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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
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  725. /home/user/scratch60/hg38.fa : chr # 396  "chrUn_KI270363v1" chrStart: 3051356160
  726. /home/user/scratch60/hg38.fa : chr # 397  "chrUn_KI270364v1" chrStart: 3051618304
  727. /home/user/scratch60/hg38.fa : chr # 398  "chrUn_KI270362v1" chrStart: 3051880448
  728. /home/user/scratch60/hg38.fa : chr # 399  "chrUn_KI270366v1" chrStart: 3052142592
  729. /home/user/scratch60/hg38.fa : chr # 400  "chrUn_KI270378v1" chrStart: 3052404736
  730. /home/user/scratch60/hg38.fa : chr # 401  "chrUn_KI270379v1" chrStart: 3052666880
  731. /home/user/scratch60/hg38.fa : chr # 402  "chrUn_KI270389v1" chrStart: 3052929024
  732. /home/user/scratch60/hg38.fa : chr # 403  "chrUn_KI270390v1" chrStart: 3053191168
  733. /home/user/scratch60/hg38.fa : chr # 404  "chrUn_KI270387v1" chrStart: 3053453312
  734. /home/user/scratch60/hg38.fa : chr # 405  "chrUn_KI270395v1" chrStart: 3053715456
  735. /home/user/scratch60/hg38.fa : chr # 406  "chrUn_KI270396v1" chrStart: 3053977600
  736. /home/user/scratch60/hg38.fa : chr # 407  "chrUn_KI270388v1" chrStart: 3054239744
  737. /home/user/scratch60/hg38.fa : chr # 408  "chrUn_KI270394v1" chrStart: 3054501888
  738. /home/user/scratch60/hg38.fa : chr # 409  "chrUn_KI270386v1" chrStart: 3054764032
  739. /home/user/scratch60/hg38.fa : chr # 410  "chrUn_KI270391v1" chrStart: 3055026176
  740. /home/user/scratch60/hg38.fa : chr # 411  "chrUn_KI270383v1" chrStart: 3055288320
  741. /home/user/scratch60/hg38.fa : chr # 412  "chrUn_KI270393v1" chrStart: 3055550464
  742. /home/user/scratch60/hg38.fa : chr # 413  "chrUn_KI270384v1" chrStart: 3055812608
  743. /home/user/scratch60/hg38.fa : chr # 414  "chrUn_KI270392v1" chrStart: 3056074752
  744. /home/user/scratch60/hg38.fa : chr # 415  "chrUn_KI270381v1" chrStart: 3056336896
  745. /home/user/scratch60/hg38.fa : chr # 416  "chrUn_KI270385v1" chrStart: 3056599040
  746. /home/user/scratch60/hg38.fa : chr # 417  "chrUn_KI270382v1" chrStart: 3056861184
  747. /home/user/scratch60/hg38.fa : chr # 418  "chrUn_KI270376v1" chrStart: 3057123328
  748. /home/user/scratch60/hg38.fa : chr # 419  "chrUn_KI270374v1" chrStart: 3057385472
  749. /home/user/scratch60/hg38.fa : chr # 420  "chrUn_KI270372v1" chrStart: 3057647616
  750. /home/user/scratch60/hg38.fa : chr # 421  "chrUn_KI270373v1" chrStart: 3057909760
  751. /home/user/scratch60/hg38.fa : chr # 422  "chrUn_KI270375v1" chrStart: 3058171904
  752. /home/user/scratch60/hg38.fa : chr # 423  "chrUn_KI270371v1" chrStart: 3058434048
  753. /home/user/scratch60/hg38.fa : chr # 424  "chrUn_KI270448v1" chrStart: 3058696192
  754. /home/user/scratch60/hg38.fa : chr # 425  "chrUn_KI270521v1" chrStart: 3058958336
  755. /home/user/scratch60/hg38.fa : chr # 426  "chrUn_GL000195v1" chrStart: 3059220480
  756. /home/user/scratch60/hg38.fa : chr # 427  "chrUn_GL000219v1" chrStart: 3059482624
  757. /home/user/scratch60/hg38.fa : chr # 428  "chrUn_GL000220v1" chrStart: 3059744768
  758. /home/user/scratch60/hg38.fa : chr # 429  "chrUn_GL000224v1" chrStart: 3060006912
  759. /home/user/scratch60/hg38.fa : chr # 430  "chrUn_KI270741v1" chrStart: 3060269056
  760. /home/user/scratch60/hg38.fa : chr # 431  "chrUn_GL000226v1" chrStart: 3060531200
  761. /home/user/scratch60/hg38.fa : chr # 432  "chrUn_GL000213v1" chrStart: 3060793344
  762. /home/user/scratch60/hg38.fa : chr # 433  "chrUn_KI270743v1" chrStart: 3061055488
  763. /home/user/scratch60/hg38.fa : chr # 434  "chrUn_KI270744v1" chrStart: 3061317632
  764. /home/user/scratch60/hg38.fa : chr # 435  "chrUn_KI270745v1" chrStart: 3061579776
  765. /home/user/scratch60/hg38.fa : chr # 436  "chrUn_KI270746v1" chrStart: 3061841920
  766. /home/user/scratch60/hg38.fa : chr # 437  "chrUn_KI270747v1" chrStart: 3062104064
  767. /home/user/scratch60/hg38.fa : chr # 438  "chrUn_KI270748v1" chrStart: 3062366208
  768. /home/user/scratch60/hg38.fa : chr # 439  "chrUn_KI270749v1" chrStart: 3062628352
  769. /home/user/scratch60/hg38.fa : chr # 440  "chrUn_KI270750v1" chrStart: 3062890496
  770. /home/user/scratch60/hg38.fa : chr # 441  "chrUn_KI270751v1" chrStart: 3063152640
  771. /home/user/scratch60/hg38.fa : chr # 442  "chrUn_KI270752v1" chrStart: 3063414784
  772. /home/user/scratch60/hg38.fa : chr # 443  "chrUn_KI270753v1" chrStart: 3063676928
  773. /home/user/scratch60/hg38.fa : chr # 444  "chrUn_KI270754v1" chrStart: 3063939072
  774. /home/user/scratch60/hg38.fa : chr # 445  "chrUn_KI270755v1" chrStart: 3064201216
  775. /home/user/scratch60/hg38.fa : chr # 446  "chrUn_KI270756v1" chrStart: 3064463360
  776. /home/user/scratch60/hg38.fa : chr # 447  "chrUn_KI270757v1" chrStart: 3064725504
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  778. /home/user/scratch60/hg38.fa : chr # 449  "chrUn_KI270742v1" chrStart: 3065249792
  779. /home/user/scratch60/hg38.fa : chr # 450  "chrUn_GL000216v2" chrStart: 3065511936
  780. /home/user/scratch60/hg38.fa : chr # 451  "chrUn_GL000218v1" chrStart: 3065774080
  781. /home/user/scratch60/hg38.fa : chr # 452  "chrX" chrStart: 3066036224
  782. /home/user/scratch60/hg38.fa : chr # 453  "chrY" chrStart: 3222274048
  783. /home/user/scratch60/hg38.fa : chr # 454  "chrY_KI270740v1_random" chrStart: 3279683584
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