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 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 --genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/ - -readFilesIn /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R1_001.fastq,/h pcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fastq,/hpcdata/bcbb/lee rkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_ FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_ VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/J B37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GG CTCTGA_L007_R1_001.fastq /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R2_ 001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R2_001.fastq,/hpcd ata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fastq,/hpcdata/bcbb/leerke sm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP _48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGT I_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37 _ATTACTCG-GGCTCTGA_L007_R2_001.fastq --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMultimapNm ax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 1 --outFilterMismatchNmax 2 --runThreadN 4 --outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-G GCTCTGA ##### Initial USER parameters from Command Line: outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GG CTCTGA ###### All USER parameters from Command Line: genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/ ~RE-DEFINED readFilesIn /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L00 1_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fastq, /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq,/hpcdata/bcbb/l eerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGE T_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_62 7_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download /JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTC G-GGCTCTGA_L001_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002 _R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fastq,/ hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/bcbb/le erkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET _FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627 _VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED quantMode GeneCounts ~RE-DEFINED outFilterMultimapNmax 1 ~RE-DEFINED outFilterScoreMinOverLread 0 ~RE-DEFINED outFilterMatchNminOverLread 0 ~RE-DEFINED outFilterMatchNmin 1 ~RE-DEFINED outFilterMismatchNmax 2 ~RE-DEFINED runThreadN 4 ~RE-DEFINED outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GGCTCT GA ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 4 genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/ readFilesIn /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA _L001_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fa stq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq,/hpcdata/bc bb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM /WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FT P_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_down load/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATT ACTCG-GGCTCTGA_L001_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_ L002_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fas tq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/bcb b/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/ WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP _627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GG CTCTGA outSAMtype BAM SortedByCoordinate outFilterMultimapNmax 1 outFilterScoreMinOverLread 0 outFilterMatchNmin 1 outFilterMatchNminOverLread 0 outFilterMismatchNmax 2 quantMode GeneCounts ------------------------------- ##### Final effective command line: /hpcdata/lmm/lmm_data/muddjc/STAR-2.5.2b/bin/Linux_x86_64/STAR --runThreadN 4 --genomeDir /hpcdata/lmm/lmm_data/m uddjc/Mmul_8.0.1/ --readFilesIn /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA _L001_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fa stq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq,/hpcdata/bc bb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM /WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FT P_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_down load/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATT ACTCG-GGCTCTGA_L001_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_ L002_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fas tq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/bcb b/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/ WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP _627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq --outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/STA Rindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GGCTCTGA --outSAMtype BAM SortedByCoordinate --outFilterMul timapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 1 --outFilterMatchNminOverLread 0 --outFilter MismatchNmax 2 --quantMode GeneCounts ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 4 runDirPerm User_RWX runRNGseed 777 genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/ genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 readFilesIn /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA _L001_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fa stq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq,/hpcdata/bc bb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM /WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FT P_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_down load/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATT ACTCG-GGCTCTGA_L001_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_ L002_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fas tq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/bcb b/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/ WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP _627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq 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 /hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GG CTCTGA outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM SortedByCoordinate 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 1 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0 outFilterMatchNmin 1 outFilterMatchNminOverLread 0 outFilterMismatchNmax 2 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 GeneCounts quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Input read files for mate 1, from input string /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_A TTACTCG-GGCTCTGA_L001_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTG A_L002_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.f astq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/b cbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AG M/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/F TP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 666790221 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L001_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656995965 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L002_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656034791 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L003_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 649712788 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L004_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 659414483 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L005_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 660493219 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L006_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 661592981 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L007_R1_001.fastq readsCommandsFile: exec > "/hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GGCTCTGA_STARtmp/tmp.fifo.re ad1" echo FILE 0 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R1_001.fastq" echo FILE 1 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fastq" echo FILE 2 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq" echo FILE 3 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq" echo FILE 4 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq" echo FILE 5 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq" echo FILE 6 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq" Input read files for mate 2, from input string /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_A TTACTCG-GGCTCTGA_L001_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTG A_L002_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.f astq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/b cbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AG M/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/F TP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 666790221 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L001_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656995965 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L002_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656034791 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L003_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 649712788 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L004_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 659414483 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L005_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 660493219 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L006_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 661592981 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L007_R2_001.fastq readsCommandsFile: exec > "/hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GGCTCTGA_STARtmp/tmp.fifo.re ad2" echo FILE 0 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R2_001.fastq" echo FILE 1 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R2_001.fastq" echo FILE 2 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fastq" echo FILE 3 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq" echo FILE 4 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq" echo FILE 5 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq" echo FILE 6 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq" WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna ~ RE-DEFINED genomeSAindexNbases 13 ~RE-DEFINED genomeChrBinNbits 0 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.gff ~RE- DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscriptParent ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 284728 1 NC_027893.1 225584828 0 2 NC_027894.1 204787373 225584830 3 NC_027895.1 185818997 430372205 4 NC_027896.1 172585720 616191204 5 NC_027897.1 190429646 788776926 6 NC_027898.1 180051392 979206574 7 NC_027899.1 169600520 1159257968 8 NC_027900.1 144306982 1328858490 9 NC_027901.1 129882849 1473165474 10 NC_027902.1 92844088 1603048325 11 NC_027903.1 133663169 1695892415 12 NC_027904.1 125506784 1829555586 13 NC_027905.1 108979918 1955062372 14 NC_027906.1 127894412 2064042292 15 NC_027907.1 111343173 2191936706 16 NC_027908.1 77216781 2303279881 17 NC_027909.1 95684472 2380496664 18 NC_027910.1 70235451 2476181138 19 NC_027911.1 53671032 2546416591 20 NC_027912.1 74971481 2600087625 21 NC_027913.1 149150640 2675059108 22 NC_027914.1 11753682 2824209750 23 NW_014806053.1 1653 2835963434 24 NW_014806054.1 997 2835965089 25 NW_014806055.1 843 2835966088 26 NW_014806056.1 783 2835966933 27 NW_014806057.1 655 2835967718 28 NW_014806058.1 712 2835968375 29 NW_014806059.1 994 2835969089 30 NW_014806060.1 7901 2835970085 #########################################################...etc...################################################################# Processing splice junctions database sjdbN=235800, sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 winBinNbits=16 > genomeChrBinNbits=0 redefining: winBinNbits=0 Created thread # 1 Created thread # 2 Created thread # 3 Starting to map file # 0 mate 1: /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R1_001.fastq mate 2: /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R2_001.fastq