RicardoPluto
commented
7 years ago I have been trying to build again and I have get a log.out in my genomeDir. It seems that the step of generating Suffix Array index is wrong.
Closed RicardoPluto closed 5 years ago
RicardoPluto
commented
7 years ago I have been trying to build again and I have get a log.out in my genomeDir. It seems that the step of generating Suffix Array index is wrong.
RicardoPluto
commented
7 years ago STAR version=STAR_2.5.2b STAR compilation time,server,dir=Tue Nov 1 14:54:50 CST 2016 :/mnt/tools/STAR-2.5.2b/source
DEFAULT parameters:
versionSTAR 20201 versionGenome 20101 20200
parametersFiles -
sysShell - runMode alignReads runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles -
genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 readFilesIn Read1 Read2
readFilesCommand -
readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator /
inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outFileNamePrefix ./ outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype SAM
outSAMmode Full outSAMstrandField None outSAMattributes Standard
outSAMunmapped None
outSAMorder Paired outSAMprimaryFlag OneBestScore outSAMreadID Standard outSAMmapqUnique 255 outSAMflagOR 0 outSAMflagAND 65535 outSAMattrRGline -
outSAMheaderHD -
outSAMheaderPG -
outSAMheaderCommentFile - outBAMcompression 1 outBAMsortingThreadN 0 outSAMfilter None
outSAMmultNmax 18446744073709551615 outSAMattrIHstart 1 outSJfilterReads All outSJfilterCountUniqueMin 3 1 1 1
outSJfilterCountTotalMin 3 1 1 1
outSJfilterOverhangMin 30 12 12 12
outSJfilterDistToOtherSJmin 10 0 5 10
outSJfilterIntronMaxVsReadN 50000 100000 200000
outWigType None
outWigStrand Stranded
outWigReferencesPrefix - outWigNorm RPM
outFilterType Normal outFilterMultimapNmax 10 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.3 outFilterMismatchNoverReadLmax 1 outFilterIntronMotifs None clip5pNbases 0
clip3pNbases 0
clip3pAfterAdapterNbases 0
clip3pAdapterSeq -
clip3pAdapterMMp 0.1
winBinNbits 16 winAnchorDistNbins 9 winFlankNbins 4 winAnchorMultimapNmax 50 winReadCoverageRelativeMin 0.5 winReadCoverageBasesMin 0 scoreGap 0 scoreGapNoncan -8 scoreGapGCAG -4 scoreGapATAC -8 scoreStitchSJshift 1 scoreGenomicLengthLog2scale -0.25 scoreDelBase -2 scoreDelOpen -2 scoreInsOpen -2 scoreInsBase -2 seedSearchLmax 0 seedSearchStartLmax 50 seedSearchStartLmaxOverLread 1 seedPerReadNmax 1000 seedPerWindowNmax 50 seedNoneLociPerWindow 10 seedMultimapNmax 10000 alignIntronMin 21 alignIntronMax 0 alignMatesGapMax 0 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 5 alignSJDBoverhangMin 3 alignSJstitchMismatchNmax 0 -1 0 0
alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes alignEndsProtrude 0 ConcordantPair
chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN
chimSegmentReadGapMax 0 sjdbFileChrStartEnd -
sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode -
quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode NoneCommand Line:
STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /mnt/data/shenpan/V83/V83_homo_chr/STAR-index --genomeFastaFiles /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /mnt/data/shenpan/V83/Homo_sapiens.GRCh38.83.gtf/Homo_sapiens.GRCh38.83.gtf
Initial USER parameters from Command Line:
All USER parameters from Command Line:
runThreadN 8 ~RE-DEFINED runMode genomeGenerate ~RE-DEFINED genomeDir /mnt/data/shenpan/V83/V83_homo_chr/STAR-index ~RE-DEFINED genomeFastaFiles /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa ~RE-DEFINED sjdbGTFfile /mnt/data/shenpan/V83/Homo_sapiens.GRCh38.83.gtf/Homo_sapiens.GRCh38.83.gtf ~RE-DEFINED
Finished reading parameters from all sources
runMode genomeGenerate
runThreadN 8
genomeDir /mnt/data/shenpan/V83/V83_homo_chr/STAR-index
genomeFastaFiles /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa
sjdbGTFfile /mnt/data/shenpan/V83/Homo_sapiens.GRCh38.83.gtf/Homo_sapiens.GRCh38.83.gtf
STAR --runMode genomeGenerate --runThreadN 8 --genomeDir /mnt/data/shenpan/V83/V83_homo_chr/STAR-index --genomeFastaFiles /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /mnt/data/shenpan/V83/Homo_sapiens.GRCh38.83.gtf/Homo_sapiens.GRCh38.83.gtf
Finished loading and checking parameters Mar 03 18:54:16 ... starting to generate Genome files /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 0 "1" chrStart: 0 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 1 "10" chrStart: 249036800 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 2 "11" chrStart: 382992384 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 3 "12" chrStart: 518258688 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 4 "13" chrStart: 651689984 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 5 "14" chrStart: 766246912 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 6 "15" chrStart: 873463808 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 7 "16" chrStart: 975699968 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 8 "17" chrStart: 1066139648 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 9 "18" chrStart: 1149501440 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 10 "19" chrStart: 1229979648 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 11 "2" chrStart: 1288699904 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 12 "20" chrStart: 1530920960 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 13 "21" chrStart: 1595408384 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 14 "22" chrStart: 1642332160 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 15 "3" chrStart: 1693188096 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 16 "4" chrStart: 1891631104 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 17 "5" chrStart: 2081947648 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 18 "6" chrStart: 2263613440 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 19 "7" chrStart: 2434531328 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 20 "8" chrStart: 2593914880 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 21 "9" chrStart: 2739142656 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 22 "MT" chrStart: 2877554688 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 23 "X" chrStart: 2877816832 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 24 "Y" chrStart: 3034054656 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 25 "KI270728.1" chrStart: 3091464192 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 26 "KI270727.1" chrStart: 3093561344 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 27 "KI270442.1" chrStart: 3094085632 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 28 "KI270729.1" chrStart: 3094609920 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 29 "GL000225.1" chrStart: 3095134208 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 30 "KI270743.1" chrStart: 3095396352 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 31 "GL000008.2" chrStart: 3095658496 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 32 "GL000009.2" chrStart: 3095920640 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 33 "KI270747.1" chrStart: 3096182784 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 34 "KI270722.1" chrStart: 3096444928 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 35 "GL000194.1" chrStart: 3096707072 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 36 "KI270742.1" chrStart: 3096969216 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 37 "GL000205.2" chrStart: 3097231360 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 38 "GL000195.1" chrStart: 3097493504 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 39 "KI270736.1" chrStart: 3097755648 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 40 "KI270733.1" chrStart: 3098017792 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 41 "GL000224.1" chrStart: 3098279936 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 42 "GL000219.1" chrStart: 3098542080 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 43 "KI270719.1" chrStart: 3098804224 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 44 "GL000216.2" chrStart: 3099066368 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 45 "KI270712.1" chrStart: 3099328512 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 46 "KI270706.1" chrStart: 3099590656 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 47 "KI270725.1" chrStart: 3099852800 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 48 "KI270744.1" chrStart: 3100114944 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 49 "KI270734.1" chrStart: 3100377088 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 50 "GL000213.1" chrStart: 3100639232 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 51 "GL000220.1" chrStart: 3100901376 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 52 "KI270715.1" chrStart: 3101163520 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 53 "GL000218.1" chrStart: 3101425664 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 54 "KI270749.1" chrStart: 3101687808 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 55 "KI270741.1" chrStart: 3101949952 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 56 "GL000221.1" chrStart: 3102212096 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 57 "KI270716.1" chrStart: 3102474240 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 58 "KI270731.1" chrStart: 3102736384 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 59 "KI270751.1" chrStart: 3102998528 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 60 "KI270750.1" chrStart: 3103260672 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 61 "KI270519.1" chrStart: 3103522816 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 62 "GL000214.1" chrStart: 3103784960 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 63 "KI270708.1" chrStart: 3104047104 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 64 "KI270730.1" chrStart: 3104309248 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 65 "KI270438.1" chrStart: 3104571392 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 66 "KI270737.1" chrStart: 3104833536 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 67 "KI270721.1" chrStart: 3105095680 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 68 "KI270738.1" chrStart: 3105357824 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 69 "KI270748.1" chrStart: 3105619968 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 70 "KI270435.1" chrStart: 3105882112 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 71 "GL000208.1" chrStart: 3106144256 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 72 "KI270538.1" chrStart: 3106406400 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 73 "KI270756.1" chrStart: 3106668544 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 74 "KI270739.1" chrStart: 3106930688 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 75 "KI270757.1" chrStart: 3107192832 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 76 "KI270709.1" chrStart: 3107454976 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 77 "KI270746.1" chrStart: 3107717120 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 78 "KI270753.1" chrStart: 3107979264 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 79 "KI270589.1" chrStart: 3108241408 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 80 "KI270726.1" chrStart: 3108503552 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 81 "KI270735.1" chrStart: 3108765696 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 82 "KI270711.1" chrStart: 3109027840 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 83 "KI270745.1" chrStart: 3109289984 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 84 "KI270714.1" chrStart: 3109552128 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 85 "KI270732.1" chrStart: 3109814272 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 86 "KI270713.1" chrStart: 3110076416 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 87 "KI270754.1" chrStart: 3110338560 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 88 "KI270710.1" chrStart: 3110600704 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 89 "KI270717.1" chrStart: 3110862848 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 90 "KI270724.1" chrStart: 3111124992 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 91 "KI270720.1" chrStart: 3111387136 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 92 "KI270723.1" chrStart: 3111649280 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 93 "KI270718.1" chrStart: 3111911424 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 94 "KI270317.1" chrStart: 3112173568 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 95 "KI270740.1" chrStart: 3112435712 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 96 "KI270755.1" chrStart: 3112697856 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 97 "KI270707.1" chrStart: 3112960000 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 98 "KI270579.1" chrStart: 3113222144 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 99 "KI270752.1" chrStart: 3113484288 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 100 "KI270512.1" chrStart: 3113746432 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 101 "KI270322.1" chrStart: 3114008576 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 102 "GL000226.1" chrStart: 3114270720 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 103 "KI270311.1" chrStart: 3114532864 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 104 "KI270366.1" chrStart: 3114795008 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 105 "KI270511.1" chrStart: 3115057152 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 106 "KI270448.1" chrStart: 3115319296 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 107 "KI270521.1" chrStart: 3115581440 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 108 "KI270581.1" chrStart: 3115843584 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 109 "KI270582.1" chrStart: 3116105728 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 110 "KI270515.1" chrStart: 3116367872 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 111 "KI270588.1" chrStart: 3116630016 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 112 "KI270591.1" chrStart: 3116892160 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 113 "KI270522.1" chrStart: 3117154304 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 114 "KI270507.1" chrStart: 3117416448 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 115 "KI270590.1" chrStart: 3117678592 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 116 "KI270584.1" chrStart: 3117940736 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 117 "KI270320.1" chrStart: 3118202880 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 118 "KI270382.1" chrStart: 3118465024 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 119 "KI270468.1" chrStart: 3118727168 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 120 "KI270467.1" chrStart: 3118989312 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 121 "KI270362.1" chrStart: 3119251456 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 122 "KI270517.1" chrStart: 3119513600 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 123 "KI270593.1" chrStart: 3119775744 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 124 "KI270528.1" chrStart: 3120037888 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 125 "KI270587.1" chrStart: 3120300032 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 126 "KI270364.1" chrStart: 3120562176 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 127 "KI270371.1" chrStart: 3120824320 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 128 "KI270333.1" chrStart: 3121086464 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 129 "KI270374.1" chrStart: 3121348608 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 130 "KI270411.1" chrStart: 3121610752 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 131 "KI270414.1" chrStart: 3121872896 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 132 "KI270510.1" chrStart: 3122135040 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 133 "KI270390.1" chrStart: 3122397184 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 134 "KI270375.1" chrStart: 3122659328 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 135 "KI270420.1" chrStart: 3122921472 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 136 "KI270509.1" chrStart: 3123183616 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 137 "KI270315.1" chrStart: 3123445760 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 138 "KI270302.1" chrStart: 3123707904 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 139 "KI270518.1" chrStart: 3123970048 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 140 "KI270530.1" chrStart: 3124232192 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 141 "KI270304.1" chrStart: 3124494336 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 142 "KI270418.1" chrStart: 3124756480 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 143 "KI270424.1" chrStart: 3125018624 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 144 "KI270417.1" chrStart: 3125280768 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 145 "KI270508.1" chrStart: 3125542912 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 146 "KI270303.1" chrStart: 3125805056 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 147 "KI270381.1" chrStart: 3126067200 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 148 "KI270529.1" chrStart: 3126329344 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 149 "KI270425.1" chrStart: 3126591488 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 150 "KI270396.1" chrStart: 3126853632 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 151 "KI270363.1" chrStart: 3127115776 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 152 "KI270386.1" chrStart: 3127377920 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 153 "KI270465.1" chrStart: 3127640064 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 154 "KI270383.1" chrStart: 3127902208 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 155 "KI270384.1" chrStart: 3128164352 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 156 "KI270330.1" chrStart: 3128426496 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 157 "KI270372.1" chrStart: 3128688640 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 158 "KI270548.1" chrStart: 3128950784 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 159 "KI270580.1" chrStart: 3129212928 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 160 "KI270387.1" chrStart: 3129475072 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 161 "KI270391.1" chrStart: 3129737216 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 162 "KI270305.1" chrStart: 3129999360 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 163 "KI270373.1" chrStart: 3130261504 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 164 "KI270422.1" chrStart: 3130523648 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 165 "KI270316.1" chrStart: 3130785792 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 166 "KI270340.1" chrStart: 3131047936 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 167 "KI270338.1" chrStart: 3131310080 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 168 "KI270583.1" chrStart: 3131572224 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 169 "KI270334.1" chrStart: 3131834368 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 170 "KI270429.1" chrStart: 3132096512 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 171 "KI270393.1" chrStart: 3132358656 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 172 "KI270516.1" chrStart: 3132620800 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 173 "KI270389.1" chrStart: 3132882944 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 174 "KI270466.1" chrStart: 3133145088 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 175 "KI270388.1" chrStart: 3133407232 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 176 "KI270544.1" chrStart: 3133669376 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 177 "KI270310.1" chrStart: 3133931520 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 178 "KI270412.1" chrStart: 3134193664 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 179 "KI270395.1" chrStart: 3134455808 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 180 "KI270376.1" chrStart: 3134717952 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 181 "KI270337.1" chrStart: 3134980096 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 182 "KI270335.1" chrStart: 3135242240 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 183 "KI270378.1" chrStart: 3135504384 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 184 "KI270379.1" chrStart: 3135766528 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 185 "KI270329.1" chrStart: 3136028672 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 186 "KI270419.1" chrStart: 3136290816 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 187 "KI270336.1" chrStart: 3136552960 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 188 "KI270312.1" chrStart: 3136815104 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 189 "KI270539.1" chrStart: 3137077248 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 190 "KI270385.1" chrStart: 3137339392 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 191 "KI270423.1" chrStart: 3137601536 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 192 "KI270392.1" chrStart: 3137863680 /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 193 "KI270394.1" chrStart: 3138125824 Number of SA indices: 5891698134 Mar 03 18:55:06 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 27; chunks size limit: 1854240296 bytes Mar 03 18:55:21 ... sorting Suffix Array chunks and saving them to disk... Writing 1624408768 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_2 ; empty space on disk = 1985918341120 bytes ... done Writing 1841378792 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_6 ; empty space on disk = 1984292335616 bytes ... done Writing 1789714872 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_7 ; empty space on disk = 1982449147904 bytes ... done Writing 1693291528 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_3 ; empty space on disk = 1980657676288 bytes ... done Writing 1730742336 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_4 ; empty space on disk = 1978962722816 bytes ... done Writing 1815767296 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_0 ; empty space on disk = 1977230278656 bytes ... done Writing 1640585088 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_1 ; empty space on disk = 1975412731904 bytes ... done Writing 1800795608 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_5 ; empty space on disk = 1973770534912 bytes ... done Writing 1737704576 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_10 ; empty space on disk = 1971967971328 bytes ... done Writing 1815304384 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_9 ; empty space on disk = 1970228559872 bytes ... done Writing 1609091464 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_8 ; empty space on disk = 1968411475968 bytes ... done Writing 1776015312 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_11 ; empty space on disk = 1966800805888 bytes ... done Writing 1831994016 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_15 ; empty space on disk = 1965023047680 bytes ... done Writing 1729296464 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_14 ; empty space on disk = 1963189256192 bytes ... done Writing 1747220456 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_12 ; empty space on disk = 1961458262016 bytes ... done Writing 1665910992 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_13 ; empty space on disk = 1959709327360 bytes ... done Writing 1829304048 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_17 ; empty space on disk = 1958041780224 bytes ... done Writing 1815573112 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_16 ; empty space on disk = 1956210679808 bytes ... done Writing 1815828304 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_19 ; empty space on disk = 1954393325568 bytes ... done Writing 1702801672 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_18 ; empty space on disk = 1952575717376 bytes ... done Writing 1700126776 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_20 ; empty space on disk = 1950871244800 bytes ... done Writing 1702616416 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_23 ; empty space on disk = 1949169446912 bytes ... done Writing 1776826504 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_21 ; empty space on disk = 1947465162752 bytes ... done Writing 1542633240 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_25 ; empty space on disk = 1945686593536 bytes ... done Writing 1757272088 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_22 ; empty space on disk = 1944142446592 bytes ... done Writing 1825606584 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_24 ; empty space on disk = 1942383452160 bytes ... done Writing 1815774376 bytes into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index/SA_26 ; empty space on disk = 1940556054528 bytes ... done Mar 03 19:32:11 ... loading chunks from disk, packing SA... Mar 03 19:37:54 ... finished generating suffix array Mar 03 19:37:54 ... generating Suffix Array index
BUG: next index is smaller than previous, EXITING
Mar 03 19:37:57 ...... FATAL ERROR, exiting
alexdobin
commented
7 years ago Hi Ricardo,
please try to use pre-compiled executables from bin/Linux_x86_64 and bin/Linux_x86_64_static . Also, before running a new job, please remove all the files from the run directory.
Cheers Alex
RicardoPluto
commented
7 years ago Hi Alex,
I have followed your guidance but the same error still occurs. Are there any other solutions? Thank you！
Ricardo Shen
RicardoPluto
commented
7 years ago Hi Alex,
I found in the step of loading chunks from disk, packing SA, the run directory appeared a set of SA* (0, 1, 2, ...) and then these SA* disappeared one by one. When it reached the step of starting to generate Suffix Array index, the BUG occured and the run directory only contained five files: chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt. And there was no log.out (I have build at least ten times, only one time the log.out appeared). Is the problem in the step of starting to generate Suffix Array index? Thank you！
Ricardo Shen
alexdobin
commented
7 years ago Hi Ricardo,
are you using the files GTF/FASTA files download directly from ENSEMBL? I will run genome generation with these files to see if I can reproduce this problem. If it works fine, I will post the indexes so that you can download them and try mapping. The behavior with disappearing SA_* files is normal - these are uncompressed pieces of the index that are loaded in RAM one by one. After they are all loaded, STAR begins yet another indexing operation, which fails with the BUG message. The Log.out should appear in the run directory, which may not coincide with the genomeDir. If you cd into /mnt/data/shenpan/V83/V83_homo_chr/STAR-index before running, Log.out should appear in that directory.
Cheers Alex
RicardoPluto
commented
7 years ago Hi Alex,
The GTF/FASTA files are download directly from ENSEMBL (GTF file: ftp://ftp.ensembl.org/pub/release-83/gtf/homo_sapiens/Homo_sapiens.GRCh38.83.gtf.gz; FASTA file: ftp://ftp.ensembl.org/pub/release-83/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz). Thank you！
Ricardo Shen
alexdobin
commented
7 years ago Hi Ricardo,
I have generated the genome indexes without any issues. Please download them and run a mapping job, let us see if it works: http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/ENSEMBL/homo_sapiens/ENSEMBL.homo_sapiens.release-83/
Cheers Alex
RicardoPluto
commented
7 years ago Hi Alex,
Eventually I got the correct result. Thank you very much！
Ricardo Shen
alexdobin
commented
7 years ago Hi Ricardo,
that's good to hear - what did you do to resolve the problem?
Cheers Alex
RicardoPluto
commented
7 years ago Hi Alex,
I used the genome indexes you generated and run mapping jobs without any errors. Thank you very much！
Ricardo Shen
alexdobin
commented
7 years ago Hi Ricardo,
thanks! At some point I would like to figure out why the genome generation did not work.
Cheers Alex
BreenMS
commented
7 years ago I'm getting the exact same issue here...
Apr 07 16:08:51 ..... Started STAR run Apr 07 16:08:51 ... Starting to generate Genome files Apr 07 16:09:29 ... starting to sort Suffix Array. This may take a long time... Apr 07 16:09:45 ... sorting Suffix Array chunks and saving them to disk... Apr 07 16:11:25 ... loading chunks from disk, packing SA... Apr 07 16:11:32 ... Finished generating suffix array Apr 07 16:11:32 ... starting to generate Suffix Array index...
BUG: next index is smaller than previous, EXITING
Apr 07 16:11:32 ...... FATAL ERROR, exiting
Still figuring this one out... Michael
alexdobin
commented
7 years ago Hi Michael.
please send me the Log.out file of this run.
Cheers Alex
antonkulaga
commented
6 years ago I had the same error when running Index without gtf. This error looks very misterious to me
alexdobin
commented
6 years ago Hi Anton,
could you please send me the Log.out file of this run, and also the fasta and gtf files (or links to them)?
Cheers Alex
algunion
commented
6 years ago @alexdobin,
The same error here: BUG: next index is smaller than previous, EXITING
I attached the log file. Log.out.LOG
alexdobin
commented
6 years ago Hi @algunion
I have never been able to trace this bug, none of my tests show it. Could you please send me the link to the Homo_sapiens.GRCh38.dna.chromosome.1.fa fasta file?
Cheers Alex
christianwake
commented
6 years ago Hi,
In case it is helpful for troubleshooting, I have also encountered this error when attempting to build a STAR index from miRBase microRNA hairpin sequences. Except for the sake of consistency with other analyses, my use of STAR isn’t necessary with small RNA reads, but I hope this info might be helpful.
I’ve attached the log file. The fasta file is the miRBase v21 hairpin fasta file, filtered for hsa sequences. STAR_create_index.log
Best, Chris
alexdobin
commented
6 years ago Hi Chris,
could you please send me the Log.out file, and the FASTA file you are using.
Thanks! Alex
lauscherin
commented
6 years ago Dear Alex, unfortunately, I have the same issue. My genome is not a real one, it is only the sequence of a LINE1, without GTF-file.
My command: STAR --runThreadN 10 --runMode genomeGenerate --genomeDir STARgenomes/L1 --genomeFastaFiles L1_Hs_consensus.fas
Error message: Nov 27 14:45:23 ..... Started STAR run Nov 27 14:45:23 ... Starting to generate Genome files Nov 27 14:45:23 ... starting to sort Suffix Array. This may take a long time... Nov 27 14:45:23 ... sorting Suffix Array chunks and saving them to disk... Nov 27 14:45:23 ... loading chunks from disk, packing SA... Nov 27 14:45:23 ... Finished generating suffix array Nov 27 14:45:23 ... Generating Suffix Array index
BUG: next index is smaller than previous, EXITING
Nov 27 14:45:23 ...... FATAL ERROR, exiting
Attached, you will find the Log- and the "genome"-file.
Many thanks in advance!
alexdobin
commented
6 years ago Hi Angela,
for such a small genome you need to reduce --genomeSAindexNbases 6 , then the problem will go away.
Cheer Alex
scottkall
commented
6 years ago I just encountered this bug as well. I've never seen it before. I'm in the process of testing a snakemake pipeline that submits to SGE, but this is the 50th time it's been run. It's only the second time my colleague has run it, though -- it's possible this is related to a permissions issue, since she's operating in my directory, but it didn't happen the first time, and the first half of the pipeline ran just fine.
Hope this helps (both of us)! Thanks for a super tool.
EDIT: P.S. I just ran the Snakemake pipeline again, and it worked this time. Hard to debug an error that isn't reproducible!
alexdobin
commented
6 years ago Hi Scott,
is it possible that several jobs were run at the same time with the same genomeDir? That would create a problem.
Cheers Alex
SaiyiW
commented
6 years ago Hi Alex,
I encountered the same issue. The fasta I am using is hg19 and when I generated the index on one machine it works perfect. But when I moved to another and try to generate one with the same fasta there, it gives me this bug.
One difference of the two machines I have noticed is that the first machine is with intel little-endian cpu while the second is a power7 server with ibm big-endian cpu. I don't know if the endianness could be the problem. Maybe you can have a look if you have time.
Thank you for the great tool! :)
Saiyi
alexdobin
commented
6 years ago Hi Saiyi
STAR will not work on big-endian machines, unfortunately.
Cheers Alex
EvelyneC
commented
6 years ago Hi For me a dos2unix on my reference.fa fixed this 'bug'...
gprashant17
commented
5 years ago Hi, I'm using the latest version of STAR (2.7.1a) and I face the same problem. Also, the link which was posted before which contained the generated genome indexes did not work in the new version and gave this error: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.1a
Is it possible to get the genome indexes which will be compatible with the new version?
alexdobin
commented
5 years ago Hi @gprashant123
please send me the Log.out file of the failed genome generation run. Which genome assembly are you working with?
Cheers Alex
gprashant17
commented
5 years ago Hi Alex,
The issue is now resolved after I downloaded the latest version of the human genome from http://gencodegenes.org/ (along with annotations).
Previously I was working with NCBI's RefSeq human genome dataset, whose extension of the file was .fna, and this created the problem. I think the log.out file was not generated during the run.
Thanks
alexdobin
commented
5 years ago Great - thanks for letting me know!
anpanche
commented
3 years ago Hi Alex, I am also getting similar error while generating the genome index. I have attached the log.out file. Log.out.tar.gz
Thanks
Error: Apr 07 17:03:00 ..... Started STAR run Apr 07 17:03:00 ... Starting to generate Genome files Apr 07 17:03:53 ... starting to sort Suffix Array. This may take a long time... Apr 07 17:04:08 ... sorting Suffix Array chunks and saving them to disk... Killed
alexdobin
commented
3 years ago Hi Archana,
this is likely a different issue.
How much RAM do you have? You would need ~35GB to generate this genome. Also, what's the output of ulimit -a
Cheers Alex
anpanche
commented
3 years ago Hi Alex, Thank you for the reply. My system has only 24GB RAM. The output of ulimit -a is as below,
core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 111902 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 111902 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited
Can I go for parallel computing on cluster? If yes how? Please let me know how should I proceed to do it? Thanks in advance.
SebsCarrillo
commented
2 years ago Hi Alex, I have downloaded assemblies from NCI Assembly and also downloaded them from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Achromobacter_xylosoxidans/
I run: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /mnt/Adenina/drobles/scarrillo/alm_an/star_db/Achromobacter_xylosoxidans -- genomeFastaFiles /mnt/Adenina/drobles/scarrillo/alm_an/star_db/Achromobacter_xylosoxidans/GCF_003031105.1_ASM303110v1_genomic.fna.gz
And get the following error: Aug 29 17:51:57 ..... Started STAR run Aug 29 17:51:57 ... Starting to generate Genome files Aug 29 17:51:57 ... starting to sort Suffix Array. This may take a long time... Aug 29 17:51:57 ... sorting Suffix Array chunks and saving them to disk... Aug 29 17:51:57 ... loading chunks from disk, packing SA... Aug 29 17:51:57 ... Finished generating suffix array Aug 29 17:51:57 ... starting to generate Suffix Array index...
BUG: next index is smaller than previous, EXITING
Aug 29 17:51:57 ...... FATAL ERROR, exiting
I'm attaching my Log.out Log.txt
alexdobin
commented
2 years ago Hi @SebsCarrillo
you need to gunzip the FASTA file.
Cheers Alex
mptrsen
commented
2 years ago Just as an information: For really short sequences in the reference, and with little diversity, --genomeSAindexNbases needs to be very small. I had to reduce it to 3 to make it work with my barcode reference (some 350 seqs of length 51, differing only in 10 nucleotides or so).
pc297
commented
2 years ago Hi Saiyi
STAR will not work on big-endian machines, unfortunately.
Cheers Alex
It does however look like there are debian m68k and OpenSuse ppc64 versions (both big-endian) that must have passed the post-compilation tests as they are both hosted by their legitimate repositories:
https://packages.debian.org/sid/m68k/rna-star/download
Usually when building under debian, with dpkg-buildpackage or debuild, tests are performed post compilation, although they can be bypassed. I have been able to build it under debian ppc64 however it fails the dummy test afterwards (with foo.fa and foo.gtf). Can't test the opensuse version yet but I might try it in a VM to see if it is functional. As for the m68k version I do happen to have an old 68k mac to test it :D I might give m68k debian a try to see if it does work, however given how slow these CPUs are I am not sure what that version would be of any use for beyond viral and maybe some bacterial genomes :D
I would be interested to know how whoever compiled these solved the endianness issue (if they really did, that is), haven't been able to find any build information about those builds, but will keep looking.
pc297
commented
2 years ago So re the ppc64 (big endian) Suse version, I don't know yet as it needs glibc 2.34 which I am having to build. Having checked the diff files I don't see how it would be functional, as far as I can tell nothing was changed in the source. I will test it once I have a working 2.34 ppc64 glibc
Re the m68k version I haven't actually tried it (I did install qemu-m68k rather), however after consulting the build logs of that version and of the s390x version (also big endian, https://launchpad.net/ubuntu/+source/rna-star/2.5.0a+dfsg-1/+build/8788404), testing with foo.fa and foo.gtf was most likely not carried out (only carried out in later builds). So very likely these builds also cause the next index smaller bug. Will test the m68k version to be sure.
Cheers,
pc297
commented
2 years ago So re the ppc64 (big endian) Suse version, I don't know yet as it needs glibc 2.34 which I am having to build. Having checked the diff files I don't see how it would be functional, as far as I can tell nothing was changed in the source. I will test it once I have a working 2.34 ppc64 glibc
The ppc64 version provided by OpenSuse is non functional as well, the same bug arises when building indexes. And when trying to run STAR in alignment mode (using an index built on x64) a bad allocation exception is thrown. This confirms that these big-endian versions are not functional and might as well be removed
Cheers,
alexdobin
commented
2 years ago Hi @pc297
thanks for testing it. I will add a strong disclaimer that STAR cannot work on big-endian architectures.
Cheers Alex
Hi Alex,
I'm trying to build the genome index for GRCh38 downloaded from Ensembl and I get the following error: BUG: next index is smaller than previous, EXITING Additionally, I don't find log.out in my genomeDir. The log information in terminal as shown below: Mar 03 17:09:38 ..... started STAR run Mar 03 17:09:38 ... starting to generate Genome files Mar 03 17:10:44 ... starting to sort Suffix Array. This may take a long time... Mar 03 17:10:58 ... sorting Suffix Array chunks and saving them to disk... Mar 03 17:51:06 ... loading chunks from disk, packing SA... Mar 03 17:57:29 ... finished generating suffix array Mar 03 17:57:29 ... generating Suffix Array index BUG: next index is smaller than previous, EXITING Mar 03 17:57:34 ...... FATAL ERROR, exiting
Thank you very much!
Ricardo Shen