STAR version=STAR_2.5.2b STAR compilation time,server,dir=Thu Aug 18 17:20:47 EDT 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 - 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 None ##### Command Line: /hpcdata/lmm/lmm_data/muddjc/STAR-2.5.2b/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 24 --genomeDir /hpcdata/lm m/lmm_data/muddjc/Mmul_8.0.1/ --genomeFastaFiles /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna --sjdbGTFfile /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.gff --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang -1 --genomeChrBinNbits=min --genomeSAindexNbases 13,14 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: runMode genomeGenerate ~RE-DEFINED runThreadN 24 ~RE-DEFINED genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/ ~RE-DEFINED genomeFastaFiles /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna ~RE-DEFINED sjdbGTFfile /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.gff ~RE-DEFINED sjdbGTFtagExonParentTranscriptParent ~RE-DEFINED sjdbOverhang 18446744073709551615 ~RE-DEFINED genomeChrBinNbits 0 ~RE-DEFINED genomeSAindexNbases 13 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runMode genomeGenerate runThreadN 24 genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/ genomeFastaFiles /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna genomeSAindexNbases 13 genomeChrBinNbits 0 sjdbGTFfile /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.gff sjdbGTFtagExonParentTranscript Parent sjdbOverhang 18446744073709551615 ------------------------------- ##### Final effective command line: /hpcdata/lmm/lmm_data/muddjc/STAR-2.5.2b/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 24 --genomeDir /hpcd ata/lmm/lmm_data/muddjc/Mmul_8.0.1/ --genomeFastaFiles /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_gen omic.fna --genomeSAindexNbases 13 --genomeChrBinNbits 0 --sjdbGTFfile /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_0007 72875.2_Mmul_8.0.1_genomic.gff --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang 18446744073709551615 ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode genomeGenerate runThreadN 24 runDirPerm User_RWX runRNGseed 777 genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/ genomeLoad NoSharedMemory genomeFastaFiles /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna genomeSAindexNbases 13 genomeChrBinNbits 0 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 /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.gff sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript Parent sjdbGTFtagExonParentGene gene_id sjdbOverhang 18446744073709551615 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Finished loading and checking parameters Nov 08 12:25:07 ... starting to generate Genome files /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna : chr # 0 "NC_027893.1" chrStart: 0 /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna : chr # 1 "NC_027894.1" chrStart: 225584830 #######etc########### Writing 2408032 bytes into /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1//SA_104 ; empty space on disk = 1280342361112576 bytes ... done Writing 435973920 bytes into /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1//SA_98 ; empty space on disk = 1280331875352576 bytes ...Writing 381016024 bytes into /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1//SA_100 ; empty space on disk = 1280332296880128 bytes ...Writing 372743744 bytes into /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1//SA_102 ; empty space on disk = 1280332460457984 bytes ... done done done Writing 496735088 bytes into /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1//SA_99 ; empty space on disk = 1280331930927104 bytes ... done Writing 429529872 bytes into /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1//SA_101 ; empty space on disk = 1280332006424576 bytes ... done Writing 747343112 bytes into /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1//SA_103 ; empty space on disk = 1280319432949760 bytes ... done Nov 08 12:50:31 ... loading chunks from disk, packing SA...