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  1. ##### DEFAULT parameters:
  2. versionSTAR 20201
  3. versionGenome 20101 20200
  4. parametersFiles -
  5. sysShell -
  6. runMode alignReads
  7. runThreadN 1
  8. runDirPerm User_RWX
  9. runRNGseed 777
  10. genomeDir ./GenomeDir/
  11. genomeLoad NoSharedMemory
  12. genomeFastaFiles -
  13. genomeChainFiles -
  14. genomeSAindexNbases 14
  15. genomeChrBinNbits 18
  16. genomeSAsparseD 1
  17. genomeSuffixLengthMax 18446744073709551615
  18. genomeFileSizes 0
  19. readFilesIn Read1 Read2
  20. readFilesCommand -
  21. readMatesLengthsIn NotEqual
  22. readMapNumber 18446744073709551615
  23. readNameSeparator /
  24. inputBAMfile -
  25. bamRemoveDuplicatesType -
  26. bamRemoveDuplicatesMate2basesN 0
  27. limitGenomeGenerateRAM 31000000000
  28. limitIObufferSize 150000000
  29. limitOutSAMoneReadBytes 100000
  30. limitOutSJcollapsed 1000000
  31. limitOutSJoneRead 1000
  32. limitBAMsortRAM 0
  33. limitSjdbInsertNsj 1000000
  34. outTmpDir -
  35. outTmpKeep None
  36. outStd Log
  37. outReadsUnmapped None
  38. outQSconversionAdd 0
  39. outMultimapperOrder Old_2.4
  40. outSAMtype SAM
  41. outSAMmode Full
  42. outSAMstrandField None
  43. outSAMattributes Standard
  44. outSAMunmapped None
  45. outSAMorder Paired
  46. outSAMprimaryFlag OneBestScore
  47. outSAMreadID Standard
  48. outSAMmapqUnique 255
  49. outSAMflagOR 0
  50. outSAMflagAND 65535
  51. outSAMattrRGline -
  52. outSAMheaderHD -
  53. outSAMheaderPG -
  54. outSAMheaderCommentFile -
  55. outBAMcompression 1
  56. outBAMsortingThreadN 0
  57. outSAMfilter None
  58. outSAMmultNmax 18446744073709551615
  59. outSAMattrIHstart 1
  60. outSJfilterReads All
  61. outSJfilterCountUniqueMin 3 1 1 1
  62. outSJfilterCountTotalMin 3 1 1 1
  63. outSJfilterOverhangMin 30 12 12 12
  64. outSJfilterDistToOtherSJmin 10 0 5 10
  65. outSJfilterIntronMaxVsReadN 50000 100000 200000
  66. outWigType None
  67. outWigStrand Stranded
  68. outWigReferencesPrefix -
  69. outWigNorm RPM
  70. outFilterType Normal
  71. outFilterMultimapNmax 10
  72. outFilterMultimapScoreRange 1
  73. outFilterScoreMin 0
  74. outFilterScoreMinOverLread 0.66
  75. outFilterMatchNmin 0
  76. outFilterMatchNminOverLread 0.66
  77. outFilterMismatchNmax 10
  78. outFilterMismatchNoverLmax 0.3
  79. outFilterMismatchNoverReadLmax 1
  80. outFilterIntronMotifs None
  81. clip5pNbases 0
  82. clip3pNbases 0
  83. clip3pAfterAdapterNbases 0
  84. clip3pAdapterSeq -
  85. clip3pAdapterMMp 0.1
  86. winBinNbits 16
  87. winAnchorDistNbins 9
  88. winFlankNbins 4
  89. winAnchorMultimapNmax 50
  90. winReadCoverageRelativeMin 0.5
  91. winReadCoverageBasesMin 0
  92. scoreGap 0
  93. scoreGapNoncan -8
  94. scoreGapGCAG -4
  95. scoreGapATAC -8
  96. scoreStitchSJshift 1
  97. scoreGenomicLengthLog2scale -0.25
  98. scoreDelBase -2
  99. scoreDelOpen -2
  100. scoreInsOpen -2
  101. scoreInsBase -2
  102. seedSearchLmax 0
  103. seedSearchStartLmax 50
  104. seedSearchStartLmaxOverLread 1
  105. seedPerReadNmax 1000
  106. seedPerWindowNmax 50
  107. seedNoneLociPerWindow 10
  108. seedMultimapNmax 10000
  109. alignIntronMin 21
  110. alignIntronMax 0
  111. alignMatesGapMax 0
  112. alignTranscriptsPerReadNmax 10000
  113. alignSJoverhangMin 5
  114. alignSJDBoverhangMin 3
  115. alignSJstitchMismatchNmax 0 -1 0 0
  116. alignSplicedMateMapLmin 0
  117. alignSplicedMateMapLminOverLmate 0.66
  118. alignWindowsPerReadNmax 10000
  119. alignTranscriptsPerWindowNmax 100
  120. alignEndsType Local
  121. alignSoftClipAtReferenceEnds Yes
  122. alignEndsProtrude 0 ConcordantPair
  123. chimSegmentMin 0
  124. chimScoreMin 0
  125. chimScoreDropMax 20
  126. chimScoreSeparation 10
  127. chimScoreJunctionNonGTAG -1
  128. chimMainSegmentMultNmax 10
  129. chimJunctionOverhangMin 20
  130. chimOutType SeparateSAMold
  131. chimFilter banGenomicN
  132. chimSegmentReadGapMax 0
  133. sjdbFileChrStartEnd -
  134. sjdbGTFfile -
  135. sjdbGTFchrPrefix -
  136. sjdbGTFfeatureExon exon
  137. sjdbGTFtagExonParentTranscript transcript_id
  138. sjdbGTFtagExonParentGene gene_id
  139. sjdbOverhang 100
  140. sjdbScore 2
  141. sjdbInsertSave Basic
  142. quantMode -
  143. quantTranscriptomeBAMcompression 1
  144. quantTranscriptomeBan IndelSoftclipSingleend
  145. twopass1readsN 18446744073709551615
  146. twopassMode None
  147. ##### Command Line:
  148. STAR --runThreadN 10 --runMode genomeGenerate --genomeDir /home/user/scratch60/beargenomes --genomeFastaFiles /home/user/scratch60/hg38.fa --readFilesIn /home/user/scratch60/SRR7059137.fastq --sjdbGTFfile /home/user/scratch60/gencode.v28.annotation.gtf --sjdbOverhang 99 --outFileNamePrefix /home/user/scratch60/SRR7059137 --outSAMtype BAM
  149. ##### Initial USER parameters from Command Line:
  150. outFileNamePrefix /home/user/scratch60/SRR7059137
  151. ###### All USER parameters from Command Line:
  152. runThreadN 10 ~RE-DEFINED
  153. runMode genomeGenerate ~RE-DEFINED
  154. genomeDir /home/user/scratch60/beargenomes ~RE-DEFINED
  155. genomeFastaFiles /home/user/scratch60/hg38.fa ~RE-DEFINED
  156. readFilesIn /home/user/scratch60/SRR7059137.fastq ~RE-DEFINED
  157. sjdbGTFfile /home/user/scratch60/gencode.v28.annotation.gtf ~RE-DEFINED
  158. sjdbOverhang 99 ~RE-DEFINED
  159. outFileNamePrefix /home/user/scratch60/SRR7059137 ~RE-DEFINED
  160. outSAMtype BAM ~RE-DEFINED
  161. ##### Finished reading parameters from all sources
  162.  
  163. ##### Final user re-defined parameters-----------------:
  164. runMode genomeGenerate
  165. runThreadN 10
  166. genomeDir /home/user/scratch60/beargenomes
  167. genomeFastaFiles /home/user/scratch60/hg38.fa
  168. readFilesIn /home/user/scratch60/SRR7059137.fastq
  169. outFileNamePrefix /home/user/scratch60/SRR7059137
  170. outSAMtype BAM
  171. sjdbGTFfile /home/user/scratch60/gencode.v28.annotation.gtf
  172. sjdbOverhang 99
  173.  
  174. -------------------------------
  175. ##### Final effective command line:
  176. STAR --runMode genomeGenerate --runThreadN 10 --genomeDir /home/user/scratch60/beargenomes --genomeFastaFiles /home/user/scratch60/hg38.fa --readFilesIn /home/user/scratch60/SRR7059137.fastq --outFileNamePrefix /home/user/scratch60/SRR7059137 --outSAMtype BAM --sjdbGTFfile /home/user/scratch60/gencode.v28.annotation.gtf --sjdbOverhang 99
  177.  
  178. ##### Final parameters after user input--------------------------------:
  179. versionSTAR 20201
  180. versionGenome 20101 20200
  181. parametersFiles -
  182. sysShell -
  183. runMode genomeGenerate
  184. runThreadN 10
  185. runDirPerm User_RWX
  186. runRNGseed 777
  187. genomeDir /home/user/scratch60/beargenomes
  188. genomeLoad NoSharedMemory
  189. genomeFastaFiles /home/user/scratch60/hg38.fa
  190. genomeChainFiles -
  191. genomeSAindexNbases 14
  192. genomeChrBinNbits 18
  193. genomeSAsparseD 1
  194. genomeSuffixLengthMax 18446744073709551615
  195. genomeFileSizes 0
  196. readFilesIn /home/user/scratch60/SRR7059137.fastq
  197. readFilesCommand -
  198. readMatesLengthsIn NotEqual
  199. readMapNumber 18446744073709551615
  200. readNameSeparator /
  201. inputBAMfile -
  202. bamRemoveDuplicatesType -
  203. bamRemoveDuplicatesMate2basesN 0
  204. limitGenomeGenerateRAM 31000000000
  205. limitIObufferSize 150000000
  206. limitOutSAMoneReadBytes 100000
  207. limitOutSJcollapsed 1000000
  208. limitOutSJoneRead 1000
  209. limitBAMsortRAM 0
  210. limitSjdbInsertNsj 1000000
  211. outFileNamePrefix /home/user/scratch60/SRR7059137
  212. outTmpDir -
  213. outTmpKeep None
  214. outStd Log
  215. outReadsUnmapped None
  216. outQSconversionAdd 0
  217. outMultimapperOrder Old_2.4
  218. outSAMtype BAM
  219. outSAMmode Full
  220. outSAMstrandField None
  221. outSAMattributes Standard
  222. outSAMunmapped None
  223. outSAMorder Paired
  224. outSAMprimaryFlag OneBestScore
  225. outSAMreadID Standard
  226. outSAMmapqUnique 255
  227. outSAMflagOR 0
  228. outSAMflagAND 65535
  229. outSAMattrRGline -
  230. outSAMheaderHD -
  231. outSAMheaderPG -
  232. outSAMheaderCommentFile -
  233. outBAMcompression 1
  234. outBAMsortingThreadN 0
  235. outSAMfilter None
  236. outSAMmultNmax 18446744073709551615
  237. outSAMattrIHstart 1
  238. outSJfilterReads All
  239. outSJfilterCountUniqueMin 3 1 1 1
  240. outSJfilterCountTotalMin 3 1 1 1
  241. outSJfilterOverhangMin 30 12 12 12
  242. outSJfilterDistToOtherSJmin 10 0 5 10
  243. outSJfilterIntronMaxVsReadN 50000 100000 200000
  244. outWigType None
  245. outWigStrand Stranded
  246. outWigReferencesPrefix -
  247. outWigNorm RPM
  248. outFilterType Normal
  249. outFilterMultimapNmax 10
  250. outFilterMultimapScoreRange 1
  251. outFilterScoreMin 0
  252. outFilterScoreMinOverLread 0.66
  253. outFilterMatchNmin 0
  254. outFilterMatchNminOverLread 0.66
  255. outFilterMismatchNmax 10
  256. outFilterMismatchNoverLmax 0.3
  257. outFilterMismatchNoverReadLmax 1
  258. outFilterIntronMotifs None
  259. clip5pNbases 0
  260. clip3pNbases 0
  261. clip3pAfterAdapterNbases 0
  262. clip3pAdapterSeq -
  263. clip3pAdapterMMp 0.1
  264. winBinNbits 16
  265. winAnchorDistNbins 9
  266. winFlankNbins 4
  267. winAnchorMultimapNmax 50
  268. winReadCoverageRelativeMin 0.5
  269. winReadCoverageBasesMin 0
  270. scoreGap 0
  271. scoreGapNoncan -8
  272. scoreGapGCAG -4
  273. scoreGapATAC -8
  274. scoreStitchSJshift 1
  275. scoreGenomicLengthLog2scale -0.25
  276. scoreDelBase -2
  277. scoreDelOpen -2
  278. scoreInsOpen -2
  279. scoreInsBase -2
  280. seedSearchLmax 0
  281. seedSearchStartLmax 50
  282. seedSearchStartLmaxOverLread 1
  283. seedPerReadNmax 1000
  284. seedPerWindowNmax 50
  285. seedNoneLociPerWindow 10
  286. seedMultimapNmax 10000
  287. alignIntronMin 21
  288. alignIntronMax 0
  289. alignMatesGapMax 0
  290. alignTranscriptsPerReadNmax 10000
  291. alignSJoverhangMin 5
  292. alignSJDBoverhangMin 3
  293. alignSJstitchMismatchNmax 0 -1 0 0
  294. alignSplicedMateMapLmin 0
  295. alignSplicedMateMapLminOverLmate 0.66
  296. alignWindowsPerReadNmax 10000
  297. alignTranscriptsPerWindowNmax 100
  298. alignEndsType Local
  299. alignSoftClipAtReferenceEnds Yes
  300. alignEndsProtrude 0 ConcordantPair
  301. chimSegmentMin 0
  302. chimScoreMin 0
  303. chimScoreDropMax 20
  304. chimScoreSeparation 10
  305. chimScoreJunctionNonGTAG -1
  306. chimMainSegmentMultNmax 10
  307. chimJunctionOverhangMin 20
  308. chimOutType SeparateSAMold
  309. chimFilter banGenomicN
  310. chimSegmentReadGapMax 0
  311. sjdbFileChrStartEnd -
  312. sjdbGTFfile /home/user/scratch60/gencode.v28.annotation.gtf
  313. sjdbGTFchrPrefix -
  314. sjdbGTFfeatureExon exon
  315. sjdbGTFtagExonParentTranscript transcript_id
  316. sjdbGTFtagExonParentGene gene_id
  317. sjdbOverhang 99
  318. sjdbScore 2
  319. sjdbInsertSave Basic
  320. quantMode -
  321. quantTranscriptomeBAMcompression 1
  322. quantTranscriptomeBan IndelSoftclipSingleend
  323. twopass1readsN 18446744073709551615
  324. twopassMode None
  325. ----------------------------------------
  326.  
  327. Finished loading and checking parameters
  328. Aug 09 21:55:52 ... starting to generate Genome files
  329. /home/user/scratch60/hg38.fa : chr # 0 "chr1" chrStart: 0
  330. /home/user/scratch60/hg38.fa : chr # 1 "chr10" chrStart: 249036800
  331. /home/user/scratch60/hg38.fa : chr # 2 "chr11" chrStart: 382992384
  332. /home/user/scratch60/hg38.fa : chr # 3 "chr11_KI270721v1_random" chrStart: 518258688
  333. /home/user/scratch60/hg38.fa : chr # 4 "chr12" chrStart: 518520832
  334. /home/user/scratch60/hg38.fa : chr # 5 "chr13" chrStart: 651952128
  335. /home/user/scratch60/hg38.fa : chr # 6 "chr14" chrStart: 766509056
  336. /home/user/scratch60/hg38.fa : chr # 7 "chr14_GL000009v2_random" chrStart: 873725952
  337. /home/user/scratch60/hg38.fa : chr # 8 "chr14_GL000225v1_random" chrStart: 873988096
  338. /home/user/scratch60/hg38.fa : chr # 9 "chr14_KI270722v1_random" chrStart: 874250240
  339. /home/user/scratch60/hg38.fa : chr # 10 "chr14_GL000194v1_random" chrStart: 874512384
  340. /home/user/scratch60/hg38.fa : chr # 11 "chr14_KI270723v1_random" chrStart: 874774528
  341. /home/user/scratch60/hg38.fa : chr # 12 "chr14_KI270724v1_random" chrStart: 875036672
  342. /home/user/scratch60/hg38.fa : chr # 13 "chr14_KI270725v1_random" chrStart: 875298816
  343. /home/user/scratch60/hg38.fa : chr # 14 "chr14_KI270726v1_random" chrStart: 875560960
  344. /home/user/scratch60/hg38.fa : chr # 15 "chr15" chrStart: 875823104
  345. /home/user/scratch60/hg38.fa : chr # 16 "chr15_KI270727v1_random" chrStart: 978059264
  346. /home/user/scratch60/hg38.fa : chr # 17 "chr16" chrStart: 978583552
  347. /home/user/scratch60/hg38.fa : chr # 18 "chr16_KI270728v1_random" chrStart: 1069023232
  348. /home/user/scratch60/hg38.fa : chr # 19 "chr17" chrStart: 1071120384
  349. /home/user/scratch60/hg38.fa : chr # 20 "chr17_GL000205v2_random" chrStart: 1154482176
  350. /home/user/scratch60/hg38.fa : chr # 21 "chr17_KI270729v1_random" chrStart: 1154744320
  351. /home/user/scratch60/hg38.fa : chr # 22 "chr17_KI270730v1_random" chrStart: 1155268608
  352. /home/user/scratch60/hg38.fa : chr # 23 "chr18" chrStart: 1155530752
  353. /home/user/scratch60/hg38.fa : chr # 24 "chr19" chrStart: 1236008960
  354. /home/user/scratch60/hg38.fa : chr # 25 "chr1_KI270706v1_random" chrStart: 1294729216
  355. /home/user/scratch60/hg38.fa : chr # 26 "chr1_KI270707v1_random" chrStart: 1294991360
  356. /home/user/scratch60/hg38.fa : chr # 27 "chr1_KI270708v1_random" chrStart: 1295253504
  357. /home/user/scratch60/hg38.fa : chr # 28 "chr1_KI270709v1_random" chrStart: 1295515648
  358. /home/user/scratch60/hg38.fa : chr # 29 "chr1_KI270710v1_random" chrStart: 1295777792
  359. /home/user/scratch60/hg38.fa : chr # 30 "chr1_KI270711v1_random" chrStart: 1296039936
  360. /home/user/scratch60/hg38.fa : chr # 31 "chr1_KI270712v1_random" chrStart: 1296302080
  361. /home/user/scratch60/hg38.fa : chr # 32 "chr1_KI270713v1_random" chrStart: 1296564224
  362. /home/user/scratch60/hg38.fa : chr # 33 "chr1_KI270714v1_random" chrStart: 1296826368
  363. /home/user/scratch60/hg38.fa : chr # 34 "chr2" chrStart: 1297088512
  364. /home/user/scratch60/hg38.fa : chr # 35 "chr20" chrStart: 1539309568
  365. /home/user/scratch60/hg38.fa : chr # 36 "chr21" chrStart: 1603796992
  366. /home/user/scratch60/hg38.fa : chr # 37 "chr22" chrStart: 1650720768
  367. /home/user/scratch60/hg38.fa : chr # 38 "chr22_KI270731v1_random" chrStart: 1701576704
  368. /home/user/scratch60/hg38.fa : chr # 39 "chr22_KI270732v1_random" chrStart: 1701838848
  369. /home/user/scratch60/hg38.fa : chr # 40 "chr22_KI270733v1_random" chrStart: 1702100992
  370. /home/user/scratch60/hg38.fa : chr # 41 "chr22_KI270734v1_random" chrStart: 1702363136
  371. /home/user/scratch60/hg38.fa : chr # 42 "chr22_KI270735v1_random" chrStart: 1702625280
  372. /home/user/scratch60/hg38.fa : chr # 43 "chr22_KI270736v1_random" chrStart: 1702887424
  373. /home/user/scratch60/hg38.fa : chr # 44 "chr22_KI270737v1_random" chrStart: 1703149568
  374. /home/user/scratch60/hg38.fa : chr # 45 "chr22_KI270738v1_random" chrStart: 1703411712
  375. /home/user/scratch60/hg38.fa : chr # 46 "chr22_KI270739v1_random" chrStart: 1703673856
  376. /home/user/scratch60/hg38.fa : chr # 47 "chr2_KI270715v1_random" chrStart: 1703936000
  377. /home/user/scratch60/hg38.fa : chr # 48 "chr2_KI270716v1_random" chrStart: 1704198144
  378. /home/user/scratch60/hg38.fa : chr # 49 "chr3" chrStart: 1704460288
  379. /home/user/scratch60/hg38.fa : chr # 50 "chr3_GL000221v1_random" chrStart: 1902903296
  380. /home/user/scratch60/hg38.fa : chr # 51 "chr4" chrStart: 1903165440
  381. /home/user/scratch60/hg38.fa : chr # 52 "chr4_GL000008v2_random" chrStart: 2093481984
  382. /home/user/scratch60/hg38.fa : chr # 53 "chr5" chrStart: 2093744128
  383. /home/user/scratch60/hg38.fa : chr # 54 "chr5_GL000208v1_random" chrStart: 2275409920
  384. /home/user/scratch60/hg38.fa : chr # 55 "chr6" chrStart: 2275672064
  385. /home/user/scratch60/hg38.fa : chr # 56 "chr7" chrStart: 2446589952
  386. /home/user/scratch60/hg38.fa : chr # 57 "chr8" chrStart: 2605973504
  387. /home/user/scratch60/hg38.fa : chr # 58 "chr9" chrStart: 2751201280
  388. /home/user/scratch60/hg38.fa : chr # 59 "chr9_KI270717v1_random" chrStart: 2889613312
  389. /home/user/scratch60/hg38.fa : chr # 60 "chr9_KI270718v1_random" chrStart: 2889875456
  390. /home/user/scratch60/hg38.fa : chr # 61 "chr9_KI270719v1_random" chrStart: 2890137600
  391. /home/user/scratch60/hg38.fa : chr # 62 "chr9_KI270720v1_random" chrStart: 2890399744
  392. /home/user/scratch60/hg38.fa : chr # 63 "chr1_KI270762v1_alt" chrStart: 2890661888
  393. /home/user/scratch60/hg38.fa : chr # 64 "chr1_KI270766v1_alt" chrStart: 2891186176
  394. /home/user/scratch60/hg38.fa : chr # 65 "chr1_KI270760v1_alt" chrStart: 2891448320
  395. /home/user/scratch60/hg38.fa : chr # 66 "chr1_KI270765v1_alt" chrStart: 2891710464
  396. /home/user/scratch60/hg38.fa : chr # 67 "chr1_GL383518v1_alt" chrStart: 2891972608
  397. /home/user/scratch60/hg38.fa : chr # 68 "chr1_GL383519v1_alt" chrStart: 2892234752
  398. /home/user/scratch60/hg38.fa : chr # 69 "chr1_GL383520v2_alt" chrStart: 2892496896
  399. /home/user/scratch60/hg38.fa : chr # 70 "chr1_KI270764v1_alt" chrStart: 2893021184
  400. /home/user/scratch60/hg38.fa : chr # 71 "chr1_KI270763v1_alt" chrStart: 2893283328
  401. /home/user/scratch60/hg38.fa : chr # 72 "chr1_KI270759v1_alt" chrStart: 2894331904
  402. /home/user/scratch60/hg38.fa : chr # 73 "chr1_KI270761v1_alt" chrStart: 2894856192
  403. /home/user/scratch60/hg38.fa : chr # 74 "chr2_KI270770v1_alt" chrStart: 2895118336
  404. /home/user/scratch60/hg38.fa : chr # 75 "chr2_KI270773v1_alt" chrStart: 2895380480
  405. /home/user/scratch60/hg38.fa : chr # 76 "chr2_KI270774v1_alt" chrStart: 2895642624
  406. /home/user/scratch60/hg38.fa : chr # 77 "chr2_KI270769v1_alt" chrStart: 2895904768
  407. /home/user/scratch60/hg38.fa : chr # 78 "chr2_GL383521v1_alt" chrStart: 2896166912
  408. /home/user/scratch60/hg38.fa : chr # 79 "chr2_KI270772v1_alt" chrStart: 2896429056
  409. /home/user/scratch60/hg38.fa : chr # 80 "chr2_KI270775v1_alt" chrStart: 2896691200
  410. /home/user/scratch60/hg38.fa : chr # 81 "chr2_KI270771v1_alt" chrStart: 2896953344
  411. /home/user/scratch60/hg38.fa : chr # 82 "chr2_KI270768v1_alt" chrStart: 2897215488
  412. /home/user/scratch60/hg38.fa : chr # 83 "chr2_GL582966v2_alt" chrStart: 2897477632
  413. /home/user/scratch60/hg38.fa : chr # 84 "chr2_GL383522v1_alt" chrStart: 2897739776
  414. /home/user/scratch60/hg38.fa : chr # 85 "chr2_KI270776v1_alt" chrStart: 2898001920
  415. /home/user/scratch60/hg38.fa : chr # 86 "chr2_KI270767v1_alt" chrStart: 2898264064
  416. /home/user/scratch60/hg38.fa : chr # 87 "chr3_JH636055v2_alt" chrStart: 2898526208
  417. /home/user/scratch60/hg38.fa : chr # 88 "chr3_KI270783v1_alt" chrStart: 2898788352
  418. /home/user/scratch60/hg38.fa : chr # 89 "chr3_KI270780v1_alt" chrStart: 2899050496
  419. /home/user/scratch60/hg38.fa : chr # 90 "chr3_GL383526v1_alt" chrStart: 2899312640
  420. /home/user/scratch60/hg38.fa : chr # 91 "chr3_KI270777v1_alt" chrStart: 2899574784
  421. /home/user/scratch60/hg38.fa : chr # 92 "chr3_KI270778v1_alt" chrStart: 2899836928
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