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  1.  
  2. > lifebit-biotech-platform@0.0.0 test-env /home/diogo/Diogo/Science/Lifebit/deploit/lifebit-platform/api-server
  3. > cross-env NODE_ENV=test nodemon -i "*.test.js" -r dotenv-safe/config .
  4.  
  5. [nodemon] 1.15.0
  6. [nodemon] to restart at any time, enter `rs`
  7. [nodemon] watching: *.*
  8. [nodemon] starting `node -r dotenv-safe/config .`
  9. Could not create predefined file: pipelines/CalliNGS-NF-data/known_variants.vcf.gz
  10. Could not create predefined folder: ref owner: { _id: c4ca4238a0b923820dcc509a,
  11. updatedAt: 2018-10-16T11:05:07.045Z,
  12. createdAt: 2018-10-16T11:05:07.045Z,
  13. email: 'tests@lifebit.ai',
  14. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  15. name: 'tests',
  16. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  17. __v: 0,
  18. keywords: [ 'tests', 'tests lifebit ai' ],
  19. favoritedPublicBuckets: [],
  20. git:
  21. { gitlab: { scope: [], token_type: 'bearer' },
  22. bitbucket: { scope: [], token_type: 'bearer' },
  23. github: { scope: [], token_type: 'bearer' } },
  24. role: 'admin',
  25. isPredefined: true,
  26. isSuspended: false } folder: { _id: 6ea373520f2ad04ce35b5e43,
  27. name: 'ref',
  28. s3BucketName: 'lifebit-featured-datasets',
  29. s3Prefix: 'pipelines/RepeatExpansion/ExpansionHunter/repeat-specs/grch37',
  30. user: { _id: c4ca4238a0b923820dcc509a,
  31. updatedAt: 2018-10-16T11:05:07.045Z,
  32. createdAt: 2018-10-16T11:05:07.045Z,
  33. email: 'tests@lifebit.ai',
  34. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  35. name: 'tests',
  36. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  37. __v: 0,
  38. keywords: [ 'tests', 'tests lifebit ai' ],
  39. favoritedPublicBuckets: [],
  40. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  41. role: 'admin',
  42. isPredefined: true,
  43. isSuspended: false },
  44. folderType: 'S3Folder',
  45. isPredefined: true,
  46. parent: { kind: 'Workflow', id: 'faaaf63001f6f2d43e7b4a64' } }
  47. Could not create predefined folder: reads owner: { _id: c4ca4238a0b923820dcc509a,
  48. updatedAt: 2018-10-16T11:05:07.045Z,
  49. createdAt: 2018-10-16T11:05:07.045Z,
  50. email: 'tests@lifebit.ai',
  51. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  52. name: 'tests',
  53. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  54. __v: 0,
  55. keywords: [ 'tests', 'tests lifebit ai' ],
  56. favoritedPublicBuckets: [],
  57. git:
  58. { gitlab: { scope: [], token_type: 'bearer' },
  59. bitbucket: { scope: [], token_type: 'bearer' },
  60. github: { scope: [], token_type: 'bearer' } },
  61. role: 'admin',
  62. isPredefined: true,
  63. isSuspended: false } folder: { _id: c48dd084ebfb10e2b62f9177,
  64. name: 'reads',
  65. s3BucketName: 'lifebit-featured-datasets',
  66. s3Prefix: 'pipelines/rnatoy-data',
  67. user: { _id: c4ca4238a0b923820dcc509a,
  68. updatedAt: 2018-10-16T11:05:07.045Z,
  69. createdAt: 2018-10-16T11:05:07.045Z,
  70. email: 'tests@lifebit.ai',
  71. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  72. name: 'tests',
  73. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  74. __v: 0,
  75. keywords: [ 'tests', 'tests lifebit ai' ],
  76. favoritedPublicBuckets: [],
  77. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  78. role: 'admin',
  79. isPredefined: true,
  80. isSuspended: false },
  81. folderType: 'S3Folder',
  82. isPredefined: true,
  83. parent: { kind: 'Workflow', id: '38b259992a6390824039158b' } }
  84. Could not create predefined folder: repeats owner: { _id: c4ca4238a0b923820dcc509a,
  85. updatedAt: 2018-10-16T11:05:07.045Z,
  86. createdAt: 2018-10-16T11:05:07.045Z,
  87. email: 'tests@lifebit.ai',
  88. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  89. name: 'tests',
  90. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  91. __v: 0,
  92. keywords: [ 'tests', 'tests lifebit ai' ],
  93. favoritedPublicBuckets: [],
  94. git:
  95. { gitlab: { scope: [], token_type: 'bearer' },
  96. bitbucket: { scope: [], token_type: 'bearer' },
  97. github: { scope: [], token_type: 'bearer' } },
  98. role: 'admin',
  99. isPredefined: true,
  100. isSuspended: false } folder: { _id: d5178fa3b52acf8173fcad0a,
  101. name: 'repeats',
  102. s3BucketName: 'lifebit-featured-datasets',
  103. s3Prefix: 'pipelines/RepeatExpansion/ExpansionHunter/repeat-specs/hg19',
  104. user: { _id: c4ca4238a0b923820dcc509a,
  105. updatedAt: 2018-10-16T11:05:07.045Z,
  106. createdAt: 2018-10-16T11:05:07.045Z,
  107. email: 'tests@lifebit.ai',
  108. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  109. name: 'tests',
  110. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  111. __v: 0,
  112. keywords: [ 'tests', 'tests lifebit ai' ],
  113. favoritedPublicBuckets: [],
  114. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  115. role: 'admin',
  116. isPredefined: true,
  117. isSuspended: false },
  118. folderType: 'S3Folder',
  119. isPredefined: true,
  120. parent: { kind: 'Workflow', id: 'dca407d35ad845806f946294' } }
  121. Could not create predefined file: pipelines/freebayes-data/ucsc.hg19.chr20.unittest.fasta.fai
  122. Could not create predefined file: pipelines/grape-nf-data/ggal/ggal_test_1.fq
  123. Could not create predefined folder: bam_folder owner: { _id: c4ca4238a0b923820dcc509a,
  124. updatedAt: 2018-10-16T11:05:07.045Z,
  125. createdAt: 2018-10-16T11:05:07.045Z,
  126. email: 'tests@lifebit.ai',
  127. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  128. name: 'tests',
  129. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  130. __v: 0,
  131. keywords: [ 'tests', 'tests lifebit ai' ],
  132. favoritedPublicBuckets: [],
  133. git:
  134. { gitlab: { scope: [], token_type: 'bearer' },
  135. bitbucket: { scope: [], token_type: 'bearer' },
  136. github: { scope: [], token_type: 'bearer' } },
  137. role: 'admin',
  138. isPredefined: true,
  139. isSuspended: false } folder: { _id: d0faf194ea29484e75376cee,
  140. name: 'bam_folder',
  141. s3BucketName: 'lifebit-featured-datasets',
  142. s3Prefix: 'pipelines/DeepVariant/hg19-testSmall1.1',
  143. user: { _id: c4ca4238a0b923820dcc509a,
  144. updatedAt: 2018-10-16T11:05:07.045Z,
  145. createdAt: 2018-10-16T11:05:07.045Z,
  146. email: 'tests@lifebit.ai',
  147. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  148. name: 'tests',
  149. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  150. __v: 0,
  151. keywords: [ 'tests', 'tests lifebit ai' ],
  152. favoritedPublicBuckets: [],
  153. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  154. role: 'admin',
  155. isPredefined: true,
  156. isSuspended: false },
  157. folderType: 'S3Folder',
  158. isPredefined: true,
  159. parent: { kind: 'Workflow', id: 'e7ddd4c88573cba170af6b3b' } }
  160. Could not create predefined file: containers/cellbase/NA12878.exome.vcf
  161. Could not create predefined file: pipelines/workflows-proteogenomics-data/small-yeast.fasta
  162. Could not create predefined folder: reads owner: { _id: c4ca4238a0b923820dcc509a,
  163. updatedAt: 2018-10-16T11:05:07.045Z,
  164. createdAt: 2018-10-16T11:05:07.045Z,
  165. email: 'tests@lifebit.ai',
  166. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  167. name: 'tests',
  168. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  169. __v: 0,
  170. keywords: [ 'tests', 'tests lifebit ai' ],
  171. favoritedPublicBuckets: [],
  172. git:
  173. { gitlab: { scope: [], token_type: 'bearer' },
  174. bitbucket: { scope: [], token_type: 'bearer' },
  175. github: { scope: [], token_type: 'bearer' } },
  176. role: 'admin',
  177. isPredefined: true,
  178. isSuspended: false } folder: { _id: 09aa180992cdb76cf094dc26,
  179. name: 'reads',
  180. s3BucketName: 'lifebit-featured-datasets',
  181. s3Prefix: 'pipelines/CalliNGS-NF-data/reads',
  182. user: { _id: c4ca4238a0b923820dcc509a,
  183. updatedAt: 2018-10-16T11:05:07.045Z,
  184. createdAt: 2018-10-16T11:05:07.045Z,
  185. email: 'tests@lifebit.ai',
  186. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  187. name: 'tests',
  188. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  189. __v: 0,
  190. keywords: [ 'tests', 'tests lifebit ai' ],
  191. favoritedPublicBuckets: [],
  192. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  193. role: 'admin',
  194. isPredefined: true,
  195. isSuspended: false },
  196. folderType: 'S3Folder',
  197. isPredefined: true,
  198. parent: { kind: 'Workflow', id: '9ad3cda6c5b9852336f5a0ca' } }
  199. Could not create predefined file: pipelines/RepeatExpansion/Reference/hs37d5.fa
  200. Could not create predefined file: pipelines/nextflow_variant_calling/adapters.fasta
  201. Could not create predefined file: pipelines/nextflow_assembly_data/adapters.fasta
  202. Could not create predefined folder: reads owner: { _id: c4ca4238a0b923820dcc509a,
  203. updatedAt: 2018-10-16T11:05:07.045Z,
  204. createdAt: 2018-10-16T11:05:07.045Z,
  205. email: 'tests@lifebit.ai',
  206. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  207. name: 'tests',
  208. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  209. __v: 0,
  210. keywords: [ 'tests', 'tests lifebit ai' ],
  211. favoritedPublicBuckets: [],
  212. git:
  213. { gitlab: { scope: [], token_type: 'bearer' },
  214. bitbucket: { scope: [], token_type: 'bearer' },
  215. github: { scope: [], token_type: 'bearer' } },
  216. role: 'admin',
  217. isPredefined: true,
  218. isSuspended: false } folder: { _id: 28a2c2b16a722778f916532f,
  219. name: 'reads',
  220. s3BucketName: 'lifebit-featured-datasets',
  221. s3Prefix: 'pipelines/kallisto-nf-data/reads',
  222. user: { _id: c4ca4238a0b923820dcc509a,
  223. updatedAt: 2018-10-16T11:05:07.045Z,
  224. createdAt: 2018-10-16T11:05:07.045Z,
  225. email: 'tests@lifebit.ai',
  226. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  227. name: 'tests',
  228. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  229. __v: 0,
  230. keywords: [ 'tests', 'tests lifebit ai' ],
  231. favoritedPublicBuckets: [],
  232. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  233. role: 'admin',
  234. isPredefined: true,
  235. isSuspended: false },
  236. folderType: 'S3Folder',
  237. isPredefined: true,
  238. parent: { kind: 'Workflow', id: '395e4e814103490d2b889302' } }
  239. Could not create predefined folder: reads_folder owner: { _id: c4ca4238a0b923820dcc509a,
  240. updatedAt: 2018-10-16T11:05:07.045Z,
  241. createdAt: 2018-10-16T11:05:07.045Z,
  242. email: 'tests@lifebit.ai',
  243. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  244. name: 'tests',
  245. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  246. __v: 0,
  247. keywords: [ 'tests', 'tests lifebit ai' ],
  248. favoritedPublicBuckets: [],
  249. git:
  250. { gitlab: { scope: [], token_type: 'bearer' },
  251. bitbucket: { scope: [], token_type: 'bearer' },
  252. github: { scope: [], token_type: 'bearer' } },
  253. role: 'admin',
  254. isPredefined: true,
  255. isSuspended: false } folder: { _id: 5583e0fbcaa61ec5879718f4,
  256. name: 'reads_folder',
  257. s3BucketName: 'lifebit-featured-datasets',
  258. s3Prefix: 'pipelines/methylseq-data/ngi-bisulfite_test_set',
  259. user: { _id: c4ca4238a0b923820dcc509a,
  260. updatedAt: 2018-10-16T11:05:07.045Z,
  261. createdAt: 2018-10-16T11:05:07.045Z,
  262. email: 'tests@lifebit.ai',
  263. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  264. name: 'tests',
  265. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  266. __v: 0,
  267. keywords: [ 'tests', 'tests lifebit ai' ],
  268. favoritedPublicBuckets: [],
  269. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  270. role: 'admin',
  271. isPredefined: true,
  272. isSuspended: false },
  273. folderType: 'S3Folder',
  274. isPredefined: true,
  275. parent: { kind: 'Workflow', id: '16239cc7804f8285e1c839da' } }
  276. Could not create predefined file: pipelines/freebayes-data/ucsc.hg19.chr20.unittest.fasta.gz.fai
  277. Could not create predefined file: pipelines/RepeatExpansion/Reference/hs37d5.fa
  278. Could not create predefined file: pipelines/lncRNA-Annotation-nf-data/genome_chr38.fa
  279. Could not create predefined file: pipelines/mta-nf-data/12asA_1atiA.fasta
  280. Could not create predefined file: pipelines/CalliNGS-NF-data/blacklist.bed
  281. Could not create predefined file: pipelines/nextflow_variant_calling/SRR957824.fastq
  282. Could not create predefined file: pipelines/nextflow_assembly_data/ERR486840_1.fastq.gz
  283. Could not create predefined folder: bismark_index owner: { _id: c4ca4238a0b923820dcc509a,
  284. updatedAt: 2018-10-16T11:05:07.045Z,
  285. createdAt: 2018-10-16T11:05:07.045Z,
  286. email: 'tests@lifebit.ai',
  287. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  288. name: 'tests',
  289. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  290. __v: 0,
  291. keywords: [ 'tests', 'tests lifebit ai' ],
  292. favoritedPublicBuckets: [],
  293. git:
  294. { gitlab: { scope: [], token_type: 'bearer' },
  295. bitbucket: { scope: [], token_type: 'bearer' },
  296. github: { scope: [], token_type: 'bearer' } },
  297. role: 'admin',
  298. isPredefined: true,
  299. isSuspended: false } folder: { _id: df78b4224073422b81ec59a0,
  300. name: 'bismark_index',
  301. s3BucketName: 'lifebit-featured-datasets',
  302. s3Prefix: 'pipelines/methylseq-data/ngi-bisulfite_test_set/references/BismarkIndex',
  303. user: { _id: c4ca4238a0b923820dcc509a,
  304. updatedAt: 2018-10-16T11:05:07.045Z,
  305. createdAt: 2018-10-16T11:05:07.045Z,
  306. email: 'tests@lifebit.ai',
  307. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  308. name: 'tests',
  309. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  310. __v: 0,
  311. keywords: [ 'tests', 'tests lifebit ai' ],
  312. favoritedPublicBuckets: [],
  313. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  314. role: 'admin',
  315. isPredefined: true,
  316. isSuspended: false },
  317. folderType: 'S3Folder',
  318. isPredefined: true,
  319. parent: { kind: 'Workflow', id: '16239cc7804f8285e1c839da' } }
  320. Could not create predefined file: pipelines/freebayes-data/ucsc.hg19.chr20.unittest.fasta.gz
  321. Could not create predefined file: pipelines/grape-nf-data/ggal/ggal_test_2.fq
  322. Could not create predefined file: pipelines/ampa-nf-data/example.fa
  323. Could not create predefined file: containers/cellbase/NA12878.exome.json
  324. Could not create predefined file: pipelines/workflows-proteogenomics-data/demo.ms2
  325. Could not create predefined file: pipelines/CalliNGS-NF-data/genome.fa
  326. Could not create predefined file: pipelines/RepeatExpansion/Bams/HG00472.mapped.ILLUMINA.bwa.CHS.exome.20121211.bam
  327. Could not create predefined file: pipelines/rnatoy-data/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
  328. Could not create predefined file: pipelines/nextflow_variant_calling/pO157_Sakai.fasta
  329. Could not create predefined file: pipelines/RepeatExpansion/Reference/hg19.fa
  330. Could not create predefined file: pipelines/kallisto-nf-data/transcriptome/transcriptome.fa
  331. Could not create predefined file: pipelines/methylseq-data/conf/multiqc_config.yaml
  332. Could not create predefined file: pipelines/freebayes-data/ucsc.hg19.chr20.unittest.fasta.gz.gzi
  333. Could not create predefined file: pipelines/grape-nf-data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
  334. Could not create predefined file: pipelines/RepeatExpansion/Bams/HG00472.mapped.ILLUMINA.bwa.CHS.exome.20121211.bam
  335. Could not create predefined file: pipelines/lncRNA-Annotation-nf-data/annotation_chr38.gtf
  336. Could not create predefined folder: reads owner: { _id: c4ca4238a0b923820dcc509a,
  337. updatedAt: 2018-10-16T11:05:07.045Z,
  338. createdAt: 2018-10-16T11:05:07.045Z,
  339. email: 'tests@lifebit.ai',
  340. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  341. name: 'tests',
  342. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  343. __v: 0,
  344. keywords: [ 'tests', 'tests lifebit ai' ],
  345. favoritedPublicBuckets: [],
  346. git:
  347. { gitlab: { scope: [], token_type: 'bearer' },
  348. bitbucket: { scope: [], token_type: 'bearer' },
  349. github: { scope: [], token_type: 'bearer' } },
  350. role: 'admin',
  351. isPredefined: true,
  352. isSuspended: false } folder: { _id: 394eeca55bc7cb5a8ee62dff,
  353. name: 'reads',
  354. s3BucketName: 'lifebit-featured-datasets',
  355. s3Prefix: 'pipelines/rnaseq-nf-data/',
  356. user: { _id: c4ca4238a0b923820dcc509a,
  357. updatedAt: 2018-10-16T11:05:07.045Z,
  358. createdAt: 2018-10-16T11:05:07.045Z,
  359. email: 'tests@lifebit.ai',
  360. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  361. name: 'tests',
  362. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  363. __v: 0,
  364. keywords: [ 'tests', 'tests lifebit ai' ],
  365. favoritedPublicBuckets: [],
  366. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  367. role: 'admin',
  368. isPredefined: true,
  369. isSuspended: false },
  370. folderType: 'S3Folder',
  371. isPredefined: true,
  372. parent: { kind: 'Workflow', id: '09490a8aa76d1668004a961e' } }
  373. Could not create predefined file: pipelines/piper-nf-data/5_RNA_queries.fa
  374. Could not create predefined file: pipelines/RepeatExpansion/GangSTR/hs37_ver8.bed
  375. Could not create predefined file: pipelines/rnatoy-data/ggal_1_48850000_49020000.bed.gff
  376. Could not create predefined file: pipelines/RepeatExpansion/ExpansionHunter/small/bam/bamlet.bam
  377. Could not create predefined file: pipelines/kallisto-nf-data/experiment/hiseq_info.txt
  378. Could not create predefined file: pipelines/freebayes-data/ucsc.hg19.chr20.unittest.fasta
  379. Could not create predefined folder: bam_folder owner: { _id: c4ca4238a0b923820dcc509a,
  380. updatedAt: 2018-10-16T11:05:07.045Z,
  381. createdAt: 2018-10-16T11:05:07.045Z,
  382. email: 'tests@lifebit.ai',
  383. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  384. name: 'tests',
  385. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  386. __v: 0,
  387. keywords: [ 'tests', 'tests lifebit ai' ],
  388. favoritedPublicBuckets: [],
  389. git:
  390. { gitlab: { scope: [], token_type: 'bearer' },
  391. bitbucket: { scope: [], token_type: 'bearer' },
  392. github: { scope: [], token_type: 'bearer' } },
  393. role: 'admin',
  394. isPredefined: true,
  395. isSuspended: false } folder: { _id: 984a1bdf2c4c250b872601ca,
  396. name: 'bam_folder',
  397. s3BucketName: 'lifebit-featured-datasets',
  398. s3Prefix: 'pipelines/freebayes-data/',
  399. user: { _id: c4ca4238a0b923820dcc509a,
  400. updatedAt: 2018-10-16T11:05:07.045Z,
  401. createdAt: 2018-10-16T11:05:07.045Z,
  402. email: 'tests@lifebit.ai',
  403. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  404. name: 'tests',
  405. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  406. __v: 0,
  407. keywords: [ 'tests', 'tests lifebit ai' ],
  408. favoritedPublicBuckets: [],
  409. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  410. role: 'admin',
  411. isPredefined: true,
  412. isSuspended: false },
  413. folderType: 'S3Folder',
  414. isPredefined: true,
  415. parent: { kind: 'Workflow', id: '02e2a3b324b7a1c71e572cbb' } }
  416. Could not create predefined file: pipelines/grape-nf-data/ggal/ggal_1_48850000_49020000.bed.gff
  417. Could not create predefined file: pipelines/RepeatExpansion/HipSTR/GRCh37.hipstr_reference.bed
  418. Could not create predefined folder: reads owner: { _id: c4ca4238a0b923820dcc509a,
  419. updatedAt: 2018-10-16T11:05:07.045Z,
  420. createdAt: 2018-10-16T11:05:07.045Z,
  421. email: 'tests@lifebit.ai',
  422. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  423. name: 'tests',
  424. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  425. __v: 0,
  426. keywords: [ 'tests', 'tests lifebit ai' ],
  427. favoritedPublicBuckets: [],
  428. git:
  429. { gitlab: { scope: [], token_type: 'bearer' },
  430. bitbucket: { scope: [], token_type: 'bearer' },
  431. github: { scope: [], token_type: 'bearer' } },
  432. role: 'admin',
  433. isPredefined: true,
  434. isSuspended: false } folder: { _id: 222a889a3781bb32da777f9c,
  435. name: 'reads',
  436. s3BucketName: 'lifebit-featured-datasets',
  437. s3Prefix: 'pipelines/lncRNA-Annotation-nf-data/reads',
  438. user: { _id: c4ca4238a0b923820dcc509a,
  439. updatedAt: 2018-10-16T11:05:07.045Z,
  440. createdAt: 2018-10-16T11:05:07.045Z,
  441. email: 'tests@lifebit.ai',
  442. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  443. name: 'tests',
  444. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  445. __v: 0,
  446. keywords: [ 'tests', 'tests lifebit ai' ],
  447. favoritedPublicBuckets: [],
  448. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  449. role: 'admin',
  450. isPredefined: true,
  451. isSuspended: false },
  452. folderType: 'S3Folder',
  453. isPredefined: true,
  454. parent: { kind: 'Workflow', id: '356099becc5d5c8d6a734570' } }
  455. Could not create predefined file: pipelines/rnaseq-nf-data/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
  456. Could not create predefined folder: genomes-folder owner: { _id: c4ca4238a0b923820dcc509a,
  457. updatedAt: 2018-10-16T11:05:07.045Z,
  458. createdAt: 2018-10-16T11:05:07.045Z,
  459. email: 'tests@lifebit.ai',
  460. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  461. name: 'tests',
  462. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  463. __v: 0,
  464. keywords: [ 'tests', 'tests lifebit ai' ],
  465. favoritedPublicBuckets: [],
  466. git:
  467. { gitlab: { scope: [], token_type: 'bearer' },
  468. bitbucket: { scope: [], token_type: 'bearer' },
  469. github: { scope: [], token_type: 'bearer' } },
  470. role: 'admin',
  471. isPredefined: true,
  472. isSuspended: false } folder: { _id: 6b5a33b5f061ffaaf47df3a3,
  473. name: 'genomes-folder',
  474. s3BucketName: 'lifebit-featured-datasets',
  475. s3Prefix: 'pipelines/piper-nf-data/genomes',
  476. user: { _id: c4ca4238a0b923820dcc509a,
  477. updatedAt: 2018-10-16T11:05:07.045Z,
  478. createdAt: 2018-10-16T11:05:07.045Z,
  479. email: 'tests@lifebit.ai',
  480. picture: 'https://gravatar.com/avatar/1fbf378e45719862b7fd450c53a089a1?d=identicon',
  481. name: 'tests',
  482. password: '$2a$04$n/ced.GEKuLyN7K7fmcFXuSV8v89PWCrt.Mr8C7HcX/PhOr5ly30e',
  483. __v: 0,
  484. keywords: [ 'tests', 'tests lifebit ai' ],
  485. favoritedPublicBuckets: [],
  486. git: { gitlab: [Object], bitbucket: [Object], github: [Object] },
  487. role: 'admin',
  488. isPredefined: true,
  489. isSuspended: false },
  490. folderType: 'S3Folder',
  491. isPredefined: true,
  492. parent: { kind: 'Workflow', id: 'b4227d250b6babe0bd132af0' } }
  493. Error while inserting predefined data: TypeError: Cannot read property 'equals' of null
  494. at _callee$ (/home/diogo/Diogo/Science/Lifebit/deploit/lifebit-platform/api-server/src/api/data/dataItemCommon.js:46:62)
  495. at tryCatch (/home/diogo/Diogo/Science/Lifebit/deploit/lifebit-platform/api-server/node_modules/regenerator-runtime/runtime.js:62:40)
  496. at Generator.invoke [as _invoke] (/home/diogo/Diogo/Science/Lifebit/deploit/lifebit-platform/api-server/node_modules/regenerator-runtime/runtime.js:296:22)
  497. at Generator.prototype.(anonymous function) [as next] (/home/diogo/Diogo/Science/Lifebit/deploit/lifebit-platform/api-server/node_modules/regenerator-runtime/runtime.js:114:21)
  498. at step (/home/diogo/Diogo/Science/Lifebit/deploit/lifebit-platform/api-server/node_modules/babel-runtime/helpers/asyncToGenerator.js:17:30)
  499. at /home/diogo/Diogo/Science/Lifebit/deploit/lifebit-platform/api-server/node_modules/babel-runtime/helpers/asyncToGenerator.js:28:13
  500. at <anonymous>
  501. at process._tickDomainCallback (internal/process/next_tick.js:229:7)
  502. Looking for broken jobs on start.
  503. Looking for broken jobs on start.
  504. Looking for broken jobs on start.
  505. Looking for broken jobs on start.
  506. Looking for broken jobs on start.
  507. Billing: ensuring users are invoiced for month Sep.
  508. Found 0 broken jobs on start.
  509. Found 0 broken jobs on start.
  510. Found 0 broken jobs on start.
  511. Found 0 broken jobs on start.
  512. Found 0 broken jobs on start.
  513. Express server listening on http://localhost:3002, in test mode
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