Amyris (AMRSQ) 10-Q 12 Nov 19 2019 Q3 Quarterly report Financial data

Document And Entity Information

Document And Entity Information - shares	9 Months Ended
	Sep. 30, 2019	Oct. 31, 2019
Document And Entity Information
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		105,502,887
Document Type	10-Q
Document Period End Date	Sep. 30, 2019
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q3
Amendment Flag	false

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 1,632	$ 45,353
Restricted cash	476	741
Accounts receivable, net of allowance of $116 and $642	17,072	16,003
Accounts receivable - related party, net of allowance of $21 and $0	3,692	1,349
Contract assets	2,567	0
Accounts receivable, unbilled - related party	0	8,021
Inventories	15,944	9,693
Deferred cost of products sold - related party	968	489
Prepaid expenses and other current assets	12,849	10,566
Total current assets	55,200	92,215
Property, plant and equipment, net	24,436	19,756
Accounts receivable, unbilled, noncurrent - related party	1,203	1,203
Deferred cost of products sold, noncurrent - related party	15,894	2,828
Restricted cash, noncurrent	960	960
Recoverable taxes from Brazilian government entities	2,866	3,005
Right-of-use assets under leases	21,936
Other assets	5,620	7,958
Total assets	128,115	127,925
Current liabilities:
Accounts payable	24,925	26,844
Accrued and other current liabilities	42,686	28,979
Lease liabilities	7,973
Contract liabilities	4,737	8,236
Debt, current portion (instrument measured at fair value $63,152 and $57,918, respectively)	65,495	124,010
Related party debt, current portion	13,221	23,667
Total current liabilities	159,037	211,736
Long-term debt, net of current portion	20,045	43,331
Related party debt, net of current portion	105,482	18,689
Lease liabilities, net of current portion	15,472
Derivative liabilities	9,357	42,796
Other noncurrent liabilities	26,801	23,192
Total liabilities	336,194	339,744
Commitments and contingencies
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of September 30, 2019 and December 31, 2018, and 14,656 shares issued and outstanding as of September 30, 2019 and December 31, 2018, respectively	0	0
Common stock - $0.0001 par value, 250,000,000 shares authorized as of September 30, 2019 and December 31, 2018; 103,400,207 and 76,564,829 shares issued and outstanding as of September 30, 2019 and December 31, 2018, respectively	10	8
Additional paid-in capital	1,507,298	1,346,996
Accumulated other comprehensive loss	(44,545)	(43,343)
Accumulated deficit	(1,676,779)	(1,521,417)
Total Amyris, Inc. stockholders’ deficit	(214,016)	(217,756)
Noncontrolling interest	937	937
Total stockholders' deficit	(213,079)	(216,819)
Total liabilities, mezzanine equity and stockholders' deficit	128,115	127,925
Contingently redeemable common stock
Current liabilities:
Contingently redeemable common stock	$ 5,000	$ 5,000

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parentheticals) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Accounts receivable, allowance	$ 116	$ 642
Accounts receivable, allowance, related parties	21	0
Fair value of debt	$ 63,152	$ 57,918
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)	14,656	14,656
Preferred stock, shares outstanding (in shares)	14,656	14,656
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (in shares)	250,000,000	250,000,000
Common stock, shares issued (in shares)	103,400,207	76,564,829
Common stock, shares outstanding (in shares)	103,400,207	76,564,829

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues [Abstract]
Revenue	$ 34,953	$ 14,315	$ 112,021	$ 47,233
Cost and operating expenses:
Cost of products sold	20,654	8,574	53,482	20,423
Research and development	19,032	16,445	56,093	49,939
Sales, general and administrative	33,341	27,239	92,456	64,793
Total cost and operating expenses	73,027	52,258	202,031	135,155
Loss from operations	(38,074)	(37,943)	(90,010)	(87,922)
Other income (expense):
Loss on divestiture	0	0	0	(1,778)
Interest expense	(16,857)	(9,180)	(44,608)	(28,738)
Loss from change in fair value of derivative instruments	(398)	(24,797)	(2,437)	(61,164)
Loss from change in fair value of debt	(2,055)	0	(18,629)	0
Loss upon extinguishment of debt	(2,721)	0	(8,596)	(26)
Other income (expense), net	1,076	(2,533)	920	(2,009)
Total other expense, net	(20,955)	(36,510)	(73,350)	(93,715)
Loss before income taxes	(59,029)	(74,453)	(163,360)	(181,637)
Provision for income taxes	(533)	0	(533)	0
Net loss attributable to Amyris, Inc.	(59,562)	(74,453)	(163,893)	(181,637)
Less: deemed dividend to preferred shareholder on issuance and modification of common stock warrants	0	0	(34,964)	0
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D preferred stock	0	(6,852)	0	(6,852)
Less: losses allocated to participating securities	1,655	4,491	6,233	12,824
Net loss attributable to Amyris, Inc. common stockholders	$ (57,907)	$ (76,814)	$ (192,624)	$ (175,665)
Loss per share attributable to common stockholders, basic and diluted	$ (0.56)	$ (1.26)	$ (2.11)	$ (3.15)
Weighted-average shares of common stock outstanding used in computing loss per share of common stock, basic and diluted	103,449,612	60,966,071	91,344,150	55,735,571
Product
Revenues [Abstract]
Revenue	$ 17,363	$ 9,639	$ 41,367	$ 21,467
Licenses and Royalties
Revenues [Abstract]
Revenue	2,305	142	43,387	7,584
Grants and Collaborations
Revenues [Abstract]
Revenue	$ 15,285	$ 4,534	$ 27,267	$ 18,182

Condensed Consolidated Statem_2

Condensed Consolidated Statements of Operations (Parentheticals) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues, related party	$ 844	$ 1,171	$ 44,190	$ 11,341
Product
Revenues, related party	0	13	2	308
Licenses and Royalties
Revenues, related party	0	(39)	40,302	7,366
Grants and Collaborations
Revenues, related party	$ 844	$ 1,197	$ 3,886	$ 3,667

Condensed Consolidated Statem_3

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Comprehensive loss:
Net loss attributable to Amyris, Inc.	$ (59,562)	$ (74,453)	$ (163,893)	$ (181,637)
Foreign currency translation adjustment	(1,066)	(194)	(1,202)	(1,158)
Comprehensive loss attributable to Amyris, Inc.	$ (60,628)	$ (74,647)	$ (165,095)	$ (182,795)

Consolidated Statements of Stoc

Consolidated Statements of Stockholders' Deficit and Mezzanine Equity Consolidated Statements of Stockholders' Deficit and Mezzanine Equity - USD ($) $ in Thousands	Total	Preferred Stock	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Noncontrolling Interest	Mezzanine Equity - Common Stock
Balance (in shares) at Dec. 31, 2017		22,171,000	45,637,433,000
Balance at Dec. 31, 2017	$ (217,088)	$ 0	$ 5	$ 1,114,546	$ (42,156)	$ (1,290,420)	$ 937	$ 5,000
Issuance of common stock upon exercise of warrants (in shares)			162,392,000
Issuance of common stock upon exercise of warrants	835			835
Issuance of common stock upon exercise of stock options (in shares)			7,004,000
Issuance of common stock upon exercise of stock options	81			81
Issuance of common stock upon restricted stock settlement (in shares)			30,489,000
Issuance of common stock upon restricted stock settlement	(66)			(66)
Stock-based compensation	1,278			1,278
Other	93			93
Foreign currency translation adjustment	(137)				(137)
Issuance of common stock in private placement, net of issuance costs (in shares)			13,529,000
Issuance of common stock in private placement, net of issuance costs	92			92
Net loss	(92,802)					(92,802)
Balance (in shares) at Mar. 31, 2018		22,171,000	45,850,847,000
Balance at Mar. 31, 2018	(308,517)	$ 0	$ 5	1,116,859	(42,293)	(1,384,025)	937	5,000
Issuance of common stock upon ESPP purchase (in shares)			87,768,000
Issuance of common stock upon ESPP purchase	269			269
Issuance of common stock upon exercise of warrants (in shares)			3,638,938,000
Issuance of common stock upon exercise of warrants	24,788			24,788
Issuance of common stock upon exercise of stock options (in shares)			36,051,000
Issuance of common stock upon exercise of stock options	195			195
Issuance of common stock upon restricted stock settlement (in shares)			85,130,000
Issuance of common stock upon restricted stock settlement	(147)			(147)
Issuance of warrants in connection with debt accounted for at fair value	9,438			9,438
Stock-based compensation	1,900			1,900
Foreign currency translation adjustment	(827)				(827)
Issuance of common stock in private placement, net of issuance costs (in shares)			191,639,000
Issuance of common stock in private placement, net of issuance costs	$ 1,323			1,323
Issuance of common stock upon conversion of preferred stock (in shares)	0	(2,837,000)	450,307,000
Net loss	$ (14,382)					(14,382)
Balance (in shares) at Jun. 30, 2018		19,334,000	50,340,680,000
Balance at Jun. 30, 2018	(285,960)	$ 0	$ 5	1,154,625	(43,120)	(1,398,407)	937	5,000
Issuance of common stock upon exercise of warrants (in shares)			12,558,721,000
Issuance of common stock upon exercise of warrants	80,979		$ 1	80,978
Issuance of common stock upon exercise of stock options (in shares)			18,695,000
Issuance of common stock upon exercise of stock options	53			53
Issuance of common stock upon restricted stock settlement (in shares)			74,176,000
Issuance of common stock upon restricted stock settlement	(11)			(11)
Issuance of warrants in connection with debt accounted for at fair value	30,097			30,097
Stock-based compensation	2,937			2,937
Foreign currency translation adjustment	$ (194)				(194)
Issuance of common stock upon conversion of preferred stock (in shares)	0	(4,678,000)	1,098,173,000
Net loss	$ (74,453)					(74,453)
Balance (in shares) at Sep. 30, 2018		14,656,000	64,090,445,000
Balance at Sep. 30, 2018	$ (246,552)	$ 0	$ 6	1,268,679	(43,314)	(1,472,860)	937	5,000
Balance (in shares) at Dec. 31, 2018	76,564,829	14,656,000	76,564,829,000
Balance at Dec. 31, 2018	$ (216,819)	$ 0	$ 8	1,346,996	(43,343)	(1,521,417)	937	5,000
Issuance of common stock upon exercise of warrants (in shares)	479,751		450,568,000
Issuance of common stock upon exercise of warrants	$ 1			1
Issuance of common stock upon exercise of stock options (in shares)			3,612,000
Issuance of common stock upon exercise of stock options	13			13
Issuance of common stock upon restricted stock settlement (in shares)			191,672,000
Issuance of common stock upon restricted stock settlement	(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
Net loss	(66,243)					(66,243)
Balance (in shares) at Mar. 31, 2019		14,656,000	77,210,681,000
Balance at Mar. 31, 2019	$ (237,200)	$ 0	$ 8	1,383,363	(42,379)	(1,579,129)	937	5,000
Balance (in shares) at Dec. 31, 2018	76,564,829	14,656,000	76,564,829,000
Balance at Dec. 31, 2018	$ (216,819)	$ 0	$ 8	1,346,996	(43,343)	(1,521,417)	937	5,000
Issuance of common stock upon exercise of warrants (in shares)	2,500,000
Issuance of common stock upon exercise of stock options (in shares)	3,612
Balance (in shares) at Sep. 30, 2019		14,656,000	103,400,207,000
Balance at Sep. 30, 2019	$ (213,079)	$ 0	$ 10	1,507,298	(44,545)	(1,676,779)	937	5,000
Balance (in shares) at Mar. 31, 2019		14,656,000	77,210,681,000
Balance at Mar. 31, 2019	(237,200)	$ 0	$ 8	1,383,363	(42,379)	(1,579,129)	937	5,000
Issuance of common stock in private placement (in shares)			3,610,944,000
Issuance of common stock in private placement, net of issuance costs	14,221		$ 0	14,221
Issuance of common stock in private placement - related party (in shares)			10,478,338,000
Issuance of common stock in private placement - related party	39,500		$ 1	39,499
Issuance of common stock upon conversion of debt (in shares)			7,101,468,000
Issuance of common stock upon conversion of debt	34,651		$ 1	34,650
Issuance of common stock upon ESPP purchase (in shares)			131,460,000
Issuance of common stock upon ESPP purchase	$ 464			464
Issuance of common stock upon exercise of warrants (in shares)	2,170,231		2,064,606,000
Issuance of common stock upon exercise of warrants	$ 0			0
Issuance of common stock upon restricted stock settlement (in shares)			589,241,000
Issuance of common stock upon restricted stock settlement	(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
Other	(238)			(238)
Foreign currency translation adjustment	(1,100)				(1,100)
Net loss	(38,088)					(38,088)
Balance (in shares) at Jun. 30, 2019		14,656,000	101,186,738,000
Balance at Jun. 30, 2019	(180,334)	$ 0	$ 10	1,479,415	(43,479)	(1,617,217)	937	5,000
Issuance of common stock and warrants upon conversion of debt (in shares)			1,767,632,000
Issuance of common stock and warrants upon conversion of debt	7,829			7,829
Issuance of common stock upon restricted stock settlement (in shares)			445,837,000
Issuance of common stock upon restricted stock settlement	(271)			(271)
Issuance of warrants in connection with related party debt issuance	13,279			13,279
Issuance of warrants in connection with related party debt modification	2,882			2,882
Issuance of warrants in connection with debt accounted for at fair value	930			930
Stock-based compensation	3,234			3,234
Foreign currency translation adjustment	(1,066)				(1,066)
Net loss	(59,562)					(59,562)
Balance (in shares) at Sep. 30, 2019		14,656,000	103,400,207,000
Balance at Sep. 30, 2019	$ (213,079)	$ 0	$ 10	$ 1,507,298	$ (44,545)	$ (1,676,779)	$ 937	$ 5,000

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Net Cash Provided by (Used in) Operating Activities [Abstract]
Net loss	$ (163,893)	$ (181,637)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss from change in fair value of debt	18,629	0
Stock-based compensation	10,061	6,115
Amortization of debt discount	9,701	12,244
Amortization of right-of-use assets under operating leases	10,237	0
Loss upon extinguishment of debt	8,596	26
Expense for warrants issued for covenant waivers	5,358	0
Depreciation and amortization	2,691	3,957
Loss from change in fair value of derivative liability	2,437	61,164
Impairment of property, plant and equipment	1,263	0
Loss on disposal of property, plant and equipment	122	943
Gain on foreign currency exchange rates	(361)	(1,132)
Changes in assets and liabilities:
Accounts receivable	(3,482)	2,226
Contract assets	(2,567)	0
Accounts receivable, unbilled - related party	8,021	7,457
Inventories	(6,609)	(890)
Deferred cost of products sold - related party	(13,545)	0
Prepaid expenses and other assets	(4,445)	(2,387)
Accounts payable	(2,050)	(4,795)
Accrued and other liabilities	22,310	8,348
Lease liabilities	(12,453)	0
Contract liabilities	3,488	1,086
Net cash used in operating activities	(113,467)	(89,447)
Net cash used in investing activities
Purchases of property, plant and equipment	(9,013)	(6,362)
Purchases of property, plant and equipment	(9,013)	(6,362)
Cash flows from financing activities
Proceeds from issuance of debt, net of issuance costs	89,217	36,643
Proceeds from issuance of common stock in private placements, net of issuance costs - related party	39,500	0
Proceeds from issuance of common stock in private placements, net of issuance costs	14,221	1,415
Proceeds from issuance of common stock upon ESPP purchase	464	269
Proceeds from exercises of common stock options	13	329
Proceeds from exercises of warrants	1	60,544
Principal payments on debt	(63,675)	(41,970)
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(627)	(224)
Principal payments on financing leases	(372)	(846)
Net cash provided by financing activities	78,742	56,160
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(248)	(101)
Net decrease in cash, cash equivalents and restricted cash	(43,986)	(39,750)
Cash, cash equivalents and restricted cash at beginning of period	47,054	61,012
Cash, cash equivalents and restricted cash at end of the period	3,068	21,262
Cash and cash equivalents	1,632	19,045
Restricted cash, current	476	1,258
Restricted cash, noncurrent	960	959
Total cash, cash equivalents and restricted cash	47,054	61,012
Supplemental disclosures of cash flow information:
Cash paid for interest	10,390	14,783
Supplemental disclosures of non-cash investing and financing activities:
Right-of-use assets under operating leases recorded upon adoption of ASC 842	29,713	0
Lease liabilities recorded upon adoption of ASC 842	33,552	0
Cumulative effect of change in accounting principle	41,043	0
Issuance of common stock upon conversion of convertible notes	42,479	0
Fair value of warrants recorded as debt discount in connection with debt issuances - related party	16,155	0
Fair value of warrants recorded as debt discount in connection with debt issuances	8,965	0
Acquisition of right-of-use assets under operating leases	2,361	0
Accrued interest added to debt principal	986	2,029
Fair value of warrants recorded as debt discount in connection with debt modification	398	0
Acquisition of property, plant and equipment under accounts payable, accrued liabilities and notes payable	134	783
Derecognition of derivative liabilities upon exercise of warrants	0	85,912
Financing of equipment	$ 0	$ 764

Basis of Presentation and Summa

Basis of Presentation and Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2019
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 industrial biotechnology company that applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness, Clean Beauty, and Flavor & Fragrance markets. The Company's proven technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. The Company's biotechnology platform and industrial fermentation process replace existing complex and expensive manufacturing processes. The Company has successfully used its technology to develop and produce 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/A for the year ended December 31, 2018 (the 2018 Form 10-K/A), from which the condensed consolidated balance sheet as of December 31, 2018 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, since they are interim statements, the accompanying 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 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. If such conditions are not satisfied by December 31, 2019, the joint venture will automatically terminate. However, the termination date can be extended by mutual agreement of the parties. 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. Upon the closing of the joint venture, each party will make an initial capital contribution to the joint venture of 2.5 million Brazilian Real ( R$2.5 million ) and the joint venture will be owned 50% by the Company and 50% by Raizen. Within 60 days of the formation, the parties will make an aggregate cash contribution to the joint venture of U.S. $9.0 million to purchase certain fixed assets currently owned by the Company and located at the site of the Company’s former joint venture with Sao Martinho S.A. in Pradopolis, Brazil for U.S. $3.0 million , as well as to pay for costs related to the removal and transportation of such assets to the site of the Sweetener Plant. In addition, within six months of the formation, the Company will contribute to the joint venture its existing supply agreements related to its alternative sweetener product, subject to certain exceptions, in exchange for shares of dividend-bearing preferred stock in the joint venture, which will be entitled, for a period of 10 years commencing from the initial date of operation of the Sweetener Plant, to certain priority fixed cumulative dividends including, in the event that certain technological and economic milestones are met in any fiscal quarter, a percentage of the operating cash flow of the joint venture in such quarter. After the formation of the joint venture, subject to certain exceptions, the parties will not conduct activities similar or identical to the joint venture except through the joint venture. In the event that certain technological and economic milestones are not met in any fiscal year beginning with the third fiscal year after formation of the joint venture and ending with the seventh fiscal year after formation of the joint venture, Raizen shall have the right to sell all of its shares in the joint venture to the Company at a price per share equal to the higher of the book value and the amount of Raizen’s investments in the joint venture, as adjusted for Raizen’s cost of capital. 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. 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 for at least the next 12 months following the issuance of these condensed consolidated financial statements. As of September 30, 2019 , the Company had negative working capital of $103.8 million (compared to negative working capital of $119.5 million as of December 31, 2018 ), and an accumulated deficit of $1.7 billion . As of September 30, 2019 , the Company's debt (including related party debt), net of debt discount of $37.5 million , totaled $204.2 million , of which $78.7 million is classified as current. The Company's debt service obligations through September 30, 2020 are $109.3 million , including $27.4 million of anticipated cash interest payments. 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 and cross-default clauses. A failure to comply with, or cure non-compliance events or obtain waivers for covenant violations, 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 such indebtedness. If such indebtedness is accelerated, it would generally constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of the Company's outstanding indebtedness. On September 16, 2019, the Company failed to pay an aggregate of $63.6 million of outstanding principal and accrued interest on the Second Exchange Note (see Note 4, “Debt”), when due. Such failure resulted in an event of default under the Second Exchange Note and also triggered cross-defaults under other debt instruments of the Company with an aggregate principal amount of approximately $148.7 million , which permitted the holders of such indebtedness to accelerate the amounts owing under such instruments. The Company subsequently received waivers from all the holders of the $148.7 million principal amount of such debt instruments to waive their right to accelerate. As a result, the indebtedness with respect to which the Company has obtained such waivers continues to be classified as long-term debt on the Company’s balance sheet. The indebtedness reflected by the Second Exchange Note continues to be classified as a current liability on the Company’s balance sheet. On November 8, 2019, the Company entered into a Securities Exchange Agreement with certain private investors (the “Investors”), pursuant to which, upon the purchase by the Investors of the Second Exchange Note, the Second Exchange Note would be exchanged for new senior convertible notes with an aggregate principal amount of $66.0 million (see Note 12, “Subsequent Events”). In connection with the entry into the Securities Exchange Agreement, (i) the holder of the Second Exchange Note and the Investors entered into a Securities Purchase Agreement providing for the purchase by the Investors of the Second Exchange Note and (ii) the Company and the holder of the Second Exchange Note entered into an agreement by which such holder agreed to immediately dismiss its complaint against the Company (see Note 8, “Commitments and Contingencies”) with prejudice upon the purchase of the Second Exchange Note by the Investors. Cash and cash equivalents of $1.6 million as of September 30, 2019 are not sufficient to fund expected future negative cash flows from operations and cash debt service obligations through September 30, 2020 . These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date that 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 raise additional capital through equity offerings or debt financings and extend or refinance existing debt maturities by restructuring a majority of its convertible debt, which is uncertain and outside the control of the Company. Further, the Company's operating plan for the 12 months ending September 30, 2020 contemplates a significant reduction in its net operating cash outflows as compared to the year ended December 31, 2018 , resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) significantly increased cash inflows from grants and collaborations, and (iii) reduced production costs as a result of manufacturing and technical developments. If the Company is unable to complete these actions, it expects to be unable to meet its operating cash flow needs and its obligations under its existing debt facilities. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and it may be required 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 the Company receives for its assets in liquidation or dissolution could be significantly lower than the value reflected in these condensed consolidated financial statements. Significant Accounting Policies Note 1, "Basis of Presentation and Summary of Significant Accounting Policies", to the audited consolidated financial statements in the 2018 Form 10-K/A 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 three and nine months ended September 30, 2019 , except for the Company's adoption of these accounting standards on January 1, 2019: • Accounting Standards Codification (ASC) Topic 842 (ASC 842), Leases; and • ASU 2017-11, Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging (Topic 815): Accounting for Certain Financial Instruments with Down Round Features. Revenue Recognition The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer and recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does not incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred. The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators among others when determining whether it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does not meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis. The Company’s significant contracts and contractual terms with its customers are presented in Note 10, "Revenue Recognition" in Part II, Item 8 of the 2018 Form 10-K/A. The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. The Company’s renewable products are delivered to customers from the Company’s facilities with shipping terms typically specifying F.O.B. shipping point. Performance Obligations A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts may contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis. The following is a description of the principal goods and services from which the Company generates revenue. Renewable Product Sales Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the first transportation carrier. The Company, on occasion, may recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does not have the ability to direct the product to a different customer. It is at this point that the Company has the right to payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do not include rights of return. Returns are accepted only if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a two-year assurance-type warranty to replace squalane products that do not meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated. Licenses and Royalties Licensing of Intellectual Property: When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized. Royalties from Licensing of Intellectual Property: The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits. When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception and revenue is estimated and recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends. When the Company’s intellectual property license is not the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts. Grants and Collaborative Research and Development Services Collaborative Research and Development Services: The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaborators with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include one or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits. Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Generally, revenue is recognized using an input-based measure of progress towards the satisfaction of the performance obligations, which can be based on labor hours expended or time-based in proportion to the estimated total project effort or total projected time to complete. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. Certain performance obligations are associated with milestones agreed between the Company and its customer. Revenue generated from the performance of services in accordance with these milestones is recognized upon confirmation from the customer that the milestone has been achieved. In these cases, amounts recognized are constrained to the amount of consideration received upon achievement of the milestone. The Company generally invoices its collaborators on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Contract liability arises from amounts received in advance of performing the research and development activities and is recognized as revenue in future periods as the performance obligations are satisfied. Grants: The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements. The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. For descriptions of the Company's other significant accounting policies, see the 2018 Form 10-K/A. Accounting Standards or Updates Recently Adopted In the nine months ended September 30, 2019 , the Company adopted these accounting standards or updates: Leases In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842). The standard requires the recognition of lease liabilities and right-of-use (ROU) assets on the balance sheet arising from lease transactions at the lease commencement date and the disclosure of key information about leasing arrangements. In July 2018, the FASB issued ASU 2018-11, Leases (Topic 842): Targeted Improvements , which provided entities the option to use the effective date as the date of initial application on transition to the new guidance. The Company elected this transition method, and as a result, the Company did not adjust comparative information for prior periods. The Company elected certain additional practical expedients permitted by the new guidance allowing the Company to carry forward historical accounting related to lease identification and classification for existing leases upon adoption. The Company adopted this standard on January 1, 2019 using the modified retrospective approach and elected the package of practical expedients permitted under transition guidance, which allowed the Company to carry forward its historical assessments of: (1) whether contracts are or contain leases, (2) lease classification and (3) initial direct costs, where applicable. The Company did not elect the practical expedient allowing the use-of-hindsight which would require the Company to reassess the lease term of its leases based on all facts and circumstances through the effective date and did not elect the practical expedient pertaining to land easements as this is not applicable to the Company’s current contracts. The Company elected the post-transition practical expedient to not separate lease components from non-lease components for all leases of manufacturing equipment. The Company also elected a policy of not recording leases on its condensed consolidated balance sheets when the leases have a term of 12 months or less and the Company is not reasonably certain to elect an option to purchase the leased asset. The adoption of this standard had the net effect of increasing both assets and liabilities by $25.7 million , after considering prepaid and other current and noncurrent assets previously recorded on the condensed consolidated balance sheet, but did not have a material impact on the condensed consolidated statements of operations or cash flows. The most significant impact relates to (1) the recognition of new ROU assets and lease liabilities on the balance sheet for the Company's operating leases; and (2) providing significant new disclosures about the Company's leasing activities. Upon adoption, the Company recognized operating lease liabilities of $33.6 million , based on the present value of the remaining minimum rental payments under current leasing standards for existing operating leases. The Company also recognized ROU assets of $29.7 million , which represents the operating lease liability, adjusted for prepaid expenses and deferred rent. The difference between the operating lease ROU assets and lease liabilities reflects the net of advanced rent payments and deferred rent balances that were derecognized at the time of adoption. Financial Instruments with "Down Round" Features In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging (Topic 815): Accounting for Certain Financial Instruments with Down Round Features . The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update became effective in the first quarter of fiscal year 2019, and the Company adopted the standard using a modified retrospective approach. Since the adoption of ASU 2017-11 would have classified the warrants effected as equity at inception, the cumulative-effect adjustment should (i) record the issuance date value of the warrants as if they had been equity classified at the issuance date, (ii) reverse the effects of changes in the fair value of the warrants that had been recorded in the statement of operations of each period, and (iii) eliminate the derivative liabilities from the balance sheet. Upon adoption, the Company (i) recorded an increase of $32.5 million to additional paid-in capital, (ii) recorded a decrease to accumulated deficit of $8.5 million and (iii) decreased the warrant liability by $41.0 million . Recent Accounting Standards or Updates Not Yet Effective 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. The accounting standard update will be effective beginning 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 Company is in the initial stages of evaluating the impact of the standard on its condensed consolidated financial statements. Collaborative Revenue Arrangements In

Balance Sheet Details

Balance Sheet Details	9 Months Ended
	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Balance Sheet Details	Balance Sheet Details Inventories (In thousands) September 30, 2019 December 31, 2018 Raw materials $ 5,753 $ 3,901 Work-in-process 2,243 539 Finished goods 7,948 5,253 Inventories $ 15,944 $ 9,693 Deferred cost of products sold - related party (In thousands) September 30, 2019 December 31, 2018 Deferred cost of products sold - related party $ 968 $ 489 Deferred cost of products sold, noncurrent - related party 15,894 2,828 Total $ 16,862 $ 3,317 In November 2018, the Company amended the supply agreement with DSM to secure capacity at the Brotas 1 facility for sweetener production through 2022. See Note 10, “Revenue Recognition” in Part II, Item 8 of the 2018 Form 10-K/A for information regarding the November 2018 Supply Agreement Amendment. The supply agreement was included as an element of a combined transaction with DSM, which resulted in a fair value allocation of $24.4 million to the manufacturing capacity fees, of which $3.3 million was recorded as deferred cost of products sold at December 31, 2018. During the nine months ended September 30, 2019 , the Company paid an additional $14.1 million of reservation capacity fees, which was recorded as additional deferred cost of products sold. The remaining $6.9 million capacity fees will be recorded as deferred cost of products sold in the period the additional payments are made to DSM. The 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 sold over the five -year term of the supply agreement. Each quarter, the Company evaluates its future production volumes and adjusts the unit cost to be expensed over the remaining estimated production volume. During the three and nine months ended September 30, 2019 , the Company expensed $0.4 million and $0.5 million , respectively, of the deferred cost of products sold asset to cost of products sold. The deferred cost of products sold asset is evaluated for recoverability at each period end. Prepaid expenses and other current assets (In thousands) September 30, 2019 December 31, 2018 Prepayments, advances and deposits $ 3,706 $ 5,644 Recoverable taxes from Brazilian government entities 3,270 631 Other 5,873 4,291 Total prepaid expenses and other current assets $ 12,849 $ 10,566 Property, Plant and Equipment, Net (In thousands) September 30, 2019 December 31, 2018 Machinery and equipment $ 47,960 $ 43,713 Leasehold improvements 41,152 39,922 Computers and software 10,305 9,987 Furniture and office equipment, vehicles and land 3,330 3,016 Construction in progress 650 1,749 103,397 98,387 Less: accumulated depreciation and amortization (78,961 ) (78,631 ) Property, plant and equipment, net $ 24,436 $ 19,756 During the three and nine months ended September 30, 2019 and 2018 , the Company capitalized the following amounts of internal labor costs required to automate, integrate and ready certain laboratory and plant equipment for its intended use: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2019 2018 2019 2018 Capitalized internal labor $ — $ 501 $ 320 $ 2,083 During the three and nine months ended September 30, 2019 and 2018 , Depreciation and amortization expense, including amortization of assets under capital leases, was as follows: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2019 2018 2019 2018 Depreciation and amortization expense $ 969 $ 1,013 $ 2,691 $ 3,957 Leases Operating Leases The Company has entered into operating leases primarily for administrative offices, laboratory equipment and other facilities. The operating leases have remaining terms that range from 1 year 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 September 30, 2019 Consolidated Balance Sheet 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 September 30, 2019 Consolidated Balance Sheet. Based on the present value of the lease payments for the remaining lease term of the Company's existing leases, the Company recognized right-of-use assets of $29.7 million and lease liabilities for operating leases of $33.6 million on January 1, 2019. Operating lease right-of-use assets and liabilities commencing after January 1, 2019 are recognized at commencement date based on the present value of lease payments over the lease term. As of September 30, 2019 , total right-of-use assets and operating lease liabilities were $21.9 million and $23.1 million , respectively. All operating lease expense is recognized on a straight-line basis over the lease term. In the three and nine months ended September 30, 2019 , respectively, the Company recorded $4.7 million and $14.1 million of operating lease amortization that was charged to expense, of which $1.7 million and $5.2 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: Nine Months Ended September 30, 2019 Cash paid for operating lease liabilities, in thousands $ 15,908 Right-of-use assets obtained in exchange for new operating lease obligations (1) $ 32,074 Weighted-average remaining lease term 2.6 Weighted-average discount rate 17.5 % (1) Includes $29.7 million for operating leases existing on January 1, 2019 and $2.4 million for operating leases that commenced during the nine months ended September 30, 2019 . Financing Leases The Company has entered into financing leases primarily for laboratory and computer equipment. Assets purchased under financing leases are included in "Property, plant and equipment, 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. Property, plant and equipment, net includes $2.3 million and $5.0 million of machinery and equipment under financing leases as of September 30, 2019 and December 31, 2018 , respectively. Accumulated amortization of assets under financing leases totaled $1.1 million and $2.3 million as of September 30, 2019 and December 31, 2018 , respectively. Maturities of Financing and Operating Leases Maturities of lease liabilities as of September 30, 2019 were as follows: Years ending December 31: (In thousands) Financing Operating Total Leases 2019 (remaining three months) $ 116 $ 3,346 $ 3,462 2020 198 9,652 9,850 2021 1 7,220 7,221 2022 — 7,392 7,392 2023 — 3,033 3,033 Thereafter — — — Total lease payments 315 30,643 30,958 Less: amount representing interest (8 ) (7,505 ) (7,513 ) Total lease liability $ 307 $ 23,138 $ 23,445 Current lease liability $ 295 $ 7,678 $ 7,973 Noncurrent lease liability 12 15,460 15,472 Total lease liability $ 307 $ 23,138 $ 23,445 Other Assets (In thousands) September 30, 2019 December 31, 2018 Contingent consideration $ 4,286 $ 4,286 Deposits 293 2,465 Other 1,041 1,207 Total other assets $ 5,620 $ 7,958 Accrued and Other Current Liabilities (In thousands) September 30, 2019 December 31, 2018 Accrued interest $ 15,297 $ 3,853 Payroll and related expenses 7,677 9,220 Contract termination fees 5,241 4,092 Ginkgo partnership payments obligation 3,267 2,155 Asset retirement obligation 2,990 3,063 Professional services 2,854 1,173 Tax-related liabilities 2,402 2,139 Other 2,958 3,284 Total accrued and other current liabilities $ 42,686 $ 28,979 Other noncurrent liabilities (In thousands) September 30, 2019 December 31, 2018 Refund liability $ 12,500 $ — Liability for unrecognized tax benefit 7,115 6,582 Ginkgo partnership payments obligation, net of current portion 4,937 6,185 Contract liability, net of current portion (Note 9) 1,449 1,587 Deferred rent, net of current portion (1) — 6,440 Contract termination fees, net of current portion — 1,530 Other 800 868 Total other noncurrent liabilities $ 26,801 $ 23,192 (1) Deferred rent at December 31, 2018 was reclassified to ROU asset upon the adoption on January 1, 2019 of ASC 842, "Leases". In April 2019, the Company assigned the Value Sharing Agreement to DSM. See Note 9, "Revenue Recognition and Contract Assets and Liabilities" 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 of prepaid variable consideration is recorded as a refund liability and represents a stand ready obligation to refund some or all of the $12.5 million prepaid consideration if certain criteria outlined in the assignment agreement is not met before December 2021. The Company will update its assessment of amounts it expects to be entitled to keep at the end of each reporting period, by reducing the refund liability and recording additional license and royalty revenue, as the criterion is met.

Fair Value Measurement

Fair Value Measurement	9 Months Ended
	Sep. 30, 2019
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) September 30, 2019 December 31, 2018 Level 1 Level 2 Level 3 Total Level 1 Level 2 Level 3 Total Liabilities 6% Convertible Notes $ — $ — $ 63,152 $ 63,152 $ — $ — $ 57,918 $ 57,918 Freestanding derivative instruments in connection with the issuance of debt and equity instruments — — 8,325 8,325 — — 42,796 42,796 Embedded derivative instruments in connection with the issuance of debt instruments — — 1,032 1,032 — — — — Total liabilities measured and recorded at fair value $ — $ — $ 72,509 $ 72,509 $ — $ — $ 100,714 $ 100,714 There were no transfers between levels during the periods presented. 6% Convertible Notes The Company issued $60.0 million of 6% Convertible Notes on December 10, 2018 and elected the fair value option of accounting for this instrument. At September 30, 2019 , outstanding principal was $62.8 million , and the fair value was $63.2 million , which was measured at the noteholders’ put option price of 125% of outstanding principal. See Note 4, “Debt” for further information related to this debt instrument and the noteholders’ put option. For the nine months ended September 30, 2019 , the Company recorded a $18.6 million loss from change in fair value of debt in connection with the 6% Convertible Notes, as follows: In thousands Fair value at December 31, 2018 $ 57,918 Less: principal paid (13,395 ) Loss on change in fair value 18,629 Fair value at September 30, 2019 $ 63,152 Derivative Liabilities Recognized in Connection with the Issuance of Debt and Equity 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 and equity instruments – either freestanding or compound embedded – measured at fair value using significant unobservable inputs (Level 3): (In thousands) Equity-related Derivative Liability Debt-related Derivative Liability Total Derivative Liability Balance at December 31, 2018 $ 41,272 $ 1,524 $ 42,796 Derecognition upon adoption of ASU 2017-11 (39,513 ) (1,524 ) (41,037 ) Fair value of derivative liabilities issued during the period — 8,959 8,959 Change in fair value of derivative liabilities 2,039 398 2,437 Derecognition on extinguishment (3,798 ) — (3,798 ) Balance at September 30, 2019 $ — $ 9,357 $ 9,357 As of September 30, 2019 , a $3.8 million derivative liability recorded in connection with the November 2018 Securities Purchase Agreement with DSM was settled and extinguished through a cash payment in April 2019. Also, during the three and nine months ended September 30, 2019 , the Company issued three debt instruments with an embedded mandatory redemption feature and a related freestanding liability classified warrant with conversion rate adjustment and antidilution provisions. See Note 4, “Debt” for a description of the transactions and the initial accounting treatment for these debt related derivatives. There is no current observable market for these types of derivatives and, as such, the Company determined the fair value of the embedded mandatory redemption feature using a probability weighted discounted cash flow model measuring the fair value of the debt instrument both with and without the embedded feature and the freestanding warrant derivative using a Black-Scholes option pricing model. See Note 6, “Stockholders’ Deficit” for information regarding the initial Black-Scholes assumptions use to fair value the freestanding liability warrant. The freestanding liability warrant issued on September 10, 2019 had an initial fair value of $7.9 million and was recorded as a derivative liability and a debt discount. The warrant will be remeasured each reporting period until settled or extinguished with subsequent changes in fair value recorded through the statement of operations as a gain or loss on change in fair value of derivative liabilities. At September 30, 2019 the warrant derivative had a fair value of $8.3 million . The $0.4 million increase in fair value was recorded as a loss on change in fair value of derivative liabilities in the statement of operations during the three and nine months ended September 30, 2019 . The embedded mandatory redemption features were measured using a probability weighted discounted cash flow model to determine if the debt instruments would be called or held at each decision point. Within the model, the following assumption is made: the note will be called early if the change in control redemption value is greater than the holding value. If the note 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 note including the embedded derivative is defined as the "with", and the fair value of each note 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 collective fair value of the three embedded derivatives totaled $1.0 million at issuance date and was recorded as a derivative liability and a debt discount. There has been no change to the collective fair value of the three derivatives from issuance date to September 30, 2019 . Assets and Liabilities Recorded at Carrying Value Financial Assets and Liabilities The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. Loans payable, credit facilities and convertible notes are recorded at carrying value (except for the 6% Convertible Notes, which are recorded at fair value), which is representative of fair value at the date of acquisition. For loans payable and credit facilities recorded at carrying value, the Company estimates fair value using observable market-based inputs (Level 2); for convertible notes, the Company estimates fair value based on rates currently offered for instruments with similar maturities and terms (Level 3). The carrying amount (the total amount of net debt presented on the balance sheet) of the Company's debt at September 30, 2019 , excluding the 6% Convertible Notes that the Company records at fair value, was $141.1 million . The fair value of such debt at September 30, 2019 was $153.8 million 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.

Debt

Debt	9 Months Ended
	Sep. 30, 2019
Debt Disclosure [Abstract]
Debt	Debt Net carrying amounts of debt are as follows: September 30, 2019 December 31, 2018 (In thousands) Principal Unamortized Debt (Discount) Premium Change in Fair Value Net Balance Principal Unamortized Debt (Discount) Premium Change in Fair Value Net Balance Convertible notes payable 6% convertible notes $ 62,825 $ — $ 327 $ 63,152 $ 60,000 $ — $ (2,082 ) $ 57,918 August 2013 financing convertible note — — — — 4,415 (70 ) — 4,345 2015 Rule 144A convertible notes — — — — 37,887 (2,413 ) — 35,474 2014 Rule 144A convertible notes — — — — 24,004 (867 ) — 23,137 62,825 — 327 63,152 126,306 (3,350 ) (2,082 ) 120,874 Related party convertible notes payable 2014 Rule 144A convertible notes 9,705 — — 9,705 24,705 (1,038 ) — 23,667 Loans payable and credit facilities Ginkgo note 12,000 (3,377 ) — 8,623 12,000 (4,047 ) — 7,953 Nikko notes 9,122 (938 ) — 8,184 4,598 (1,047 ) — 3,551 Schottenfeld notes 12,500 (8,151 ) 4,349 — — — — Other loans payable 1,280 — — 1,280 312 — — 312 GACP secured term loan facility — — — — 36,000 (1,349 ) — 34,651 34,902 (12,466 ) — 22,436 52,910 (6,443 ) — 46,467 Related party loans payable Foris secured term loan facility 71,041 (8,829 ) — 62,212 — — — — Foris unsecured note 19,000 (6,681 ) — 12,319 — — — — DSM notes 33,000 (5,135 ) — 27,865 25,000 (6,311 ) — 18,689 Naxyris note 10,957 (4,403 ) — 6,554 — — — — 133,998 (25,048 ) — 108,950 25,000 (6,311 ) — 18,689 Total debt 241,430 (37,514 ) 327 204,243 228,921 (17,142 ) (2,082 ) 209,697 Less: current portion (78,716 ) (147,677 ) Long-term debt, net of current portion $ 125,527 $ 62,020 August 2013 Financing Convertible Note On January 14, 2019, Wolverine Flagship Fund Trading Limited (Wolverine) agreed to waive payment of the August 2013 Financing Convertible Note held by Wolverine at its January 15, 2019 maturity until July 15, 2019 in exchange for a fee, payable on or prior to July 15, 2019, of $0.6 million . The due date of the waiver fee was extended to October 13, 2019 and was subsequently paid on October 29, 2019. The Company concluded that the maturity date extension represented a debt modification, and the fee was accounted for as additional debt discount to be amortized over the remaining term. On July 8, 2019, $5.1 million principal balance of the convertible note and unpaid interest was exchanged for 1.8 million shares of common stock with a total fair value of $5.9 million or $3.30 per share and a warrant to purchase 1.1 million shares of common stock with a fair value of $1.9 million . The Company recorded a $2.7 million loss on debt extinguishment in the three and nine months ended September 30, 2019 for the difference between the carrying value of the debt and the sum of the fair values of the common stock and warrant. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of the common stock and warrant issued in connection with this exchange. Foris Credit Agreements On April 8, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $8.0 million (the April Foris Credit Agreement), which the Company borrowed in full on April 8, 2019 and issued to Foris a promissory note in the principal amount of $8.0 million (the April Foris Note). The April Foris Note has a maturity date of October 14, 2019, which has no stated interest rate. The Company agreed to pay Foris a fee of $1.0 million , payable on or prior to the maturity date; provided, that the fee will be reduced to $0.5 million if the Company repays the April Foris Note in full by July 15, 2019. The Company accrues this fee as interest expense over the six-month term of the note. On June 11, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $8.5 million , which the Company borrowed in full on June 11, 2019 and issued to Foris a promissory note in the principal amount of $8.5 million (the June Foris Note). The June Foris Note (i) accrues interest at a rate of 12.5% per annum and is payable on the maturity date or the earlier repayment or other satisfaction of the June Foris Note, and (ii) matured on August 28, 2019. On July 10, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $16.0 million (the July Foris Credit Agreement), of which the Company borrowed $8.0 million on July 10, 2019 and $8.0 million on July 26, 2019 and issued to Foris promissory notes, each in the principal amount of $8.0 million , on such dates (the July Foris Notes). The July Foris Notes (i) accrue interest at a rate of 12.5% per annum, which is payable on the maturity date or the earlier repayment or other satisfaction of the applicable July Foris Note, and (ii) mature on December 31, 2019. In connection with the entry into the July Foris Credit Agreement, the Company and Foris amended the warrant issued to Foris on August 17, 2018 to reduce the exercise price of such warrant from $7.52 per share to $2.87 per share. The warrant modification resulted in $4.0 million of incremental value which was accounted for as a debt discount to the $16 million July Foris Notes. See Note 6, “Stockholders’ Deficit” for additional information regarding the fair value measurement of the modified warrant. On August 14, 2019, the April Foris Note, the June Foris Note and the July Foris Notes were added to the loans under the LSA, made subject to the LSA and secured by the security interest in the collateral granted to Foris under the LSA, and such notes were cancelled in connection therewith. See "LSA Assignment, Amendments and Waiver" below for further information. 2015 and 2014 Rule 144A Convertible Notes On April 16, 2019, the Company repaid in cash the $37.9 million outstanding principal, as well as accrued and unpaid interest, under its 9.50% Convertible Senior Notes due 2019 (the 2015 Rule 144A Convertible Notes). On May 10, 2019, the Company exchanged $13.5 million aggregate principal amount of its 6.50% Convertible Senior Note (the 2014 Rule 144A Convertible Notes) held by certain non-affiliated investors, including accrued and unpaid interest thereon for an aggregate of 3.5 million shares of common stock and warrants to purchase an aggregate of 1.4 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act of 1933, as amended (the Securities Act). On May 14, 2019, the Company exchanged $5.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Foris, including accrued and unpaid interest thereon, for 1.1 million shares of common stock and a warrant to purchase up to 0.4 million shares of common stock at an exercise price of $4.56 per share, with an exercise term of two years from issuance, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. On August 28, 2019, the Company and Foris agreed to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share. See “August 2019 Foris Credit Agreements” below and Note 6, “Stockholders’ Deficit” for additional information. On May 15, 2019, the Company exchanged $10.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Maxwell (Mauritius) Pte Ltd for 2.5 million shares of common stock in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The Company evaluated the May 2019 exchanges described above and concluded that the transactions resulted in a debt extinguishment. The Company recorded a $5.9 million loss on debt extinguishment of the 2014 144A Convertible Notes in the three months ended June 30, 2019. The loss represented the difference between the $30.8 million fair value of 7.1 million common shares issued upon exchange, $3.8 million fair value of warrants issued to purchase 1.7 million shares of common stock and $0.4 million of fees incurred, less the $29.1 million carrying value of the debt that was extinguished. See Note 6. "Stockholders’ Deficit" for further information regarding the fair value measurement of the common stock and warrants issued in connection with the May 2019 exchanges discussed above. On May 15, 2019, the Company exchanged $9.7 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Total Raffinage Chimie (Total) for a new senior convertible note with an equal principal amount and with substantially identical terms, except that the new note had a maturity date of June 14, 2019, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. Effective June 14, 2019, the Company and Total agreed to extend the maturity date of the new note from June 14, 2019 to July 18, 2019. Effective July 18, 2019, the Company and Total agreed to (i) further extend the maturity date of the new note from July 18, 2019 to August 28, 2019 and (ii) increase the interest rate on the new note to 10.5% per annum, beginning July 18, 2019. Effective August 28, 2019, the Company and Total agreed to (i) further extend the maturity date of the new note from August 28, 2019 to October 28, 2019 and (ii) increase the interest rate on the new note to 12% per annum, beginning August 28, 2019. See Note 12, “Subsequent Events” for information regarding further modifications to the new note subsequent to September 30, 2019. The Company accounted for the series of exchanges with Total as a debt modification; however, no additional fees were paid, and the modifications had no impact on the debt discount or interest expense in the three and nine months ended September 30, 2019. 6% Convertible Notes Exchanges On May 15, 2019 and June 24, 2019, the Company exchanged $53.3 million and $4.7 million principal amount, respectively, of the 6% Convertible Notes, including accrued and unpaid interest thereon, representing all then-outstanding 6% Convertible Notes, for new senior convertible notes with an equal principal amount and warrants to purchase up to 2.0 million and 0.2 million shares of common stock, respectively, at an exercise price of $5.12 per share, with an exercise term of two years from issuance, in private exchanges pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The new notes have substantially identical terms as the 6% Convertible Notes being exchanged, except that (i) the holders agreed to waive, until July 22, 2019, certain covenants relating to the effectiveness of the registration statement covering the shares of common stock issuable upon conversion of, or otherwise pursuant to, the new notes and the filing by the Company of reports with the SEC and (ii) during the period from July 22, 2019 to July 29, 2019, inclusive, the holders have the right to require the Company to redeem the new notes, in whole or in part, at a price equal to 125% of the principal amount being redeemed. Since the Company has elected the fair value accounting option for the 6% Convertible Notes and records all changes in fair value through the gain/loss on change in fair value of debt line item in the statement of operations each reporting period, this exchange is not required to be evaluated for modification or extinguishment accounting treatment. However, the Company considered the issuance of the warrant as compensation to the noteholders for waiving certain covenant violations during the period, and recorded a $4.4 million increase to additional paid in capital and a charge to interest expense for the fair value of the equity-classified May 15, 2019 and June 24, 2019 warrants. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant. On July 24, 2019, the Company further exchanged $53.3 million principal amount of the previously-exchanged 6% Convertible Senior Notes, as well as the warrant to purchase up to 2.0 million shares of common stock issued on May 15, 2019, for a new senior convertible note with a principal amount of $68.3 million (the Second Exchange Note) and a new warrant to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from May 15, 2019 (the Second Exchange Warrant) in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The Second Exchange Note and Second Exchange Warrant have substantially similar terms as the note and warrant, respectively, issued on May 15, 2019, except that (i) the principal amount of the Second Exchange Note would be $68.3 million , reflecting accrued and unpaid interest and late charges under the exchanged note and a 25% premium accruing as a result of the Company’s failure to make an installment payment on the exchanged note due July 1, 2019 in the amount of $6.4 million , provided that upon an event of default under the Second Exchange Note, the Company would not be required to redeem the Second Exchange Note in cash at a price greater than the intrinsic value of the shares of common stock underlying the Second Exchange Note, (ii) the Second Exchange Note bears interest at a rate of 18% per annum, (iii) the holder agreed to extend its waiver of certain covenant breaches relating to the failure by the Company to timely file periodic reports with the SEC from July 22, 2019 to September 16, 2019, (iv) the Company is required to (A) make principal payments on the Second Exchange Note in the amount of $3.2 million on each of August 2, 2019 and August 22, 2019, and (B) pay all remaining amounts then outstanding under the Second Exchange Note on September 16, 2019, and if the Company fails to make any such payment on the applicable payment date, the conversion price of the Second Exchange Note would be reset to the volume-weighted average price of the common stock on the trading day immediately following the Company’s filing of a Current Report on Form 8-K with respect to its failure to make the payment due on September 16, 2019, if such volume-weighted average price is lower than the conversion price of the Second Exchange Note then in effect, subject to a price floor and (v) the Second Exchange Warrant has an exercise price of $2.87 per share. Since the Company has elected the fair value accounting option for the 6% Convertible Notes and records all changes in fair value through the gain/loss on change in fair value of debt line item in the statement of operations each reporting period, this second note exchange is not required to be evaluated for modification or extinguishment accounting treatment. However, the Company considered the modification of the warrant as compensation to the noteholder for waiving certain covenant violations during the period, and recorded a $0.9 million increase to additional paid in capital and a charge to interest expense for the incremental fair value of the modification. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement of this warrant modification. On July 26, 2019, one of the holders of $4.7 million principal amount of the 6% Convertibles Notes issued on June 24, 2019, exercised their right to require the Company to redeem such note in whole at a price equal to 125% of the principal amount being redeemed, plus accrued and unpaid interest on such note to the date of repayment. Redemption of such note was initially due on July 30, 2019 and subsequently extended to August 30, 2019. The Company redeemed such note in full on August 30, 2019. On September 16, 2019, the Company failed to pay an aggregate of $63.6 million of outstanding principal and accrued interest on the Second Exchange Note when due. The failure resulted in an event of default under the Second Exchange Note and also triggered cross-defaults under other debt instruments of the Company which permitted the holders of such indebtedness to accelerate the amounts owing under such instruments. The Company subsequently received waivers from all holders of such other debt instruments to waive the right to accelerate. As a result, the indebtedness with respect to which the Company has obtained such waivers continues to be classified as long-term on the Company’s balance sheet. The indebtedness reflected by the Second Exchange Note continues to be classified as a current liability on the Company’s balance sheet. In addition, as a result of the payment default, the conversion price of the Second Exchange Note is subject to adjustment in accordance with the terms of the Second Exchange Note. On November 8, 2019, the Company entered into a Securities Exchange Agreement with certain private investors (the “Investors”), pursuant to which, upon the purchase by the Investors of the Second Exchange Note, the Second Exchange Note would be exchanged for new senior convertible notes with an aggregate principal amount of $66.0 million (see Note 12, “Subsequent Events”). In connection with the entry into the Securities Exchange Agreement, (i) the holder of the Second Exchange Note and the Investors entered into a Securities Purchase Agreement providing for the purchase by the Investors of the Second Exchange Note and (ii) the Company and the holder of the Second Exchange Note entered into an agreement by which such holder agreed to immediately dismiss its complaint against the Company (see Note 8, “Commitments and Contingencies”) with prejudice upon the purchase of the Second Exchange Note by the Investors. Nikko Loan Agreement On July 29, 2019, the Company and Nikko Chemicals Co., Ltd. (Nikko) entered into a loan agreement (the Nikko Loan Agreement) to make available to the Company secured loans in an aggregate principal amount of $5.0 million , to be issued in separate installments of $3.0 million and $2.0 million , respectively, with each installment being subject to certain closing conditions, including the entry into certain commercial agreements and other arrangements relating to the Aprinnova JV (see Note 11, “Related Party Transactions” in Part II, Item 8 of the 2018 Form 10-K/A). On July 30, 2019, the Company borrowed the first installment of $3.0 million under the Nikko Loan Agreement and received net cash proceeds of $2.8 million , with the remaining $0.2 million being withheld by Nikko as prepayment of the interest payable on such loan through the maturity date. On August 8, 2019, the Company borrowed the remaining $2.0 million available under the Nikko Loan Agreement and received net cash proceeds of $1.9 million , with the remaining $0.1 million being withheld by Nikko as prepayment of the interest payable on such loan through the maturity date. The loans (i) mature on December 18, 2020, (ii) accrue interest at a rate of 5% per annum from and including the applicable loan date through the maturity date, which interest is required to be prepaid in full on the date of the applicable loan, and (iii) are secured by a first-priority lien on 12.8% of the Aprinnova JV interests owned by the Company. Aprinnova Working Capital Loan Effective July 31, 2019, the Company and Nikko agreed to extend the term of the Second Aprinnova Note (see Note 5, “Debt” in Part II, Item 8 of the 2018 Form 10-K/A) from August 1, 2019 to August 1, 2020. LSA Assignment, Amendments and Waivers On April 4, 2019, the Company and GACP Finance Co., LLC (GACP) amended the Loan and Security Agreement, dated June 29, 2018 (as amended, the LSA), to (i) effective December 31, 2018, eliminate the conditions giving rise to the early maturity date, so that loans under the GACP Term Loan Facilities would have a maturity date of July 1, 2021, (ii) remove certain Company intellectual property related to the Cannabinoid Agreement from the lien granted by the Company to GACP under the LSA, (iii) eliminate the Company’s ability to obtain an incremental term loan facility, (iv) eliminate the Company’s reinvestment rights with respect to mandatory prepayments upon asset sales, (v) restrict the Company’s ability to pay interest and principal on other indebtedness without the consent of GACP, and (vi) provide that the Company must have at all times at least $15 million of unrestricted, unencumbered cash subject to a control agreement in favor of GACP. Also, on April 4, 2019, the Company and GACP entered into a waiver agreement, pursuant to which GACP agreed to waive breaches of certain covenants under the LSA occurring prior to, as of and after December 31, 2018 through April 8, 2019, including covenants related to quarterly minimum revenues, minimum liquidity amounts and a minimum asset coverage ratio. In connection with such waiver, the Company agreed to pay GACP fees of $0.8 million , which the Company paid in April 2019. This waiver fee was recorded as interest expense in the statement of operations in the nine months ended September 30, 2019. On April 15, 2019, the Company, GACP and Foris Ventures, LLC (Foris), 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) entered into a Loan Purchase Agreement, pursuant to which Foris agreed to purchase and assume from GACP, and GACP agreed to sell and assign to Foris, the outstanding loans under the LSA and all documents and assets related thereto. In connection with such purchase and assignment, the Company agreed to repay Foris $2.5 million of the purchase price and accrued interest paid by Foris to GACP (the LSA Obligation). The Company accounted for the LSA Obligation as a debt modification and recorded the $2.5 million fee as additional debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA. The closing of the loan purchase and assignment occurred on April 16, 2019. On August 14, 2019, the Company and Foris entered into an Amendment No 5 and Waiver to the LSA (the LSA Amendment and Waiver), pursuant to which (i) the maturity date of the loans under the LSA was extended from July 1, 2021 to July 1, 2022, (ii) the interest rate for the loans under the LSA was modified from the sum of (A) the greater of (x) the prime rate as reported in the Wall Street Journal or (y) 4.75% plus (B) 9% to the greater of (A) 12% or (B) the rate of interest payable with respect to any indebtedness of the Company, (iii) the amortization of the loans under the LSA was delayed until December 16, 2019, (iv) certain accrued and future interest and agency fee payments under the LSA were delayed until December 16, 2019, (v) certain covenants under the LSA, including related definitions, were amended to provide the Company with greater operational and financial flexibility, including, without limitation, to permit the incurrence of the indebtedness under the Naxyris Loan Facility (as described below) and the granting of liens with respect thereto, subject to the terms of an intercreditor agreement between Foris and Naxyris S.A. (Naxyris) governing the respective rights of the parties with respect to, among other things, the assets securing the Naxyris Loan Agreement (as defined below) and the LSA (the Intercreditor Agreement), (vi) certain outstanding unsecured promissory notes issued by the Company to Foris on April 8, 2019, June 11, 2019, July 10, 2019 and July 26, 2019 (as described in the “Foris Credit Agreements” section above), in an aggregate principal amount of $32.5 million , as well as the $2.5 million LSA Obligation, were added to the loans under the LSA, made subject to the LSA and secured by the security interest in the collateral granted to Foris under the LSA, and such promissory notes and contractual obligation were canceled in connection therewith, and (vii) Foris agreed to waive certain existing defaults under the LSA, including with respect to covenants related to quarterly minimum revenues, minimum liquidity amounts and a minimum asset coverage ratio. After giving effect to the LSA Amendment and Waiver, there is $71.0 million aggregate principal amount of loans outstanding under the LSA. The Company also issued to Foris a warrant (the LSA Warrant) on August 14, 2019 to purchase up to 1.4 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The warrant had a fair value of $2.9 million which was measured using a Black-Scholes option pricing model. See Note 6, “Stockholders’ Deficit” for further information regarding the fair value measurement and issuance of this warrant. Due to multiple changes in key provisions of the LSA from April 15, 2019 through August 14, 2019, the Company analyzed the before and after cash flows resulting from the increased principal balance, decreased interest rate, extended maturity date, waiver of default interest and the fair value of the new LSA Warrant provided to Foris in order to determine if these changes result in a modification or extinguishment of the original LSA. Based on the combined before and after cash flows of the five separate note balances making up the new principal balance of the LSA and the fair value of the LSA warrant, the change in cash flows was not significantly different. Consequently, the LSA Amendment and Waiver was accounting for as a debt modification with the $2.9 million fair value of the LSA Warrant recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA. See Note 12, “Subsequent Events” for more information regarding the LSA. Naxyris Loan and Security Agreement On August 14, 2019, the Company, certain of the Company’s subsidiaries (the Subsidiary Guarantors) and, as lender, Naxyris, an existing stockholder of the Company and an investment vehicle owned by Naxos Capital Partners SCA Sicar, which is affiliated with NAXOS S.A.R.L. (Switzerland), for which director Carole Piwnica serves as director, entered into a Loan and Security Agreement (the Naxyris Loan Agreement) to make available to the Company a secured term loan facility in an aggregate principal amount of up to $10.4 million (the Naxyris Loan Facility), which the Company borrowed in full on August 14, 2019. In connection with the funding of the Naxyris Loan Facility, the Company paid Naxyris an upfront fee of $0.4 million . Loans under the Naxyris Loan Facility have a maturity date of July 1, 2022 and accrue interest at a rate per annum equal to the greater of (i) 12% or (ii) the rate of interest payable with respect to any indebtedness of the Company plus 25 basis points, which interest will be payable monthly in arrears, provided that all interest accruing from and after August 14, 2019 through December 1, 2019 shall be due and payable on December 15, 2019. The obligations of the Company under the Naxyris Loan Facility are (i) guaranteed by the Subsidiary Guarantors and (ii) secured by a perfected security interest in substantially all of the assets of the Company and the Subsidiary Guarantors (the Collateral), junior in payment priority to Foris subject to certain limitations and exceptions, as well as the terms of the Intercreditor Agreement. Mandatory prepayments of the outstanding amounts under the Naxyris Loan Facility will be required upon the occurrence of certain events, including asset sales, a change in control, and the incurrence of additional indebtedness, subject to certain exceptions and reinvestment rights. Outstanding amounts under the Naxyris Loan Facility must also be prepaid to the extent that the borrowing base exceeds the outstanding principal amount of the loans under the Naxyris Loan Facility. In addition, the Company may at its option prepay the outstanding principal amount of the loans under the Naxyris Loan Facility in full before the maturity date. Any prepayment of the loans under the Naxyris Loan Facility prior to the maturity date, whether pursuant to a mandatory or optional prepayment, is subject to a prepayment charge equal to one year’s interest at the then-current interest rate for the Naxyris Loan Facility. Upon any repayment of the loans under the Naxyris loan facility, whether on the maturity date or earlier pursuant to an optional or mandatory prepayment, the Company will pay Naxyris an end of term fee based on a percentage of the aggregate amount borrowed. In addition, (i) the Company will be required to pay a fee equal to 6% of any amount the Company fails to pay within three business days of its due date and (ii) any interest that is not paid when due will be added to principal and will bear compound interest at the applicable rate. The affirmative and negative covenants in the Naxyris Loan Agreement relate to, among other items: (i) payment of taxes; (ii) financial reporting; (iii) maintenance of insurance; and (iv) limitations on indebtedness, liens, mergers, consolidations and acquisitions, transfers of assets, dividends and other distributions in respect of capital stock, investments, loans and advances, and corporate changes. The Naxyris Loan Agreement also contains financial covenants, including covenants related to minimum revenue, liquidity, and asset coverage. The Naxyris Loan Facility also contained a mandatory redemption feature that was not clearly and closely related to the debt host instrument, and thus, required bifurcation and separate accounting as a derivative liability. The embedded feature had an initial fair value of $0.3 million and was recorded as a derivative liability and a debt discount to be amortized to interest expense under the effective interest method over the term of the Naxyris Loan Facility. See Note 3, “Fair Value Measurements” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature. In connection with the entry into the Naxyris Loan Agreement, on August 14, 2019 the Company issued to Naxyris a warrant (the Naxyris LSA Warrant) to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. See Note 6, “Stockholders’ Deficit” for information regarding the fair value measurement and issuance of this warrant. The warrant had a $4.0 million Black-Scholes fair value and a $3.0 million relative fair value after allocating the Naxyris Loan Facility proceeds to the $0.3 million fair value of the embedded mandatory redemption feature contained in the Naxyris Loan Facility, and allocating on a residual basis, to the relative fair values of the Naxyris Loan Facility and the Naxyris LSA Warrant. The $3.0 million relative fair value of the Naxyris LSA Warrant was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the term of the Naxyris Loan Agreement. In addition to the $3.0 million relative fair value of the Naxyris LSA Warrant and the $0.3 million fair value of the embedded mandatory redemption feature, the Naxyris Loan Facility contained $0.4 million original issue discount, $0.5 million mandatory end of term fee and $0.3 million of issuances costs, all totaling $4.5 million . All such amounts were recorded as a debt discount to be amortized as interest expense over the term of the Naxyris Loan Agreement. See Note 12, “Subsequent Events” for more information regarding the Naxyris Loan Agreement. August 2019 Foris Credit Agreements On August 28, 2019, the Company and Foris entered into a credit agreement to make available to the Company an unsecured credit facility in an aggregate principal amount of $19.0 million (the August 2019 Foris Credit Agreement), which the Company borrowed in full on August 28, 2019 and issued to Foris a promissory note in the principal amount of $19.0 million (the August 2019 Foris Note). The August 2019 Foris Note (i) accrues interest at a rate of 12% per annum from and including August 28, 2019, which interest is payable quarterly in arrears on each March 31, June 30, September 30 and December 31, beginning December 31, 2019, and (ii) matures on January 1, 2023. The Company may at its option repay the amounts outstanding under the August 2019 Foris Note before the maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount

Mezzanine Equity

Mezzanine Equity	9 Months Ended
	Sep. 30, 2019
Temporary Equity Disclosure [Abstract]
Mezzanine Equity	Mezzanine Equity Mezzanine equity at September 30, 2019 and December 31, 2018 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 September 30, 2019 , the Company's remaining research and development obligation under this arrangement was $0.5 million

Stockholders' Deficit

Stockholders' Deficit	9 Months Ended
	Sep. 30, 2019
Equity [Abstract]
Stockholders' Deficit	Stockholders' Deficit Private Placements On April 16, 2019, the Company sold and issued to Foris 6,732,369 shares of common stock at a price of $2.87 per share, for aggregate proceeds to the Company of $20.0 million (the Foris Investment), as well as a warrant to purchase up to 5.4 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance, in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act, for aggregate cash proceeds to the Company of $20.0 million . The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity. On April 26, 2019, the Company sold and issued (i) 2,832,440 shares of common stock at a price of $5.12 per share, as well as a warrant to purchase up to 4.0 million shares of common stock at an exercise price of $5.12 per share, with an exercise term of two years from issuance, to Foris and (ii) an aggregate of 2,043,781 shares of common stock at a price of $4.02 per share, as well as warrants to purchase up to an aggregate of 1.6 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to certain other non-affiliated investors, in each case 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, for aggregate cash proceeds to the Company of $15.0 million from Foris and and $8.2 million from non-affiliated investors, for a total of $23.2 million . The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity. On April 29, 2019, the Company sold and issued (i) 913,529 shares of common stock at a price of $4.76 per share, as well as warrants to purchase up to an aggregate of 1.2 million shares of common stock at an exercise price of $4.76 per share, with an exercise term of two years from issuance, to affiliates of Vivo Capital LLC (Vivo), an entity affiliated with director Frank Kung and which owns greater than five percent of our outstanding common stock and has the right to designate one member of the Company’s Board of Directors) and (ii) an aggregate of 0.3 million shares of common stock at a price of $4.02 per share, as well as warrants to purchase up to an aggregate of 0.3 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to certain other non-affiliated investors, in each case 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, for aggregate cash proceeds to the Company of $4.5 million from Vivo and $1.3 million from non-affiliated investors, for a total of $5.8 million . The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity. On May 3, 2019, the Company sold and issued 1.2 million shares of common stock at a price of $4.02 per share, as well as a warrant to purchase up to 1.0 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, to a non-affiliated investor in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act, for aggregate cash proceeds to the Company of $5 million . The Company evaluated the warrants for derivative liability treatment and concluded that the instruments met the indexation criteria to be accounted for in equity. The exercise price of the warrants issued in the foregoing private placements is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of issuance of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, in connection with the foregoing private placements, the Company agreed not to effect any exercise or conversion of any Company security, and the investors agreed not to exercise or convert any portion of any Company security, to the extent that after giving effect to such exercise or conversion, the applicable investor, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding immediately after giving effect to such exercise or conversion, and the warrant contained a similar limitation. The Company is seeking stockholder approval for Foris to exceed such limitation in accordance with Nasdaq rules and regulations at its 2019 annual meeting of stockholders. August 2013 Financing Convertible Note Conversion into Equity On July 8, 2019, Wolverine exchanged $5.1 million principal and accrued and unpaid interest related to its August 2013 Financing Convertible Note for 1.8 million shares of common stock and a warrant to purchase 1.1 million shares of common stock in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The common stock had a fair value of $5.9 million or $3.30 per share and the warrant had a fair value of $1.9 million . The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the convertible note and will be classified in equity as the warrant is both indexed to the Company’s own stock and meets the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasured to fair value at each reporting period, unless new events trigger a requirement for the warrant to be reclassified to an asset or liability. The fair value of the warrant was measured using the Black-Scholes option pricing model, with the following parameters: stock price $3.33 , strike price $2.87 , volatility 94% , risk-free interest rate 1.88% , and expected dividend yield 0% . See Note 4, “Debt” for additional information regarding the loss on debt extinguishment. 2014 Rule 144A Convertible Notes Exchanges On May 10, 2019, the Company exchanged $13.5 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by certain non-affiliated investors, including accrued and unpaid interest thereon, for an aggregate of 3.5 million shares of common stock and warrants to purchase an aggregate of 1.4 million shares of common stock at an exercise price of $5.02 per share, with an exercise term of two years from issuance, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. On May 14, 2019, the Company exchanged $5.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Foris, including accrued and unpaid interest thereon, for 1.1 million shares of common stock and a warrant to purchase up to 0.4 million shares of common stock at an exercise price of $4.56 per share, with an exercise term of two years from issuance, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. On August 28, 2019, the Company and Foris agreed to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share. See “August 2019 Foris Warrant Issuance” below for additional information. On May 15, 2019, the Company exchanged $10.0 million aggregate principal amount of the 2014 Rule 144A Convertible Notes held by Maxwell (Mauritius) Pte Ltd for 2.5 million shares of common stock in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The Company issued 7.1 million shares of common stock with a fair value totaling $30.8 million based on the Company's closing stock price at the date of each exchange upon exchange of the 2014 Rule 144A Convertible Notes described above. The Company also issued warrants to purchase a total of 1.7 million shares of common stock with a fair value of $3.8 million . The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the convertible notes and will be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasured to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrants were measured using the Black-Scholes option pricing model with the following parameters: stock price $4.27 - $4.54 , strike price $4.56 - $5.02 , volatility 96% , risk-free interest rate 2.20% - 2.26% , and expected dividend yield 0% . The warrant had a fair value of $5.9 million that was recorded as a loss of debt extinguishment. See Note 4, "Debt" for information about the accounting treatment for this debt exchange and fair value of the warrant. The exercise price of the warrants issued in the foregoing exchanges is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of the exercisability of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, (i) the exercisability of the warrant issued to Foris is subject to stockholder approval in accordance with Nasdaq rules and regulations, which the Company is seeking at its 2019 annual meeting of stockholders, and (ii) each other warrant provides that the Company may not effect any exercise of such warrant to the extent that, after giving effect to such exercise, the applicable holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding after giving effect to such exercise. Standstill Agreement In connection with the September 10, 2019 entry into the Investor Credit Agreements discussed in Note 4, “Debt” and the issuance of the September 2019 Investor Warrants discussed in the "Warrant - September 2019 Investor Warrants" section below, the Company and the Investors entered into a Standstill Agreement (the Investor Standstill Agreement), pursuant to which the Investors agreed that, until the earliest to occur of (i) the Investors no longer beneficially owning any shares underlying the warrants, (ii) the Company entering into a definitive agreement involving the direct or indirect acquisition of all or a majority of the Company’s equity securities or all or substantially all of the Company’s assets or (iii) a person or group, with the prior approval of the Company’s Board of Directors (the Board), commencing a tender offer for all or a majority of the Company's equity securities, neither the Investors nor any of their respective affiliates (together, the Investor Group) will (without the prior written consent of the Board), among other things, (i) acquire any loans, debt securities, equity securities, or assets of the Company or any of its subsidiaries, or rights or options with respect thereto, except that the Investor Group shall be permitted to (a) purchase the shares underlying the warrants pursuant to the exercise of the warrants and (b) acquire beneficial ownership of up to 6.99% of the Company's common stock, or (ii) make any proposal, public announcement, solicitation or offer with respect to, or otherwise solicit, seek or offer to effect, or instigate, encourage, or assist any third party with respect to: (a) any business combination, merger, tender offer, exchange offer, or similar transaction involving the Company or any of its subsidiaries; (b) any restructuring, recapitalization, liquidation, or similar transaction involving the Company or any of its subsidiaries; (c) any acquisition of any of the Company’s loans, debt securities, equity securities or assets, or rights or options with respect thereto; or (d) any proposal to seek representation on the Board or otherwise seek to control or influence the management, Board, or policies of the Company, in each case subject to certain exceptions. Warrants In connection with various debt and equity transactions (see Note 4, “Debt” above and Note 5, "Debt" and Note 7, “Stockholders’ Deficit” in Part II, Item 8 of the 2018 Form 10-K/A), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrants activity for the current year interim periods ended September 30, 2019 : Transaction Outstanding at December 31, 2018 Exercises Outstanding at March 31, 2019 Additional Warrants Issued Exercises Outstanding at June 30, 2019 Additional Warrants Issued Expiration Outstanding at September 30, 2019 July 2015 related party debt exchange 663,228 (471,204 ) 192,024 245,558 (245,558 ) 192,024 — — 192,024 July 2015 private placement 81,197 (8,547 ) 72,650 — — 72,650 — — 72,650 February 2016 related party private placement 171,429 — 171,429 — — 171,429 — — 171,429 May 2017 cash and dilution warrants 6,292,798 — 6,292,798 4,795,924 (1,924,673 ) 9,164,049 — — 9,164,049 August 2017 cash and dilution warrants 3,968,116 — 3,968,116 3,028,983 — 6,997,099 — — 6,997,099 April 2018 warrant exercise agreements 3,616,174 — 3,616,174 — — 3,616,174 — (3,616,174 ) — August 2018 warrant exercise agreements 12,097,164 — 12,097,164 — — 12,097,164 — — 12,097,164 April 2019 PIPE warrants — — — 8,084,770 — 8,084,770 — — 8,084,770 April 2019 Foris warrant — — — 5,424,804 — 5,424,804 — — 5,424,804 May 2019 6.50% Note Exchange Warrants — — — 1,744,241 — 1,744,241 — — 1,744,241 May-June 2019 6% Note Exchange Warrants — — — 2,181,818 — 2,181,818 — — 2,181,818 July 2019 Wolverine warrant — — — — — — 1,080,000 — 1,080,000 August 2019 Foris LSA warrant — — — — — — 1,438,829 — 1,438,829 August 2019 Foris Credit Agreement warrant — — — — — — 4,871,795 — 4,871,795 August 2019 Naxyris LSA warrant — — — — — — 2,000,000 — 2,000,000 September 2019 Investor Credit Agreement warrant — — — — — — 3,205,128 — 3,205,128 Other 1,406 — 1,406 — — 1,406 — — 1,406 26,891,512 (479,751 ) 26,411,761 25,506,098 (2,170,231 ) 49,747,628 12,595,752 (3,616,174 ) 58,727,206 Due to certain down-round adjustments to other equity-related instruments during the three months ended June 30, 2019, approximately 8.1 million shares became available under the May 2017 and August 2017 cash and dilution warrants and the Temasek Funding Warrant (see Note 7, “Stockholders’ Deficit” in Part II, Item 8 of the 2018 Form 10-K/A). Approximately 2.6 million shares were exercised under the May 2017 and August 2017 dilution warrants and the Temasek Funding Warrant during the nine months ended September 30, 2019, which resulted in zero proceeds to the Company. A portion of the warrant exercises occurring during the nine months ended September 30, 2019 was net share settled, and 2.5 million shares were issued upon exercise of warrants during the nine months ended September 30, 2019 . July 2019 Foris Credit Agreement Warrant Modification In connection with the entry into the July Foris Credit Agreement on July 10, 2019 (see Note 4, “Debt”), the Company and Foris amended a warrant to purchase up to 4.9 million shares of common stock issued to Foris on August 17, 2018 to reduce the exercise price of such warrant from $7.52 per share to $2.87 per share. The warrant modification was measured on a before and after modification basis using a Black-Scholes option pricing model with the following parameters: stock price $3.21 , strike price $2.87 , volatility 124% , risk-free interest rate 1.82% , term 0.9 years, and expected dividend yield 0% . The warrant had an incremental fair value of $4.0 million , which was accounted for as an increase to additional paid in capital and a debt discount to the $16 million July Foris Notes. See Note 4, “Debt” for additional information regarding the debt discount recorded in connection with the modification of the warrant. 6% Convertible Note Exchange Warrants and Modification In connection with the May 15, 2019 and June 24, 2019 6% Convertible Note Exchanges (see Note 4, “Debt”), the Company issued warrants to purchase up to 2.0 million and 0.2 million shares of common stock, respectively, at an exercise price of $5.12 per share, with an exercise term of two years from issuance, in private exchanges pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The exercise price of the warrants is subject to standard adjustments, but the warrants do not contain anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, the holders may not exercise the warrants, and the Company may not affect any exercise of the warrants, to the extent that, after giving effect to such exercise, the applicable holder, together with its affiliates, would beneficially own in excess of 4.99% of the number of shares of common stock outstanding after giving effect to such exercise. The Company concluded the warrants are freestanding instruments that are legally detachable and separately exercisable from the convertible notes and will be classified in equity as the warrants are both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrants within equity and will not subsequently remeasured to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The fair value of the warrants totaled $4.4 million and were measured using the Black-Scholes option pricing model with the following parameters: 94% - 96% volatility, 1.72% - 2.16% risk-free interest rate, $3.55 - $4.39 issuance-date stock price, term 2.0 years, and 0% expected dividend yield. The Company concluded that the $4.4 million fair value of the equity-classified May 15, 2019 and June 24, 2019 warrants should be recorded as an increase to additional paid in capital and a charge to interest expense in the statement of operations at the date of issuance. See Note 4, “Debt” for additional information regarding the accounting for the fair value of these warrants. Further, on July 24, 2019, Company exchanged the May 15, 2019 warrant to purchase up to 2.0 million shares of common stock, for a new warrant to purchase up to 2.0 million shares of common stock at an exercise price of $2.87 per share, with an exercise term of two years from May 15, 2019 (the Second Exchange Warrant) in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The Second Exchange Warrant has substantially identical terms as the original warrant issued on May 15, 2019, except that the exercise price was reduced from $5.12 to $2.87 per share. The warrant modification was measured on a before and after modification basis using a Black-Scholes option pricing model with the following parameters: strike price $2.87 , volatility 93% , risk-free interest rate 1.86% , term 1.8 years, and expected dividend yield 0% ; and resulted in $0.9 million of incremental fair value. The Company concluded that the increase in the fair value of the Second Exchange Warrant should be recorded as an increase to additional paid in capital and a charge to interest expense in the statement of operations at the date of modification. See Note 4, “Debt” for additional information regarding the charge to interest expense in connection with the fair value of this warrant. LSA Warrant Issuance In connection with the entry into the LSA Amendment and Waiver (see Note 4, “Debt”), on August 14, 2019 the Company issued to Foris a warrant to purchase up to 1.4 million shares of Common Stock at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permit “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. Pursuant to the terms of the warrant, Foris may not exercise the LSA Warrant to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company is seeking at its 2019 annual meeting of stockholders. The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the LSA Amendment and Waiver and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasured to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes option pricing model with the following parameters: stock price $3.59 , strike price $2.87 , volatility 94% , risk-free interest rate 1.58% , term 2.0 years, and expected dividend yield 0% . The warrant had a fair value of $2.9 million which was recorded as an increase to additional paid in capital and as a debt discount to be amortized to interest expense under the effective interest method over the remaining term of the LSA. See Note 4, “Debt” for further information regarding the accounting treatment for the fair value of this warrant. Naxyris LSA Warrant Issuance In connection with the entry into the Naxyris Loan Agreement (see Note 4, “Debt”), on August 14, 2019 the Company issued to Naxyris a warrant to purchase up to 2.0 million shares of the Company’s common stock, par value $0.0001 per share at an exercise price of $2.87 per share, with an exercise term of two years from issuance. The exercise price of the warrant is subject to standard adjustments and permits “cashless” or “net” exercise any time after issuance. The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the Naxyris Loan Facility and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasured to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes option pricing model with the following parameters: stock price $3.59 , strike price $2.87 , volatility 94% , risk-free interest rate 1.58% , term 2.0 years, and expected dividend yield 0% . The warrant had a $4.0 million Black-Scholes fair value and a $3.0 million relative fair value after allocating the Naxyris Loan Facility proceeds to the $0.3 million fair value of an embedded mandatory redemption feature contained in the Naxyris Loan Facility, and allocating on a residual basis, to the relative fair values of the Naxyris Loan Facility and the Naxyris LSA Warrant. See Note 4, “Debt” for further information regarding the initial accounting treatment for the embedded mandatory redemption feature and the accounting treatment for the relative fair value of this warrant, and see Note 3, “Fair Value Measurements” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature. August 2019 Foris Warrant Issuance In connection with the entry into the August 2019 Foris Credit Agreement (see Note 4, “Debt”), on August 28, 2019 the Company issued to Foris a warrant to purchase up to 4.9 million shares of Common Stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act. The exercise price of the warrant is subject to standard adjustments but does not contain any anti-dilution protection, and the warrant only permits “cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the warrant. In addition, Foris may not exercise the warrant to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the Company is seeking at its 2019 annual meeting of stockholders. The Company concluded the warrant is a freestanding instrument that is legally detachable and separately exercisable from the August 2019 Foris Note and will be classified in equity as the warrant is both indexed to the Company’s own stock and meet the equity classification criteria. As such, the Company will account for the fair value of the warrant within equity and will not subsequently remeasured to fair value at each reporting period, unless new events trigger a requirement for the warrants to be reclassified to an asset or liability. The warrant was measured using the Black-Scholes option pricing model with the following parameters: stock price $3.67 , strike price $3.90 , volatility 94% , risk-free interest rate 1.50% , term 2.0 years, and expected dividend yield 0% . The warrant had a $8.7 million Black-Scholes fair value and a $5.2 million relative fair value after allocating the August 2019 Foris Note proceeds to the $0.5 million fair value of an embedded mandatory redemption feature contained in the August 2019 Foris Note, and allocating on a residual basis, to the relative fair values of the August 2019 Foris Note and the August 2019 Foris Warrant. See Note 4, “Debt” for further information regarding the initial accounting treatment for the embedded mandatory redemption feature and the accounting treatment for the relative fair value of this warrant, and see Note 3, “Fair Value Measurements” for information regarding the fair value measurement and subsequent accounting for the embedded mandatory redemption feature. Also, on August 28, 2019 in connection with the entry into the August 2019 Foris Credit Agreement, the Company and Foris amended the warrant to purchase up to 3.9 million shares of common stock issued to Foris on April 26, 2019 to reduce the exercise price of such warrant from $5.12 per share to $3.90 per share, and amended the warrant to purchase up to 0.4 million shares of common stock issued to Foris on May 14, 2019 to reduce the exercise price of such warrant from $4.56 per share to $3.90 per share (see above under “ Private Placements ” for more information regarding these warrants). The warrant modifications were measured on a before and after modification basis using a Black-Scholes option pricing model with the following parameters: stock price $3.67 , strike price $3.90 , volatility 98% - 100% , risk-free interest rate 1.50% , term 1.7 years, and expected dividend yield 0% , resulting in $1.1 million of incremental fair value, which was accounted for as an increase to additional paid in capital and a debt discount to the $19 million August 2019 Foris Note. See Note 4, “Debt” for additional information regarding the debt discount recorded in connection with the modification of these warrants. September 2019 Investor Warrants Issuance In connection with the entry into the Investor Credit Agreements (see Note 4, “Debt”), on September 10, 2019, the Company issued to the Investors warrants (the Investor Warrants) to purchase up to an aggregate of 3.2 million shares of common stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act. The exercise price of the warrants is subject to standard adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise after the six-month anniversary of issuance of the applicable warrant, and only to the extent that there is not an effective registration statement covering the resale of the shares of common stock underlying the applicable warrant. In addition, no Investor may exercise its warrant to the extent that, after giving effect to such exercise, such Investor, together with its affiliates, would beneficially own in excess of 9.99% of the number of shares of common stock outstanding after giving effect to such exercise. In addition, the Company agreed to file a registration statement providing for the resale by the Investors of the shares of common stock underlying the warrants with the SEC within 60 days following the date of the issuance of the warrants and to use commercially reasonable efforts to (i) cause such registration statement to become effective within 120 days following the date of the issuance of the warrants and (ii) keep such registration statement effective until the Investors no longer beneficially own any such shares of common stock or such shares of common stock are eligible for resale under Rule 144 under the Securities Act without regard to volume limitations. If the Company fails to file the registration statement by the filing deadline or the registration statement is not declared effective by the effectiveness deadline, or the Company fails to maintain the effectiveness of the registration statement as required by the warrants, then the exercise price of the warrants will be reduced by 10% , and by an additional 5% if such failure continues for longer than 90 days , subject to an exercise price floor of $3.31 per share, provided that upon the cure by the Company of such failure, the exercise price of the warrants will revert to $3.90 per share. The Company concluded the Investor Warrants are freestanding instruments that are legally detachable and separately exercisable from the Investor Notes and should be classified and accounted for as a liability because the warrants contain certain price and share count adjustment protection and other modification protection provisions that cause the warrants to not meet the fixed-for-fixed criterion, and thus, are not considered indexed to the Company’s stock. As such, the Company has accounted for the Investor Warrants as a liability and will subsequently remeasure to fair value at each reporting period with changes in fair value recorded in the statement of operations. The warrants were measured using the Black-Scholes option pricing model with the following parameters as of the September 10, 2019 issuance date and September 30, 2019 balance sheet date, respectively: stock price $4.56 and $4.76 , strike price $3.90 , volatility 94% and 95% , risk-free interest rate 1.67% and 1.63% , term 2.0 years, and expected dividend yield 0% . The warrants had an initial fair value of $7.9 million and was recorded as a derivative liability and debt discount to be amortized to interest expense under the effective interest method over the term of the Investor Notes; at September 30, 2019, the fair value of the warrants was $8.3 million . See Note 4, “Debt” for fu

Loss Per Share

Loss Per Share	9 Months Ended
	Sep. 30, 2019
Earnings Per Share [Abstract]
Loss Per Share	Loss per Share For the three and nine months ended September 30, 2019 and September 30, 2018 , 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 September 30, Nine Months Ended September 30, (In thousands, except shares and per share amounts) 2019 2018 2019 2018 Numerator: Net loss attributable to Amyris, Inc. $ (59,562 ) $ (74,453 ) $ (163,893 ) $ (181,637 ) Less: deemed dividend to preferred shareholder on issuance and modification of common stock warrants — — (34,964 ) — Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D preferred stock — (6,852 ) — (6,852 ) Less: losses allocated to participating securities 1,655 4,491 6,233 12,824 Net loss attributable to Amyris, Inc. common stockholders $ (57,907 ) $ (76,814 ) $ (192,624 ) $ (175,665 ) — — — — Denominator: Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted 103,449,612 60,966,071 91,344,150 55,735,571 Loss per share attributable to common stockholders, basic and diluted $ (0.56 ) $ (1.26 ) $ (2.11 ) $ (3.15 ) 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 September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Period-end stock options to purchase common stock 5,398,834 5,449,701 5,398,834 5,449,701 Convertible promissory notes (1) 14,259,214 9,397,134 14,259,214 9,397,134 Period-end common stock warrants 52,612,330 25,986,432 52,612,330 25,986,432 Period-end restricted stock units 4,543,190 5,324,092 4,543,190 5,324,092 Period-end preferred stock 2,955,732 2,955,732 2,955,732 2,955,732 Total potentially dilutive securities excluded from computation of diluted loss per share 79,769,300 49,113,091 79,769,300 49,113,091 ______________ (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.

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2019
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 13, “Divestiture” in Part II, Item 8 of the 2018 Form 10-K/A) 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 alleges securities law violations based on statements and omissions made by the Company during such period. 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., Case No. 4:19-cv-03621 and Carlson v. Doerr, et al., Case No. 4:19-cv-06230) based on similar allegations to those made in the securities class action complaint described above. On October 18, 2019, the first of these derivative cases was dismissed. The remaining derivative complaint names Amyris, Inc. as a nominal defendant and certain of the Company’s current and former officers and directors as additional defendants. The derivative lawsuit seeks 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 complaint also seeks a series of changes to the Company’s corporate governance policies, restitution to the Company from the individual defendants, and an award of attorneys’ fees. This case is in the initial pleadings stage. The Company believes that complaint lacks merit, and intends to defend itself 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 November 1, 2019 CVI Investments, Inc. (“CVI”) filed a complaint against the Company in the United States District Court for the Southern District of New York. The complaint contained causes of action for breach of contract and declaratory judgment. Both causes of action arise out of the Company’s alleged failure to issue shares under a Senior Convertible Note originally issued by the Company to CVI in December 2018 (the “Note”). Under the Note, as modified in two subsequent amendments (See Note 4, Debt, 6% Convertible Notes Exchanges), the Company would repay in cash or common stock over time with interest and certain other charges. Through the complaint, CVI sought to convert certain amounts owed under the Note into shares of the Company’s common stock. The complaint was never served on the Company. On November 8, 2019 the Company and CVI entered into an agreement by which CVI agreed to immediately dismiss its complaint with prejudice upon the satisfaction by the Company of all amounts due under the Note pursuant to the Second Note Exchange Agreement. 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 are not predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, 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.

Revenue Recognition and Contrac

Revenue Recognition and Contract Assets and Liabilities	9 Months Ended
	Sep. 30, 2019
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 September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total Europe $ 2,609 $ 2,305 $ 1,354 $ 6,268 $ 1,176 $ 142 $ 3,909 $ 5,227 United States 9,927 — 9,114 19,041 4,883 — 625 5,508 Asia 2,398 — 4,789 7,187 3,544 — — 3,544 South America 2,272 — 28 2,300 36 — — 36 Other 157 — — 157 — — — — $ 17,363 $ 2,305 $ 15,285 $ 34,953 $ 9,639 $ 142 $ 4,534 $ 14,315 Nine Months Ended September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total Europe $ 7,565 $ 43,387 $ 6,180 $ 57,132 $ 6,597 $ 7,584 $ 11,725 $ 25,906 United States 22,806 — 16,015 38,821 9,184 — 6,457 15,641 Asia 8,015 — 5,038 13,053 5,335 — — 5,335 South America 2,787 — 34 2,821 251 — — 251 Other 194 — — 194 100 — — 100 $ 41,367 $ 43,387 $ 27,267 $ 112,021 $ 21,467 $ 7,584 $ 18,182 $ 47,233 Significant Revenue Agreements During the Nine Months Ended September 30, 2019 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. Under the agreement, the Company would perform research and development activities and Lavvan would be responsible for the manufacturing and commercialization of the cannabinoids developed under the agreement. The Cannabinoid Agreement is being principally funded on a milestone basis, with the Company also entitled to receive certain supplementary research and development funding from Lavvan. 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. Additionally, the Cannabinoid Agreement provides for profit share to the Company on Lavvan's gross profit margin once products are commercialized; these payments will be due for the next 20 years . On May 2, 2019, the parties consummated the transactions contemplated by the Cannabinoid Agreement, including the formation of 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 LSA (see Note 5, “Debt” in Part II, Item 8 of the 2018 Form 10-K/A). 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 obligations, which the Company concluded to be research and development services. The Company estimated the total unconstrained transaction price to be $135 million , based on a high probability of achieving certain underlying milestones. As of September 30, 2019 , the Company has constrained $165 million of variable consideration related to milestones that have not met the criteria under ASC 606 necessary to be included in the transaction price. The Company determined 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 $8.2 million and $11.7 million of collaboration revenue under the Cannabinoid Agreement for the three and nine months ended September 30, 2019 based on proportional performance delivered to date. At September 30, 2019 , $1.7 million of the $11.7 million of collaboration revenues recognized in the nine months ended September 30, 2019 was recorded as a contract asset. See the "Contract Assets and Liabilities" section below for further information regarding this contract asset. DSM Agreements On April 16, 2019, the Company assigned to DSM, and DSM assumed, all of the Company’s rights and obligations under the December 2017 DSM Value Sharing Agreement, as amended, for aggregate consideration to the Company of $57.0 million , which included $7.4 million of the third and final annual royalty payment due under the original agreement received on March 29, 2019 (see Note 10, "Revenue Recognition" in Part II, Item 8 of the 2018 Form 10-K/A). On April 16, 2019, the Company received net cash of $21.7 million , with the remaining $27.9 million used by the Company to offset past due trade payables (including interest) under the 2017 Supply Agreement, the obligation under the November 2018 Securities Purchase Agreement, and manufacturing capacity fees under the provisions of Amendment No. 1 to the 2017 Supply Agreement (see Note 11, "Related Party Transactions" in Part II, Item 8 of the 2018 Form 10-K/A). The original 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 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 refund obligation. The effect of the contract modification on the transaction price, and on the Company’s measure of progress toward complete satisfaction of the performance obligation, was recognized as an adjustment to revenue at the date of the contract modification on a cumulative catch-up basis. As a result, the Company recognized $37.1 million of licenses and royalties revenue in the nine months ended September 30, 2019 , due to fully satisfying the performance obligation. The $12.5 million of prepaid variable consideration is recorded as a refund liability in other noncurrent liabilities and represents a stand ready obligation to refund some or all of the $12.5 million prepaid consideration if certain criteria outlined in the assignment agreement is not met before December 2021. The Company will update its assessment of amounts it expects to be entitled to keep at the end of each reporting period, by reducing the refund liability and recording additional license and royalty revenue as the criteria is met. The Company also recognized $3.6 million of previously deferred revenue under the December 2017 DSM Value Sharing Agreement, as the remaining underlying performance obligation was fully satisfied through the April 16, 2019 assignment of the Value Sharing Agreement to DSM. In addition, on April 16, 2019 the Company and DSM entered into amendments to the 2017 Supply Agreement and the 2017 Performance Agreement, as well as the Quota Purchase Agreement relating to the December 2017 sale of Amyris Brasil to DSM (see Note 10, “Revenue Recognition” and Note 13, “Divestiture” in Part II, Item 8 of the 2018 Form 10-K/A ), pursuant to which (i) DSM agreed to reduce certain manufacturing costs and fees paid by the Company related to the production of farnesene under the Supply Agreement through 2021, as well as remove the priority of certain customers over the Company with respect to production capacity at the Brotas, Brazil facility, (ii) the Company agreed to provide DSM rights to conduct certain process and downstream recovery improvements under the Performance Agreement at facilities other than the Brotas, Brazil facility in exchange for DSM providing the Company with a license to such improvements and (iii) the Company released DSM from its obligation to provide manufacturing and support services under the Quota Purchase Agreement in connection with the Company’s planned new manufacturing facility, which is no longer to be located at the Brotas, Brazil location. In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 10, “Revenue Recognition ” in Part II, Item 8 of the 2018 Form 10-K/A) , the Company recognized the following revenues for the three and nine months ended September 30, 2019 and 2018 : Three Months Ended September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total DSM - related party $ — $ — $ 844 $ 844 $ — $ (39 ) $ 1,197 $ 1,158 Givaudan 3,312 — — 3,312 525 — 1,500 2,025 Firmenich 4,556 2,305 400 7,261 903 181 1,212 2,296 Lavvan — — 8,238 8,238 — — — — Subtotal revenue from significant revenue agreements 7,868 2,305 9,482 19,655 1,428 142 3,909 5,479 Revenue from all other customers 9,495 — 5,803 15,298 8,211 — 625 8,836 Total revenue from all customers $ 17,363 $ 2,305 $ 15,285 $ 34,953 $ 9,639 $ 142 $ 4,534 $ 14,315 Nine Months Ended September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total DSM - related party $ 2 $ 40,302 $ 3,886 $ 44,190 $ — $ 7,366 $ 3,667 $ 11,033 Givaudan 6,127 — — 6,127 3,710 — 4,358 8,068 Firmenich 6,439 3,085 1,413 10,937 1,110 218 3,698 5,026 Lavvan — — 11,742 11,742 — — — — Subtotal revenue from significant revenue agreements 12,568 43,387 17,041 72,996 4,820 7,584 11,723 24,127 Revenue from all other customers 28,799 — 10,226 39,025 16,647 — 6,459 23,106 Total revenue from all customers $ 41,367 $ 43,387 $ 27,267 $ 112,021 $ 21,467 $ 7,584 $ 18,182 $ 47,233 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 accounts receivable are recorded 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 for sale of goods or the performance of services. Contract Balances The following table provides information about accounts receivable, contract liabilities and refund liability from contracts with customers: (In thousands) September 30, 2019 December 31, 2018 Accounts receivable, net $ 17,072 $ 16,003 Accounts receivable - related party, net $ 3,692 $ 1,349 Contract assets $ 2,567 $ — Accounts receivable, unbilled - related party $ — $ 8,021 Accounts receivable, unbilled, noncurrent - related party $ 1,203 $ 1,203 Contract liabilities, current $ 4,737 $ 8,236 Contract liabilities, noncurrent (1) $ 1,449 $ 1,587 Refund liability - related party $ 12,500 $ — (1) As of September 30, 2019 and December 31, 2018 , contract liabilities, noncurrent is presented in Other Noncurrent Liabilities in the condensed consolidated balance sheets. Accounts receivable, unbilled - related party decreased from December 31, 2018 to September 30, 2019, primarily as the result of issuing an $8.0 million invoice and receiving early payment from DSM in April 2019 for the final installment of the December 2017 minimum guaranteed value share payments originally due on December 31, 2019. The Company received a $7.4 million cash payment in April 2019 and the $0.6 million difference between the original amount due and the $7.4 million cash payment was recorded as a $0.4 million reduction of royalty revenue during the quarter and a $0.2 million charge to interest expense. The contract asset balance at September 30, 2019 consists of $1.7 million related to the Lavvan collaboration agreement and $0.8 million related to the Yifan collaboration agreements (see Note 10, "Revenue Recognition" in Part II, Item 8 of the 2018 Form 10-K/A for information regarding the Yifan collaboration agreements), for which the Company does not yet have the contractual right to bill. 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 September 30, 2019 . (In thousands) As of September 30, 2019 Remaining 2019 $ 12,523 2020 77,029 2021 48,354 2022 and thereafter 333 Total from all customers $ 138,239 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 $180.9 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

Related Party Transactions

Related Party Transactions	9 Months Ended
	Sep. 30, 2019
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Related Party Debt See Note 4, "Debt" above for related party debt as of September 30, 2019 and December 31, 2018 . Related Party Accounts Receivable and Unbilled Receivables Related party accounts receivable and unbilled receivables as of September 30, 2019 and December 31, 2018 were as follows: (In thousands) September 30, 2019 December 31, 2018 Related party accounts receivable: DSM $ 3,692 $ 1,071 Novvi — 188 Total — 90 $ 3,692 $ 1,349 Related party accounts receivable, unbilled, current: DSM $ — $ 8,021 Related party accounts receivable, unbilled, noncurrent: DSM $ 1,203 $ 1,203

Stock-based Compensation

Stock-based Compensation	9 Months Ended
	Sep. 30, 2019
Share-based Payment Arrangement [Abstract]
Stock-based Compensation	Stock-based Compensation The Company’s stock option activity and related information for the nine months ended September 30, 2019 was as follows: Quantity of Stock Options Weighted- Weighted-average Aggregate Outstanding - December 31, 2018 5,390,270 $ 11.55 8.5 $ 29 Granted 270,633 $ 3.67 Exercised (3,612 ) $ 5.48 Forfeited or expired (251,557 ) $ 18.00 Outstanding - September 30, 2019 5,405,734 $ 10.57 8.1 $ 705 Vested or expected to vest after September 30, 2019 4,781,072 $ 11.28 8.0 $ 682 Exercisable at September 30, 2019 1,247,627 $ 28.74 6.3 $ 416 The Company’s restricted stock units (RSUs) activity and related information for the nine months ended September 30, 2019 was as follows: Quantity of Restricted Stock Units Weighted-average Grant-date Fair Value Weighted-average Remaining Contractual Life, in Years Outstanding - December 31, 2018 5,294,803 $ 5.50 1.7 Awarded 1,148,866 $ 3.73 RSUs released (1,389,466 ) $ 4.98 RSUs forfeited (511,013 ) $ 4.91 Outstanding - September 30, 2019 4,543,190 $ 5.07 1.5 Vested or expected to vest after September 30, 2019 4,196,792 $ 5.08 1.4 Stock-based compensation expense related to employee and non-employee options, RSUs and ESPP during the three and nine months ended September 30, 2019 and 2018 was allocated to research and development expense and sales, general and administrative expense as follows: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2019 2018 2019 2018 Research and development $ 663 $ 495 $ 2,002 $ 1,191 Sales, general and administrative 2,571 2,442 8,058 4,924 Total stock-based compensation expense $ 3,234 $ 2,937 $ 10,060 $ 6,115 As of September 30, 2019 , there was unrecognized compensation expense of $24.9 million related to stock options and RSUs. The Company expects to recognize this expense over a weighted-average period of 2.8 years. Evergreen Shares for 2010 Equity Incentive Plan and 2010 Employee Stock Purchase Plan In February 2019, 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 3,828,241 shares. This increase is equal to approximately 5.0% of the 76,564,829 total outstanding shares of the Company’s common stock as of December 31, 2018. This automatic increase was effective as of January 1, 2019. 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 383,824 shares. This increase is equal to approximately 0.5% of the 76,564,829 total outstanding shares of the Company’s common stock as of December 31, 2018. This automatic increase was effective as of January 1, 2019.

Subsequent Events

Subsequent Events	9 Months Ended
	Sep. 30, 2019
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events LSA Amendments, Additional Loan and Warrant Issuance On October 10, 2019, the Company, the Subsidiary Guarantors and Foris entered into Amendment No. 6 to the LSA (the October 2019 LSA Amendment), pursuant to which the maximum loan commitment of Foris under the LSA (see Note 4, “Debt”) was increased by $10.0 million . In connection with the entry into the October 2019 LSA Amendment, on October 11, 2019, the Company borrowed an additional $10.0 million from Foris under the LSA (the October 2019 LSA Loan), which loan is subject to the terms and provisions of the LSA, including the lien on substantially all of the assets of the Company and the Subsidiary Guarantors. After giving effect to the LSA Loan, there is $81.0 million aggregate principal amount of loans outstanding under the LSA. Also, in connection with the entry into the October 2019 LSA Amendment, on October 11, 2019 the Company issued to Foris a warrant to purchase up to 2.0 million shares of common stock, at an exercise price of $2.87 per share, with an exercise term of two years from issuance (the October 2019 Foris Warrant). Pursuant to the terms of the October 2019 Foris Warrant, Foris may not exercise the October 2019 Foris Warrant to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of shares of Common Stock outstanding after giving effect to such exercise, unless the Company has obtained stockholder approval to exceed such limit, which the Company is seeking at its 2019 annual meeting of stockholders. The October 2019 Foris Warrant was issued in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act. On October 28, 2019, the Company, the Subsidiary Guarantors and Foris entered into an amended and restated LSA (as amended and restated, the A&R LSA), pursuant to which, among other things, certain covenants and related definitions were amended to permit the incurrence of the indebtedness under the October 2019 Naxyris Loan (as defined below), subject to the terms of an amended and restated intercreditor agreement, dated October 28, 2019, between Foris and Naxyris governing the respective rights of the parties with respect to, among other things, the assets securing the A&R Naxyris LSA (as defined below) and the A&R LSA, and additional covenants were added relating to, among other things, maintenance of intellectual property, compliance with laws, delivery of reports and repayment of indebtedness. Series B Preferred Stock Beneficial Ownership Limitation On October 24, 2019, the Company filed a certificate of amendment (the Certificate of Amendment) to the Certificate of Designation (the Certificate of Designation) relating to the Company’s Series B 17.38% Convertible Preferred Stock, par value $0.0001 per share (the Series B Preferred Stock), with the Secretary of State of Delaware. The Company had originally filed the Certificate of Designation on May 8, 2017, pursuant to which the conversion of the Series B Preferred Stock was subject to a beneficial ownership limitation of 4.99% , or such other percentage as determined by the holder, not to exceed 9.99% of the number of shares of the Company’s common stock outstanding after giving effect to such conversion (the Beneficial Ownership Limitation). In addition, pursuant to the Certificate of Designation, each share of Series B Preferred Stock automatically converted on October 9, 2017, subject to the Beneficial Ownership Limitation. Pursuant to the Certificate of Amendment, the Beneficial Ownership Limitation was eliminated, permitting the conversion of any outstanding shares of Series B Preferred Stock, the conversion of which was previously prevented by the Beneficial Ownership Limitation. As such, on October 24, 2019, the remaining 6,376.28 shares of Series B Preferred Stock, which were all held by Foris, automatically converted into 1.0 million shares of the Company’s common stock, including the related Make-Whole shares (see Note 7, “Stockholders’ Deficit” in Part II, Item 8 of the 2018 Form 10-K/A). Naxyris LSA Amendment On October 28, 2019, the Company, the Subsidiary Guarantors and Naxyris amended and restated the Naxyris Loan Agreement (as amended and restated, the A&R Naxyris LSA), pursuant to which the maximum loan commitment of Naxyris under the Naxyris Loan Facility (see Note 4, “Debt”) was increased by $10.4 million . In connection with the entry into the A&R Naxyris LSA, on October 29, 2019, the Company borrowed an additional $10.4 million from Naxyris under the A&R Naxyris LSA (the October 2019 Naxyris Loan), which loan is subject to the terms and provisions of the A&R Naxyris LSA, including the lien on substantially all of the assets of the Company and the Subsidiary Guarantors. In connection with the funding of the October 2019 Naxyris Loan, the Company paid Naxyris an upfront fee of $0.4 million . After giving effect to the October 2019 Naxyris LSA Loan, there is $20.9 million aggregate principal amount of loans outstanding under the A&R Naxyris LSA. Also, in connection with the entry into the A&R Naxyris LSA, on October 28, 2019 the Company issued to Naxyris a warrant to purchase up to 2.0 million shares of common stock, at an exercise price of $3.87 per share, with an exercise term of two years from issuance (the Naxyris October 2019 Warrant). The Naxyris October 2019 Warrant was issued in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act, and Regulation D promulgated under the Securities Act. Second Exchange Note Exchange Agreement On November 8, 2019, the Company entered into a Securities Exchange Agreement with certain private investors, pursuant to which, upon the purchase by the investors of the Second Exchange Note (see Note 4, “Debt”) from its current holder, the Second Exchange Note would be exchanged for new senior convertible notes with an aggregate principal amount of $66.0 million (the “New Notes”) that (i) bear interest at 5% per annum, which interest is payable monthly in arrears beginning February 1, 2020, in either cash or, at the Company’s option, subject to the satisfaction of certain equity conditions, in shares of common stock at a discount to the then-current market price, subject to a price floor (the “Installment Conversion Price”), (ii) are convertible into shares of the Company’s common stock at an initial conversion price of $5.00 per share, and (iii) mature on September 30, 2022, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act. The New Notes will be payable in monthly installments beginning February 1, 2020 in either cash or, at the Company’s option, subject to the satisfaction of certain equity conditions, in shares of common stock at the Installment Conversion Price. Each installment payment will reduce the principal amount under the New Notes by 90% of the amount of such installment payment. The New Notes contain customary terms and covenants, including (i) a restriction on the Company’s ability to incur additional indebtedness, (ii) covenants related to minimum revenue, liquidity, financing activity and the conversion or exchange of existing indebtedness into equity, (iii) certain events of default, after which the holders may (A) require the Company to redeem all or any portion of their New Notes in cash at a price equal to 115% of the amount being redeemed and (B) convert all or any portion of their New Notes at a discount to the Installment Conversion Price and (iv) certain other events, after which the holders may convert all or any portion of their New Notes at a discount to the Installment Conversion Price. The Company may at its option redeem the New Notes, in full, at a price equal to 115% of the greater of (A) the principal amount of the New Notes being redeemed and (B) the intrinsic value of the shares of Common Stock underlying the principal amount of the New Notes being redeemed. In addition, the Company is required to (i) redeem the New Notes in an aggregate amount of $10.0 million following the receipt by the Company of at least $75.0 million of aggregate net cash proceeds from one or more financing transactions, at a price equal to 110% of the amount being redeemed and (ii) redeem the New Notes in an aggregate amount of $10.0 million on December 31, 2019, at a price equal to 110% of the amount being redeemed, in each case unless such redemption is deferred by the holder. The issuance of shares upon conversion of the New Notes or otherwise is limited by (i) a 4.99% beneficial ownership limitation, and (ii) the limitation imposed by Nasdaq Listing Standard Rule 5635(d), unless the Company’s obtains stockholder approval to exceed such limit. Under the New Notes, the Company will agree to use commercially reasonable efforts to obtain such approval on or prior to May 31, 2020. The Securities Exchange Agreement prohibits the Company, subject to certain exceptions, from (i) disposing of any common stock or securities convertible into or exchangeable for shares of common stock from the date of the Securities Exchange Agreement through 90 days after the closing of the exchange and (ii) effecting or entering into an agreement to effect a variable rate transaction while the New Notes are outstanding. The closing of the issuance and sale of the New Notes is expected to occur on or about November 12, 2019, subject to customary closing conditions, including the purchase by the investors of the Second Exchange Note.

Basis of Presentation and Sum_2

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2019
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, since they are interim statements, the accompanying 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.
Revenue Recognition	Revenue Recognition The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer and recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does not incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred. The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators among others when determining whether it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does not meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis. The Company’s significant contracts and contractual terms with its customers are presented in Note 10, "Revenue Recognition" in Part II, Item 8 of the 2018 Form 10-K/A. The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. The Company’s renewable products are delivered to customers from the Company’s facilities with shipping terms typically specifying F.O.B. shipping point. Performance Obligations A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts may contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis. The following is a description of the principal goods and services from which the Company generates revenue. Renewable Product Sales Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the first transportation carrier. The Company, on occasion, may recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does not have the ability to direct the product to a different customer. It is at this point that the Company has the right to payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do not include rights of return. Returns are accepted only if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a two-year assurance-type warranty to replace squalane products that do not meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated. Licenses and Royalties Licensing of Intellectual Property: When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized. Royalties from Licensing of Intellectual Property: The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits. When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception and revenue is estimated and recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends. When the Company’s intellectual property license is not the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts. Grants and Collaborative Research and Development Services Collaborative Research and Development Services: The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaborators with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include one or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits. Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Generally, revenue is recognized using an input-based measure of progress towards the satisfaction of the performance obligations, which can be based on labor hours expended or time-based in proportion to the estimated total project effort or total projected time to complete. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized. Certain performance obligations are associated with milestones agreed between the Company and its customer. Revenue generated from the performance of services in accordance with these milestones is recognized upon confirmation from the customer that the milestone has been achieved. In these cases, amounts recognized are constrained to the amount of consideration received upon achievement of the milestone. The Company generally invoices its collaborators on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Contract liability arises from amounts received in advance of performing the research and development activities and is recognized as revenue in future periods as the performance obligations are satisfied. Grants: The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements. The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.
Accounting Standards or Updates Recently Adopted and Recent Accounting Standards or Updates Not Yet Effective	Accounting Standards or Updates Recently Adopted In the nine months ended September 30, 2019 , the Company adopted these accounting standards or updates: Leases In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842). The standard requires the recognition of lease liabilities and right-of-use (ROU) assets on the balance sheet arising from lease transactions at the lease commencement date and the disclosure of key information about leasing arrangements. In July 2018, the FASB issued ASU 2018-11, Leases (Topic 842): Targeted Improvements , which provided entities the option to use the effective date as the date of initial application on transition to the new guidance. The Company elected this transition method, and as a result, the Company did not adjust comparative information for prior periods. The Company elected certain additional practical expedients permitted by the new guidance allowing the Company to carry forward historical accounting related to lease identification and classification for existing leases upon adoption. The Company adopted this standard on January 1, 2019 using the modified retrospective approach and elected the package of practical expedients permitted under transition guidance, which allowed the Company to carry forward its historical assessments of: (1) whether contracts are or contain leases, (2) lease classification and (3) initial direct costs, where applicable. The Company did not elect the practical expedient allowing the use-of-hindsight which would require the Company to reassess the lease term of its leases based on all facts and circumstances through the effective date and did not elect the practical expedient pertaining to land easements as this is not applicable to the Company’s current contracts. The Company elected the post-transition practical expedient to not separate lease components from non-lease components for all leases of manufacturing equipment. The Company also elected a policy of not recording leases on its condensed consolidated balance sheets when the leases have a term of 12 months or less and the Company is not reasonably certain to elect an option to purchase the leased asset. The adoption of this standard had the net effect of increasing both assets and liabilities by $25.7 million , after considering prepaid and other current and noncurrent assets previously recorded on the condensed consolidated balance sheet, but did not have a material impact on the condensed consolidated statements of operations or cash flows. The most significant impact relates to (1) the recognition of new ROU assets and lease liabilities on the balance sheet for the Company's operating leases; and (2) providing significant new disclosures about the Company's leasing activities. Upon adoption, the Company recognized operating lease liabilities of $33.6 million , based on the present value of the remaining minimum rental payments under current leasing standards for existing operating leases. The Company also recognized ROU assets of $29.7 million , which represents the operating lease liability, adjusted for prepaid expenses and deferred rent. The difference between the operating lease ROU assets and lease liabilities reflects the net of advanced rent payments and deferred rent balances that were derecognized at the time of adoption. Financial Instruments with "Down Round" Features In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging (Topic 815): Accounting for Certain Financial Instruments with Down Round Features . The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update became effective in the first quarter of fiscal year 2019, and the Company adopted the standard using a modified retrospective approach. Since the adoption of ASU 2017-11 would have classified the warrants effected as equity at inception, the cumulative-effect adjustment should (i) record the issuance date value of the warrants as if they had been equity classified at the issuance date, (ii) reverse the effects of changes in the fair value of the warrants that had been recorded in the statement of operations of each period, and (iii) eliminate the derivative liabilities from the balance sheet. Upon adoption, the Company (i) recorded an increase of $32.5 million to additional paid-in capital, (ii) recorded a decrease to accumulated deficit of $8.5 million and (iii) decreased the warrant liability by $41.0 million . Recent Accounting Standards or Updates Not Yet Effective 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. The accounting standard update will be effective beginning 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 Company is in the initial stages of evaluating the impact of the standard on its 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. The accounting standard update will be effective beginning in the first quarter of fiscal year 2020 retroactively. The Company does not believe that the impact of the new standard on its condensed consolidated financial statements will be material. 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 will become effective for the Company beginning in the first quarter of fiscal year 2020. The Company does not believe that the impact of the new standard on its condensed consolidated financial statements will be material.
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.

Balance Sheet Details (Tables)

Balance Sheet Details (Tables)	9 Months Ended
	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Inventories	Inventories (In thousands) September 30, 2019 December 31, 2018 Raw materials $ 5,753 $ 3,901 Work-in-process 2,243 539 Finished goods 7,948 5,253 Inventories $ 15,944 $ 9,693
Deferred Cost of Products Sold	Deferred cost of products sold - related party (In thousands) September 30, 2019 December 31, 2018 Deferred cost of products sold - related party $ 968 $ 489 Deferred cost of products sold, noncurrent - related party 15,894 2,828 Total $ 16,862 $ 3,317
Prepaid Expenses and Other Current Assets	Prepaid expenses and other current assets (In thousands) September 30, 2019 December 31, 2018 Prepayments, advances and deposits $ 3,706 $ 5,644 Recoverable taxes from Brazilian government entities 3,270 631 Other 5,873 4,291 Total prepaid expenses and other current assets $ 12,849 $ 10,566
Property, Plant and Equipment, Net	Property, Plant and Equipment, Net (In thousands) September 30, 2019 December 31, 2018 Machinery and equipment $ 47,960 $ 43,713 Leasehold improvements 41,152 39,922 Computers and software 10,305 9,987 Furniture and office equipment, vehicles and land 3,330 3,016 Construction in progress 650 1,749 103,397 98,387 Less: accumulated depreciation and amortization (78,961 ) (78,631 ) Property, plant and equipment, net $ 24,436 $ 19,756
Schedule of Capitalized Software	During the three and nine months ended September 30, 2019 and 2018 , the Company capitalized the following amounts of internal labor costs required to automate, integrate and ready certain laboratory and plant equipment for its intended use: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2019 2018 2019 2018 Capitalized internal labor $ — $ 501 $ 320 $ 2,083
Schedule Of Depreciation and Amortization	During the three and nine months ended September 30, 2019 and 2018 , Depreciation and amortization expense, including amortization of assets under capital leases, was as follows: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2019 2018 2019 2018 Depreciation and amortization expense $ 969 $ 1,013 $ 2,691 $ 3,957
Lease, Cost	Information related to the Company's right-of-use assets and related lease liabilities were as follows: Nine Months Ended September 30, 2019 Cash paid for operating lease liabilities, in thousands $ 15,908 Right-of-use assets obtained in exchange for new operating lease obligations (1) $ 32,074 Weighted-average remaining lease term 2.6 Weighted-average discount rate 17.5 % (1) Includes $29.7 million for operating leases existing on January 1, 2019 and $2.4 million for operating leases that commenced during the nine months ended September 30, 2019 .
Lessee, Lease Liability, Maturity	Maturities of lease liabilities as of September 30, 2019 were as follows: Years ending December 31: (In thousands) Financing Operating Total Leases 2019 (remaining three months) $ 116 $ 3,346 $ 3,462 2020 198 9,652 9,850 2021 1 7,220 7,221 2022 — 7,392 7,392 2023 — 3,033 3,033 Thereafter — — — Total lease payments 315 30,643 30,958 Less: amount representing interest (8 ) (7,505 ) (7,513 ) Total lease liability $ 307 $ 23,138 $ 23,445 Current lease liability $ 295 $ 7,678 $ 7,973 Noncurrent lease liability 12 15,460 15,472 Total lease liability $ 307 $ 23,138 $ 23,445
Other Assets	Other Assets (In thousands) September 30, 2019 December 31, 2018 Contingent consideration $ 4,286 $ 4,286 Deposits 293 2,465 Other 1,041 1,207 Total other assets $ 5,620 $ 7,958
Accrued and Other Current Liabilities	Accrued and Other Current Liabilities (In thousands) September 30, 2019 December 31, 2018 Accrued interest $ 15,297 $ 3,853 Payroll and related expenses 7,677 9,220 Contract termination fees 5,241 4,092 Ginkgo partnership payments obligation 3,267 2,155 Asset retirement obligation 2,990 3,063 Professional services 2,854 1,173 Tax-related liabilities 2,402 2,139 Other 2,958 3,284 Total accrued and other current liabilities $ 42,686 $ 28,979
Other Liabilities	Other noncurrent liabilities (In thousands) September 30, 2019 December 31, 2018 Refund liability $ 12,500 $ — Liability for unrecognized tax benefit 7,115 6,582 Ginkgo partnership payments obligation, net of current portion 4,937 6,185 Contract liability, net of current portion (Note 9) 1,449 1,587 Deferred rent, net of current portion (1) — 6,440 Contract termination fees, net of current portion — 1,530 Other 800 868 Total other noncurrent liabilities $ 26,801 $ 23,192 (1) Deferred rent at December 31, 2018 was reclassified to ROU asset upon the adoption on January 1, 2019 of ASC 842, "Leases".

Fair Value Measurement (Tables)

Fair Value Measurement (Tables)	9 Months Ended
	Sep. 30, 2019
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) September 30, 2019 December 31, 2018 Level 1 Level 2 Level 3 Total Level 1 Level 2 Level 3 Total Liabilities 6% Convertible Notes $ — $ — $ 63,152 $ 63,152 $ — $ — $ 57,918 $ 57,918 Freestanding derivative instruments in connection with the issuance of debt and equity instruments — — 8,325 8,325 — — 42,796 42,796 Embedded derivative instruments in connection with the issuance of debt instruments — — 1,032 1,032 — — — — Total liabilities measured and recorded at fair value $ — $ — $ 72,509 $ 72,509 $ — $ — $ 100,714 $ 100,714
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation	For the nine months ended September 30, 2019 , the Company recorded a $18.6 million loss from change in fair value of debt in connection with the 6% Convertible Notes, as follows: In thousands Fair value at December 31, 2018 $ 57,918 Less: principal paid (13,395 ) Loss on change in fair value 18,629 Fair value at September 30, 2019 $ 63,152
Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation	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 and equity instruments – either freestanding or compound embedded – measured at fair value using significant unobservable inputs (Level 3): (In thousands) Equity-related Derivative Liability Debt-related Derivative Liability Total Derivative Liability Balance at December 31, 2018 $ 41,272 $ 1,524 $ 42,796 Derecognition upon adoption of ASU 2017-11 (39,513 ) (1,524 ) (41,037 ) Fair value of derivative liabilities issued during the period — 8,959 8,959 Change in fair value of derivative liabilities 2,039 398 2,437 Derecognition on extinguishment (3,798 ) — (3,798 ) Balance at September 30, 2019 $ — $ 9,357 $ 9,357

Debt (Tables)

Debt (Tables)	9 Months Ended
	Sep. 30, 2019
Debt Disclosure [Abstract]
Schedule of Debt	Net carrying amounts of debt are as follows: September 30, 2019 December 31, 2018 (In thousands) Principal Unamortized Debt (Discount) Premium Change in Fair Value Net Balance Principal Unamortized Debt (Discount) Premium Change in Fair Value Net Balance Convertible notes payable 6% convertible notes $ 62,825 $ — $ 327 $ 63,152 $ 60,000 $ — $ (2,082 ) $ 57,918 August 2013 financing convertible note — — — — 4,415 (70 ) — 4,345 2015 Rule 144A convertible notes — — — — 37,887 (2,413 ) — 35,474 2014 Rule 144A convertible notes — — — — 24,004 (867 ) — 23,137 62,825 — 327 63,152 126,306 (3,350 ) (2,082 ) 120,874 Related party convertible notes payable 2014 Rule 144A convertible notes 9,705 — — 9,705 24,705 (1,038 ) — 23,667 Loans payable and credit facilities Ginkgo note 12,000 (3,377 ) — 8,623 12,000 (4,047 ) — 7,953 Nikko notes 9,122 (938 ) — 8,184 4,598 (1,047 ) — 3,551 Schottenfeld notes 12,500 (8,151 ) 4,349 — — — — Other loans payable 1,280 — — 1,280 312 — — 312 GACP secured term loan facility — — — — 36,000 (1,349 ) — 34,651 34,902 (12,466 ) — 22,436 52,910 (6,443 ) — 46,467 Related party loans payable Foris secured term loan facility 71,041 (8,829 ) — 62,212 — — — — Foris unsecured note 19,000 (6,681 ) — 12,319 — — — — DSM notes 33,000 (5,135 ) — 27,865 25,000 (6,311 ) — 18,689 Naxyris note 10,957 (4,403 ) — 6,554 — — — — 133,998 (25,048 ) — 108,950 25,000 (6,311 ) — 18,689 Total debt 241,430 (37,514 ) 327 204,243 228,921 (17,142 ) (2,082 ) 209,697 Less: current portion (78,716 ) (147,677 ) Long-term debt, net of current portion $ 125,527 $ 62,020
Schedule of Long-term Debt Instruments	Future minimum payments under the Company's debt agreements as of September 30, 2019 are as follows: (In thousands) Convertible Notes Loans Related Party Convertible Notes Related Party Loans Payable and Credit Facilities Total 2019 (remaining three months) $ 66,506 $ 2,737 $ 10,124 $ 9,955 $ 89,322 2020 — 9,356 — 21,807 31,163 2021 — 3,342 — 45,963 49,305 2022 — 15,177 — 83,277 98,454 2023 — 12,899 — 19,000 31,899 Thereafter — 2,268 — — 2,268 Total future minimum payments 66,506 45,779 10,124 180,002 302,411 Less: amount representing interest (3,681 ) (10,877 ) (419 ) (46,004 ) (60,981 ) Less: future conversion of accrued interest to principal — — — — — Present value of minimum debt payments 62,825 34,902 9,705 133,998 241,430 Less: current portion of debt principal (62,825 ) (2,534 ) (9,705 ) (6,842 ) (81,906 ) Noncurrent portion of debt principal $ — $ 32,368 $ — $ 127,156 $ 159,524

Stockholders' Deficit (Tables)

Stockholders' Deficit (Tables)	9 Months Ended
	Sep. 30, 2019
Equity [Abstract]
Schedule of Stockholders' Equity Note, Warrants or Rights	The following table summarizes warrants activity for the current year interim periods ended September 30, 2019 : Transaction Outstanding at December 31, 2018 Exercises Outstanding at March 31, 2019 Additional Warrants Issued Exercises Outstanding at June 30, 2019 Additional Warrants Issued Expiration Outstanding at September 30, 2019 July 2015 related party debt exchange 663,228 (471,204 ) 192,024 245,558 (245,558 ) 192,024 — — 192,024 July 2015 private placement 81,197 (8,547 ) 72,650 — — 72,650 — — 72,650 February 2016 related party private placement 171,429 — 171,429 — — 171,429 — — 171,429 May 2017 cash and dilution warrants 6,292,798 — 6,292,798 4,795,924 (1,924,673 ) 9,164,049 — — 9,164,049 August 2017 cash and dilution warrants 3,968,116 — 3,968,116 3,028,983 — 6,997,099 — — 6,997,099 April 2018 warrant exercise agreements 3,616,174 — 3,616,174 — — 3,616,174 — (3,616,174 ) — August 2018 warrant exercise agreements 12,097,164 — 12,097,164 — — 12,097,164 — — 12,097,164 April 2019 PIPE warrants — — — 8,084,770 — 8,084,770 — — 8,084,770 April 2019 Foris warrant — — — 5,424,804 — 5,424,804 — — 5,424,804 May 2019 6.50% Note Exchange Warrants — — — 1,744,241 — 1,744,241 — — 1,744,241 May-June 2019 6% Note Exchange Warrants — — — 2,181,818 — 2,181,818 — — 2,181,818 July 2019 Wolverine warrant — — — — — — 1,080,000 — 1,080,000 August 2019 Foris LSA warrant — — — — — — 1,438,829 — 1,438,829 August 2019 Foris Credit Agreement warrant — — — — — — 4,871,795 — 4,871,795 August 2019 Naxyris LSA warrant — — — — — — 2,000,000 — 2,000,000 September 2019 Investor Credit Agreement warrant — — — — — — 3,205,128 — 3,205,128 Other 1,406 — 1,406 — — 1,406 — — 1,406 26,891,512 (479,751 ) 26,411,761 25,506,098 (2,170,231 ) 49,747,628 12,595,752 (3,616,174 ) 58,727,206

Loss Per Share (Tables)

Loss Per Share (Tables)	9 Months Ended
	Sep. 30, 2019
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 September 30, Nine Months Ended September 30, (In thousands, except shares and per share amounts) 2019 2018 2019 2018 Numerator: Net loss attributable to Amyris, Inc. $ (59,562 ) $ (74,453 ) $ (163,893 ) $ (181,637 ) Less: deemed dividend to preferred shareholder on issuance and modification of common stock warrants — — (34,964 ) — Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D preferred stock — (6,852 ) — (6,852 ) Less: losses allocated to participating securities 1,655 4,491 6,233 12,824 Net loss attributable to Amyris, Inc. common stockholders $ (57,907 ) $ (76,814 ) $ (192,624 ) $ (175,665 ) — — — — Denominator: Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted 103,449,612 60,966,071 91,344,150 55,735,571 Loss per share attributable to common stockholders, basic and diluted $ (0.56 ) $ (1.26 ) $ (2.11 ) $ (3.15 )
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 September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Period-end stock options to purchase common stock 5,398,834 5,449,701 5,398,834 5,449,701 Convertible promissory notes (1) 14,259,214 9,397,134 14,259,214 9,397,134 Period-end common stock warrants 52,612,330 25,986,432 52,612,330 25,986,432 Period-end restricted stock units 4,543,190 5,324,092 4,543,190 5,324,092 Period-end preferred stock 2,955,732 2,955,732 2,955,732 2,955,732 Total potentially dilutive securities excluded from computation of diluted loss per share 79,769,300 49,113,091 79,769,300 49,113,091 ______________ (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.

Revenue Recognition and Contr_2

Revenue Recognition and Contract Assets and Liabilities (Tables)	9 Months Ended
	Sep. 30, 2019
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 September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total Europe $ 2,609 $ 2,305 $ 1,354 $ 6,268 $ 1,176 $ 142 $ 3,909 $ 5,227 United States 9,927 — 9,114 19,041 4,883 — 625 5,508 Asia 2,398 — 4,789 7,187 3,544 — — 3,544 South America 2,272 — 28 2,300 36 — — 36 Other 157 — — 157 — — — — $ 17,363 $ 2,305 $ 15,285 $ 34,953 $ 9,639 $ 142 $ 4,534 $ 14,315 Nine Months Ended September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total Europe $ 7,565 $ 43,387 $ 6,180 $ 57,132 $ 6,597 $ 7,584 $ 11,725 $ 25,906 United States 22,806 — 16,015 38,821 9,184 — 6,457 15,641 Asia 8,015 — 5,038 13,053 5,335 — — 5,335 South America 2,787 — 34 2,821 251 — — 251 Other 194 — — 194 100 — — 100 $ 41,367 $ 43,387 $ 27,267 $ 112,021 $ 21,467 $ 7,584 $ 18,182 $ 47,233
Revenue in Connection with Significant Revenue Agreement	In connection with the significant revenue agreements discussed above and others previously disclosed (see Note 10, “Revenue Recognition ” in Part II, Item 8 of the 2018 Form 10-K/A) , the Company recognized the following revenues for the three and nine months ended September 30, 2019 and 2018 : Three Months Ended September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total DSM - related party $ — $ — $ 844 $ 844 $ — $ (39 ) $ 1,197 $ 1,158 Givaudan 3,312 — — 3,312 525 — 1,500 2,025 Firmenich 4,556 2,305 400 7,261 903 181 1,212 2,296 Lavvan — — 8,238 8,238 — — — — Subtotal revenue from significant revenue agreements 7,868 2,305 9,482 19,655 1,428 142 3,909 5,479 Revenue from all other customers 9,495 — 5,803 15,298 8,211 — 625 8,836 Total revenue from all customers $ 17,363 $ 2,305 $ 15,285 $ 34,953 $ 9,639 $ 142 $ 4,534 $ 14,315 Nine Months Ended September 30, (In thousands) 2019 2018 Renewable Products Licenses and Royalties Grants and Collaborations Total Renewable Products Licenses and Royalties Grants and Collaborations Total DSM - related party $ 2 $ 40,302 $ 3,886 $ 44,190 $ — $ 7,366 $ 3,667 $ 11,033 Givaudan 6,127 — — 6,127 3,710 — 4,358 8,068 Firmenich 6,439 3,085 1,413 10,937 1,110 218 3,698 5,026 Lavvan — — 11,742 11,742 — — — — Subtotal revenue from significant revenue agreements 12,568 43,387 17,041 72,996 4,820 7,584 11,723 24,127 Revenue from all other customers 28,799 — 10,226 39,025 16,647 — 6,459 23,106 Total revenue from all customers $ 41,367 $ 43,387 $ 27,267 $ 112,021 $ 21,467 $ 7,584 $ 18,182 $ 47,233
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) September 30, 2019 December 31, 2018 Accounts receivable, net $ 17,072 $ 16,003 Accounts receivable - related party, net $ 3,692 $ 1,349 Contract assets $ 2,567 $ — Accounts receivable, unbilled - related party $ — $ 8,021 Accounts receivable, unbilled, noncurrent - related party $ 1,203 $ 1,203 Contract liabilities, current $ 4,737 $ 8,236 Contract liabilities, noncurrent (1) $ 1,449 $ 1,587 Refund liability - related party $ 12,500 $ — (1) As of September 30, 2019 and December 31, 2018 , 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 September 30, 2019 . (In thousands) As of September 30, 2019 Remaining 2019 $ 12,523 2020 77,029 2021 48,354 2022 and thereafter 333 Total from all customers $ 138,239

Related Party Transactions (Tab

Related Party Transactions (Tables)	9 Months Ended
	Sep. 30, 2019
Related Party Transactions [Abstract]
Schedule of Related Party Accounts Receivables	Related party accounts receivable and unbilled receivables as of September 30, 2019 and December 31, 2018 were as follows: (In thousands) September 30, 2019 December 31, 2018 Related party accounts receivable: DSM $ 3,692 $ 1,071 Novvi — 188 Total — 90 $ 3,692 $ 1,349 Related party accounts receivable, unbilled, current: DSM $ — $ 8,021 Related party accounts receivable, unbilled, noncurrent: DSM $ 1,203 $ 1,203

Stock-based Compensation (Table

Stock-based Compensation (Tables)	9 Months Ended
	Sep. 30, 2019
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 nine months ended September 30, 2019 was as follows: Quantity of Stock Options Weighted- Weighted-average Aggregate Outstanding - December 31, 2018 5,390,270 $ 11.55 8.5 $ 29 Granted 270,633 $ 3.67 Exercised (3,612 ) $ 5.48 Forfeited or expired (251,557 ) $ 18.00 Outstanding - September 30, 2019 5,405,734 $ 10.57 8.1 $ 705 Vested or expected to vest after September 30, 2019 4,781,072 $ 11.28 8.0 $ 682 Exercisable at September 30, 2019 1,247,627 $ 28.74 6.3 $ 416
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 nine months ended September 30, 2019 was as follows: Quantity of Restricted Stock Units Weighted-average Grant-date Fair Value Weighted-average Remaining Contractual Life, in Years Outstanding - December 31, 2018 5,294,803 $ 5.50 1.7 Awarded 1,148,866 $ 3.73 RSUs released (1,389,466 ) $ 4.98 RSUs forfeited (511,013 ) $ 4.91 Outstanding - September 30, 2019 4,543,190 $ 5.07 1.5 Vested or expected to vest after September 30, 2019 4,196,792 $ 5.08 1.4
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 nine months ended September 30, 2019 and 2018 was allocated to research and development expense and sales, general and administrative expense as follows: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2019 2018 2019 2018 Research and development $ 663 $ 495 $ 2,002 $ 1,191 Sales, general and administrative 2,571 2,442 8,058 4,924 Total stock-based compensation expense $ 3,234 $ 2,937 $ 10,060 $ 6,115

Basis of Presentation and Sum_3

Basis of Presentation and Summary of Significant Accounting Policies (Details) R$ in Millions	Sep. 16, 2019USD ($)	May 10, 2019USD ($)monthday	Jan. 01, 2019USD ($)	Nov. 08, 2019USD ($)	Sep. 30, 2019USD ($)	May 15, 2019USD ($)	May 10, 2019BRL (R$)monthday	Dec. 31, 2018USD ($)	Sep. 30, 2018USD ($)
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Working capital					$ (103,800,000)			$ (119,500,000)
Accumulated deficit					1,676,779,000			1,521,417,000
Unamortized debt (discount) premium					37,514,000			17,142,000
Long-term debt, total					204,243,000			209,697,000
Fair value of debt					63,152,000			57,918,000
Long-term debt, current maturities, including due to related parties					(78,716,000)			(147,677,000)
Long-term debt, current maturities due within 60 days, including due to related parties					109,300,000
Long-term debt, current maturities due within 60 days, including due to related parties, anticipated interest portion					27,400,000
Cash and cash equivalents					1,632,000			45,353,000	$ 19,045,000
Assets					128,115,000			127,925,000
Liabilities					336,194,000			$ 339,744,000
Operating lease liability					23,138,000
Right-of-use assets under leases					$ 21,936,000
Accounting Standards Update 2016-02
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Assets			$ 25,700,000
Liabilities			25,700,000
Operating lease liability			33,600,000
Right-of-use assets under leases			29,700,000
Accounting Standards Update 2017-11
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Accumulated deficit			8,500,000
Additional paid-in capital, ending balance			32,500,000
Increase (decrease) in derivative liabilities			$ 41,000,000
Convertible Senior Notes, 6.0% Due in 2021, Second Exchange
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, debt default, amount	$ 63,600,000
Extinguishment of debt, amount	$ 148,700,000
Debt instrument, face amount						$ 68,300,000
Second Exchange Note Agreement | Subsequent Event
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Debt instrument, face amount				$ 66,000,000
The Joint Venture
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Percentage of venture owned		50.00%					50.00%
Maximum days to make aggregate cash contribution to joint venture | day		60					60
Aggregate cash contribution due		$ 9,000,000
Agreed purchase price of fixed assets		$ 3,000,000					R$ 2.5
Maximum months to contribute existing supply agreements | month		6					6
Period of entitlement to certain priority fixed cumulative dividends (years)		10 years
Raizen | The Joint Venture
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Percentage of venture owned		50.00%					50.00%

Balance Sheet Details - Invento

Balance Sheet Details - Inventory, Current (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Raw materials	$ 5,753	$ 3,901
Work-in-process	2,243	539
Finished goods	7,948	5,253
Inventories	$ 15,944	$ 9,693

Balance Sheet Details - Deferre

Balance Sheet Details - Deferred Cost of Products Sold - Related Party (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Deferred cost of products sold - related party	$ 968	$ 489
Deferred cost of products sold, noncurrent - related party	15,894	2,828
Total	$ 16,862	$ 3,317

Balance Sheet Details - Additio

Balance Sheet Details - Additional Information (Details) - USD ($) $ in Thousands	Jan. 01, 2019	Sep. 30, 2019	Sep. 30, 2019	Sep. 30, 2018	Apr. 30, 2019	Dec. 31, 2018
Property, Plant and Equipment [Line Items]
Deferred cost of products sold, related party		$ 16,862	$ 16,862			$ 3,317
Supply agreement term (years)			5 years
Right-of-use assets under leases		21,936	$ 21,936
Operating lease liability		23,138	23,138
Operating lease expense		4,700	14,100
Operating lease, right of use asset amortization			10,237	$ 0
Acquisition of right-of-use assets under operating leases	$ 29,700		2,361	$ 0
Finance lease, right-of-use asset amortization		1,100	1,100			2,300
Deferred Cost of Products Sold, Amortization		400	500
Lease, Cost		1,700	5,200
DSM International B.V.
Property, Plant and Equipment [Line Items]
Manufacturing capacity reservation fee, current						24,400
Deferred cost of products sold, related party		$ 6,900	6,900			3,300
Payments of reservation capacity fees			$ 14,100
Minimum
Property, Plant and Equipment [Line Items]
Operating lease remaining lease term (years)			1 year
Operating lease renewal term (years)		1 year	1 year
Maximum
Property, Plant and Equipment [Line Items]
Operating lease remaining lease term (years)			5 years
Operating lease renewal term (years)		5 years	5 years
Accounting Standards Update 2016-02
Property, Plant and Equipment [Line Items]
Right-of-use assets under leases	29,700
Operating lease liability	$ 33,600
Property, Plant and Equipment, Net
Property, Plant and Equipment [Line Items]
Finance lease, right-of-use asset		$ 2,300	$ 2,300			$ 5,000
DSM International B.V.
Property, Plant and Equipment [Line Items]
Prepaid variable consideration		$ 12,500	$ 12,500		$ 12,500

Balance Sheet Details - Prepaid

Balance Sheet Details - Prepaid Expenses and Other Current Assets (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Prepayments, advances and deposits	$ 3,706	$ 5,644
Recoverable taxes from Brazilian government entities	3,270	631
Other	5,873	4,291
Total prepaid expenses and other current assets	$ 12,849	$ 10,566

Balance Sheet Details - Propert

Balance Sheet Details - Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	$ 103,397	$ 98,387
Less: accumulated depreciation and amortization	(78,961)	(78,631)
Property, plant and equipment, net	24,436	19,756
Machinery and equipment
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	47,960	43,713
Leasehold improvements
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	41,152	39,922
Computers and software
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	10,305	9,987
Furniture and office equipment, vehicles and land
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	3,330	3,016
Construction in progress
Property, Plant and Equipment [Line Items]
Property, plant and equipment, gross	$ 650	$ 1,749

Balance Sheet Details - Capital

Balance Sheet Details - Capitalized Software (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Capitalized internal labor	$ 0	$ 501	$ 320	$ 2,083

Balance Sheet Details - Depreci

Balance Sheet Details - Depreciation and Amortization (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Depreciation and amortization expense	$ 969	$ 1,013	$ 2,691	$ 3,957

Balance Sheet Details Balance S

Balance Sheet Details Balance Sheet Details - Right-of-use Assets and Related Lease Liabilities (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2019USD ($)
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Cash paid for operating lease liabilities, in thousands	$ 15,908
Right-of-use assets obtained in exchange for new operating lease obligations	$ 32,074
Weighted-average remaining lease term	2 years 7 months 6 days
Weighted-average discount rate	17.50%

Balance Sheet Details - Maturit

Balance Sheet Details - Maturities of Financing and Operating Leases (Details) $ in Thousands	Sep. 30, 2019USD ($)
Finance Lease, Liability, Payment, Due [Abstract]
2019 (remaining three months), financing leases	$ 116
2020, financing leases	198
2021, financing leases	1
2022, financing leases	0
2023, financing leases	0
Thereafter, financing leases	0
Total lease payments, financing leases	315
Less: amount representing interest	(8)
Total lease liability, financing leases	307
Current lease liability, financing leases	295
Noncurrent lease liability, financing leases	12
Lessee, Operating Lease, Liability, Payment, Due [Abstract]
2019 (remaining three months), operating leases	3,346
2020, operating leases	9,652
2021, operating leases	7,220
2022, operating leases	7,392
2023, operating leases	3,033
Thereafter, operating leases	0
Total lease payments, operating leases	30,643
Less: amount representing interest	(7,505)
Total lease liability, operating leases	23,138
Current lease liability, operating leases	7,678
Noncurrent lease liability, operating leases	15,460
2019 (remaining three months), total leases	3,462
2020, total leases	9,850
2021, total leases	7,221
2022, total leases	7,392
2023, total leases	3,033
Thereafter, total leases	0
Total lease payments, total leases	30,958
Less: amount representing interest	(7,513)
Total lease liability, total leases	23,445
Lease liabilities	7,973
Lease liabilities, net of current portion	$ 15,472

Balance Sheet Details - Other A

Balance Sheet Details - Other Assets (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Contingent consideration	$ 4,286	$ 4,286
Deposits	293	2,465
Other	1,041	1,207
Total other assets	$ 5,620	$ 7,958

Balance Sheet Details - Accrued

Balance Sheet Details - Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Accrued interest	$ 15,297	$ 3,853
Payroll and related expenses	7,677	9,220
Contract termination fees	5,241	4,092
Ginkgo partnership payments obligation	3,267	2,155
Asset retirement obligation	2,990	3,063
Professional services	2,854	1,173
Tax-related liabilities	2,402	2,139
Other	2,958	3,284
Total accrued and other current liabilities	$ 42,686	$ 28,979

Balance Sheet Details - Other N

Balance Sheet Details - Other Noncurrent Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Refund liability	$ 12,500	$ 0
Liability for unrecognized tax benefit	7,115	6,582
Ginkgo partnership payments obligation, net of current portion	4,937	6,185
Contract liability, net of current portion	1,449	1,587
Deferred rent, net of current portion	0	6,440
Contract termination fees, net of current portion	0	1,530
Other	800	868
Total other noncurrent liabilities	$ 26,801	$ 23,192

Fair Value Measurement - Fair V

Fair Value Measurement - Fair Value, Assets, and Liabilities Measured on Recurring Basis (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	$ 63,152	$ 57,918
Fair Value, Measurements, Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	63,152	57,918
Freestanding derivative instruments in connection with the issuance of equity instruments	8,325	42,796
Embedded derivative instruments in connection with the issuance of debt instruments	1,032	0
Total liabilities measured and recorded at fair value	72,509	100,714
Fair Value, Measurements, Recurring | Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Freestanding derivative instruments in connection with the issuance of equity instruments	0	0
Embedded derivative instruments in connection with the issuance of debt instruments	0	0
Total liabilities measured and recorded at fair value	0	0
Fair Value, Measurements, Recurring | Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	0	0
Freestanding derivative instruments in connection with the issuance of equity instruments	0	0
Embedded derivative instruments in connection with the issuance of debt instruments	0	0
Total liabilities measured and recorded at fair value	0	0
Fair Value, Measurements, Recurring | Level 3
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of debt	63,152	57,918
Freestanding derivative instruments in connection with the issuance of equity instruments	8,325	42,796
Embedded derivative instruments in connection with the issuance of debt instruments	1,032	0
Total liabilities measured and recorded at fair value	$ 72,509	$ 100,714

Fair Value Measurement - Additi

Fair Value Measurement - Additional Information (Details)	3 Months Ended	9 Months Ended
	Sep. 30, 2019USD ($)instrument	Sep. 30, 2019USD ($)instrument	Sep. 10, 2019USD ($)	Dec. 31, 2018USD ($)	Dec. 10, 2018USD ($)
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt Instrument, Number Issued | instrument	3	3
Long-term debt, gross	$ 241,430,000	$ 241,430,000		$ 228,921,000
Combined debt amount	141,100,000	141,100,000	$ 7,900,000
Warrant derivative, fair value	8,300,000	8,300,000
Fair value adjustment of warrants	$ 400,000	$ 400,000
Embedded Derivative, Number Of Instruments Held | instrument	3	3
Debt instrument fair value disclosure	$ 153,800,000	$ 153,800,000
Embedded derivative, fair value of embedded derivative liability	1,000,000	1,000,000
DSM Securities Purchase Agreement
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Derivative Liability	$ 3,800,000	$ 3,800,000
6% convertible notes due 2021
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Debt instrument, face amount					$ 60,000,000
Debt instrument, interest rate, stated percentage	6.00%	6.00%			6.00%
Measurement Input, Put Option Price | 6% convertible notes due 2021
Fair Value Measurement Inputs and Valuation Techniques [Line Items]
Measurement input (percentage)	1.25	1.25

Fair Value Measurement - Conver

Fair Value Measurement - Convertible Debt (Details) - Long-term Debt $ in Thousands	9 Months Ended
	Sep. 30, 2019USD ($)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Fair value, beginning balance	$ 57,918
Less: principal paid	(13,395)
Loss on change in fair value	(18,629)
Fair value, ending balance	$ 63,152

Fair Value Measurement - Reconc

Fair Value Measurement - Reconciliation for Compound Embedded Derivative Liability (Details) - Level 3 $ in Thousands	9 Months Ended
	Sep. 30, 2019USD ($)
Equity-related Derivative Liability
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	$ 41,272
Derecognition upon adoption of ASU 2017-11	(39,513)
Fair value of derivative liabilities issued during the period	0
Change in fair value of derivative liabilities	2,039
Derecognition upon extinguishment of derivative liabilities	3,798
Fair value, ending balance	0
Debt-related Derivative Liability
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	1,524
Derecognition upon adoption of ASU 2017-11	(1,524)
Fair value of derivative liabilities issued during the period	8,959
Change in fair value of derivative liabilities	398
Derecognition upon extinguishment of derivative liabilities	0
Fair value, ending balance	9,357
Total Derivative Liability
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value, beginning balance	42,796
Derecognition upon adoption of ASU 2017-11	(41,037)
Fair value of derivative liabilities issued during the period	8,959
Change in fair value of derivative liabilities	2,437
Derecognition upon extinguishment of derivative liabilities	3,798
Fair value, ending balance	$ 9,357

Debt - Debt Components (Details

Debt - Debt Components (Details) - USD ($) $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2019	Dec. 31, 2018	Jul. 29, 2019
Debt Instrument [Line Items]
Principal	$ 241,430	$ 228,921
Unamortized Debt (Discount) Premium	(37,514)	(17,142)
Change in Fair Value	327	(2,082)
Net Balance	204,243	209,697
Less: current portion	(78,716)	(147,677)
Long-term debt, net of current portion	125,527	62,020
Nikko notes
Debt Instrument [Line Items]
Net Balance			$ 100
Convertible notes payable
Debt Instrument [Line Items]
Principal	62,825	126,306
Unamortized Debt (Discount) Premium		(3,350)
Change in Fair Value	327	(2,082)
Net Balance	63,152	120,874
Convertible notes payable | 6% convertible notes due 2021
Debt Instrument [Line Items]
Principal	62,825	60,000
Change in Fair Value	327	(2,082)
Net Balance	63,152	57,918
Convertible notes payable | August 2013 financing convertible note
Debt Instrument [Line Items]
Principal		4,415
Unamortized Debt (Discount) Premium		(70)
Net Balance		4,345
Convertible notes payable | 2015 Rule 144A convertible notes
Debt Instrument [Line Items]
Principal		37,887
Unamortized Debt (Discount) Premium		(2,413)
Net Balance		35,474
Convertible notes payable | 2014 Rule 144A convertible notes
Debt Instrument [Line Items]
Principal		24,004
Unamortized Debt (Discount) Premium		(867)
Net Balance		23,137
Related party convertible notes payable | 2014 Rule 144A convertible notes
Debt Instrument [Line Items]
Principal	9,705	24,705
Unamortized Debt (Discount) Premium		(1,038)
Net Balance	9,705	23,667
Loans payable and credit facilities
Debt Instrument [Line Items]
Principal	34,902	52,910
Unamortized Debt (Discount) Premium	(12,466)	(6,443)
Net Balance	22,436	46,467
Loans payable and credit facilities | Ginkgo notes
Debt Instrument [Line Items]
Principal	12,000	12,000
Unamortized Debt (Discount) Premium	(3,377)	(4,047)
Net Balance	8,623	7,953
Loans payable and credit facilities | Nikko notes
Debt Instrument [Line Items]
Principal	9,122	4,598
Unamortized Debt (Discount) Premium	(938)	(1,047)
Net Balance	8,184	3,551
Loans payable and credit facilities | Schottenfeld notes
Debt Instrument [Line Items]
Principal	12,500
Unamortized Debt (Discount) Premium	(8,151)
Net Balance	4,349
Loans payable and credit facilities | Other loans payable
Debt Instrument [Line Items]
Principal	1,280	312
Net Balance	1,280	312
Loans payable and credit facilities | GACP secured term loan facility
Debt Instrument [Line Items]
Principal		36,000
Unamortized Debt (Discount) Premium		(1,349)
Net Balance		34,651
Related party loans payable
Debt Instrument [Line Items]
Principal	133,998	25,000
Unamortized Debt (Discount) Premium	(25,048)	(6,311)
Net Balance	108,950	18,689
Related party loans payable | Foris secured term loan facility
Debt Instrument [Line Items]
Principal	71,041
Unamortized Debt (Discount) Premium	(8,829)
Net Balance	62,212
Related party loans payable | Foris unsecured notes
Debt Instrument [Line Items]
Principal	19,000
Unamortized Debt (Discount) Premium	(6,681)
Net Balance	12,319
Related party loans payable | DSM note
Debt Instrument [Line Items]
Principal	33,000	25,000
Unamortized Debt (Discount) Premium	(5,135)	(6,311)
Net Balance	27,865	$ 18,689
Related party loans payable | Naxyris note
Debt Instrument [Line Items]
Principal	10,957
Unamortized Debt (Discount) Premium	(4,403)
Net Balance	$ 6,554

Debt - August 2013 Financing No

Debt - August 2013 Financing Note (Details) - USD ($) $ / shares in Units, $ in Thousands, shares in Millions	Jul. 08, 2019	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Aug. 28, 2019	Jan. 14, 2019
Obligation with Joint and Several Liability Arrangement [Line Items]
Debt instrument fair value disclosure		$ 153,800		$ 153,800
Warrants and rights outstanding						$ 8,700
Loss upon extinguishment of debt		$ 2,721	$ 0	$ 8,596	$ 26
Warrants Issued in Exchange for August 2013 Financing Convertible Note
Obligation with Joint and Several Liability Arrangement [Line Items]
Debt conversion, converted instrument (in shares)	1.8
Debt instrument fair value disclosure	$ 5,900
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.30
Class of warrant or right, number of securities called by warrants or rights (in shares)	1.1
Warrants and rights outstanding	$ 1,900
Loss upon extinguishment of debt	2,700
Related party convertible notes payable | Second Tranche
Obligation with Joint and Several Liability Arrangement [Line Items]
Debt instrument, cash waiver fee amount payable							$ 600
Convertible notes payable	$ 5,100

Debt - Foris Credit Agreements

Debt - Foris Credit Agreements (Details) - USD ($)	Jul. 10, 2019	Sep. 30, 2019	Sep. 30, 2019	Aug. 17, 2019	Jul. 26, 2019	Jul. 09, 2019	Jun. 11, 2019	Apr. 08, 2019
Line of Credit Facility [Line Items]
Fair Value Adjustment of Warrants		$ (400,000)	$ (400,000)
July Foris Credit Agreement
Line of Credit Facility [Line Items]
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 2.87			$ 7.52		$ 7.52
Fair Value Adjustment of Warrants	$ 4,000,000
Debt instrument, unamortized discount	4,000,000
Foris Ventures LLC | July Foris Credit Agreement
Line of Credit Facility [Line Items]
Debt instrument, face amount	8,000,000				$ 8,000,000
Line of credit facility, maximum borrowing capacity	$ 8,000,000
Debt instrument, interest rate, stated percentage	12.50%				12.50%
Long-term, line of credit	$ 16,000,000				$ 8,000,000
Foris Ventures LLC | April Foris Credit Agreement
Line of Credit Facility [Line Items]
Debt instrument, face amount								$ 8,000,000
Line of credit facility, maximum borrowing capacity								8,000,000
Debt instrument, fee amount								$ 1,000,000
Debt instrument, interest rate, stated percentage								0.00%
Foris Ventures LLC | June Foris Credit Agreement
Line of Credit Facility [Line Items]
Debt instrument, face amount							$ 8,500,000
Line of credit facility, maximum borrowing capacity							$ 8,500,000
Debt instrument, interest rate, stated percentage							12.50%
Foris Ventures LLC | Maximum | April Foris Credit Agreement
Line of Credit Facility [Line Items]
Debt instrument, fee amount								$ 500,000

Debt - 2015 and 2014 Rule 144A

Debt - 2015 and 2014 Rule 144A Convertible Notes (Details) - USD ($) $ / shares in Units, $ in Thousands

Aug. 28, 2019

May 15, 2019

May 14, 2019

May 10, 2019

Sep. 30, 2019

Sep. 30, 2018

Sep. 30, 2019

Sep. 30, 2018

Jul. 18, 2019

Jun. 30, 2019

Apr. 16, 2019

Mar. 31, 2019

Dec. 31, 2018

Debt Instrument [Line Items]

Long-term debt, gross

$ 241,430

$ 241,430

$ 228,921

Warrants and rights outstanding

$ 8,700

Loss upon extinguishment of debt

$ 2,721

$ 0

$ 8,596

$ 26

Class of warrant or right, outstanding

58,727,206

58,727,206

49,747,628

26,411,761

26,891,512

Issuance of common stock upon conversion of convertible notes

$ 42,479

$ 0

Rule 144A Convertible Notes

Debt Instrument [Line Items]

Loss upon extinguishment of debt

$ 5,900

August Foris Credit Agreement

Debt Instrument [Line Items]

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 3.90

Class of warrant or right, term

2 years

Warrants and rights outstanding

$ 5,200

Convertible notes payable

Debt Instrument [Line Items]

Long-term debt, gross

62,825

62,825

$ 126,306

Convertible notes payable | Rule 144A Convertible Notes

Debt Instrument [Line Items]

Long-term debt, gross

$ 37,900

Debt instrument, interest rate, stated percentage

9.50%

Maxwell (Mauritius) Pte Ltd | Rule 144A Convertible Notes

Debt Instrument [Line Items]

Debt conversion, original debt, amount

$ 10,000

Debt conversion, converted instrument (in shares)

2,500,000

Other Non-affiliated Investors | Rule 144A Convertible Notes

Debt Instrument [Line Items]

Debt conversion, original debt, amount

$ 5,000

$ 13,500

Debt conversion, converted instrument (in shares)

1,100,000

3,500,000

Debt conversion, converted instrument, warrants issued (in shares)

1,400,000

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 5.02

Debt instrument, interest rate, stated percentage

6.50%

Total | Rule 144A Convertible Notes

Debt Instrument [Line Items]

Debt conversion, original debt, amount

$ 9,700

Debt instrument, interest rate, stated percentage

12.00%

10.50%

Foris Ventures LLC | August Foris Credit Agreement

Debt Instrument [Line Items]

Warrants and rights outstanding

$ 8,700

Debt instrument, interest rate, stated percentage

12.00%

Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors

Debt Instrument [Line Items]

Class of warrant or right, term

2 years

Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Other Non-affiliated Investors | Rule 144A Convertible Notes

Debt Instrument [Line Items]

Debt conversion, converted instrument, warrants issued (in shares)

1,400,000

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 5.02

Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges | Foris Ventures LLC

Debt Instrument [Line Items]

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 3.90

$ 4.56

Warrants Issued in Connection with Rule 144A Convertible Notes Conversion

Debt Instrument [Line Items]

Warrants and rights outstanding

$ 3,800

$ 3,800

Class of warrant or right, outstanding

1,700,000

1,700,000

Foris Ventures LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges

Debt Instrument [Line Items]

Debt conversion, converted instrument, warrants issued (in shares)

400,000

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 3.90

$ 4.56

Class of warrant or right, term

2 years

Rule 144A Convertible Notes Converted to Common Stock

Debt Instrument [Line Items]

Debt conversion, original debt, amount

$ 29,100

Debt conversion, converted instrument (in shares)

7,100,000

Issuance of common stock upon conversion of convertible notes

$ 30,800

Debt issuance costs, net

$ 400

$ 400

Debt - 6% Convertible Notes Exc

Debt - 6% Convertible Notes Exchanges (Details) - USD ($) $ / shares in Units, shares in Millions

Aug. 22, 2019

Aug. 02, 2019

Jul. 26, 2019

Jul. 24, 2019

Jul. 01, 2019

Jun. 24, 2019

May 15, 2019

Sep. 30, 2019

Sep. 30, 2018

Sep. 30, 2019

Sep. 30, 2018

Nov. 08, 2019

Sep. 16, 2019

Debt Instrument [Line Items]

Interest expense

$ 16,857,000

$ 9,180,000

$ 44,608,000

$ 28,738,000

Convertible Senior Notes, 6.0% Due in 2021

Debt Instrument [Line Items]

Debt conversion, original debt, amount

$ 4,700,000

$ 4,700,000

$ 53,300,000

Debt instrument, interest rate, stated percentage

6.00%

6.00%

Debt instrument repayment price, percent of face amount

125.00%

125.00%

Interest expense

$ 4,400,000

Debt instrument, face amount

$ 68,300,000

Debt instrument, periodic payment, principal

$ 6,400,000

Convertible Senior Notes, 6.0% Due in 2021, Second Exchange

Debt Instrument [Line Items]

Debt instrument, interest rate, stated percentage

18.00%

25.00%

Debt instrument, face amount

$ 68,300,000

Debt instrument, periodic payment, principal

$ 3,200,000

$ 3,200,000

Debt instrument, debt default, amount

$ 63,600,000

Second Exchange Note Agreement | Subsequent Event

Debt Instrument [Line Items]

Debt instrument, interest rate, stated percentage

5.00%

Debt instrument repayment price, percent of face amount

110.00%

Debt instrument, face amount

$ 66,000,000

Warrants Issued in Exchange for 6% Convertible Notes Due 2021

Debt Instrument [Line Items]

Class of warrant or right, number of securities called by warrants or rights (in shares)

2

0.2

2

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 5.12

$ 5.12

Class of warrant or right, term

2 years

Debt instrument repayment price, percent of face amount

4.99%

Warrants Issued in Exchange for Convertible Senior Notes, 6.0% Due 2021, Second Exchange

Debt Instrument [Line Items]

Class of warrant or right, number of securities called by warrants or rights (in shares)

2

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 2.87

Class of warrant or right, term

2 years

Adjustments to additional paid in capital, other

$ 0

Debt - Nikko Loan Agreement (De

Debt - Nikko Loan Agreement (Details) - USD ($)	Aug. 08, 2019	Jul. 30, 2019	Sep. 30, 2019	Jul. 29, 2019	Dec. 31, 2018
Debt Instrument [Line Items]
Long-term debt, total			$ 204,243,000		$ 209,697,000
Nikko notes
Debt Instrument [Line Items]
Debt instrument, face amount				$ 5,000,000
Long-term debt, total				$ 100,000
Debt instrument, interest rate, stated percentage				5.00%
Nikko notes | Aprinnova JV
Debt Instrument [Line Items]
First priority lien on interests owned by the company				12.80%
Nikko Loan Agreement, First Installment
Debt Instrument [Line Items]
Debt instrument, face amount		$ 3,000,000		$ 3,000,000
Proceeds from issuance of long-term debt		2,800,000
Nikko Loan Agreement, First Installment | Nikko
Debt Instrument [Line Items]
Proceeds from issuance of long-term debt, withheld as prepayment of interest payable		$ 200,000
Nikko Loan Agreement, Second Installment
Debt Instrument [Line Items]
Debt instrument, face amount	$ 2,000,000			$ 2,000,000
Proceeds from issuance of long-term debt	$ 1,900,000

Debt - LSA Assignment, Amendmen

Debt - LSA Assignment, Amendments and Waivers (Details) - USD ($) $ / shares in Units, shares in Millions	Aug. 28, 2019	Aug. 14, 2019	Apr. 15, 2019	Apr. 04, 2019	May 14, 2019	Apr. 26, 2019
Debt Instrument [Line Items]
Warrants and rights outstanding	$ 8,700,000
LSA Amendment Warrants
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		1.4
Class of warrant or right, exercise price of warrants or rights (in dollars per share)		$ 2.87
Class of warrant or right, term		2 years
Warrants and rights outstanding		$ 2,900,000
The Naxyris Loan Agreement
Debt Instrument [Line Items]
Debt instrument, failure to pay fee		6.00%
Debt instrument, interest rate, stated percentage		12.00%
Debt instrument, basis spread on variable rate		0.25%
Debt instrument, face amount		$ 10,400,000
The Naxyris Loan Agreement | LSA Amendment Warrants
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)		2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)		$ 2.87
Warrants and rights outstanding		$ 4,000,000
August Foris Credit Agreement
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	4.9				0.4	3.9
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90
Class of warrant or right, term	2 years
Warrants and rights outstanding	$ 5,200,000
Loan and Security Agreement Amendment and Waiver
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage		4.75%
Debt instrument, face amount		$ 71,000,000
Foris unsecured notes | Loan and Security Agreement Amendment and Waiver
Debt Instrument [Line Items]
Debt instrument, face amount		$ 32,500,000
Foris Ventures LLC
Debt Instrument [Line Items]
Purchases from related party			$ 2,500,000
Great American Capital Partners, LLC | Loan and Security Agreement Amendment and Waiver
Debt Instrument [Line Items]
Debt instrument, requirement, unrestricted, unencumbered cash				$ 15,000,000
Payments for debt agreement amendment				$ 800,000
Base Rate | Loan and Security Agreement Amendment and Waiver | Minimum
Debt Instrument [Line Items]
Debt instrument, basis spread on variable rate		9.00%
Base Rate | Loan and Security Agreement Amendment and Waiver | Maximum
Debt Instrument [Line Items]
Debt instrument, basis spread on variable rate		12.00%

Debt - Naxyris Loan and Securit

Debt - Naxyris Loan and Security Agreement (Details) - USD ($) $ / shares in Units, shares in Millions	Sep. 30, 2019	Aug. 28, 2019	Aug. 14, 2019
Debt Instrument [Line Items]
Embedded derivative, fair value of embedded derivative liability	$ 1,000,000
Warrants and rights outstanding		$ 8,700,000
Loan and Security Agreement Amendment and Waiver
Debt Instrument [Line Items]
Debt instrument, face amount			$ 71,000,000
Debt instrument, interest rate, stated percentage			4.75%
The Naxyris Loan Agreement
Debt Instrument [Line Items]
Debt instrument, face amount			$ 10,400,000
Debt instrument, failure to pay fee			6.00%
Debt instrument, interest rate, stated percentage			12.00%
Debt instrument, fee amount			$ 400,000
The Naxyris Loan Agreement
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)			2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)			$ 2.87
Warrants and rights outstanding			$ 4,000,000
Debt instrument, unamortized discount			400,000
Debt instrument, fee amount			500,000
Debt issuance costs, gross			300,000
Debt issuance costs, net			4,500,000
The Naxyris Loan Agreement | Loan and Security Agreement Amendment and Waiver
Debt Instrument [Line Items]
Embedded derivative, fair value of embedded derivative liability			300,000
Warrants and rights outstanding			$ 3,000,000

Debt - August 2019 Foris Credit

Debt - August 2019 Foris Credit Agreements (Details) - USD ($)	Aug. 28, 2019	Sep. 30, 2019	Sep. 30, 2019	Jul. 18, 2019	May 14, 2019	Apr. 26, 2019
Debt Instrument [Line Items]
Fair Value Adjustment of Warrants		$ (400,000)	$ (400,000)
Warrants and rights outstanding	$ 8,700,000
Embedded derivative, fair value of embedded derivative liability		$ 1,000,000	$ 1,000,000
Rule 144A Convertible Notes | Total
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage	12.00%			10.50%
August Foris Credit Agreement
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	4,900,000				400,000	3,900,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90
Class of warrant or right, term	2 years
Warrants and rights outstanding	$ 5,200,000
Embedded derivative, fair value of embedded derivative liability	$ 500,000
Foris Ventures LLC | Private Placement, April 26, 2019
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)						3,900,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90					$ 5.12
Foris Ventures LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Debt Instrument [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)					400,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90				$ 4.56
Foris Ventures LLC | August Foris Credit Agreement
Debt Instrument [Line Items]
Debt instrument, face amount	$ 19,000,000
Line of credit facility, maximum borrowing capacity	$ 19,000,000
Debt instrument, interest rate, stated percentage	12.00%
Debt instrument repayment price, percent of face amount	100.00%
Fair Value Adjustment of Warrants	$ 1,100,000
Debt instrument, fee amount	100,000
Warrants and rights outstanding	8,700,000
Warrants And Rights Outstanding, Relative Fair Value	5,200,000
Embedded derivative, fair value of embedded derivative liability	500,000
Debt instrument, unamortized discount	$ 6,800,000

Debt - September 2019 Credit Ag

Debt - September 2019 Credit Agreement (Details) - USD ($) $ / shares in Units, shares in Millions	Sep. 10, 2019	Sep. 30, 2019
Debt Instrument [Line Items]
Embedded derivative, fair value of embedded derivative liability		$ 1,000,000
Combined debt amount	$ 7,900,000	141,100,000
The Investor Notes | Investor Credit Agreements
Debt Instrument [Line Items]
Debt instrument, face amount	$ 12,500,000
Debt instrument, interest rate, stated percentage	12.00%
Embedded derivative, fair value of embedded derivative liability	$ 300,000
Investors Warrants
Debt Instrument [Line Items]
Warrant exercise, beneficial common stock ownership maximum percentage	100.00%
Class of warrant or right, number of securities called by warrants or rights (in shares)	3.2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90
Class of warrant or right, term	2 years
Investors Warrants | Investor Credit Agreements
Debt Instrument [Line Items]
Embedded derivative, fair value of embedded derivative liability	$ 7,900,000	$ 8,300,000
Class of warrant or right, number of securities called by warrants or rights (in shares)	3.2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90
Class of warrant or right, term	2 years

Debt - DSM Credit Agreement (D

Debt - DSM Credit Agreement (Details) - DSM International B.V. - USD ($)	Sep. 23, 2019	Sep. 30, 2019	Sep. 19, 2019	Sep. 17, 2019
The 2019 DSM Credit Agreement, First Installment
Debt Instrument [Line Items]
Debt instrument, face amount				$ 3,000,000
Line of credit facility, incremental draw down amount				3,000,000
The 2019 DSM Credit Agreement, Second Installment
Debt Instrument [Line Items]
Debt instrument, face amount			$ 3,000,000
Line of credit facility, incremental draw down amount				3,000,000
The 2019 DSM Credit Agreement, Third Installment
Debt Instrument [Line Items]
Debt instrument, face amount	$ 2,000,000
Line of credit facility, incremental draw down amount	2,000,000			2,000,000
Extinguishment of debt, amount	$ 1,500,000
The 2019 DSM Credit Agreement
Debt Instrument [Line Items]
Line of credit facility, maximum borrowing capacity				$ 8,000,000
Debt instrument, interest rate, stated percentage				12.50%
Debt instrument repayment price, percent of face amount				100.00%
Proceeds from sale of equity securities, gross, trigger repayment of amounts outstanding under line of credit		$ 50,000,000
Debt instrument, fee amount				$ 300,000

Debt - Ginkgo Note Amendment (D

Debt - Ginkgo Note Amendment (Details) - Secured Promissory Note in Connection with Termination of Ginkgo Collaboration Agreement - USD ($) $ in Millions	Oct. 01, 2019	Sep. 29, 2019
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage	12.00%	10.50%
Debt instrument, cash waiver fee amount payable		$ 1.3

Debt - Long-term Debt Instrumen

Debt - Long-term Debt Instruments (Details) $ in Thousands	Sep. 30, 2019USD ($)
Obligation with Joint and Several Liability Arrangement [Line Items]
2019 (remaining nine months)	$ 89,322
2020	31,163
2021	49,305
2022	98,454
2023	31,899
Thereafter	2,268
Total future minimum payments	302,411
Less: amount representing interest	(60,981)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	241,430
Less: current portion of debt principal	(81,906)
Noncurrent portion of debt principal	159,524
Convertible notes payable
Obligation with Joint and Several Liability Arrangement [Line Items]
2019 (remaining nine months)	66,506
2020	0
2021	0
2022	0
2023	0
Thereafter	0
Total future minimum payments	66,506
Less: amount representing interest	(3,681)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	62,825
Less: current portion of debt principal	(62,825)
Noncurrent portion of debt principal	0
Loans Payable and Credit Facilities
Obligation with Joint and Several Liability Arrangement [Line Items]
2019 (remaining nine months)	2,737
2020	9,356
2021	3,342
2022	15,177
2023	12,899
Thereafter	2,268
Total future minimum payments	45,779
Less: amount representing interest	(10,877)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	34,902
Less: current portion of debt principal	(2,534)
Noncurrent portion of debt principal	32,368
Related Party Convertible Notes
Obligation with Joint and Several Liability Arrangement [Line Items]
2019 (remaining nine months)	10,124
2020	0
2021	0
2022	0
2023	0
Thereafter	0
Total future minimum payments	10,124
Less: amount representing interest	(419)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	9,705
Less: current portion of debt principal	(9,705)
Noncurrent portion of debt principal	0
Related Party Loans Payable and Credit Facilities
Obligation with Joint and Several Liability Arrangement [Line Items]
2019 (remaining nine months)	9,955
2020	21,807
2021	45,963
2022	83,277
2023	19,000
Thereafter	0
Total future minimum payments	180,002
Less: amount representing interest	(46,004)
Less: future conversion of accrued interest to principal	0
Present value of minimum debt payments	133,998
Less: current portion of debt principal	(6,842)
Noncurrent portion of debt principal	$ 127,156

Mezzanine Equity (Details Textu

Mezzanine Equity (Details Textual) - Gates Foundation Purchase Agreement $ / shares in Units, $ in Millions	9 Months Ended
	Sep. 30, 2019USD ($)$ / 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 | $	$ 0.5

Stockholders' Deficit - Warrant

Stockholders' Deficit - Warrant Activity (Details) - shares	3 Months Ended			9 Months Ended
	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Sep. 30, 2019
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	49,747,628	26,411,761	26,891,512	26,891,512
Additional warrants issued (in shares)	12,595,752	25,506,098
Issuance of common stock upon exercise of warrants (in shares)		(2,170,231)	(479,751)	(2,500,000)
Expiration (in shares)	(3,616,174)
Number outstanding, ending balance (in shares)	58,727,206	49,747,628	26,411,761	58,727,206
July 2015 related party debt exchange
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	192,024	192,024	663,228	663,228
Additional warrants issued (in shares)		245,558
Issuance of common stock upon exercise of warrants (in shares)		(245,558)	(471,204)
Number outstanding, ending balance (in shares)	192,024	192,024	192,024	192,024
July 2015 private placement
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	72,650	72,650	81,197	81,197
Issuance of common stock upon exercise of warrants (in shares)			(8,547)
Number outstanding, ending balance (in shares)	72,650	72,650	72,650	72,650
February 2016 related party private placement
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	171,429	171,429	171,429	171,429
Number outstanding, ending balance (in shares)	171,429	171,429	171,429	171,429
May 2017 cash and dilution warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	9,164,049	6,292,798	6,292,798	6,292,798
Additional warrants issued (in shares)		4,795,924
Issuance of common stock upon exercise of warrants (in shares)		(1,924,673)
Number outstanding, ending balance (in shares)	9,164,049	9,164,049	6,292,798	9,164,049
August 2017 cash and dilution warrants
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	6,997,099	3,968,116	3,968,116	3,968,116
Additional warrants issued (in shares)		3,028,983
Number outstanding, ending balance (in shares)	6,997,099	6,997,099	3,968,116	6,997,099
April 2018 warrant exercise agreements
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	3,616,174	3,616,174	3,616,174	3,616,174
Expiration (in shares)	(3,616,174)
Number outstanding, ending balance (in shares)	0	3,616,174	3,616,174	0
August 2018 warrant exercise agreements
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	12,097,164	12,097,164	12,097,164	12,097,164
Number outstanding, ending balance (in shares)	12,097,164	12,097,164	12,097,164	12,097,164
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)		8,084,770
Number outstanding, ending balance (in shares)	8,084,770	8,084,770		8,084,770
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)		5,424,804
Number outstanding, ending balance (in shares)	5,424,804	5,424,804		5,424,804
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)		1,744,241
Number outstanding, ending balance (in shares)	1,744,241	1,744,241		1,744,241
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)		2,181,818
Number outstanding, ending balance (in shares)	2,181,818	2,181,818		2,181,818
July 2019 Wolverine warrant
Class of Warrant or Right [Line Items]
Additional warrants issued (in shares)	1,080,000
Number outstanding, ending balance (in shares)	1,080,000			1,080,000
August 2019 Foris LSA warrant
Class of Warrant or Right [Line Items]
Additional warrants issued (in shares)	1,438,829
Number outstanding, ending balance (in shares)	1,438,829			1,438,829
August 2019 Foris Credit Agreement warrant
Class of Warrant or Right [Line Items]
Additional warrants issued (in shares)	4,871,795
Number outstanding, ending balance (in shares)	4,871,795			4,871,795
August 2019 Naxyris LSA warrant
Class of Warrant or Right [Line Items]
Additional warrants issued (in shares)	2,000,000
Number outstanding, ending balance (in shares)	2,000,000			2,000,000
September 2019 Investor Credit Agreement warrant
Class of Warrant or Right [Line Items]
Additional warrants issued (in shares)	3,205,128
Number outstanding, ending balance (in shares)	3,205,128			3,205,128
Other
Class of Warrant or Right [Line Items]
Number outstanding, beginning balance (in shares)	1,406	1,406	1,406	1,406
Number outstanding, ending balance (in shares)	1,406	1,406	1,406	1,406

Stockholders' Deficit - Private

Stockholders' Deficit - Private Placements (Details) - USD ($) $ / shares in Units, $ in Millions	May 03, 2019	Apr. 29, 2019	Apr. 26, 2019	Apr. 16, 2019	Sep. 10, 2019
Class of Stock [Line Items]
Warrant exercise, beneficial common stock ownership maximum percentage					6.99%
Private Placement
Class of Stock [Line Items]
Proceeds from issuance of common stock	$ 5	$ 5.8	$ 23.2
Warrant exercise, beneficial common stock ownership maximum percentage	19.99%
Foris Ventures LLC
Class of Stock [Line Items]
Proceeds from issuance of common stock			$ 15
Foris Ventures LLC | Private Placement, April 16, 2019
Class of Stock [Line Items]
Class of warrant or right, term				2 years
Class of warrant or right, number of securities called by warrants or rights (in shares)				5,400,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)				$ 2.87
Foris Ventures LLC | Private Placement, April 26, 2019
Class of Stock [Line Items]
Class of warrant or right, term			2 years
Class of warrant or right, number of securities called by warrants or rights (in shares)			4,000,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)			$ 5.12
Foris Ventures LLC | Private Placement
Class of Stock [Line Items]
Shares issued (in dollars per share)			$ 5.12	$ 2.87
Proceeds from issuance of common stock				$ 20
Issuance of common stock in private placement, net of issuance costs (in shares)			2,832,440	6,732,369
Other Non-affiliated Investors | Private Placement, April 26, 2019
Class of Stock [Line Items]
Class of warrant or right, term			2 years
Class of warrant or right, number of securities called by warrants or rights (in shares)			1,600,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)			$ 5.02
Other Non-affiliated Investors | Private Placement, April 29, 2019
Class of Stock [Line Items]
Class of warrant or right, term		2 years
Class of warrant or right, number of securities called by warrants or rights (in shares)		300,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)		$ 5.02
Other Non-affiliated Investors | Private Placement, May 3, 2019
Class of Stock [Line Items]
Class of warrant or right, term	2 years
Class of warrant or right, number of securities called by warrants or rights (in shares)	1,000,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 5.02
Other Non-affiliated Investors | Private Placement
Class of Stock [Line Items]
Shares issued (in dollars per share)	$ 4.02	$ 4.02	$ 4.02
Issuance of common stock in private placement, net of issuance costs (in shares)	1,200,000	300,000	2,043,781
Vivo Capital LLC
Class of Stock [Line Items]
Proceeds from issuance of common stock		$ 4.5
Vivo Capital LLC | Private Placement, April 29, 2019
Class of Stock [Line Items]
Class of warrant or right, term		2 years
Class of warrant or right, number of securities called by warrants or rights (in shares)		1,200,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)		$ 4.76
Vivo Capital LLC | Private Placement
Class of Stock [Line Items]
Shares issued (in dollars per share)		$ 4.76
Issuance of common stock in private placement, net of issuance costs (in shares)		913,529
Non-affiliated Investors
Class of Stock [Line Items]
Proceeds from issuance of common stock		$ 1.3	$ 8.2

Stockholders' Deficit - August

Stockholders' Deficit - August 2013 Financing Convertible Note Conversion into Equity (Details) shares in Millions, $ in Millions	Jul. 08, 2019USD ($)$ / sharesshares	Sep. 30, 2019USD ($)	Jul. 10, 2019$ / shares
Class of Stock [Line Items]
Warrant derivative, fair value | $		$ 8.3
Wolverine | August 2013 financing convertible note
Class of Stock [Line Items]
Debt conversion, original debt, amount | $	$ 5.1
Debt conversion, converted instrument (in shares) | shares	1.8
Debt conversion, converted instrument shares converted | $	$ 5.9
Shares issued (in dollars per share) | $ / shares	$ 3.30
Warrants Issued For August 2013 Convertible Notes | Wolverine | August 2013 financing convertible note
Class of Stock [Line Items]
Debt conversion, converted instrument, warrants issued (in shares) | shares	1.1
Warrant derivative, fair value | $	$ 1.9
Share price
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input | $ / shares			3.21
Share price | Warrants Issued For August 2013 Convertible Notes | Wolverine
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	3.33
Strike price | Warrants Issued For August 2013 Convertible Notes | Wolverine
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	2.87
Stock price volatility | Warrants Issued For August 2013 Convertible Notes | Wolverine
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input	0.94
Risk-free interest rate | Warrants Issued For August 2013 Convertible Notes | Wolverine
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input	0.0188
Expected diviend yield | Warrants Issued For August 2013 Convertible Notes | Wolverine
Class of Stock [Line Items]
Warrants and rights outstanding, measurement input	0

Stockholders' Deficit - 2014 Ru

Stockholders' Deficit - 2014 Rule 144A Convertible Notes Exchanges (Details) $ in Thousands, shares in Millions	May 15, 2019USD ($)$ / sharesshares	May 14, 2019USD ($)$ / sharesshares	May 10, 2019USD ($)$ / sharesshares	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Sep. 30, 2019USD ($)	Aug. 28, 2019$ / shares	Jul. 10, 2019$ / shares
Class of Warrant or Right [Line Items]
Issuance of common stock in private placement, net of issuance costs | $				$ 1,323	$ 92
Warrant derivative, fair value | $						$ 8,300
Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Class of warrant or right, stock ownership percentage, restriction on ability to exercise	4.99%
Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Class of warrant or right, term			2 years
Warrant derivative, fair value | $	$ 5,900
Other Non-affiliated Investors | Rule 144A Convertible Notes
Class of Warrant or Right [Line Items]
Debt conversion, original debt, amount | $		$ 5,000	$ 13,500
Debt conversion, converted instrument (in shares) | shares		1.1	3.5
Debt conversion, converted instrument, warrants issued (in shares) | shares			1.4
Class of warrant or right, exercise price of warrants or rights (in dollars per share) | $ / shares			$ 5.02
Other Non-affiliated Investors | Rule 144A Convertible Notes | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument, warrants issued (in shares) | shares			1.4
Class of warrant or right, exercise price of warrants or rights (in dollars per share) | $ / shares			$ 5.02
Issuance of common stock in private placement, net of issuance costs (in shares) | shares	7.1
Issuance of common stock in private placement, net of issuance costs | $	$ 30,800
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	1.7
Warrant derivative, fair value | $	$ 3,800
Foris Ventures LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Debt conversion, converted instrument (in shares) | shares		1.1
Debt conversion, converted instrument, warrants issued (in shares) | shares		0.4
Class of warrant or right, exercise price of warrants or rights (in dollars per share) | $ / shares		$ 4.56					$ 3.90
Class of warrant or right, term		2 years
Foris Ventures LLC | Rule 144A Convertible Notes
Class of Warrant or Right [Line Items]
Debt conversion, original debt, amount | $		$ 5,000
Maxwell (Mauritius) Pte Ltd | Rule 144A Convertible Notes
Class of Warrant or Right [Line Items]
Debt conversion, original debt, amount | $	$ 10,000
Debt conversion, converted instrument (in shares) | shares	2.5
Share price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares								3.21
Share price | Maximum | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	4.54
Share price | Minimum | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	4.27
Strike price | Maximum | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	5.02
Strike price | Minimum | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	4.56
Stock price volatility | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.96
Risk-free interest rate | Maximum | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.0226
Risk-free interest rate | Minimum | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.0220
Expected diviend yield | Other Non-affiliated Investors | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0

Stockholders' Deficit - Standst

Stockholders' Deficit - Standstill Agreement (Details)	Sep. 10, 2019
Equity [Abstract]
Warrant exercise, beneficial common stock ownership maximum percentage	6.99%

Stockholders' Deficit - Additio

Stockholders' Deficit - Additional Information (Details) - USD ($)	3 Months Ended		9 Months Ended
	Jun. 30, 2019	Mar. 31, 2019	Sep. 30, 2019	Sep. 30, 2018
Class of Warrant or Right [Line Items]
Proceeds from exercises of warrants			$ 1,000	$ 60,544,000
Issuance of common stock upon exercise of warrants (in shares)	2,170,231	479,751	2,500,000
Cash and Dilution Warrants and Temasek Funding Warrant
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares)	8,100,000
Dilution Warrants
Class of Warrant or Right [Line Items]
Class of warrant or right, exercises during the period			2,600,000
Proceeds from exercises of warrants			$ 0

Stockholders' Deficit - July 20

Stockholders' Deficit - July 2019 Foris Credit Agreement Warrant Modification (Details) $ in Thousands	3 Months Ended
	Jun. 30, 2019USD ($)	Mar. 31, 2019USD ($)	Sep. 30, 2018USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Aug. 28, 2019$ / shares	Aug. 17, 2019$ / shares	Jul. 26, 2019USD ($)	Jul. 10, 2019USD ($)$ / sharesshares	Jul. 09, 2019$ / shares	May 14, 2019$ / sharesshares
Class of Warrant or Right [Line Items]
Issuance of common stock upon exercise of warrants | $	$ 0	$ 1	$ 80,979	$ 24,788	$ 835
July Foris Credit Agreement
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares									4,900,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)							$ 7.52		$ 2.87	$ 7.52
Debt instrument, unamortized discount | $									$ 4,000
Foris Ventures LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Class of warrant or right, exercise price of warrants or rights (in dollars per share)						$ 3.90					$ 4.56
Share price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input									3.21
Measurement Input, Exercise Price | July Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input									2.87
Stock price volatility | July Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input									1.24
Risk-free interest rate | July Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input									0.0182
Measurement Input, Expected Term | July Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input									0.90
Expected diviend yield | July Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input									0
Foris Ventures LLC | July Foris Credit Agreement
Class of Warrant or Right [Line Items]
Long-term, line of credit | $								$ 8,000	$ 16,000
Foris Ventures LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares											400,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share)						$ 3.90					$ 4.56

Stockholders' Deficit - 6% Conv

Stockholders' Deficit - 6% Convertible Note Exchange Warrants and Modification (Details) $ in Thousands, shares in Millions	Jul. 24, 2019USD ($)$ / sharesshares	Jun. 24, 2019USD ($)$ / sharesshares	Sep. 30, 2019USD ($)	Sep. 30, 2018USD ($)	Sep. 30, 2019USD ($)	Sep. 30, 2018USD ($)	Sep. 10, 2019	Jul. 10, 2019$ / shares	May 15, 2019$ / sharesshares
Class of Warrant or Right [Line Items]
Warrant exercise, beneficial common stock ownership maximum percentage							6.99%
Interest expense | $			$ 16,857	$ 9,180	$ 44,608	$ 28,738
Fair Value Adjustment of Debt | $	$ 900
Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	2	0.2							2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 5.12	$ 5.12
Debt instrument repayment price, percent of face amount		4.99%
Convertible Senior Notes, 6.0% Due in 2021
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares									2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 2.87								$ 5.12
Stock price volatility | Convertible Senior Notes, 6.0% Due in 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.93
Stock price volatility | Minimum | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		0.94
Stock price volatility | Maximum | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		0.96
Risk-free interest rate | Convertible Senior Notes, 6.0% Due in 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.0186
Risk-free interest rate | Minimum | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		0.0172
Risk-free interest rate | Maximum | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		0.0216
Share price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input								3.21
Share price | Minimum | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		3.55
Share price | Maximum | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		4.39
Measurement Input, Expected Term | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		2
Measurement Input, Expected Term | Convertible Senior Notes, 6.0% Due in 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	1.80
Expected diviend yield | Warrants Issued in Exchange for 6% Convertible Notes Due 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input		0
Expected diviend yield | Convertible Senior Notes, 6.0% Due in 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0
Measurement Input, Exercise Price | Convertible Senior Notes, 6.0% Due in 2021
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	2.87
Convertible Senior Notes, 6.0% Due in 2021
Class of Warrant or Right [Line Items]
Debt instrument repayment price, percent of face amount	125.00%								125.00%
Interest expense | $		$ 4,400

Stockholders' Deficit - Foris L

Stockholders' Deficit - Foris LSA Warrant Issuance (Details) $ in Thousands, shares in Millions	Aug. 14, 2019USD ($)$ / sharesshares	Jun. 30, 2019USD ($)	Mar. 31, 2019USD ($)	Sep. 30, 2018USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Sep. 10, 2019	Jul. 10, 2019$ / shares
Class of Warrant or Right [Line Items]
Warrant exercise, beneficial common stock ownership maximum percentage							6.99%
Issuance of common stock upon exercise of warrants | $		$ 0	$ 1	$ 80,979	$ 24,788	$ 835
LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	1.4
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 2.87
Warrants and rights outstanding, term	2 years
Warrant exercise, beneficial common stock ownership maximum percentage	19.99%
Issuance of common stock upon exercise of warrants | $	$ 2,900
Share price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input								3.21
Share price | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	3.59
Measurement Input, Exercise Price | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	2.87
Stock price volatility | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.94
Risk-free interest rate | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.0158
Measurement Input, Expected Term | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	2
Expected diviend yield | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0

Stockholders' Deficit - Naxyris

Stockholders' Deficit - Naxyris LSA Warrant Issuance (Details) $ / shares in Units, shares in Millions, $ in Millions	Sep. 30, 2019USD ($)$ / shares	Aug. 28, 2019USD ($)	Aug. 14, 2019USD ($)$ / sharesshares	Jul. 10, 2019$ / shares	Dec. 31, 2018$ / shares
Class of Warrant or Right [Line Items]
Common stock, par value (in dollars per share)	$ 0.0001				$ 0.0001
Warrants and rights outstanding | $		$ 8.7
Embedded derivative, fair value of embedded derivative liability | $	$ 1
LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares			1.4
Class of warrant or right, exercise price of warrants or rights (in dollars per share)			$ 2.87
Warrants and rights outstanding | $			$ 2.9
The Naxyris Loan Agreement | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares			2
Common stock, par value (in dollars per share)			$ 0.0001
Class of warrant or right, exercise price of warrants or rights (in dollars per share)			$ 2.87
Warrants and rights outstanding | $			$ 4
Warrants And Rights Outstanding, Relative Fair Value | $			3
Embedded derivative, fair value of embedded derivative liability | $			$ 0.3
Share price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input				3.21
Share price | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			3.59
Share price | The Naxyris Loan Agreement | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			3.59
Measurement Input, Exercise Price | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			2.87
Measurement Input, Exercise Price | The Naxyris Loan Agreement | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			2.87
Stock price volatility | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			0.94
Stock price volatility | The Naxyris Loan Agreement | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			0.94
Risk-free interest rate | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			0.0158
Risk-free interest rate | The Naxyris Loan Agreement | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			0.0158
Measurement Input, Expected Term | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			2
Measurement Input, Expected Term | The Naxyris Loan Agreement | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			2
Expected diviend yield | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			0
Expected diviend yield | The Naxyris Loan Agreement | LSA Amendment Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			0

Stockholders' Deficit - Augus_2

Stockholders' Deficit - August 2019 Foris Warrant Issuance (Details)	Aug. 28, 2019USD ($)$ / sharesshares	Jun. 30, 2019USD ($)	Mar. 31, 2019USD ($)	Sep. 30, 2018USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Sep. 30, 2019USD ($)	Sep. 10, 2019	Jul. 10, 2019$ / shares	May 14, 2019$ / sharesshares	Apr. 26, 2019shares
Class of Warrant or Right [Line Items]
Warrant exercise, beneficial common stock ownership maximum percentage								6.99%
Warrants and rights outstanding	$ 8,700,000
Embedded derivative, fair value of embedded derivative liability							$ 1,000,000
Issuance of common stock upon exercise of warrants		$ 0	$ 1,000	$ 80,979,000	$ 24,788,000	$ 835,000
August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	4,900,000									400,000	3,900,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share) | $ / shares	$ 3.90
Warrant exercise, beneficial common stock ownership maximum percentage	19.99%
Warrants and rights outstanding	$ 5,200,000
Embedded derivative, fair value of embedded derivative liability	500,000
Issuance of common stock upon exercise of warrants	$ 1,100,000
Share price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares									3.21
Share price | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	3.67
Measurement Input, Exercise Price | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input | $ / shares	3.90
Stock price volatility | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.94
Risk-free interest rate | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.0150
Measurement Input, Expected Term | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	2									1.7
Expected diviend yield | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0
Minimum | Stock price volatility | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.98
Maximum | Stock price volatility | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	1
Foris Ventures LLC | Warrants Issued for 2014 Rule 144A Convertible Notes Exchanges
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares										400,000
Class of warrant or right, exercise price of warrants or rights (in dollars per share) | $ / shares	$ 3.90									$ 4.56
Foris Ventures LLC | August Foris Credit Agreement
Class of Warrant or Right [Line Items]
Warrants and rights outstanding	$ 8,700,000
Embedded derivative, fair value of embedded derivative liability	500,000
Debt instrument, face amount	19,000,000
Debt instrument, unamortized discount	$ 6,800,000

Stockholders' Deficit - Septemb

Stockholders' Deficit - September 2019 Investor Warrants Issuance (Details) $ / shares in Units, shares in Millions, $ in Millions	Sep. 10, 2019USD ($)$ / sharesshares	Sep. 30, 2019USD ($)$ / shares	Jul. 10, 2019$ / shares
Class of Warrant or Right [Line Items]
Embedded derivative, fair value of embedded derivative liability | $		$ 1
Warrant exercise, beneficial common stock ownership maximum percentage	6.99%
Warrant, Failure of Registration, Period	90 days
Investors Warrants
Class of Warrant or Right [Line Items]
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	3.2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90
Class of warrant or right, term	2 years
Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Embedded derivative, fair value of embedded derivative liability | $	$ 7.9	$ 8.3
Class of warrant or right, number of securities called by warrants or rights (in shares) | shares	3.2
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90
Class of warrant or right, term	2 years
Warrant exercise, beneficial common stock ownership maximum percentage	9.99%
Stock Repurchase Program, Period in Force	60 days
Warrants and rights outstanding, term	120 days
Warrants or rights outstanding, reduction in exercise price	10.00%
Warrants or rights outstanding, additional reduction in exercise price	5.00%
Share price
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input			3.21
Share price | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	4.56	4.76
Expected diviend yield | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0
Measurement Input, Expected Term | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	2
Risk-free interest rate | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.0167	0.0163
Stock price volatility | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	0.94	0.95
Measurement Input, Exercise Price | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Warrants and rights outstanding, measurement input	3.90
Minimum | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.31
Maximum | Investor Credit Agreements | Investors Warrants
Class of Warrant or Right [Line Items]
Class of warrant or right, exercise price of warrants or rights (in dollars per share)	$ 3.90

Loss Per Share - Calculation of

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		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Earnings Per Share, Basic and Diluted [Abstract]
Net loss attributable to Amyris, Inc.	$ (59,562)	$ (74,453)	$ (163,893)	$ (181,637)
Less: deemed dividend to preferred shareholder on issuance and modification of common stock warrants	0	0	(34,964)	0
Less: deemed dividend related to proceeds discount and issuance costs upon conversion of Series D preferred stock	0	(6,852)	0	(6,852)
Less: losses allocated to participating securities	1,655	4,491	6,233	12,824
Net loss attributable to Amyris, Inc. common stockholders	$ (57,907)	$ (76,814)	$ (192,624)	$ (175,665)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	103,449,612	60,966,071	91,344,150	55,735,571
Loss per share attributable to common stockholders, basic and diluted	$ (0.56)	$ (1.26)	$ (2.11)	$ (3.15)

Loss Per Share - Antidilutive S

Loss Per Share - Antidilutive Securities Excluded From Computation of Earnings Per Share (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
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)	79,769,300	49,113,091	79,769,300	49,113,091
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)	5,398,834	5,449,701	5,398,834	5,449,701
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)	14,259,214	9,397,134	14,259,214	9,397,134
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)	52,612,330	25,986,432	52,612,330	25,986,432
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)	4,543,190	5,324,092	4,543,190	5,324,092
Period-end preferred 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)	2,955,732	2,955,732	2,955,732	2,955,732

Revenue Recognition and Contr_3

Revenue Recognition and Contract Assets and Liabilities - Disaggregation of Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Disaggregation of Revenue [Line Items]
Revenue	$ 34,953	$ 14,315	$ 112,021	$ 47,233
United States
Disaggregation of Revenue [Line Items]
Revenue	19,041	5,508	38,821	15,641
Europe
Disaggregation of Revenue [Line Items]
Revenue	6,268	5,227	57,132	25,906
Asia
Disaggregation of Revenue [Line Items]
Revenue	7,187	3,544	13,053	5,335
South America
Disaggregation of Revenue [Line Items]
Revenue	2,300	36	2,821	251
Other
Disaggregation of Revenue [Line Items]
Revenue	157		194	100
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	17,363	9,639	41,367	21,467
Renewable Products | United States
Disaggregation of Revenue [Line Items]
Revenue	9,927	4,883	22,806	9,184
Renewable Products | Europe
Disaggregation of Revenue [Line Items]
Revenue	2,609	1,176	7,565	6,597
Renewable Products | Asia
Disaggregation of Revenue [Line Items]
Revenue	2,398	3,544	8,015	5,335
Renewable Products | South America
Disaggregation of Revenue [Line Items]
Revenue	2,272	36	2,787	251
Renewable Products | Other
Disaggregation of Revenue [Line Items]
Revenue	157		194	100
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	2,305	142	43,387	7,584
Licenses and Royalties | Europe
Disaggregation of Revenue [Line Items]
Revenue	2,305	142	43,387	7,584
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	15,285	4,534	27,267	18,182
Grants and Collaborations | United States
Disaggregation of Revenue [Line Items]
Revenue	9,114	625	16,015	6,457
Grants and Collaborations | Europe
Disaggregation of Revenue [Line Items]
Revenue	1,354	$ 3,909	6,180	$ 11,725
Grants and Collaborations | Asia
Disaggregation of Revenue [Line Items]
Revenue	4,789		5,038
Grants and Collaborations | South America
Disaggregation of Revenue [Line Items]
Revenue	$ 28		$ 34

Revenue Recognition and Contact

Revenue Recognition and Contact Assets and Liabilities - Narrative (Details) - USD ($) $ in Thousands	May 02, 2019	Apr. 16, 2019	Apr. 30, 2019	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Disaggregation of Revenue [Line Items]
Contract assets				$ 2,567		$ 2,567		$ 0
Cost of products sold				20,654	$ 8,574	53,482	$ 20,423
Interest expense				16,857	$ 9,180	44,608	$ 28,738
Revenue, remaining performance obligation, amount				180,900		180,900
Lavvan
Disaggregation of Revenue [Line Items]
Contract assets				1,700		1,700
DSM International B.V.
Disaggregation of Revenue [Line Items]
Contract with customer, liability, revenue recognized						3,600
Contract with customer, liability			$ 12,500	12,500		12,500
Consideration transferred		$ 57,000
Final annual royalty payment due under original agreement		7,400
Contract assets			8,000
Proceeds from customers		21,700	7,400
Amount used to offset past due trade payables		$ 27,900	7,400
Contract with customer, liability, cumulative catch-up adjustment to revenue, modification of contract			$ 600			37,100
Interest expense				200
DSM International B.V. | Licenses and Royalties
Disaggregation of Revenue [Line Items]
Cost of products sold				400
Yifan
Disaggregation of Revenue [Line Items]
Contract assets				800		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	$ 135,000
Variable consideration related to milestones				165,000		165,000
Contract with customer, liability, revenue recognized				8,200		11,700
Contract assets				$ 1,700		$ 1,700

Revenue Recognition and Contr_4

Revenue Recognition and Contract Assets and Liabilities - Revenue in Connection With Significant Revenue Agreement (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Disaggregation of Revenue [Line Items]
Revenue	$ 34,953	$ 14,315	$ 112,021	$ 47,233
Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	19,655	5,479	72,996	24,127
DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	844	1,158	44,190	11,033
Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	3,312	2,025	6,127	8,068
Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	7,261	2,296	10,937	5,026
DARPA | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	8,238	0	11,742	0
Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	15,298	8,836	39,025	23,106
Renewable Products
Disaggregation of Revenue [Line Items]
Revenue	17,363	9,639	41,367	21,467
Renewable Products | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	7,868	1,428	12,568	4,820
Renewable Products | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue			2
Renewable Products | Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	3,312	525	6,127	3,710
Renewable Products | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	4,556	903	6,439	1,110
Renewable Products | Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	9,495	8,211	28,799	16,647
Licenses and Royalties
Disaggregation of Revenue [Line Items]
Revenue	2,305	142	43,387	7,584
Licenses and Royalties | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	2,305	142	43,387	7,584
Licenses and Royalties | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	0	(39)	40,302	7,366
Licenses and Royalties | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	2,305	181	3,085	218
Grants and Collaborations
Disaggregation of Revenue [Line Items]
Revenue	15,285	4,534	27,267	18,182
Grants and Collaborations | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	9,482	3,909	17,041	11,723
Grants and Collaborations | DSM - related party | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	844	1,197	3,886	3,667
Grants and Collaborations | Givaudan | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue		1,500		4,358
Grants and Collaborations | Firmenich | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	400	1,212	1,413	3,698
Grants and Collaborations | DARPA | Significant Revenue Agreement
Disaggregation of Revenue [Line Items]
Revenue	8,238	0	11,742	0
Grants and Collaborations | Revenue from all other customers
Disaggregation of Revenue [Line Items]
Revenue	$ 5,803	$ 625	$ 10,226	$ 6,459

Revenue Recognition and Contr_5

Revenue Recognition and Contract Assets and Liabilities - Contract Balances (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Revenue from Contract with Customer [Abstract]
Accounts receivable, net	$ 17,072	$ 16,003
Accounts receivable - related party, net	3,692	1,349
Contract assets	2,567	0
Accounts receivable, unbilled - related party	0	8,021
Accounts receivable, unbilled, noncurrent - related party	1,203	1,203
Contract liabilities, current	4,737	8,236
Contract liability, net of current portion	1,449	1,587
Refund liability	$ 12,500	$ 0

Revenue Recognition and Contr_6

Revenue Recognition and Contract Assets and Liabilities - Remaining Performance Obligations (Details) $ in Thousands	Sep. 30, 2019USD ($)
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 138,239
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-10-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 12,523
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period	3 months
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 77,029
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]: 2021-01-01
Revenue from Contract with Customer [Abstract]
Revenue, Remaining Performance Obligation, Amount	$ 48,354
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	$ 333
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period

Related Party Transactions - Re

Related Party Transactions - Related Party Accounts Receivable (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Related Party Transaction [Line Items]
Accounts receivable	$ 3,692	$ 1,349
Accounts receivable, unbilled - related party	0	8,021
Contract assets	2,567	0
Accounts receivable, unbilled, noncurrent	1,203	1,203
DSM - related party
Related Party Transaction [Line Items]
Accounts receivable	3,692	1,071
Novvi
Related Party Transaction [Line Items]
Accounts receivable	0	188
Total
Related Party Transaction [Line Items]
Accounts receivable	$ 0	$ 90

Stock-based Compensation - Shar

Stock-based Compensation - Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2019	Dec. 31, 2018
Share-based Payment Arrangement [Abstract]
Outstanding, beginning balance (in shares)	5,390,270
Outstanding, weighted average exercise price (in dollars per share)	$ 11.55
Outstanding, weighted average remaining contractual life	8 years 1 month 2 days	8 years 6 months
Outstanding, aggregate intrinsic value, in thousands	$ 705	$ 29
Granted (in shares)	270,633
Granted, weighted average grant-date fair value (in dollars per share)	$ 3.67
Exercised (in shares)	(3,612)
Exercised, weighted average grant-date fair value (in dollars per share)	$ 5.48
Forfeited or expired (in shares)	(251,557)
Forfeited or expired, weighted average grant-date fair value (in dollars per share)	$ 18
Outstanding, ending balance (in shares)	5,405,734	5,390,270
Outstanding, weighted average exercise price (in dollars per share)	$ 10.57	$ 11.55
Vested or expected to vest (in shares)	4,781,072
Vested or expected to vest, weighted average grant-date fair value (in dollars per share)	$ 11.28
Vested or expected to vest, weighted average remaining contractual life	8 years
Vested or expected to vest, aggregate intrinsic value, in thousands	$ 682
Exercisable (in shares)	1,247,627
Exercisable, weighted average grant-date fair value (in dollars per share)	$ 28.74
Exercisable, weighted average remaining contractual life	6 years 3 months 19 days
Exercisable, aggregate intrinsic value, in thousands	$ 416

Stock-based Compensation - Temp

Stock-based Compensation - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity (Details) - Restricted Stock Units (RSUs) - $ / shares	9 Months Ended	12 Months Ended
	Sep. 30, 2019	Dec. 31, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding, RSUs (in shares)	5,294,803
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 5.50
Outstanding, weighted average remaining contractual life	1 year 6 months	1 year 8 months 12 days
Awarded, RSUs (in shares)	1,148,866
Awarded, weighted average grant-date fair value (in dollars per share)	$ 3.73
RSUs released (in shares)	(1,389,466)
RSUs released, weighted average grant-date fair value (in dollars per share)	$ 4.98
RSUs forfeited (in shares)	(511,013)
RSUs forfeited, weighted average grant-date fair value (in dollars per share)	$ 4.91
Outstanding, RSUs (in shares)	4,543,190	5,294,803
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 5.07	$ 5.50
Vested or expected to vest (in shares)	4,196,792
Vested or expected to vest, weighted average grant-date fair value (in dollars per share)	$ 5.08
Vested or expected to vest, weighted average remaining contractual life	1 year 4 months 9 days

Stock-based Compensation - Empl

Stock-based Compensation - Employee Service Share-based Compensation, Allocation of Recognized Period Costs (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	$ 3,234	$ 2,937	$ 10,060	$ 6,115
Research and development
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	663	495	2,002	1,191
Sales, general and administrative
Share-based Payment Arrangement, Expensed and Capitalized, Amount [Line Items]
Total stock-based compensation expense	$ 2,571	$ 2,442	$ 8,058	$ 4,924

Stock-based Compensation (Detai

Stock-based Compensation (Details Textual) - USD ($) $ in Millions	9 Months Ended
	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding balance (in shares)			76,564,829
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation expense related to stock options and RSUs	$ 24.9
Weighted-average period	2 years 9 months 3 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)		3,828,241
Automatic annual increase in ahares available for grant and issuance, percentage of outstanding stock		5.00%
Automatic annual increase reserved for issuance (in shares)		383,824
Automatic annual increase in shares reserved for issuance, percentage of outstanding stock		0.005

Subsequent Events (Details)

Subsequent Events (Details) - USD ($)

Nov. 08, 2019

Oct. 29, 2019

Oct. 24, 2019

Oct. 11, 2019

Aug. 28, 2019

Sep. 30, 2019

Sep. 30, 2018

Oct. 10, 2019

Sep. 10, 2019

Aug. 14, 2019

Jul. 24, 2019

May 15, 2019

May 14, 2019

Apr. 26, 2019

Dec. 31, 2018

Subsequent Event [Line Items]

Warrant exercise, beneficial common stock ownership maximum percentage

6.99%

Issuance of common stock upon conversion of convertible notes

$ 42,479,000

$ 0

Long-term debt, gross

$ 241,430,000

$ 228,921,000

Preferred stock, par value (in dollars per share)

$ 0.0001

$ 0.0001

Preferred stock, shares outstanding (in shares)

14,656

14,656

Convertible Senior Notes, 6.0% Due in 2021

Subsequent Event [Line Items]

Debt instrument, interest rate, stated percentage

6.00%

6.00%

Debt instrument, face amount

$ 68,300,000

Debt instrument repayment price, percent of face amount

125.00%

125.00%

Foris Loan And Security Amendment [Member] | Subsequent Event

Subsequent Event [Line Items]

Warrant exercise, beneficial common stock ownership maximum percentage

19.99%

Debt Instrument, Face Amount, Increase

$ 10,000,000

Debt instrument, face amount

$ 10,000,000

Long-term debt, gross

$ 81,000,000

Class of warrant or right, number of securities called by warrants or rights (in shares)

2,000,000

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 2.87

Class of warrant or right, term

2 years

The Naxyris Loan Agreement

Subsequent Event [Line Items]

Debt instrument, interest rate, stated percentage

12.00%

Debt instrument, face amount

$ 10,400,000

Debt instrument, fee amount

$ 400,000

The Naxyris Loan Agreement | Subsequent Event

Subsequent Event [Line Items]

Debt Instrument, Face Amount, Increase

$ 10,400,000

Debt instrument, face amount

$ 10,400,000

August Foris Credit Agreement

Subsequent Event [Line Items]

Warrant exercise, beneficial common stock ownership maximum percentage

19.99%

Class of warrant or right, number of securities called by warrants or rights (in shares)

4,900,000

400,000

3,900,000

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 3.90

Class of warrant or right, term

2 years

Naxyris Loan And Security Amendment [Member] | Subsequent Event

Subsequent Event [Line Items]

Debt instrument, fee amount

$ 400,000

Long-term debt, gross

$ 20,900,000

Class of warrant or right, number of securities called by warrants or rights (in shares)

2,000,000

Class of warrant or right, exercise price of warrants or rights (in dollars per share)

$ 3.87

Class of warrant or right, term

2 years

Second Exchange Note Agreement | Subsequent Event

Subsequent Event [Line Items]

Debt instrument, interest rate, stated percentage

5.00%

Debt instrument, face amount

$ 66,000,000

Preferred Stock, Beneficial Ownership Limitation, Percent

4.99%

Debt Instrument, Convertible, Conversion Price

$ 5

Debt Instrument, Reduction Principal, Percent

90.00%

Debt Instrument Repayment Price, Cash, Percent of Face Amount

115.00%

Debt Instrument, Redemption, Amount

$ 10,000,000

Debt instrument repayment price, percent of face amount

110.00%

Proceeds from sale of equity securities, gross, trigger repayment of amounts outstanding under line of credit

$ 75,000,000

Convertible Preferred Stock [Member] | Subsequent Event

Subsequent Event [Line Items]

Preferred Stock, Dividend Rate, Percentage

17.38%

Preferred stock, par value (in dollars per share)

$ 0.0001

Preferred Stock, Beneficial Ownership Limitation, Percent

4.99%

Preferred Stock, Beneficial Ownership Limitation, Percent Of Shares Outstanding After Conversion, Maximum

9.99%

Series B Preferred Stock [Member] | Subsequent Event

Subsequent Event [Line Items]

Preferred stock, shares outstanding (in shares)

6,376.28

Common Stock | Subsequent Event

Subsequent Event [Line Items]

Conversion of Stock, Shares Issued

1,000,000

Uncategorized Items - amrs-2019

Label	Element	Value
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ (803,000)
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	41,043,000
Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	(803,000)
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	8,531,000
Additional Paid-in Capital [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 32,512,000