU 2016-13, Financial Instruments—Credit Losses (Topic 326), Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires entities to measure all expected credit losses for most financial assets held at the reporting date based on an expected loss model which includes historical experience, current conditions, and reasonable and supportable forecasts. Entities will now use forward-looking information to better form their credit loss estimates. ASU 2016-13 also requires enhanced disclosures to help financial statement users better understand significant estimates and judgments used in estimating credit losses, as well as the credit quality and underwriting standards of an entity's portfolio. ASU 2016-13 is effective for the Company in the first quarter of 2021. The Company is currently evaluating the impact this standard will have on its condensed consolidated financial statements.

Accounting for Income Taxes In December 2019, the FASB issued ASU 2019-12, “Simplifying the Accounting for Income Taxes” (“ASU 2019-12”). The amendments in ASU 2019-12 simplify the accounting for income taxes by removing certain exceptions to the general principles in ASC Topic 740, Income Taxes. The amendments also improve consistent application of and simplify U.S. GAAP for other areas of ASC Topic 740 by clarifying and amending existing guidance. ASU

2019-12 will be effective for the Company commencing in the first quarter of fiscal year 2021. The transition requirements are dependent upon each amendment within this update and will be applied either prospectively or retrospectively. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Convertible Debt, and Derivatives and Hedging On August 5, 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity, to improve financial reporting associated with accounting for convertible instruments and contracts in an entity’s own equity. ASU 2020-06 is effective for the Company in the first quarter of 2022. The Company is currently evaluating the amended guidance and the impact on its condensed consolidated financial statements and related disclosures.

Use of Estimates and Judgements

Use of Estimates and Judgements

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates, judgements and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates, and such differences may be material to the condensed consolidated financial statements.

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Balance Sheet Details (Tables)

6 Months Ended

Jun. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Allowance for Doubtful Accounts

Allowance for Doubtful Accounts

(In thousands)	Balance at Beginning of Year		Provisions		Write-offs, Net		Balance at End of Period
Six months ended June 30, 2020	$	45	$	57	$	—	$	102
Year ended December 31, 2019	$	642	$	110	$	(707)	$	45

Inventories

Inventories

(In thousands)	June 30, 2020		December 31, 2019
Raw materials	$	4,487	$	3,255
Work-in-process	8,204		7,204
Finished goods	20,368		17,311
Inventories	$	33,059	$	27,770

Deferred Cost of Products Sold

Deferred cost of products sold - related party

(In thousands)	June 30, 2020		December 31, 2019
Deferred cost of products sold - related party	$	7,709	$	3,677
Deferred cost of products sold, noncurrent - related party	14,260		12,815
Total	$	21,969	$	16,492

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets

(In thousands)	June 30, 2020		December 31, 2019
Non-inventory production supplies	$	4,687	$	5,376
Prepayments, advances and deposits	6,423		4,726
Other	3,421		2,648
Total prepaid expenses and other current assets	$	14,531	$	12,750

Property, Plant and Equipment, Net

Property, Plant and Equipment, Net

(In thousands)	June 30, 2020		December 31, 2019
Machinery and equipment	$	46,568	$	48,041
Leasehold improvements	41,479		41,478
Computers and software	9,700		9,822
Furniture and office equipment, vehicles and land	3,496		3,510
Construction in progress	8,985		9,752
	110,228		112,603
Less: accumulated depreciation and amortization	(82,834)		(83,673)
Property, plant and equipment, net	$	27,394	$	28,930

Schedule Of Depreciation and Amortization

During the three and six months ended June 30, 2020 and 2019, depreciation and amortization expense was as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Depreciation and amortization expense	$	1,675	$	873	$	3,395	$	1,722

Lease, Cost

Information related to the Company's right-of-use assets and related lease liabilities were as follows:

	Six Months Ended June 30,
	2020	2019
Cash paid for operating lease liabilities, in thousands	$3,807	$10,660
Right-of-use assets obtained in exchange for new operating lease obligations(1)	$—	$31,293
Weighted-average remaining lease term	2.9	2.6
Weighted-average discount rate	18.0%	18.0%

(1) 2019 amount includes $29.7 million for operating leases existing on January 1, 2019 and $1.7 million for operating leases that commenced during the six months ended June 30, 2019.

Lessee, Lease Liability, Maturity

Maturities of lease liabilities as of June 30, 2020 were as follows:

Years ending December 31: (In thousands)	Financing Leases		Operating Leases		Total Leases
2020 (remaining six months)	$	2,185	$	3,918	$	6,103
2021	4,566		7,478		12,044
2022	—		7,654		7,654
2023	—		3,318		3,318
2024	—		152		152
Total lease payments	6,751		22,520		29,271
Less: amount representing interest	(841)		(5,170)		(6,011)
Total lease liability	$	5,910	$	17,350	$	23,260
Current lease liability	$	3,605	$	4,893	$	8,498
Noncurrent lease liability	2,305		12,457		14,762
Total lease liability	$	5,910	$	17,350	$	23,260

Other Assets

Other Assets

(In thousands)	June 30, 2020		December 31, 2019
Equity-method investment	$	4,043	$	4,734
Deposits	277		295
Contingent consideration	—		3,303
Other	1,237		1,373
Total other assets	$	5,557	$	9,705

Accrued and Other Current Liabilities

Accrued and Other Current Liabilities

(In thousands)	June 30, 2020		December 31, 2019
Accrued interest	$	10,810	$	8,209
Ginkgo partnership payments obligation	10,134		4,319
Equity issuance costs	9,983		—
Payroll and related expenses	6,718		7,296
Contract termination fees	5,490		5,347
Asset retirement obligation	2,447		3,184
Professional services	1,595		2,968
Tax-related liabilities	—		1,685
Other	1,933		3,647
Total accrued and other current liabilities	$	49,110	$	36,655

Other Liabilities

Other noncurrent liabilities

(In thousands)	June 30, 2020		December 31, 2019
Liability for unrecognized tax benefit	$	7,384	$	7,204
Liability in connection with acquisition of equity-method investment	5,962		5,249
Ginkgo partnership payments, net of current portion	725		4,492
Contract liabilities, net of current portion	245		1,449
Refund liability(1)	—		3,750
Other	938		880
Total other noncurrent liabilities	$	15,254	$	23,024

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Fair Value Measurement (Tables)

6 Months Ended

Jun. 30, 2020

Fair Value Disclosures [Abstract]

Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis

The following tables summarize liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

(In thousands)	June 30, 2020								December 31, 2019
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Liabilities
Foris Convertible Note (LSA Amendment)	$	—	$	—	$	81,551	$	81,551	$	—	$	—	$	—	$	—
Senior Convertible Notes	—		—		36,624		36,624		—		—		50,624		50,624
Embedded derivatives bifurcated from debt instruments	—		—		5,833		5,833		—		—		2,832		2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	—		—		—		—		—		—		6,971		6,971
Total liabilities measured and recorded at fair value	$	—	$	—	$	124,008	$	124,008	$	—	$	—	$	60,427	$	60,427

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation

In thousands
Fair value at December 31, 2019	$	50,624
Less: principal paid	(35,980)
Loss from change in fair value	21,980
Fair value at June 30, 2020	$	36,624

Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation

(In thousands)	Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2019	$	9,803	$	9,803
Fair value of derivative liabilities issued during the period	8,752		8,752
Change in fair value of derivative instruments	8,496		8,496
Derecognition on settlement or extinguishment	(21,218)		(21,218)
Balance at June 30, 2020	$	5,833	$	5,833

Fair Value Measurement Inputs and Valuation Techniques

Input assumptions for these freestanding instruments are as follows:

	Range for the Period
Input assumptions for liability classified warrants:	June 30, 2020		December 31, 2019
Fair value of common stock on issue date	$2.56 – $4.27		$3.09 – $4.76
Exercise price of warrants	$2.87 – $3.25		$3.87 – $3.90
Expected volatility	111% – 214%		94% – 105%
Risk-free interest rate	0.09% – 0.20%		1.58% – 1.67%
Expected term in years	0.07 – 2.51		1.51 – 2.00
Dividend yield	0.0	%	0.0 %

The market-based assumptions and estimates used in valuing the embedded derivative liabilities include amounts in the following ranges/amounts:

	June 30, 2020	December 31, 2019
Risk-free interest rate	0.09% - 0.17%	1.6% - 1.7%
Risk-adjusted discount yield	25.0% - 26.0%	20.0% - 27.0%
Probability of change in control	5.0%	5.0%
Credit spread	24.7% - 36.8%	18.4% - 25.4%
Estimated conversion dates	2022 - 2023	2022 - 2023

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Debt (Tables)

6 Months Ended

Jun. 30, 2020

Debt Disclosure [Abstract]

Schedule of Debt

Net carrying amounts of debt are as follows:

	June 30, 2020								December 31, 2019
(In thousands)	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Convertible notes payable
Senior convertible notes	$	30,020	$	—	$	6,604	$	36,624	$	66,000	$	—	$	(15,376)	$	50,624
	30,020		—		6,604		36,624		66,000		—		(15,376)		50,624
Related party convertible notes payable
Foris convertible note	50,041		—		31,510		81,551		—		—		—		—
2014 Rule 144A convertible notes	—		—		—		—		10,178		—		—		10,178
	50,041		—		31,510		81,551		10,178		—		—		10,178
Loans payable and credit facilities
Schottenfeld notes	12,500		(299)		—		12,201		20,350		(1,315)		—		19,035
Nikko notes	8,632		(830)		—		7,802		14,318		(901)		—		13,417
Ginkgo note	12,000		(2,648)		—		9,352		12,000		(3,139)		—		8,861
Other loans payable	1,034		—		—		1,034		1,828		—		—		1,828
	34,166		(3,777)		—		30,389		48,496		(5,355)		—		43,141
Related party loans payable
Foris notes	5,000		—		—		5,000		115,351		(9,516)		—		105,835
DSM notes	33,000		(3,557)		—		29,443		33,000		(4,621)		—		28,379
Naxyris note	23,559		(655)		—		22,904		24,437		(822)		—		23,615
	61,559		(4,212)		—		57,347		172,788		(14,959)		—		157,829
Total debt	$	175,786	$	(7,989)	$	38,114	205,911		$	297,462	$	(20,314)	$	(15,376)	261,772
Less: current portion							(43,482)								(63,805)
Long-term debt, net of current portion							$	162,429							$	197,967

Schedule of Long-term Debt Instruments

Future minimum payments under the Company's debt agreements as of June 30, 2020 are as follows:

(In thousands)	Convertible Notes		Loans Payable and Credit Facilities		Related Party Convertible Notes		Related Party Loans Payable and Credit Facilities		Total
2020 (remaining six months)	$	814	$	10,132	$	—	$	3,084	$	14,030
2021	33,898		4,255		—		31,777		69,930
2022	—		15,058		59,578		40,558		115,194
2023	—		12,899		—		—		12,899
2024	—		398		—		—		398
Thereafter	—		1,869		—		—		1,869
Total future minimum payments	34,712		44,611		59,578		75,419		214,320
Less: amount representing interest	(4,692)		(10,445)		(9,537)		(13,860)		(38,534)
Present value of minimum debt payments	30,020		34,166		50,041		61,559		175,786
Less: current portion of debt principal	(30,020)		(6,996)		—		—		(37,016)
Noncurrent portion of debt principal	$	—	$	27,170	$	50,041	$	61,559	$	138,770

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Stockholders' Deficit (Tables)

6 Months Ended

Jun. 30, 2020

Equity [Abstract]

Schedule of Stockholders' Equity Note, Warrants or Rights

The following table summarizes warrants activity for the six months ended June 30, 2020:

Transaction	Year Issued	Expiration Date	Number Outstanding as of December 31, 2019	Additional Warrants Issued	Exercises	Expired	Exercise Price per Share of Warrants Exercised		Number Outstanding as of June 30, 2020	Exercise Price per Share as of June 30, 2020
High Trail/Silverback warrants	2020	January 14, 2022	—	3,000,000	—	—	$	—	3,000,000	$2.87/$3.25
2020 PIPE right shares	2020	February 4, 2021	—	8,710,802	(5,226,481)	—	$	2.87	3,484,321	$	2.87
January 2020 warrant exercise right shares	2020	January 31, 2021 and January 31, 2022	—	9,939,159	—	—	$	—	9,939,159	$	2.87
Foris LSA warrants	2019	August 14, 2021	3,438,829	—	(3,438,829)	—	$	2.87	—	$	—
November 2019 Foris warrant	2019	November 27, 2021	1,000,000	—	(1,000,000)	—	$	2.87	—	$	—
August 2019 Foris warrant	2019	August 28, 2021	4,871,795	—	(4,871,795)	—	$	2.87	—	$	—
April 2019 PIPE warrants	2019	April 26, 2021, April 29, 2021 and May 3, 2021	8,084,770	—	(4,712,781)	—	$	2.87	3,371,989	$4.76/$5.02
April 2019 Foris warrant	2019	April 16, 2021	5,424,804	—	(5,424,804)	—	$	2.87	—	$	—
September and November 2019 Investor Credit Agreement warrants	2019	September 10, 2021 and November 14, 2021	5,233,551	—	—	—	$	—	5,233,551	$	2.87
Naxyris LSA warrants	2019	August 14, 2021	2,000,000	—	—	—	$	—	2,000,000	$	2.87
October 2019 Naxyris warrant	2019	October 28, 2021	2,000,000	—	—	—	$	—	2,000,000	$	3.87
May-June 2019 6% Note Exchange warrants	2019	May 15, 2021 and June 24, 2021	2,181,818	—	—	—	$	—	2,181,818	$2.87/$5.12
May 2019 6.50% Note Exchange warrants	2019	May 14, 2021 and January 31, 2022	1,744,241	—	(784,016)	—	$	2.87	960,225	$	2.87
July 2019 Wolverine warrant	2019	July 8, 2021	1,080,000	—	—	—	$	—	1,080,000	$	2.87
August 2018 warrant exercise agreements	2018	May 17, 2020 and May 20, 2020	12,097,164	—	(4,877,386)	(7,219,778)	$	2.87	—	$	—
May 2017 cash warrants	2017	July 10, 2022	6,078,156	—	—	—	$	—	6,078,156	$	2.87
August 2017 cash warrants	2017	August 7, 2022	3,968,116	—	—	—	$	—	3,968,116	$	2.87
May 2017 dilution warrants	2017	July 10, 2022	3,085,893	—	—	—	$	—	3,085,893	$	—
August 2017 dilution warrants	2017	May 23, 2023	3,028,983	—	—	—	$	—	3,028,983	$	—
February 2016 related party private placement	2016	February 12, 2021	171,429	—	(152,381)	—	$	0.15	19,048	$	0.15
July 2015 related party debt exchange	2015	July 29, 2020 and July 29, 2025	133,334	—	(133,334)	—	$	0.15	—	$	—
July 2015 private placement	2015	July 29, 2020	72,650	—	(72,650)	—	$	0.15	—	$	—
July 2015 related party debt exchange	2015	July 29, 2020	58,690	—	—	—	$	—	58,690	$	0.15
Other	2011	December 23, 2021	1,406	—	—	—	$	—	1,406	$	160.05
			65,755,629	21,649,961	(30,694,457)	(7,219,778)			49,491,355

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Loss Per Share (Tables)

6 Months Ended

Jun. 30, 2020

Earnings Per Share [Abstract]

Schedule of Earnings Per Share, Basic and Diluted

The following table presents the calculation of basic and diluted loss per share:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2020		2019		2020		2019
Numerator:
Net loss attributable to Amyris, Inc.	$	(110,422)	$	(38,088)	$	(198,266)	$	(104,331)
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D	—		(34,964)		—		(34,964)
Add: losses allocated to participating securities	6,361		2,255		7,435		4,690
Net loss attributable to Amyris, Inc. common stockholders	$	(104,061)	$	(70,797)	$	(190,831)	$	(134,605)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	184,827,330		92,785,752		169,946,482		84,831,269
Loss per share attributable to common stockholders, basic and diluted	$	(0.56)	$	(0.76)	$	(1.12)	$	(1.59)

Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted loss per share of common stock because including them would have been antidilutive:

	Three Months Ended June 30,		Six Months Ended June 30,
	2020	2019	2020	2019
Period-end common stock warrants	43,298,741	5,535,538	43,298,741	5,535,538
Convertible promissory notes(1)	8,574,399	11,007,316	8,574,399	11,007,316
Period-end stock options to purchase common stock	5,479,334	49,747,628	5,479,334	49,747,628
Period-end restricted stock units	4,468,266	5,284,742	4,468,266	5,284,742
Period-end preferred stock(2)	1,943,661	2,955,732	1,943,661	2,955,732
Total potentially dilutive securities excluded from computation of diluted loss per share	63,764,401	74,530,956	63,764,401	74,530,956

______________

⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

⁽²⁾ The 102,156 shares of Series E Preferred Stock, which is convertible into 34,052,070 common shares, is not included in this share count. The automatic conversion of the Series E Preferred Stock is contingent upon stockholder approval, and is therefore, not considered a potentially dilutive security until the contingency is resolved.

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Revenue Recognition and Contract Assets and Liabilities (Tables)

6 Months Ended

Jun. 30, 2020

Revenue from Contract with Customer [Abstract]

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

	Three Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	16,866	$	—	$	—	$	16,866	$	5,806	$	—	$	6,408	$	12,214
Europe	3,106		990		1,798		5,894		2,102		40,964		3,197		46,263
Asia	4,341		—		2,029		6,370		3,899		—		—		3,899
Brazil	670		—		—		670		295		—		5		300
Other	205		—		—		205		18		—		—		18
	$	25,188	$	990	$	3,827	$	30,005	$	12,120	$	40,964	$	9,610	$	62,694
	Six Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	28,809	$	—	$	—	$	28,809	$	12,879	$	—	$	6,901	$	19,780
Europe	6,349		6,151		5,154		17,654		4,956		41,082		4,826		50,864
Asia	6,359		—		4,788		11,147		5,617		—		250		5,867
Brazil	1,247		—		—		1,247		515		—		5		520
Other	278		—		—		278		37		—		—		37
	$	43,042	$	6,151	$	9,942	$	59,135	$	24,004	$	41,082	$	11,982	$	77,068

Revenue in Connection with Significant Revenue Agreement

In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 9, “Revenue Recognition” in Part II, Item 8 of the 2019 Form 10-K), the Company recognized the following revenues for the three and six months ended June 30, 2020 and 2019:

	Three Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	16	$	—	$	1,251	$	1,267	$	—	$	40,682	$	2,646	$	43,328
Sephora	2,442		—		—		2,442		2,397		—		—		2,397
Firmenich	933		990		339		2,262		—		282		277		559
Givaudan	1,161		—		—		1,161		1,240		—		—		1,240
Subtotal revenue from significant revenue agreements	4,552		990		1,590		7,132		3,637		40,964		2,923		47,524
Revenue from all other customers	20,636		—		2,237		22,873		8,483		—		6,687		15,170
Total revenue from all customers	$	25,188	$	990	$	3,827	$	30,005	$	12,120	$	40,964	$	9,610	$	62,694
	Six Months Ended June 30,
(In thousands)	2020								2019
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	65	$	3,750	$	4,269	$	8,084	$	2	$	40,302	$	3,042	$	43,346
Sephora	6,888		—		—		6,888		3,744		—		—		3,744
Firmenich	2,162		2,401		500		5,063		1,891		780		1,005		3,676
Givaudan	3,269		—		—		3,269		2,815		—		—		2,815
Subtotal revenue from significant revenue agreements	12,384		6,151		4,769		23,304		8,452		41,082		4,047		53,581
Revenue from all other customers	30,658		—		5,173		35,831		15,552		—		7,935		23,487
Total revenue from all customers	$	43,042	$	6,151	$	9,942	$	59,135	$	24,004	$	41,082	$	11,982	$	77,068

Contract with Customer, Asset and Liability

The following table provides information about accounts receivable, contract liabilities and refund liability from contracts with customers:

(In thousands)	June 30, 2020		December 31, 2019
Accounts receivable, net	$	22,029	$	16,322
Accounts receivable - related party, net	$	94	$	3,868
Contract assets	$	11,724	$	8,485
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Contract liabilities	$	5,180	$	1,353
Contract liabilities, noncurrent(1)	$	245	$	1,449

⁽¹⁾As of June 30, 2020 and December 31, 2019, contract liabilities, noncurrent is presented in Other noncurrent liabilities in the condensed consolidated balance sheets.

Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of June 30, 2020.

(In thousands)	As of June 30, 2020
Remaining 2020	$	4,849
2021	112,357
2022	20,750
2023 and thereafter	571
Total from all customers	$	138,527

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Related Party Transactions (Tables)

6 Months Ended

Jun. 30, 2020

Related Party Transactions [Abstract]

Schedule of Related Party Debt

Related party debt was as follows:

	June 30, 2020								December 31, 2019
In thousands	Principal		Unaccreted Debt Discount		Change in Fair Value		Net		Principal		Unaccreted Debt Discount		Change in Fair Value		Net
Foris notes	$	55,041	$	—	$	31,510	$	86,551	$	115,351	$	(9,516)	$	—	$	105,835
DSM notes	33,000		(3,557)		—		29,443		33,000		(4,621)		—		28,379
Naxyris note	23,559		(655)		—		22,904		24,437		(822)		—		23,615
Total 2014 Rule 144A convertible note	—		—		—		—		10,178		—		—		10,178
	$	111,600	$	(4,212)	$	31,510	$	138,898	$	182,966	$	(14,959)	$	—	$	168,007

Schedule of Related Party Accounts Receivables

Related party accounts receivable, unbilled receivables and accounts payable were as follows:

(In thousands)	June 30, 2020		December 31, 2019
Accounts receivable - related party	$	94	$	3,868
Contract assets - related party	$	1,203	$	—
Contract assets, noncurrent - related party	$	—	$	1,203
Accounts payable	$	5,677	$	13,957

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Stock-based Compensation (Tables)

6 Months Ended

Jun. 30, 2020

Share-based Payment Arrangement [Abstract]

Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity

The Company’s stock option activity and related information for the six months ended June 30, 2020 was as follows:

	Quantity of Stock Options	Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years	Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2019	5,620,419	$	10.27	7.8	$	24
Granted	80,507	$	2.85
Exercised	(5,227)	$	2.99
Forfeited or expired	(216,365)	$	43.33
Outstanding - June 30, 2020	5,479,334	$	8.86	7.5	$	542
Vested or expected to vest after June 30, 2020	4,904,654	$	9.31	7.5	$	518
Exercisable at June 30, 2020	1,445,710	$	19.65	6.2	$	278

Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity

The Company’s restricted stock units (RSUs) activity and related information for the six months ended June 30, 2020 was as follows:

	Quantity of Restricted Stock Units	Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2019	5,782,651	$	4.77	1.7
Awarded	410,899	$	2.89
Released	(1,249,075)	$	4.83
Forfeited	(476,209)	$	4.39
Outstanding - June 30, 2020	4,468,266	$	4.61	1.4
Vested or expected to vest after June 30, 2020	4,089,810	$	4.63	1.3

Share-based Payment Arrangement, Expensed and Capitalized, Amount

Stock-based compensation expense related to employee and non-employee options, RSUs and ESPP during the three and six months ended June 30, 2020 and 2019 was allocated to research and development expense and sales, general and administrative expense as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2020		2019		2020		2019
Research and development	$	781	$	676	$	1,846	$	1,339
Sales, general and administrative	2,150		2,699		4,589		5,488
Total stock-based compensation expense	$	2,931	$	3,375	$	6,435	$	6,827

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Basis of Presentation and Summary of Significant Accounting Policies (Details) - USD ($) $ / shares in Units, $ in Thousands					6 Months Ended
	Jun. 02, 2020	Jun. 01, 2020	Mar. 11, 2020	Jan. 31, 2020	Jun. 30, 2020	Jun. 30, 2019	May 07, 2020	Apr. 30, 2020	Dec. 31, 2019
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Working capital					$ 61,700				$ (87,500)
Accumulated deficit					1,953,919				1,755,653
Principal					175,786				297,462
Debt instrument, amount, failed to pay								$ 7,200
Debt instrument, amount, failed to pay, interest payment								2,800
Repayments of debt		$ 37,100
Proceeds from issuance or sale of equity		190,000	$ 15,000	$ 28,300
Carrying value current long term debt					37,000
Payment of accrued interest		$ 6,100
Issuance of common stock and warrants upon conversion of debt principal and accrued interest					27,650	$ 34,650
Cash and cash equivalents					99,998	$ 940			$ 270
Total Raffinage Chimie, Nikko Chemicals Co. Ltd and Schottenfeld Group LLC
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, face amount								$ 17,600
Paycheck Protection Plan Loan | Senior Notes
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, face amount							$ 10,000
Foris LSA
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Repayments of debt					$ 200,000
Foris LSA | Senior Notes
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)							$ 3.00
Rule 144A Convertible Note | Senior Notes
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$ 9,300
Induced conversion of convertible debt expense	$ 9,100

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Balance Sheet Details - Allowance for Doubtful Accounts (Details) - USD ($) $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Balance at Beginning of Year	$ 45	$ 642
Provisions	57	110
Write-offs, Net	0	(707)
Accounts Receivable, Allowance for Credit Loss, Current	$ 102	$ 45

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Balance Sheet Details - Inventories (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Raw materials	$ 4,487	$ 3,255
Work-in-process	8,204	7,204
Finished goods	20,368	17,311
Inventories	$ 33,059	$ 27,770

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Balance Sheet Details - Deferred Cost of Products Sold - Related Party (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Deferred cost of products sold - related party	$ 7,709	$ 3,677
Deferred cost of products sold, noncurrent - related party	14,260	12,815
Total	$ 21,969	$ 16,492

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Balance Sheet Details - Additional Information (Details) - USD ($) $ in Thousands		3 Months Ended		6 Months Ended		17 Months Ended	20 Months Ended
	Jan. 01, 2019	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Mar. 31, 2020	Jun. 30, 2020	Dec. 31, 2019	Apr. 30, 2019
Property, Plant and Equipment [Line Items]
Deferred cost of products sold, related party		$ 21,969		$ 21,969			$ 21,969	$ 16,492
Supply agreement term (years)				5 years
Deferred cost of products sold, amortization				$ 1,100	$ 1,300		2,300
Right-of-use assets under operating leases		11,662		11,662			11,662	13,203
Operating lease liability		17,350		17,350			17,350	19,700
Operating lease expense		1,500	$ 3,000	3,000	5,800
Lease, cost		300	$ 200	600	400
Acquisition of right-of-use assets under operating leases	$ 29,700			0	$ 1,675
Finance lease, right-of-use asset amortization		(3,100)		(3,100)			(3,100)	$ (1,700)
Proceeds from divestiture of interest in consolidated subsidiaries				3,300
Licenses and Royalties
Property, Plant and Equipment [Line Items]
Increase (decrease) in revenue				3,800
DSM International B.V.
Property, Plant and Equipment [Line Items]
Payments of reservation capacity fees						$ 17,400
Deferred cost of products sold, related party		$ 6,900		$ 6,900			$ 6,900
Minimum
Property, Plant and Equipment [Line Items]
Operating lease remaining lease term (years)		1 year		1 year			1 year
Operating lease renewal term (years)		1 year		1 year			1 year
Maximum
Property, Plant and Equipment [Line Items]
Operating lease remaining lease term (years)		5 years		5 years			5 years
Operating lease renewal term (years)		5 years		5 years			5 years
DSM International B.V.
Property, Plant and Equipment [Line Items]
Prepaid variable consideration		$ 12,500		$ 12,500			$ 12,500		$ 12,500

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Balance Sheet Details - Prepaid Expenses and Other Current Assets (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Non-inventory production supplies	$ 4,687	$ 5,376
Prepayments, advances and deposits	6,423	4,726
Other	3,421	2,648
Total prepaid expenses and other current assets	$ 14,531	$ 12,750

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Balance Sheet Details - Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	$ 110,228	$ 112,603
Less: accumulated depreciation and amortization	(82,834)	(83,673)
Property, plant and equipment, net	27,394	28,930
Machinery and equipment
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	46,568	48,041
Leasehold improvements
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	41,479	41,478
Computers and software
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	9,700	9,822
Furniture and office equipment, vehicles and land
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	3,496	3,510
Construction in progress
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	$ 8,985	$ 9,752

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Balance Sheet Details - Depreciation and Amortization (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Depreciation and amortization expense	$ 1,675	$ 873	$ 3,395	$ 1,722

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Balance Sheet Details - Right-of-use Assets and Related Lease Liabilities (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Cash paid for operating lease liabilities, in thousands	$ 3,807	$ 10,660
Right-of-use assets obtained in exchange for new operating lease obligations	$ 0	$ 31,293
Weighted-average remaining lease term	2 years 10 months 24 days	2 years 7 months 6 days
Weighted-average discount rate	18.00%	18.00%

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Balance Sheet Details - Maturities of Financing and Operating Leases (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Finance Lease, Liability, Payment, Due [Abstract]
2020 (remaining six months), finance leases	$ 2,185
2021, finance leases	4,566
2022, financing leases	0
2023, financing leases	0
2024, financing leases	0
Total lease payments, financing leases	6,751
Less: amount representing interest	(841)
Total lease liability, financing leases	5,910
Financing lease liabilities	3,605	$ 3,465
Financing lease liabilities, net of current portion	2,305	4,166
Lessee, Operating Lease, Liability, Payment, Due [Abstract]
2020 (remaining six months), operating leases	3,918
2021, operating leases	7,478
2022, operating leases	7,654
2023, operating leases	3,318
2024, operating leases	152
Total lease payments, operating leases	22,520
Less: amount representing interest	(5,170)
Total lease liability, operating leases	17,350	19,700
Operating lease liabilities	4,893	4,625
Operating lease liabilities, net of current portion	12,457	$ 15,037
2020 (remaining six months), total leases	6,103
2021, total leases	12,044
2022, total leases	7,654
2023, total leases	3,318
2024, total leases	152
Total lease payments, total leases	29,271
Less: amount representing interest	(6,011)
Total lease liability, total leases	23,260
Lease liabilities	8,498
Lease liabilities, net of current portion	$ 14,762

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Balance Sheet Details - Other Assets (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Equity-method investment	$ 4,043	$ 4,734
Contingent consideration	0	3,303
Deposits	277	295
Other	1,237	1,373
Total other assets	$ 5,557	$ 9,705

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Balance Sheet Details - Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Accrued interest	$ 10,810	$ 8,209
Ginkgo partnership payments obligation	10,134	4,319
Equity issuance costs	9,983	0
Payroll and related expenses	6,718	7,296
Contract termination fees	5,490	5,347
Professional services	1,595	2,968
Asset retirement obligation	2,447	3,184
Tax-related liabilities	0	1,685
Other	1,933	3,647
Total accrued and other current liabilities	$ 49,110	$ 36,655

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Balance Sheet Details - Other Noncurrent Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Liability for unrecognized tax benefit	$ 7,384	$ 7,204
Liability in connection with acquisition of equity-method investment	5,962	5,249
Ginkgo partnership payments, net of current portion	725	4,492
Contract liability, net of current portion	245	1,449
Refund liability	0	3,750
Other	938	880
Other noncurrent liabilities	$ 15,254	$ 23,024

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Fair Value Measurement - Fair Value, Assets, and Liabilities Measured on Recurring Basis (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	$ 36,624	$ 24,392
Fair Value, Measurements, Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	5,833	2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	0	6,971
Total liabilities measured and recorded at fair value	124,008	60,427
Fair Value, Measurements, Recurring | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	81,551	0
Fair Value, Measurements, Recurring | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	36,624	50,624
Fair Value, Measurements, Recurring | Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	0	0
Freestanding derivative instruments issued in connection with other debt and equity instruments	0	0
Total liabilities measured and recorded at fair value	0	0
Fair Value, Measurements, Recurring | Level 1 | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 1 | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	0	0
Freestanding derivative instruments issued in connection with other debt and equity instruments	0	0
Total liabilities measured and recorded at fair value	0	0
Fair Value, Measurements, Recurring | Level 2 | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 2 | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Fair Value, Measurements, Recurring | Level 3
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Embedded derivatives bifurcated from debt instruments	5,833	2,832
Freestanding derivative instruments issued in connection with other debt and equity instruments	0	6,971
Total liabilities measured and recorded at fair value	124,008	60,427
Fair Value, Measurements, Recurring | Level 3 | Foris Convertible Note (LSA Amendment)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	81,551	0
Fair Value, Measurements, Recurring | Level 3 | Senior Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	$ 36,624	$ 50,624

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Fair Value Measurement - Fair Value of Debt — Foris Convertible Note (LSA Amendment) (Details)		3 Months Ended		6 Months Ended
	Jun. 01, 2020 USD ($)	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jan. 14, 2020	Dec. 31, 2019 USD ($)
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Loss upon extinguishment of debt		$ (22,029,000)	$ (5,875,000)	$ (49,348,000)	$ (5,875,000)
Extinguishment of debt, gain (loss), net of tax	$ 72,100,000
Debt instrument fair value disclosure		77,800,000		77,800,000			$ 194,800,000
Loss from change in fair value of debt		(14,949,000)	$ (14,444,000)	(31,452,000)	$ (16,574,000)
Long-term Debt
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value of liability		36,624,000		36,624,000			$ 50,624,000
Foris Convertible Note (LSA Amendment)
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Loss from change in fair value of debt		(9,500,000)
Foris Convertible Note (LSA Amendment) | Long-term Debt
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value of liability		81,600,000		81,600,000
Foris Convertible Note (LSA Amendment) | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, convertible, conversion ratio	3.00
Loss upon extinguishment of debt	$ (22,000,000.0)
Debt instrument fair value disclosure	$ 50,000,000.0	$ 50,000,000.0		$ 50,000,000.0
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Measurement Input, Stock Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)	3.73	4.27		4.27
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Measurement Input, Discount Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)	0.26					0.25
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.0016		0.0016		0.0016
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)	0.45					0.45
Foris Convertible Note (LSA Amendment) | Convertible notes payable | Probability of Change in Control
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)						0.05

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Fair Value Measurement - Fair Value of Debt — Senior Convertible Notes (Details)			3 Months Ended		6 Months Ended
	May 01, 2020 $ / shares shares	Jan. 14, 2020 USD ($) $ / shares shares	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	May 09, 2020 $ / shares	Apr. 30, 2020 $ / shares	Mar. 11, 2020 $ / shares	Jan. 31, 2020 $ / shares shares	Jan. 13, 2020 $ / shares shares	Dec. 31, 2019 USD ($)	Nov. 15, 2019 USD ($)	May 10, 2019 $ / shares
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares										1,200,000	4,877,386
Exercise price per share (in dollars per share) | $ / shares									$ 2.87	$ 2.87	$ 2.87
Gain (loss) on extinguishment of debt			$ 22,029,000	$ 5,875,000	$ 49,348,000	$ 5,875,000
Debt instrument fair value disclosure			77,800,000		77,800,000							$ 194,800,000
Loss from change in fair value of debt			14,949,000	$ 14,444,000	31,452,000	$ 16,574,000
Long-term Debt
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value of liability			36,624,000		36,624,000							$ 50,624,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Exercise price per share (in dollars per share) | $ / shares		$ 2.87
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount		$ 66,000,000											$ 66,000,000
Gain (loss) on extinguishment of debt		(4,100,000)
Senior convertible notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Loss from change in fair value of debt			5,500,000		22,000,000.0
Senior convertible notes | Long-term Debt
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value of liability			36,600,000		36,600,000
Senior convertible notes | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount		$ 51,000,000	15,000,000.0		15,000,000.0
Debt conversion, converted instrument (in shares) | shares	2,836,364	2,742,160
Exercise price per share (in dollars per share) | $ / shares							$ 5.02							$ 2.87
Debt issuance costs, gross		$ 1,000,000.0
Gain (loss) on extinguishment of debt		5,300,000
Gain (loss) on extinguishment of debt, fair value warrants		4,100,000
Gain (loss) on extinguishment of debt, cash fee		1,000,000.0
Gain (loss) on extinguishment of debt, excess fair value		200,000
Debt instrument fair value disclosure		$ 35,800,000	$ 30,000,000.0		$ 30,000,000.0
Senior convertible notes | Convertible notes payable | Measurement Input, Stock Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		2.90	4.27		4.27
Senior convertible notes | Convertible notes payable | Measurement Input, Discount Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		2.26	2.32		2.32
Senior convertible notes | Convertible notes payable | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.0159	0.0016		0.0016
Senior convertible notes | Convertible notes payable | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.45	0.45		0.45
Senior convertible notes | Convertible notes payable | Probability of Principal Repayment in Cash
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.25
Senior convertible notes | Convertible notes payable | Probability of Principal Repayment in Stock
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.75
Senior convertible notes | Convertible notes payable | Probability of Change in Control
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)		0.05	0.05		0.05
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	431,378	2,484,321
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares		3,000,000.0
Exercise price per share (in dollars per share) | $ / shares	$ 2.87	$ 3.25						$ 3.25
Class of warrant or right, term		2 years

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Fair Value Measurement - Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Dec. 31, 2019
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Loss from change in fair value of debt	$ 14,949	$ 14,444	$ 31,452	$ 16,574
Long-term Debt
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Fair value of liability	$ 36,624		36,624		$ 50,624
Less: principal paid			(35,980)
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability, Gain (Loss) Included in Earnings			$ 21,980

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Fair Value Measurement - Reconciliation for Compound Embedded Derivative Liability (Details) - Level 3 $ in Thousands	6 Months Ended
	Jun. 30, 2020 USD ($)
Debt-related Derivative Liability
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	$ 9,803
Fair value of derivative liabilities issued during the period	8,752
Change in fair value of derivative liabilities	8,496
Derecognition upon extinguishment of derivative liabilities	21,218
Fair value, ending balance	5,833
Total Derivative Liability
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	9,803
Fair value of derivative liabilities issued during the period	8,752
Change in fair value of derivative liabilities	8,496
Derecognition upon extinguishment of derivative liabilities	21,218
Fair value, ending balance	$ 5,833

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Fair Value Measurement - Freestanding Derivative Instruments (Details) - USD ($)							3 Months Ended			6 Months Ended
	Jun. 02, 2020	May 29, 2020	Feb. 28, 2020	Jan. 31, 2020	Jan. 14, 2020	Jan. 13, 2020	Jun. 30, 2020	Mar. 31, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	May 28, 2020	May 09, 2020	May 01, 2020	Apr. 30, 2020	Apr. 06, 2020	Apr. 05, 2020	Mar. 11, 2020	Dec. 31, 2019	Nov. 15, 2019	May 10, 2019
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				1,200,000		4,877,386
Loss upon extinguishment of debt							$ (22,029,000)		$ (5,875,000)	$ (49,348,000)	$ (5,875,000)
Related party, percentage ownership in company				5.00%		5.00%
Common stock, shares authorized (in shares)		350,000,000					350,000,000			350,000,000		250,000,000							250,000,000
Exercise price per share (in dollars per share)				$ 2.87		$ 2.87												$ 2.87
Issuance of common stock and warrants upon conversion of debt principal and accrued interest										$ 27,650,000	$ 34,650,000
2014 Rule 144A Convertible Note
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative, fair value of embedded derivative liability								$ 0											$ 0
Private Placement - January 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				8,710,802
Warrants and rights outstanding				$ 8,900,000
Exercise price per share (in dollars per share)				$ 2.87
Class of warrant or right, term				12 months
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Warrants and rights outstanding					$ 4,100,000
Warrants and rights outstanding, additional paid in capital					2,400,000
Warrants and rights outstanding, derivative liability					$ 1,700,000		$ 2,800,000	1,500,000		2,800,000
Fair value adjustment of warrants							1,300,000	200,000
Exercise price per share (in dollars per share)					$ 2.87
Warrants Issued In Connection With Foris Ventures LLC
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				5,200,000
Warrants and rights outstanding				$ 5,300,000
Warrants and rights outstanding, additional paid in capital				2,300,000
Warrants and rights outstanding, derivative liability		$ 3,700,000		3,000,000.0				2,000,000.0
Fair value adjustment of warrants		$ 1,800,000						$ 1,000,000.0
Common stock, shares authorized (in shares)		355,000,000										255,000,000
Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			1,900,000
Warrants and rights outstanding			$ 3,200,000																$ 7,000,000.0
Warrants and rights outstanding, additional paid in capital				5,200,000
Warrants and rights outstanding, derivative liability			$ 3,200,000				5,200,000			5,200,000
Fair value adjustment of warrants				$ 1,800,000						2,100,000
Exercise price per share (in dollars per share)			$ 2.87
Class of warrant or right, term			2 years
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount					$ 66,000,000															$ 66,000,000
Loss upon extinguishment of debt					4,100,000
Senior convertible notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)														$ 3.50	$ 5.00
Senior convertible notes | Convertible notes payable
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount					51,000,000		15,000,000.0			15,000,000.0
Loss upon extinguishment of debt					$ (5,300,000)
Exercise price per share (in dollars per share)													$ 5.02								$ 2.87
Senior convertible notes | Convertible notes payable | Minimum
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)														5.00
Senior convertible notes | Convertible notes payable | Maximum
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Exercise price per share (in dollars per share)																					$ 5.02
Debt instrument, convertible, conversion price (in dollars per share)														3.50
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)					3,000,000.0
Exercise price per share (in dollars per share)					$ 3.25									2.87	$ 3.25
Class of warrant or right, term					2 years
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020 | Maximum
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Exercise price per share (in dollars per share)														$ 3.25
Foris $19 Million Note | Private Placement - January 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				8,800,000
2014 Rule 144A Convertible Note
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount	$ 9,300,000
Debt instrument, convertible, conversion price (in dollars per share)																$ 2.87	$ 56.16
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$ 9,300,000
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity (in shares)	3,246,489
2014 Rule 144A Convertible Note | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Warrants and rights outstanding, derivative liability	$ 6,500,000
2014 Rule 144A Convertible Note | Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value adjustment of warrants							$ 6,500,000			$ 6,500,000

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Fair Value Measurement - Bifurcated Embedded Features in Debt Instruments (Details) $ in Thousands		3 Months Ended			6 Months Ended
	Jan. 31, 2020 USD ($)	Jun. 30, 2020 USD ($)	Mar. 31, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Feb. 28, 2020 USD ($)	Dec. 31, 2019 USD ($) derivative
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Loss upon extinguishment of debt		$ (22,029)		$ (5,875)	$ (49,348)	$ (5,875)
Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Fair value adjustment of warrants	$ 1,800				2,100
Warrants and rights outstanding, derivative liability		5,200			5,200		$ 3,200
Four Derivative Liabilities
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative, fair value of embedded derivative liability		600			600			$ 2,800
Loss upon extinguishment of debt			$ 2,300
Embedded derivative, fair value, collective amount			$ 900
Fair value adjustment of warrants					500
Four Derivative Liabilities | Warrants Issued In Connection with September 2019 and November 2019 Shottenfeld Notes
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Warrants and rights outstanding, derivative liability		$ 700			$ 700
Maximum
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative, number of instruments held | derivative								4

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Fair Value Measurement - Market-based Assumption and Estimates for Compound Embedded Derivative Liabilities Valuation (Details)	Jun. 30, 2020	Dec. 31, 2019
Probability of Change in Control
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.050	0.050
Expected Diviend Yield
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.000	0.000
Minimum | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.000009	0.0158
Risk-free interest rate	0.0009	0.016
Minimum | Risk-adjusted Yields
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.250	0.200
Minimum | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	1.11	0.94
Minimum | Credit spread
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.247	0.184
Minimum | Share Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.56	3.09
Minimum | Measurement Input, Exercise Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.87	3.87
Minimum | Measurement Input, Expected Term
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.07	1.51
Maximum | Risk-free Interest Rate
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	0.000020	0.0167
Risk-free interest rate	0.0017	0.017
Maximum | Risk-adjusted Yields
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.260	0.270
Maximum | Stock Price Volatility
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.14	1.05
Maximum | Credit spread
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Risk-free interest rate	0.368	0.254
Maximum | Share Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	4.27	4.76
Maximum | Measurement Input, Exercise Price
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	3.25	3.90
Maximum | Measurement Input, Expected Term
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Embedded derivative liability, measurement input	2.51	2.00

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Fair Value Measurement - Financial Assets and Liabilities (Details) - USD ($) $ in Millions	Jun. 30, 2020	Dec. 31, 2019
Fair Value Disclosures [Abstract]
Combined debt amount	$ 87.7	$ 195.8
Debt instrument fair value disclosure	$ 77.8	$ 194.8

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Debt - Debt Components (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended	12 Months Ended
	Mar. 31, 2020	Jun. 30, 2020	Dec. 31, 2019	Feb. 18, 2020	Jan. 31, 2020
Debt Instrument [Line Items]
Principal		$ 175,786	$ 297,462
Unaccreted debt discount		(7,989)	(20,314)
Debt change in fair value gain loss	$ 1,100	38,114	(15,376)
Net		205,911	261,772		$ 60,000
Less: current portion		(43,482)	63,805
Long-term debt, net of current portion		162,429	197,967
Convertible notes payable
Debt Instrument [Line Items]
Principal		30,020	66,000
Unaccreted debt discount		0	0
Debt change in fair value gain loss		6,604	(15,376)
Net		36,624	50,624
Convertible notes payable | Senior convertible notes
Debt Instrument [Line Items]
Principal		30,020	66,000
Unaccreted debt discount		0	0
Debt change in fair value gain loss		6,604	(15,376)
Net		36,624	50,624
Related party convertible notes payable
Debt Instrument [Line Items]
Principal		50,041	10,178
Unaccreted debt discount		0	0
Debt change in fair value gain loss		31,510	0
Net		81,551	10,178
Related party convertible notes payable | Foris Convertible Note (LSA Amendment)
Debt Instrument [Line Items]
Principal		50,041	0
Unaccreted debt discount		0	0
Debt change in fair value gain loss		31,510	0
Net		81,551	0
Related party convertible notes payable | 2014 Rule 144A convertible notes
Debt Instrument [Line Items]
Principal		0	10,178
Unaccreted debt discount		0	0
Debt change in fair value gain loss		0	0
Net		0	10,178
Loans payable and credit facilities
Debt Instrument [Line Items]
Principal		34,166	48,496
Unaccreted debt discount		(3,777)	(5,355)
Debt change in fair value gain loss		0	0
Net		30,389	43,141
Loans payable and credit facilities | Schottenfeld notes
Debt Instrument [Line Items]
Principal		12,500	20,350	$ 20,400
Unaccreted debt discount		(299)	(1,315)
Debt change in fair value gain loss		0	0
Net		12,201	19,035
Loans payable and credit facilities | Nikko notes
Debt Instrument [Line Items]
Principal		8,632	14,318
Unaccreted debt discount		(830)	(901)
Debt change in fair value gain loss		0	0
Net		7,802	13,417
Loans payable and credit facilities | Ginkgo note
Debt Instrument [Line Items]
Principal		12,000	12,000
Unaccreted debt discount		(2,648)	(3,139)
Debt change in fair value gain loss		0	0
Net		9,352	8,861
Loans payable and credit facilities | Other loans payable
Debt Instrument [Line Items]
Principal		1,034	1,828
Unaccreted debt discount		0	0
Debt change in fair value gain loss		0	0
Net		1,034	1,828
Related party loans payable
Debt Instrument [Line Items]
Principal		61,559	172,788
Unaccreted debt discount		(4,212)	(14,959)
Debt change in fair value gain loss		0	0
Net		57,347	157,829
Related party loans payable | Foris notes
Debt Instrument [Line Items]
Principal		5,000	115,351
Unaccreted debt discount		0	(9,516)
Debt change in fair value gain loss		0	0
Net		5,000	105,835
Related party loans payable | DSM notes
Debt Instrument [Line Items]
Principal		33,000	33,000
Unaccreted debt discount		(3,557)	(4,621)
Debt change in fair value gain loss		0	0
Net		29,443	28,379
Related party loans payable | Naxyris note
Debt Instrument [Line Items]
Principal		23,559	24,437
Unaccreted debt discount		(655)	(822)
Debt change in fair value gain loss		0	0
Net		$ 22,904	$ 23,615

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Debt - Exchange of Senior Convertible Notes Due 2022 (Details) - USD ($)					3 Months Ended			6 Months Ended		12 Months Ended
	May 01, 2020	Mar. 01, 2020	Feb. 18, 2020	Jan. 14, 2020	Jun. 30, 2020	Mar. 31, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Dec. 31, 2019	May 09, 2020	Apr. 30, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Nov. 15, 2019	May 10, 2019
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)														1,200,000	4,877,386
Exercise price per share (in dollars per share)													$ 2.87	$ 2.87	$ 2.87
Gain (loss) on extinguishment of debt					$ 22,029,000		$ 5,875,000	$ 49,348,000	$ 5,875,000
Debt change in fair value gain loss						$ 1,100,000		38,114,000		$ (15,376,000)
Principal					175,786,000			175,786,000		297,462,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument [Line Items]
Exercise price per share (in dollars per share)				$ 2.87
Convertible notes payable
Debt Instrument [Line Items]
Debt change in fair value gain loss								6,604,000		(15,376,000)
Principal					30,020,000			30,020,000		66,000,000
Loans payable and credit facilities
Debt Instrument [Line Items]
Debt change in fair value gain loss								0		0
Principal					34,166,000			34,166,000		48,496,000
Senior convertible notes | Convertible notes payable
Debt Instrument [Line Items]
Debt instrument, face amount				$ 51,000,000	15,000,000.0			15,000,000.0
Debt conversion, converted instrument (in shares)	2,836,364			2,742,160
Exercise price per share (in dollars per share)											$ 5.02						$ 2.87
Debt issuance costs, gross				$ 1,000,000.0
Debt conversion, original debt, amount	$ 10,000,000			10,000,000				10,000,000
Debt instrument, redemption, aggregate net cash proceeds, minimum	80,000,000			$ 80,000,000
Debt instrument, redemption price, percentage				107.00%
Debt instrument, redemption, required aggregate net cash proceeds, minimum	50,000,000		$ 50,000,000
Gain (loss) on extinguishment of debt				$ 5,300,000
Gain (loss) on extinguishment of debt, fair value warrants				4,100,000
Gain (loss) on extinguishment of debt, cash fee				1,000,000.0
Gain (loss) on extinguishment of debt, excess fair value				$ 200,000
Debt change in fair value gain loss								6,604,000		(15,376,000)
Principal					30,020,000			30,020,000		66,000,000
Debt instrument, amortization stock payment price		$ 3.00
Debt instrument, amortization payment, amount	$ 8,900,000	$ 10,000,000.0
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,000,000.0
Class of warrant or right, term				2 years
Exercise price per share (in dollars per share)	$ 2.87			$ 3.25								$ 3.25
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	431,378			2,484,321
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Debt Instrument [Line Items]
Debt instrument, face amount				$ 66,000,000												$ 66,000,000
Stock exchange ownership percentage																19.99%
Gain (loss) on extinguishment of debt				$ (4,100,000)
Schottenfeld notes | Loans payable and credit facilities
Debt Instrument [Line Items]
Debt change in fair value gain loss								0		0
Principal			$ 20,400,000		$ 12,500,000			$ 12,500,000		$ 20,350,000

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Debt - Amendment to Senior Convertible Notes Due 2022 (Details) - USD ($)					6 Months Ended
	Jun. 04, 2020	May 01, 2020	Feb. 18, 2020	Jan. 14, 2020	Jun. 30, 2020	Jun. 30, 2019	May 09, 2020	Apr. 30, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Dec. 31, 2019	May 10, 2019
Debt Instrument, Redemption [Line Items]
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment					$ 10,478,000	$ 0
Class of warrant or right, outstanding (in shares)					49,491,355							65,755,629
Exercise price per share (in dollars per share)									$ 2.87	$ 2.87	$ 2.87
Class of warrant or right, number of securities called by warrants or rights (in shares)										1,200,000	4,877,386
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Exercise price per share (in dollars per share)				$ 2.87
Senior convertible notes
Debt Instrument, Redemption [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)		$ 3.50						$ 5.00
Debt conversion, converted instrument, pre-delivery (in shares)				7,500,000
Senior convertible notes | Convertible notes payable
Debt Instrument, Redemption [Line Items]
Debt conversion, original debt, amount		$ 10,000,000		$ 10,000,000	$ 10,000,000
Debt instrument, redemption, aggregate net cash proceeds, minimum		80,000,000		$ 80,000,000
Amortization of debt issuance costs		16,400,000
Debt instrument, redemption, required aggregate net cash proceeds, minimum		$ 50,000,000	$ 50,000,000
Debt instrument, redemption price, percentage				107.00%
Debt conversion, converted instrument (in shares)		2,836,364		2,742,160
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	1,363,636
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500,000
Class of warrant or right, outstanding (in shares)													960,225
Exercise price per share (in dollars per share)							$ 5.02						$ 2.87
Payments of Debt Issuance Costs		$ 16,400,000
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Class of warrant or right, outstanding (in shares)		2,000,000
Exercise price per share (in dollars per share)		$ 2.87		$ 3.25				$ 3.25
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,000,000.0
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		431,378		2,484,321
Senior convertible notes | Convertible notes payable | Debt Instrument, Redemption, Period One
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		100.00%
Senior convertible notes | Convertible notes payable | Debt Instrument, Redemption, Period Two
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		105.00%
Senior convertible notes | Convertible notes payable | Debt Instrument, Redemption, Period Three
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		110.00%
Senior convertible notes | Convertible notes payable | Minimum
Debt Instrument, Redemption [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)		$ 5.00
Senior convertible notes | Convertible notes payable | Maximum
Debt Instrument, Redemption [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)		3.50
Exercise price per share (in dollars per share)													$ 5.02
Senior convertible notes | Convertible notes payable | Maximum | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Debt Instrument, Redemption [Line Items]
Exercise price per share (in dollars per share)		$ 3.25
Senior convertible notes | Convertible notes payable | Maximum | Debt Instrument, Redemption, Period Three
Debt Instrument, Redemption [Line Items]
Debt instrument, redemption price, percentage		115.00%
Senior convertible notes | Convertible notes payable | Holders [Member]
Debt Instrument, Redemption [Line Items]
Amortization of debt issuance costs		$ 5,000,000.0
Payments of Debt Issuance Costs		$ 5,000,000
Second Amendment to New Notes and the W&F Agreements | Convertible notes payable
Debt Instrument, Redemption [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	700,000
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500,000

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Debt - Debt Equitization - Foris Related Party (Details) - USD ($)					3 Months Ended		6 Months Ended
	Jan. 31, 2020	Jan. 13, 2020	Aug. 28, 2019	Apr. 15, 2019	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Mar. 11, 2020	Dec. 31, 2019
Debt Instrument [Line Items]
Issuance of common stock upon exercise of warrants (in shares)	25,326,095	4,877,386					30,694,457
Exercise price per share (in dollars per share)	$ 2.87	$ 2.87							$ 2.87
Proceeds from exercises of warrants		$ 14,000,000.0					$ 3,332,000	$ 1,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,200,000	4,877,386
Loss upon extinguishment of debt					$ (22,029,000)	$ (5,875,000)	(49,348,000)	$ (5,875,000)
Private Placement - January 2020 Sale Of Stock To Foris
Debt Instrument [Line Items]
Issuance of common stock upon exercise of warrants (in shares)	10,200,000
Exercise price per share (in dollars per share)	$ 2.87
Number of shares issued in sale of stock (in shares)	5,279,171
Purchase price of sale of stock	$ 15,100,000
January 2020 Warrant Exercises
Debt Instrument [Line Items]
Issuance of common stock upon exercise of warrants (in shares)	19,287,780
Exercise price per share (in dollars per share)	$ 2.84
Proceeds from exercises of warrants	$ 54,800,000
January 2020 Rights Issued To Foris
Debt Instrument [Line Items]
Exercise price per share (in dollars per share)	$ 2.87
Purchase price of sale of stock	$ 69,900,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	8,778,230
Class of warrant or right, term	12 months
Foris notes | Related party loans payable
Debt Instrument [Line Items]
Debt instrument, face amount										$ 110,000,000.0
Debt instrument, capitalized interest										$ 5,300,000
Foris $19 Million Note | Related party loans payable
Debt Instrument [Line Items]
Debt conversion, original debt, amount			$ 19,000,000
Debt instrument, interest rate, stated percentage			12.00%
Debt instrument, reduction in principal	$ 60,000,000.0
Debt instrument, reduction in principal, interest and fees	9,900,000
Debt instrument, reduction in principal, capitalized interest	5,400,000
Loss upon extinguishment of debt	(5,700,000)
Gain (loss) on extinguishment of debt, unaccredited discount	6,100,000
Gain (loss) on extinguishment of debt, fair value derivative liability	400,000
Foris LSA | Related party loans payable
Debt Instrument [Line Items]
Debt conversion, original debt, amount				$ 91,000,000.0
Debt instrument, interest rate, stated percentage				12.50%
Loss upon extinguishment of debt	10,400,000
Gain (loss) on extinguishment of debt, unaccredited discount	3,100,000
Gain (loss) on extinguishment of debt, fair value derivative liability	1,600,000
Gain (Loss) On Extinguishment Of Debt, Fair Value Of Rights	$ 8,900,000
Capitalized Fair Value Of Embedded Mandatory Redemption Feature					$ 700,000		$ 700,000

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Debt - Amendment No. 1 to Foris LSA — Foris, Related Party (Details) - USD ($)			3 Months Ended		6 Months Ended
	Jun. 01, 2020	Mar. 11, 2020	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	May 31, 2020
Debt Instrument, Redemption [Line Items]
Debt instrument, interest rate during period		12.00%
Loss from change in fair value of debt			$ (14,949,000)	$ (14,444,000)	$ (31,452,000)	$ (16,574,000)
Foris LSA Amendment
Debt Instrument, Redemption [Line Items]
Debt instrument, interest rate, stated percentage	6.00%						12.50%
Debt instrument, convertible, conversion price (in dollars per share)	$ 3.00
Debt Instrument, secured indebtedness	$ 15,000,000
Debt instrument, face amount	22,000,000.0
Debt instrument, repurchase amount	$ 72,100,000
Loss from change in fair value of debt			$ 9,500,000

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Debt - Schottenfeld Forbearance Agreement (Details) - USD ($)				3 Months Ended		6 Months Ended
	Jun. 05, 2020	Jun. 01, 2020	Feb. 28, 2020	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Apr. 19, 2020	Dec. 31, 2019	Nov. 14, 2019	Sep. 10, 2019	Aug. 14, 2019
Debt Instrument [Line Items]
Forbearance agreement, forbearance period			60 days
Forbearance agreement, triggering event, minimum conversion or exchange amount			$ 60,000,000
Forbearance agreement, triggering event, minimum conversion or exchange amount, percentage of certain junior outstanding indebtedness			100.00%
Forbearance agreement, late fee percentage			5.00%
Forbearance agreement, partial payment of interest			$ 150,000
Forbearance agreement, forbearance fee			$ 150,000
Forbearance agreement, class of warrant or right, exercise price of warrants or rights			$ 2.87
Loss upon extinguishment of debt				$ (22,029,000)	$ (5,875,000)	$ (49,348,000)	$ (5,875,000)
Debt, current				43,482,000		43,482,000			$ 45,313,000
Repayments of debt		$ 37,100,000
Schottenfeld September 2019 Credit Agreements
Debt Instrument [Line Items]
Debt instrument, face amount				$ 12,500,000		12,500,000						$ 12,500,000
Debt instrument, interest rate, stated percentage											12.00%
Loss upon extinguishment of debt						(5,600,000)
Gain (loss) on extinguishment of debt, fair value warrants						3,200,000
Gain (loss) on extinguishment of debt, fair value modified warrants						1,300,000
Gain (loss) on extinguishment of debt, unaccredited discount						$ 1,100,000
Debt, current								$ 20,400,000
Repayments of debt	$ 7,900,000
Schottenfeld November 2019 Credit and Security Agreement
Debt Instrument [Line Items]
Debt instrument, additional face amount										$ 7,900,000
Debt instrument, fee amount										200,000
Embedded derivative, fair value of embedded derivative liability										$ 200,000

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Debt - 2014 Rule 144A Note Exchange and Extension - Total, Related Party (Details) - USD ($)			6 Months Ended
	Jun. 02, 2020	Mar. 11, 2020	Jun. 30, 2020	Jun. 30, 2019	Apr. 06, 2020	Jan. 31, 2020	Jan. 13, 2020
Debt Instrument, Redemption [Line Items]
Senior notes		$ 10,200,000
Repayments of senior debt, interest portion		1,500,000
Senior notes, principal amount		9,100,000
Repayments of senior debt		$ 1,100,000
Debt instrument, interest rate during period		12.00%
Exercise price per share (in dollars per share)		$ 2.87				$ 2.87	$ 2.87
Issuance of common stock and warrants upon conversion of debt principal and accrued interest			$ 27,650,000	$ 34,650,000
2014 Rule 144A Convertible Note
Debt Instrument, Redemption [Line Items]
Debt instrument, face amount	$ 9,300,000
Issuance of common stock upon conversion of debt principal and accrued interest, and the related derecognition of derivative liability to equity (in shares)	3,246,489
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$ 9,300,000
Derivative, fair value, net	$ 6,500,000
2014 Rule 144A Convertible Note
Debt Instrument, Redemption [Line Items]
Exercise price per share (in dollars per share)					$ 2.87

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Debt - Ginkgo Waiver Agreement (Details) $ in Millions	Mar. 11, 2020 USD ($)
Debt Disclosure [Abstract]
Waiver agreement, past due interest waived	$ 6.7
Waiver agreement, past due partnership payments plus interest waived	0.5
Waiver agreement, monthly payment amended	0.5
Senior notes, past due payments deferred	$ 7.2

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Debt - Nikko Secured Loan Agreement Amendment (Details) - USD ($)	Jun. 01, 2020	Mar. 12, 2020	Mar. 11, 2020	Apr. 03, 2020
Debt Instrument [Line Items]
Repayments of debt	$ 37,100,000
Debt instrument, interest rate during period			12.00%
Nikko Loan Agreement
Debt Instrument [Line Items]
Repayments of debt		$ 500,000
Long term debt, principal amount		$ 4,000,000.0		$ 4,000,000.0
Debt instrument, interest rate during period		8.00%
Debt instrument, covenant, accrued interest rate		2.75%
Debt instrument, covenant, first priority lien		27.20%

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Debt - Paycheck Protection Plan Loan (Details) - Paycheck Protection Plan Loan	May 07, 2020 USD ($)
Debt Instrument, Redemption [Line Items]
Proceeds from notes payable	$ 10,000,000
Debt instrument, interest rate, stated percentage	1.00%
Debt instrument, term	2 years

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Debt - Future Minimum Payments (Details) $ in Thousands	Jun. 30, 2020 USD ($)
Debt Instrument [Line Items]
2020 (remaining six months)	$ 14,030
2021	69,930
2022	115,194
2023	12,899
2024	398
Thereafter	1,869
Total future minimum payments	214,320
Less: amount representing interest	(38,534)
Present value of minimum debt payments	175,786
Less: current portion of debt principal	(37,016)
Noncurrent portion of debt principal	138,770
Convertible notes payable
Debt Instrument [Line Items]
2020 (remaining six months)	814
2021	33,898
2022	0
2023	0
2024	0
Thereafter	0
Total future minimum payments	34,712
Less: amount representing interest	(4,692)
Present value of minimum debt payments	30,020
Less: current portion of debt principal	(30,020)
Noncurrent portion of debt principal	0
Loans Payable and Credit Facilities
Debt Instrument [Line Items]
2020 (remaining six months)	10,132
2021	4,255
2022	15,058
2023	12,899
2024	398
Thereafter	1,869
Total future minimum payments	44,611
Less: amount representing interest	(10,445)
Present value of minimum debt payments	34,166
Less: current portion of debt principal	(6,996)
Noncurrent portion of debt principal	27,170
Related party convertible notes payable
Debt Instrument [Line Items]
2020 (remaining six months)	0
2021	0
2022	59,578
2023	0
2024	0
Thereafter	0
Total future minimum payments	59,578
Less: amount representing interest	(9,537)
Present value of minimum debt payments	50,041
Less: current portion of debt principal	0
Noncurrent portion of debt principal	50,041
Related Party Loans Payable and Credit Facilities
Debt Instrument [Line Items]
2020 (remaining six months)	3,084
2021	31,777
2022	40,558
2023	0
2024	0
Thereafter	0
Total future minimum payments	75,419
Less: amount representing interest	(13,860)
Present value of minimum debt payments	61,559
Less: current portion of debt principal	0
Noncurrent portion of debt principal	$ 61,559

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Debt - Foris $5 Million Note – Foris, Related Party (Details) - Foris $5 Million Note - Foris notes	Apr. 29, 2020 USD ($)
Debt Instrument, Redemption [Line Items]
Debt instrument, face amount	$ 5,000,000
Related party ownership percentage	5.00%
Debt instrument, interest rate, stated percentage	12.00%

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Mezzanine Equity (Details Textual) - Gates Foundation Purchase Agreement $ / shares in Units, $ in Millions	6 Months Ended
	Jun. 30, 2020 USD ($) $ / shares
Subsidiary, Sale of Stock [Line Items]
Stock price (in dollars per share) | $ / shares	$ 17.10
Compound annual return (percentage)	10.00%
Research and development obligation, remaining amount | $	$ 0.3

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Stockholders' Deficit - Foris Warrant Exercises for Cash (Details) - USD ($) $ / shares in Units, $ in Thousands						6 Months Ended
	Jun. 02, 2020	Jun. 01, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Jun. 30, 2020	Jun. 30, 2019
Class of Warrant or Right [Line Items]
Related party, percentage ownership in company				5.00%	5.00%
Class of warrant or right, number of securities called by warrants or rights (in shares)				1,200,000	4,877,386
Exercise price per share (in dollars per share)			$ 2.87	$ 2.87	$ 2.87
Proceeds from exercises of warrants					$ 14,000	$ 3,332	$ 1
Issuance of common stock upon exercise of warrants (in shares)				25,326,095	4,877,386	30,694,457
Proceeds from issuance or sale of equity		$ 190,000	$ 15,000	$ 28,300
Foris notes
Class of Warrant or Right [Line Items]
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)			5,226,481
Foris notes
Class of Warrant or Right [Line Items]
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)	5,226,481

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Stockholders' Deficit - January 2020 Warrant Amendments and Exercises, Foris Debt Equitization and Private Placement (Details) - USD ($) $ / shares in Units, $ in Thousands					6 Months Ended
	Jun. 01, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Jun. 30, 2020	Dec. 31, 2019
Class of Warrant or Right [Line Items]
Proceeds from issuance or sale of equity	$ 190,000	$ 15,000	$ 28,300
Net			60,000		$ 205,911	$ 261,772
Interest Payable			$ 9,900
Issuance of common stock upon exercise of warrants (in shares)			25,326,095	4,877,386	30,694,457
Class of warrant or right, number of securities called by warrants or rights (in shares)			1,200,000	4,877,386
Exercise price per share (in dollars per share)		$ 2.87	$ 2.87	$ 2.87
Private Placement
Class of Warrant or Right [Line Items]
Number of shares issued in sale of stock (in shares)			13,989,973
January 2020 Rights Issued
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			18,649,961
Exercise price per share (in dollars per share)			$ 2.87
Class of warrant or right, term			12 months

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Stockholders' Deficit - Warrant Amendments and Exercise by Certain Holders (Details) - USD ($) $ / shares in Units, $ in Thousands			6 Months Ended
	Jan. 31, 2020	Jan. 13, 2020	Jun. 30, 2020	Jun. 30, 2019	Mar. 11, 2020
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,200,000	4,877,386
Exercise price per share (in dollars per share)	$ 2.87	$ 2.87			$ 2.87
Issuance of common stock upon exercise of warrants (in shares)	25,326,095	4,877,386	30,694,457
Proceeds from exercises of warrants		$ 14,000	$ 3,332	$ 1
January 2020 Warrant Amendments
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,160,929
Exercise price per share (in dollars per share)	$ 2.87
Issuance of common stock upon exercise of warrants (in shares)	1,160,929
Class of warrant or right, term	12 months
Proceeds from exercises of warrants	$ 3,300

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Stockholders' Deficit - Warrant Amendments and Exercises, Common Stock Purchase and Debt Equitization by Foris- Related Party (Details)					3 Months Ended		6 Months Ended
	May 01, 2020 USD ($) $ / shares	Jan. 31, 2020 USD ($) $ / shares shares	Jan. 14, 2020 USD ($) $ / shares shares	Jan. 13, 2020 USD ($) $ / shares shares	Jun. 30, 2020 USD ($) $ / shares	Mar. 31, 2020 USD ($)	Jun. 30, 2020 USD ($) $ / shares shares	Jun. 30, 2019 USD ($)	May 09, 2020 $ / shares	Apr. 30, 2020 $ / shares	Mar. 11, 2020 $ / shares	Aug. 28, 2019 USD ($)	May 10, 2019 $ / shares
Class of Warrant or Right [Line Items]
Issuance of common stock upon exercise of warrants (in shares) | shares		25,326,095		4,877,386			30,694,457
Exercise price per share (in dollars per share)		$ 2.87		$ 2.87							$ 2.87
Proceeds from exercises of warrants | $				$ 14,000,000.0			$ 3,332,000	$ 1,000
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares		1,200,000		4,877,386
August Foris Credit Agreement | Foris notes
Class of Warrant or Right [Line Items]
Extinguishment of debt, amount | $		$ 60,000,000
Line of credit facility, maximum borrowing capacity | $												$ 19,000,000
Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)									$ 5.02				$ 2.87
Senior convertible notes | Maximum | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)													$ 5.02
Private Placement - January 2020 Sale Of Stock To Foris
Class of Warrant or Right [Line Items]
Issuance of common stock upon exercise of warrants (in shares) | shares		10,200,000
Exercise price per share (in dollars per share)		$ 2.87
Number of shares issued in sale of stock (in shares) | shares		5,279,171
Purchase price of sale of stock | $		$ 15,100,000
January 2020 Warrant Exercises
Class of Warrant or Right [Line Items]
Issuance of common stock upon exercise of warrants (in shares) | shares		19,287,780
Exercise price per share (in dollars per share)		$ 2.84
Proceeds from exercises of warrants | $		$ 54,800,000
January 2020 Rights Issued To Foris
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)		$ 2.87
Purchase price of sale of stock | $		$ 69,900,000
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares		8,778,230
Class of warrant or right, term		12 months
Ammended Foris Warrants
Class of Warrant or Right [Line Items]
Fair value adjustment of warrants | $							69,900,000
Warrants and rights outstanding | $					$ 8,900,000		$ 8,900,000
Ammended Foris Warrants | Share Price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input					2.56		2.56
Ammended Foris Warrants | Stock Price Volatility
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input					1.12		1.12
Ammended Foris Warrants | Expected Diviend Yield
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input					0		0
Ammended Foris Warrants | Risk-free Interest Rate
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input					0.0145		0.0145
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 2.87
Fair value adjustment of warrants | $					$ 1,300,000	$ 200,000
Warrants and rights outstanding | $			$ 4,100,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)	$ 2.87		$ 3.25							$ 3.25
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares			3,000,000.0
Class of warrant or right, term			2 years
Fair value of modification to previously issued common stock warrants | $	$ 1,100,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Maximum | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)	$ 3.25

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Stockholders' Deficit - Increase in Authorized Common Stock (Details) - shares	Jun. 30, 2020	May 29, 2020	May 28, 2020	Dec. 31, 2019
Equity [Abstract]
Common stock, shares authorized (in shares)	350,000,000	350,000,000	250,000,000	250,000,000

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Stockholders' Deficit - Total Conversion Price Reduction and Subsequent Conversion into Common Stock (Details) - USD ($)		6 Months Ended
	Jun. 02, 2020	Jun. 30, 2020	Jun. 30, 2019	Apr. 06, 2020	Apr. 05, 2020	Dec. 31, 2019
Debt Conversion [Line Items]
Common stock, shares outstanding (in shares)		204,618,423				117,742,677
Issuance of common stock and warrants upon conversion of debt principal and accrued interest		$ 27,650,000	$ 34,650,000
2014 Rule 144A Convertible Note
Debt Conversion [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)				$ 2.87	$ 56.16
Debt instrument, face amount	$ 9,300,000
Common stock, shares outstanding (in shares)	3,246,489
Issuance of common stock and warrants upon conversion of debt principal and accrued interest	$ 9,300,000
Derivative, fair value, net	$ 6,500,000

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Stockholders' Deficit - June 2020 PIPE (Details) - USD ($) $ / shares in Units, $ in Millions	Jun. 01, 2020	Jun. 30, 2020	Jun. 05, 2020	Dec. 31, 2019
Class of Stock [Line Items]
Common stock, par value (in dollars per share)		$ 0.0001		$ 0.0001
June 2020 PIPE
Class of Stock [Line Items]
Number of shares issued in sale of stock (in shares)	32,614,573
Common stock, par value (in dollars per share)	$ 0.0001
Purchase price of sale of stock	$ 190
June 2020 PIPE | Preferred Stock
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)			$ 1,000
Series E Convertible Preferred Stock
Class of Stock [Line Items]
Number of shares issued in sale of stock (in shares)	102,156
Common stock, par value (in dollars per share)	$ 0.0001
Conversion of stock, shares converted (in shares)	34,052,070
Sale of stock, consideration received per transaction	$ 200
Series E Convertible Preferred Stock | Common Stock
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)	$ 3.00
Series E Convertible Preferred Stock | Preferred Stock
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)	$ 1,000

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Stockholders' Deficit - January 2020 Private Placement (Details) - USD ($)					6 Months Ended
	Jun. 01, 2020	May 01, 2020	Jan. 31, 2020	Jan. 14, 2020	Jun. 30, 2020	May 09, 2020	Apr. 30, 2020	Mar. 11, 2020	Jan. 13, 2020	Nov. 15, 2019	May 10, 2019
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			1,200,000						4,877,386
Exercise price per share (in dollars per share)			$ 2.87					$ 2.87	$ 2.87
Repayments of debt	$ 37,100,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)				$ 2.87
Convertible Senior Notes 6.0% due in 2022 | Convertible notes payable
Class of Warrant or Right [Line Items]
Debt instrument, face amount				$ 66,000,000						$ 66,000,000
Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)						$ 5.02					$ 2.87
Debt instrument, face amount				$ 51,000,000	$ 15,000,000.0
Debt conversion, converted instrument (in shares)		2,836,364		2,742,160
Repayments of debt					$ 15,200,000
Senior convertible notes | Convertible notes payable | Rights Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		431,378		2,484,321
Senior convertible notes | Convertible notes payable | Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)				3,000,000.0
Exercise price per share (in dollars per share)		$ 2.87		$ 3.25			$ 3.25
Class of warrant or right, term				2 years
Private Placement - January 2020
Class of Warrant or Right [Line Items]
Number of shares issued in sale of stock (in shares)			8,710,802
Class of warrant or right, number of securities called by warrants or rights (in shares)			8,710,802
Exercise price per share (in dollars per share)			$ 2.87
Class of warrant or right, term			12 months
Purchase price of sale of stock			$ 25,000,000

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Stockholders' Deficit - Release of Pre-Delivery Shares and Amendment to Warrants Issued to Holders of Senior Convertible Notes Due 2022 (Details) - USD ($)				3 Months Ended		6 Months Ended
	Jun. 04, 2020	May 01, 2020	Jan. 14, 2020	Jun. 30, 2020	Mar. 31, 2020	Jun. 30, 2020	Jun. 30, 2019	May 09, 2020	Apr. 30, 2020	Apr. 06, 2020	Apr. 05, 2020	Mar. 11, 2020	Jan. 31, 2020	Jan. 13, 2020	Dec. 31, 2019	May 10, 2019
Class of Warrant or Right [Line Items]
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment						$ 10,478,000	$ 0
Exercise price per share (in dollars per share)												$ 2.87	$ 2.87	$ 2.87
Class of warrant or right, outstanding (in shares)				49,491,355		49,491,355									65,755,629
Class of warrant or right, number of securities called by warrants or rights (in shares)													1,200,000	4,877,386
Senior convertible notes
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)			7,500,000
Debt instrument, convertible, conversion price (in dollars per share)		$ 3.50							$ 5.00
Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	1,363,636
Debt conversion, converted instrument (in shares)		2,836,364	2,742,160
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500,000
Exercise price per share (in dollars per share)								$ 5.02								$ 2.87
Class of warrant or right, outstanding (in shares)																960,225
Return of pre-delivery shares previously issued in connection with debt agreement (in shares)	2,600,000
Senior convertible notes | Convertible notes payable | One Holder
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	700,000
Second Amendment to New Notes and the W&F Agreements | Convertible notes payable
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, pre-delivery (in shares)	3,536,364	700,000
Non-cash interest expense in connection with release of pre-delivery shares to holder in connection with debt amendment	$ 10,500,000
2014 Rule 144A Convertible Note
Class of Warrant or Right [Line Items]
Debt instrument, convertible, conversion price (in dollars per share)										$ 2.87	$ 56.16
Warrants Issued In Exchange For Convertible Senior Notes Due 2020
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 2.87
Fair value adjustment of warrants				$ 1,300,000	$ 200,000
Warrants Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)		$ 2.87	$ 3.25						$ 3.25
Class of warrant or right, outstanding (in shares)		2,000,000
Class of warrant or right, number of securities called by warrants or rights (in shares)			3,000,000.0
Rights Issued In Exchange For Convertible Senior Notes Due 2020 | Senior convertible notes | Convertible notes payable
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		431,378	2,484,321

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Stockholders' Deficit - Series E Convertible Preferred Stock and Amendment to Articles of Incorporation or Bylaws (Details) - Preferred Stock - June 2020 PIPE - USD ($)	Jun. 05, 2020	Jun. 04, 2020	Jun. 01, 2020
Class of Stock [Line Items]
Sale of stock, price per share (in dollars per share)	$ 1,000
Convertible preferred stock, shares issued upon conversion (in shares)	333.33
Debt instrument, convertible, threshold percentage of stock price trigger	19.99%
Debt instrument, convertible, beneficial conversion feature	$ 67,200,000
Stock price (in dollars per share)		$ 4.88	$ 5.35
Debt instrument, convertible, conversion price (in dollars per share)	$ 3.00

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Stockholders' Deficit - Warrant Activity (Details) - $ / shares			6 Months Ended
	Jan. 31, 2020	Jan. 13, 2020	Jun. 30, 2020	Mar. 11, 2020
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			65,755,629
Additional warrants issued (in shares)			21,649,961
Exercises (in shares)	(25,326,095)	(4,877,386)	(30,694,457)
Expiration (in shares)			(7,219,778)
Number outstanding, ending balance (in shares)			49,491,355
Exercise price per share (in dollars per share)	$ 2.87	$ 2.87		$ 2.87
High Trail/Silverback warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			0
Additional warrants issued (in shares)			3,000,000
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,000,000
Exercise price per share (in dollars per share)			$ 2.87
High trail/Silverback warrants due January 14,2022
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 3.25
2020 PIPE right shares
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			0
Additional warrants issued (in shares)			8,710,802
Exercises (in shares)			(5,226,481)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			3,484,321
Exercise price per share (in dollars per share)			$ 2.87
January 2020 warrant exercise right shares
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			0
Additional warrants issued (in shares)			9,939,159
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			9,939,159
Exercise price per share (in dollars per share)			$ 2.87
Foris LSA warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			3,438,829
Additional warrants issued (in shares)			0
Exercises (in shares)			(3,438,829)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
November 2019 Foris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			1,000,000
Additional warrants issued (in shares)			0
Exercises (in shares)			(1,000,000)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
August 2019 Foris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			4,871,795
Additional warrants issued (in shares)			0
Exercises (in shares)			(4,871,795)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
April 2019 PIPE warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			8,084,770
Additional warrants issued (in shares)			0
Exercises (in shares)			(4,712,781)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			3,371,989
April 2019 PIPE warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 4.76
April 2019 PIPE warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 5.02
April 2019 Foris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			5,424,804
Additional warrants issued (in shares)			0
Exercises (in shares)			(5,424,804)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
September and November 2019 Investor Credit Agreement warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			5,233,551
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			5,233,551
Exercise price per share (in dollars per share)			$ 2.87
Naxyris LSA warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			2,000,000
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			2,000,000
Exercise price per share (in dollars per share)			$ 2.87
October 2019 Naxyris warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			2,000,000
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			2,000,000
Exercise price per share (in dollars per share)			$ 3.87
May-June 2019 6% Note Exchange warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			2,181,818
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			2,181,818
May-June 2019 6% Note Exchange warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 2.87
May-June 2019 6% Note Exchange warrants
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			5.12
April 2019 PIPE warrants due April 29, 2021 [Member]
Class of Warrant or Right [Line Items]
Exercise price per share (in dollars per share)			$ 4.76
May 2019 6.50% Note Exchange warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			1,744,241
Additional warrants issued (in shares)			0
Exercises (in shares)			(784,016)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			960,225
Exercise price per share (in dollars per share)			$ 2.87
July 2019 Wolverine warrant
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			1,080,000
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			1,080,000
Exercise price per share (in dollars per share)			$ 2.87
August 2018 warrant exercise agreements
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			12,097,164
Additional warrants issued (in shares)			0
Exercises (in shares)			(4,877,386)
Expiration (in shares)			(7,219,778)
Exercise price per share of warrant exercised (in dollars per share)			$ 2.87
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
May 2017 cash warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			6,078,156
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			6,078,156
Exercise price per share (in dollars per share)			$ 2.87
August 2017 cash warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			3,968,116
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,968,116
Exercise price per share (in dollars per share)			$ 2.87
May 2017 dilution warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			3,085,893
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,085,893
Exercise price per share (in dollars per share)			$ 0
August 2017 dilution warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			3,028,983
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			3,028,983
Exercise price per share (in dollars per share)			$ 0
February 2016 related party private placement
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			171,429
Additional warrants issued (in shares)			0
Exercises (in shares)			(152,381)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0.15
Number outstanding, ending balance (in shares)			19,048
Exercise price per share (in dollars per share)			$ 0.15
July 2015 related party debt exchange
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			133,334
Additional warrants issued (in shares)			0
Exercises (in shares)			(133,334)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0.15
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
July 2015 private placement
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			72,650
Additional warrants issued (in shares)			0
Exercises (in shares)			(72,650)
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0.15
Number outstanding, ending balance (in shares)			0
Exercise price per share (in dollars per share)			$ 0
July 2015 related party debt exchange
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			58,690
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			58,690
Exercise price per share (in dollars per share)			$ 0.15
Other
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)			1,406
Additional warrants issued (in shares)			0
Exercises (in shares)			0
Expiration (in shares)			0
Exercise price per share of warrant exercised (in dollars per share)			$ 0
Number outstanding, ending balance (in shares)			1,406
Exercise price per share (in dollars per share)			$ 160.05

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Loss Per Share - Calculation of Basic and Diluted Net Loss Per Share of Common Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Earnings Per Share, Basic and Diluted [Abstract]
Net loss	$ (110,422)	$ (38,088)	$ (198,266)	$ (104,331)
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D	0	(34,964)	0	(34,964)
Add: losses allocated to participating securities	6,361	2,255	7,435	4,690
Net loss attributable to Amyris, Inc. common stockholders	$ (104,061)	$ (70,797)	$ (190,831)	$ (134,605)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	184,827,330	92,785,752	169,946,482	84,831,269
Loss per share attributable to common stockholders, basic and diluted (in dollars per share)	$ (0.56)	$ (0.76)	$ (1.12)	$ (1.59)

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Loss Per Share - Antidilutive Securities Excluded From Computation of Earnings Per Share (Details) - shares	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	63,764,401,000	74,530,956,000	63,764,401,000	74,530,956,000
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	184,827,330	92,785,752	169,946,482	84,831,269
Series E Preferred Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted		102,156
Common Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted		34,052,070
Period-end common stock warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	43,298,741,000	5,535,538,000	43,298,741,000	5,535,538,000
Convertible promissory notes
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	8,574,399,000	11,007,316,000	8,574,399,000	11,007,316,000
Period-end stock options to purchase common stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	5,479,334,000	49,747,628,000	5,479,334,000	49,747,628,000
Period-end restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	4,468,266,000	5,284,742,000	4,468,266,000	5,284,742,000
Period-end Preferred Shares
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive securities excluded from computation of diluted loss per share (in shares)	1,943,661,000	2,955,732,000	1,943,661,000	2,955,732,000

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Revenue Recognition and Contract Assets and Liabilities - Disaggregation of Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Disaggregation of Revenue [Line Items]
Revenue	$ 30,005	$ 62,694	$ 59,135	$ 77,068
United States
Disaggregation of Revenue [Line Items]
Revenue	16,866	12,214	28,809	19,780
Europe
Disaggregation of Revenue [Line Items]
Revenue	5,894	46,263	17,654	50,864
Asia
Disaggregation of Revenue [Line Items]
Revenue	6,370	3,899	11,147	5,867
Brazil
Disaggregation of Revenue [Line Items]
Revenue	670	300	1,247	520
Other
Disaggregation of Revenue [Line Items]
Revenue	205	18	278	37
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	25,188	12,120	43,042	24,004
Renewable Products | United States
Disaggregation of Revenue [Line Items]
Revenue	16,866	5,806	28,809	12,879
Renewable Products | Europe
Disaggregation of Revenue [Line Items]
Revenue	3,106	2,102	6,349	4,956
Renewable Products | Asia
Disaggregation of Revenue [Line Items]
Revenue	4,341	3,899	6,359	5,617
Renewable Products | Brazil
Disaggregation of Revenue [Line Items]
Revenue	670	295	1,247	515
Renewable Products | Other
Disaggregation of Revenue [Line Items]
Revenue	205	18	278	37
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	990	40,964	6,151	41,082
Licenses and Royalties | United States
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Licenses and Royalties | Europe
Disaggregation of Revenue [Line Items]
Revenue	990	40,964	6,151	41,082
Licenses and Royalties | Asia
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Licenses and Royalties | Brazil
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Licenses and Royalties | Other
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	3,827	9,610	9,942	11,982
Grants and Collaborations | United States
Disaggregation of Revenue [Line Items]
Revenue	0	6,408	0	6,901
Grants and Collaborations | Europe
Disaggregation of Revenue [Line Items]
Revenue	1,798	3,197	5,154	4,826
Grants and Collaborations | Asia
Disaggregation of Revenue [Line Items]
Revenue	2,029	0	4,788	250
Grants and Collaborations | Brazil
Disaggregation of Revenue [Line Items]
Revenue	0	5	0	5
Grants and Collaborations | Other
Disaggregation of Revenue [Line Items]
Revenue	$ 0	$ 0	$ 0	$ 0

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Revenue Recognition and Contact Assets and Liabilities - Narrative (Details) - USD ($) $ in Thousands		3 Months Ended				6 Months Ended
	May 02, 2019	Jun. 30, 2020	Mar. 31, 2020	Dec. 31, 2019	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Apr. 30, 2019
Disaggregation of Revenue [Line Items]
Revenue		$ 30,005			$ 62,694	$ 59,135	$ 77,068
Contract assets		11,724		$ 8,485		11,724
Cost of products sold		23,098			15,121	34,888	32,828
Interest expense		20,118			15,217	35,120	27,751
Revenue, remaining performance obligation, constrained variable consideration		175,400				175,400
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue		990			40,964	6,151	41,082
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue		3,827			$ 9,610	9,942	$ 11,982
DSM International B.V.
Disaggregation of Revenue [Line Items]
Contract with customer, liability		12,500				12,500		$ 12,500
Contract with customer, liability, cumulative catch-up adjustment to revenue, modification of contract			$ 3,800	$ 8,800		37,100
Yifan
Disaggregation of Revenue [Line Items]
Estimated total unconstrained transaction price		21,000				21,000
Yifan | Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue		2,000				4,700
Contract assets		2,900				2,900
Revenue from contract with customer, cumulative to date						10,800
The Cannabinoid Agreement | Lavvan
Disaggregation of Revenue [Line Items]
Agreement amount	$ 300,000
Agreement amount of research and development funding that could be received	$ 300,000
Agreement, profit sharing to be received from the counterparty, period	20 years
Estimated total unconstrained transaction price	$ 145,000
Variable consideration related to milestones		155,000				155,000
Revenue						18,300
Contract assets		8,300				8,300
Collaborative Arrangement | DSM International B.V.
Disaggregation of Revenue [Line Items]
Estimated total unconstrained transaction price		14,100				14,100
Revenue		$ 1,300				4,300
Revenue from contract with customer, cumulative to date						$ 9,100

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Revenue Recognition and Contract Assets and Liabilities - Revenue in Connection With Significant Revenue Agreement (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Disaggregation of Revenue [Line Items]
Revenue	$ 30,005	$ 62,694	$ 59,135	$ 77,068
Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	7,132	47,524	23,304	53,581
DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	1,267	43,328	8,084	43,346
Sephora | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	2,442	2,397	6,888	3,744
Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	2,262	559	5,063	3,676
Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	1,161	1,240	3,269	2,815
Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	22,873	15,170	35,831	23,487
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	25,188	12,120	43,042	24,004
Renewable Products | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	4,552	3,637	12,384	8,452
Renewable Products | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	16	0	65	2
Renewable Products | Sephora | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	2,442	2,397	6,888	3,744
Renewable Products | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	933	0	2,162	1,891
Renewable Products | Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	1,161	1,240	3,269	2,815
Renewable Products | Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	20,636	8,483	30,658	15,552
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	990	40,964	6,151	41,082
Licenses and Royalties | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	990	40,964	6,151	41,082
Licenses and Royalties | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	0	40,682	3,750	40,302
Licenses and Royalties | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	990	282	2,401	780
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	3,827	9,610	9,942	11,982
Grants and Collaborations | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	1,590	2,923	4,769	4,047
Grants and Collaborations | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	1,251	2,646	4,269	3,042
Grants and Collaborations | Sephora | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Grants and Collaborations | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	339	277	500	1,005
Grants and Collaborations | Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue		0		0
Grants and Collaborations | Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	$ 2,237	$ 6,687	$ 5,173	$ 7,935

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Revenue Recognition and Contract Assets and Liabilities - Contract Balances (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Revenue from Contract with Customer [Abstract]
Accounts receivable, net	$ 22,029	$ 16,322
Accounts receivable - related party, net	94	3,868
Contract assets	11,724	8,485
Contract assets - related party	1,203	0
Contract assets, noncurrent - related party	0	1,203
Contract liabilities	5,180	1,353
Contract liability, net of current portion	$ 245	$ 1,449

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Revenue Recognition and Contract Assets and Liabilities - Remaining Performance Obligations (Details) $ in Thousands	Jun. 30, 2020 USD ($)
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 138,527
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-07-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 4,849
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period	6 months
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 112,357
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2022-01-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 20,750
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2023-01-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 571
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period

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Related Party Transactions - Related Party Debt (Details) - USD ($)	Jun. 30, 2020	Apr. 29, 2020	Jan. 31, 2020	Dec. 31, 2019
Related Party Transaction [Line Items]
Principal	$ 175,786,000			$ 297,462,000
Change in Fair Value	36,624,000			24,392,000
Net	205,911,000		$ 60,000,000.0	261,772,000
Foris $5 Million Note | Foris notes
Related Party Transaction [Line Items]
Debt instrument, face amount		$ 5,000,000
Related Party Debt
Related Party Transaction [Line Items]
Principal	111,600,000			182,966,000
Unaccreted Debt Discount	(4,212,000)			(14,959,000)
Change in Fair Value	31,510,000			0
Net	138,898,000			168,007,000
Foris notes | Related Party Debt | Foris notes
Related Party Transaction [Line Items]
Principal	55,041,000			115,351,000
Unaccreted Debt Discount	0			(9,516,000)
Change in Fair Value	31,510,000			0
Net	86,551,000			105,835,000
DSM International B.V. | Related Party Debt | DSM notes
Related Party Transaction [Line Items]
Principal	33,000,000			33,000,000
Unaccreted Debt Discount	(3,557,000)			(4,621,000)
Change in Fair Value	0			0
Net	29,443,000			28,379,000
Naxyris note | Related Party Debt | Naxyris note
Related Party Transaction [Line Items]
Principal	23,559,000			24,437,000
Unaccreted Debt Discount	(655,000)			(822,000)
Change in Fair Value	0			0
Net	22,904,000			23,615,000
Total | Related Party Debt | 2014 Rule 144A convertible notes
Related Party Transaction [Line Items]
Principal	0			10,178,000
Unaccreted Debt Discount	0			0
Change in Fair Value	0			0
Net	$ 0			$ 10,178,000

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Related Party Transactions - Additional Information (Details) - shares	Jun. 01, 2020	Mar. 11, 2020
Series E Convertible Preferred Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)	102,156
Foris notes
Related Party Transaction [Line Items]
Issuance of common stock subsequent to exercise of common stock rights warrant in previous period - related party (in shares)		5,226,481
Foris notes | Series E Convertible Preferred Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)	30,000
Vivo Capital LLC | Series E Convertible Preferred Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)	8,932.32
Vivo Capital LLC | Series E Convertible Common Stock
Related Party Transaction [Line Items]
Number of shares issued in sale of stock (in shares)	3,689,225

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Related Party Transactions - Related Party Accounts Receivable (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Related Party Transaction [Line Items]
Due to related parties, current	$ 0	$ 18,492
DSM International B.V. | Accounts receivable - related party
Related Party Transaction [Line Items]
Accounts receivable, unbilled, related party	94	3,868
DSM International B.V. | Contract assets - related party
Related Party Transaction [Line Items]
Accounts receivable, unbilled, related party	1,203	0
DSM International B.V. | Contract assets, noncurrent - related party
Related Party Transaction [Line Items]
Accounts receivable, unbilled, related party	0	1,203
DSM International B.V. | Accounts payable
Related Party Transaction [Line Items]
Due to related parties, current	$ 5,677	$ 13,957

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Stock-based Compensation - Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity (Details) $ / shares in Units, $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2020 USD ($) $ / shares shares	Dec. 31, 2019 USD ($) $ / shares shares
Share-based Payment Arrangement [Abstract]
Outstanding, beginning balance (in shares) | shares	5,620,419
Outstanding, weighted average exercise price (in dollars per share) | $ / shares	$ 10.27
Outstanding, weighted average remaining contractual life	7 years 6 months	7 years 9 months 18 days
Outstanding, aggregate intrinsic value, in thousands | $	$ 542	$ 24
Granted (in shares) | shares	80,507
Granted, weighted average grant-date fair value (in dollars per share) | $ / shares	$ 2.85
Exercised (in shares) | shares	(5,227)
Exercised, weighted average grant-date fair value (in dollars per share) | $ / shares	$ 2.99
Forfeited or expired (in shares) | shares	(216,365)
Forfeited or expired, weighted average grant-date fair value (in dollars per share) | $ / shares	$ 43.33
Outstanding, ending balance (in shares) | shares	5,479,334	5,620,419
Outstanding, weighted average exercise price (in dollars per share) | $ / shares	$ 8.86	$ 10.27
Vested or expected to vest (in shares) | shares	4,904,654
Vested or expected to vest, weighted average grant-date fair value (in dollars per share) | $ / shares	$ 9.31
Vested or expected to vest, weighted average remaining contractual life	7 years 6 months
Vested or expected to vest, aggregate intrinsic value, in thousands | $	$ 518
Exercisable (in shares) | shares	1,445,710
Exercisable, weighted average grant-date fair value (in dollars per share) | $ / shares	$ 19.65
Exercisable, weighted average remaining contractual life	6 years 2 months 12 days
Exercisable, aggregate intrinsic value, in thousands | $	$ 278

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Stock-based Compensation - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity (Details) - Restricted Stock Units (RSUs) - $ / shares	6 Months Ended	12 Months Ended
	Jun. 30, 2020	Dec. 31, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding, RSUs (in shares)	5,782,651
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 4.77
Outstanding, weighted average remaining contractual life	1 year 4 months 24 days	1 year 8 months 12 days
Awarded, RSUs (in shares)	410,899
Awarded, weighted average grant-date fair value (in dollars per share)	$ 2.89
RSUs released (in shares)	(1,249,075)
RSUs released, weighted average grant-date fair value (in dollars per share)	$ 4.83
RSUs forfeited (in shares)	(476,209)
RSUs forfeited, weighted average grant-date fair value (in dollars per share)	$ 4.39
Outstanding, RSUs (in shares)	4,468,266	5,782,651
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 4.61	$ 4.77
Vested or expected to vest (in shares)	4,089,810
Vested or expected to vest, weighted average grant-date fair value (in dollars per share)	$ 4.63
Vested or expected to vest, weighted average remaining contractual life	1 year 3 months 18 days

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Stock-based Compensation - Employee Service Share-based Compensation, Allocation of Recognized Period Costs (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	$ 2,931	$ 3,375	$ 6,435	$ 6,827
Research and development
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	781	676	1,846	1,339
Sales, general and administrative
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	$ 2,150	$ 2,699	$ 4,589	$ 5,488

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Stock-based Compensation - Additional Information (Details) - USD ($) $ in Millions	6 Months Ended
	Jun. 30, 2020	May 31, 2020	Dec. 31, 2019	Jan. 01, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding balance (in shares)			117,742,677
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation expense related to stock options and RSUs	$ 20.1
Weighted-average period	2 years 1 month 6 days
Equity Incentive Plan, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Automatic annual increase available for grant and issuance (in shares)				5,887,133
Automatic annual increase in shares available for grant and issuance, percentage of outstanding stock			0.50%	5.00%
Automatic annual increase reserved for issuance (in shares)				588,713
2020 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant (in shares)		9,896,751

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Subsequent Events (Details) - Second Amendment to Ginkgo Note and Partnership Agreement - Subsequent Event - USD ($) $ in Millions	Aug. 07, 2020	Aug. 06, 2020
Subsequent Event [Line Items]
Debt instrument, interest rate, stated percentage	9.00%	12.00%
Debt Instrument, Redemption, Period One
Subsequent Event [Line Items]
Debt Instrument, Periodic Payment	$ 2.1
Debt Instrument, Redemption, Period Two
Subsequent Event [Line Items]
Debt Instrument, Periodic Payment	9.8
Debt Instrument, Redemption, Period Three
Subsequent Event [Line Items]
Debt Instrument, Periodic Payment	$ 10.4

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Label	Element	Value
Accounting Standards Update [Extensible List]	us-gaap_AccountingStandardsUpdateExtensibleList	us-gaap:AccountingStandardsUpdate201711Member