STAR version=STAR_2.5.1b STAR compilation time,server,dir=Fri Jan 22 14:36:39 EST 2016 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 - 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 - 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 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 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 None ##### Command Line: STAR --runMode genomeGenerate --genomeDir ./STARoutput_1 --genomeFastaFiles genome.fa --sjdbGTFfile genome_ref_notID.gtf --sjdbOverhang 99 --runThreadN 20 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: runMode genomeGenerate ~RE-DEFINED genomeDir ./STARoutput_1 ~RE-DEFINED genomeFastaFiles genome.fa ~RE-DEFINED sjdbGTFfile genome_ref_notID.gtf ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED runThreadN 20 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runMode genomeGenerate runThreadN 20 genomeDir ./STARoutput_1 genomeFastaFiles genome.fa sjdbGTFfile genome_ref_notID.gtf sjdbOverhang 99 ------------------------------- ##### Final effective command line: STAR --runMode genomeGenerate --runThreadN 20 --genomeDir ./STARoutput_1 --genomeFastaFiles genome.fa --sjdbGTFfile genome_ref_notID.gtf --sjdbOverhang 99 ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode genomeGenerate runThreadN 20 runDirPerm User_RWX runRNGseed 777 genomeDir ./STARoutput_1 genomeLoad NoSharedMemory genomeFastaFiles genome.fa 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 - 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 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 chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile genome_ref_notID.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 99 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Finished loading and checking parameters Dec 06 08:07:38 ... Starting to generate Genome files genome.fa : chr # 0 "chr10" chrStart: 0 genome.fa : chr # 1 "chr11" chrStart: 135790592 genome.fa : chr # 2 "chr12" chrStart: 271056896 genome.fa : chr # 3 "chr13" chrStart: 405012480 genome.fa : chr # 4 "chr14" chrStart: 520355840 genome.fa : chr # 5 "chr15" chrStart: 627834880 genome.fa : chr # 6 "chr16" chrStart: 730595328 genome.fa : chr # 7 "chr17" chrStart: 821035008 genome.fa : chr # 8 "chr18" chrStart: 902299648 genome.fa : chr # 9 "chr19" chrStart: 980418560 genome.fa : chr # 10 "chr1" chrStart: 1039663104 genome.fa : chr # 11 "chr20" chrStart: 1288962048 genome.fa : chr # 12 "chr21" chrStart: 1352138752 genome.fa : chr # 13 "chr22" chrStart: 1400373248 genome.fa : chr # 14 "chr2" chrStart: 1451753472 genome.fa : chr # 15 "chr3" chrStart: 1695023104 genome.fa : chr # 16 "chr4" chrStart: 1893203968 genome.fa : chr # 17 "chr5" chrStart: 2084569088 genome.fa : chr # 18 "chr6" chrStart: 2265710592 genome.fa : chr # 19 "chr7" chrStart: 2436890624 genome.fa : chr # 20 "chr8" chrStart: 2596274176 genome.fa : chr # 21 "chr9" chrStart: 2742812672 genome.fa : chr # 22 "chrM" chrStart: 2884108288 genome.fa : chr # 23 "chrX" chrStart: 2884370432 genome.fa : chr # 24 "chrY" chrStart: 3039821824 genome.fa : chr # 25 "chr10" chrStart: 3099328512 genome.fa : chr # 26 "chr11" chrStart: 3235119104 genome.fa : chr # 27 "chr12" chrStart: 3370385408 genome.fa : chr # 28 "chr13" chrStart: 3504340992 genome.fa : chr # 29 "chr14" chrStart: 3619684352 genome.fa : chr # 30 "chr15" chrStart: 3727163392 genome.fa : chr # 31 "chr16" chrStart: 3829923840 genome.fa : chr # 32 "chr17" chrStart: 3920363520 genome.fa : chr # 33 "chr18" chrStart: 4001628160 genome.fa : chr # 34 "chr19" chrStart: 4079747072 genome.fa : chr # 35 "chr1" chrStart: 4138991616 genome.fa : chr # 36 "chr20" chrStart: 4388290560 genome.fa : chr # 37 "chr21" chrStart: 4451467264 genome.fa : chr # 38 "chr22" chrStart: 4499701760 genome.fa : chr # 39 "chr2" chrStart: 4551081984 genome.fa : chr # 40 "chr3" chrStart: 4794351616 genome.fa : chr # 41 "chr4" chrStart: 4992532480 genome.fa : chr # 42 "chr5" chrStart: 5183897600 genome.fa : chr # 43 "chr6" chrStart: 5365039104 genome.fa : chr # 44 "chr7" chrStart: 5536219136 genome.fa : chr # 45 "chr8" chrStart: 5695602688 genome.fa : chr # 46 "chr9" chrStart: 5842141184 genome.fa : chr # 47 "chrM" chrStart: 5983436800 genome.fa : chr # 48 "chrX" chrStart: 5983698944 genome.fa : chr # 49 "chrY" chrStart: 6139150336 Number of SA indices: 11445374808 Dec 06 08:09:42 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 207; chunks size limit: 558079976 bytes Dec 06 08:10:10 ... sorting Suffix Array chunks and saving them to disk... Writing 64 bytes into ./STARoutput_1/SA_4 ; empty space on disk = 911866553966592 bytes ... done