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STAR version=STAR_2.5.3a
STAR compilation time,server,dir=Fri Mar 17 11:35:46 EDT 2017 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source
##### DEFAULT parameters:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 1
runDirPerm User_RWX
runRNGseed 777
genomeDir ./GenomeDir/
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeChainFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
genomeFileSizes 0
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
chimMainSegmentMultNmax 10
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 None
##### Command Line:
STAR --runThreadN 15 --runMode genomeGenerate --genomeDir /home/G/ASAJ_index/index --genomeFastaFiles /home/D/ref/GDC_ref/GRCh38.d1.vd1.fa --sjdbGTFfile /home/G/ASAJ_index/gencode.v29.annotation.gtf --sjdbOverhang 100
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runThreadN 15 ~RE-DEFINED
runMode genomeGenerate ~RE-DEFINED
genomeDir /home/G/ASAJ_index/index ~RE-DEFINED
genomeFastaFiles /home/D/ref/GDC_ref/GRCh38.d1.vd1.fa ~RE-DEFINED
sjdbGTFfile /home/G/ASAJ_index/gencode.v29.annotation.gtf ~RE-DEFINED
sjdbOverhang 100 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runMode genomeGenerate
runThreadN 15
genomeDir /home/G/ASAJ_index/index
genomeFastaFiles /home/D/ref/GDC_ref/GRCh38.d1.vd1.fa
sjdbGTFfile /home/G/ASAJ_index/gencode.v29.annotation.gtf
sjdbOverhang 100
-------------------------------
##### Final effective command line:
STAR --runMode genomeGenerate --runThreadN 15 --genomeDir /home/G/ASAJ_index/index --genomeFastaFiles /home/D/ref/GDC_ref/GRCh38.d1.vd1.fa --sjdbGTFfile /home/G/ASAJ_index/gencode.v29.annotation.gtf --sjdbOverhang 100
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode genomeGenerate
runThreadN 15
runDirPerm User_RWX
runRNGseed 777
genomeDir /home/G/ASAJ_index/index
genomeLoad NoSharedMemory
genomeFastaFiles /home/D/ref/GDC_ref/GRCh38.d1.vd1.fa
genomeChainFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
genomeFileSizes 0
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
chimMainSegmentMultNmax 10
chimJunctionOverhangMin 20
chimOutType SeparateSAMold
chimFilter banGenomicN
chimSegmentReadGapMax 0
sjdbFileChrStartEnd -
sjdbGTFfile /home/G/ASAJ_index/gencode.v29.annotation.gtf
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbGTFtagExonParentGene gene_id
sjdbOverhang 100
sjdbScore 2
sjdbInsertSave Basic
quantMode -
quantTranscriptomeBAMcompression 1
quantTranscriptomeBan IndelSoftclipSingleend
twopass1readsN 18446744073709551615
twopassMode None
----------------------------------------
Finished loading and checking parameters
Dec 13 16:22:13 ... starting to generate Genome files
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 0 "chr1" chrStart: 0
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 1 "chr2" chrStart: 249036800
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 2 "chr3" chrStart: 491257856
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 3 "chr4" chrStart: 689700864
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 4 "chr5" chrStart: 880017408
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 5 "chr6" chrStart: 1061683200
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 6 "chr7" chrStart: 1232601088
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 7 "chr8" chrStart: 1391984640
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 8 "chr9" chrStart: 1537212416
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 9 "chr10" chrStart: 1675624448
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 10 "chr11" chrStart: 1809580032
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 11 "chr12" chrStart: 1944846336
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 12 "chr13" chrStart: 2078277632
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 13 "chr14" chrStart: 2192834560
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 14 "chr15" chrStart: 2300051456
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 15 "chr16" chrStart: 2402287616
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 16 "chr17" chrStart: 2492727296
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 17 "chr18" chrStart: 2576089088
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 18 "chr19" chrStart: 2656567296
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 19 "chr20" chrStart: 2715287552
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 20 "chr21" chrStart: 2779774976
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 21 "chr22" chrStart: 2826698752
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 22 "chrX" chrStart: 2877554688
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 23 "chrY" chrStart: 3033792512
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 24 "chrM" chrStart: 3091202048
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 25 "chr1_KI270706v1_random" chrStart: 3091464192
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 26 "chr1_KI270707v1_random" chrStart: 3091726336
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 27 "chr1_KI270708v1_random" chrStart: 3091988480
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 28 "chr1_KI270709v1_random" chrStart: 3092250624
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 29 "chr1_KI270710v1_random" chrStart: 3092512768
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 30 "chr1_KI270711v1_random" chrStart: 3092774912
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 31 "chr1_KI270712v1_random" chrStart: 3093037056
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 32 "chr1_KI270713v1_random" chrStart: 3093299200
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 33 "chr1_KI270714v1_random" chrStart: 3093561344
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 34 "chr2_KI270715v1_random" chrStart: 3093823488
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 35 "chr2_KI270716v1_random" chrStart: 3094085632
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 36 "chr3_GL000221v1_random" chrStart: 3094347776
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 37 "chr4_GL000008v2_random" chrStart: 3094609920
/home/D/ref/GDC_ref/GRCh38.d1.vd1.fa : chr # 38 "chr5_GL000208v1_random" chrStart: 3094872064
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