STAR version=STAR_2.4.0j STAR compilation time,server,dir=Wed Feb 4 17:57:38 EST 2015 :/Users/alexdobin/STAR/source ##### DEFAULT parameters: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 outFileNamePrefix ./ outTmpDir - outStd Log outReadsUnmapped None outQSconversionAdd 0 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 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 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 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 0 sjdbScore 2 quantMode - quantTranscriptomeBAMcompression 1 twopass1readsN 0 twopassSJlimit 1000000 ##### Command Line: STAR --genomeDir ./GenomeDir/ --readFilesIn ./BGI_RNAseq_data_2015/15.fq --outSAMtype BAM SortedByCoordinate --runThreadN 1 --limitIObufferSize 100000000 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: genomeDir ./GenomeDir/ ~RE-DEFINED readFilesIn ./BGI_RNAseq_data_2015/15.fq ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED runThreadN 1 ~RE-DEFINED limitIObufferSize 100000000 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 1 genomeDir ./GenomeDir/ readFilesIn ./BGI_RNAseq_data_2015/15.fq limitIObufferSize 100000000 outSAMtype BAM SortedByCoordinate ------------------------------- ##### Final effective command line: STAR --runThreadN 1 --genomeDir ./GenomeDir/ --readFilesIn ./BGI_RNAseq_data_2015/15.fq --limitIObufferSize 100000000 --outSAMtype BAM SortedByCoordinate ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 readFilesIn ./BGI_RNAseq_data_2015/15.fq readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 100000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 outFileNamePrefix ./ outTmpDir - outStd Log outReadsUnmapped None outQSconversionAdd 0 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 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 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 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 0 sjdbScore 2 quantMode - quantTranscriptomeBAMcompression 1 twopass1readsN 0 twopassSJlimit 1000000 ---------------------------------------- WARNING: --limitBAMsortRAM=0, will use genome sizeas RAM linit foro BAM sorting Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles ./Mus_musculus.GRCm38.dna.primary_assembly.fa ~RE-DEFINED genomeSAindexNbases 13 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 2 ~RE-DEFINED sjdbOverhang 48 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile ./Mus_musculus.GRCm38.79.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED Genome version is compatible with current STAR version Started loading the genome: Tue Mar 31 22:06:17 2015 Read from SAindex: genomeSAindexNbases=13 nSAi=89478484 Genome file size: 2765481660 bytes; state: good=1 eof=0 fail=0 bad=0 SA file size: 11041698571 bytes; state: good=1 eof=0 fail=0 bad=0 nGenome=2765481660; nSAbyte=11041698571 GstrandBit=32 SA number of indices=2676775411 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 2765481660 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2765481660 bytes SA file size: 11041698571 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 11041698571 bytes Loading SAindex ... done: 391468488 bytes Finished loading the genome: Tue Mar 31 22:07:33 2015 Sum of all Genome bytes: 4381955250 Sum of all SA bytes: 1406848442652 Sum of all SAi bytes: 44591952253 Number of real (reference) chromosmes= 66 1 1 195471971 0 2 10 130694993 195559424 3 11 122082543 326369280 4 12 120129022 448528384 5 13 120421639 568852480 6 14 124902244 689438720 7 15 104043685 814481408 8 16 98207768 918552576 9 17 94987271 1016856576 10 18 90702639 1112014848 11 19 61431566 1202978816 12 2 182113224 1264582656 13 3 160039680 1446772736 14 4 156508116 1606942720 15 5 151834684 1763704832 16 6 149736546 1915748352 17 7 145441459 2065694720 18 8 129401213 2211184640 19 9 124595110 2340683776 20 MT 16299 2465464320 21 X 171031299 2465726464 22 Y 91744698 2636906496 23 JH584299.1 953012 2728656896 24 GL456233.1 336933 2729705472 25 JH584301.1 259875 2730229760 26 GL456211.1 241735 2730491904 27 GL456350.1 227966 2730754048 28 JH584293.1 207968 2731016192 29 GL456221.1 206961 2731278336 30 JH584297.1 205776 2731540480 31 JH584296.1 199368 2731802624 32 GL456354.1 195993 2732064768 33 JH584294.1 191905 2732326912 34 JH584298.1 184189 2732589056 35 JH584300.1 182347 2732851200 36 GL456219.1 175968 2733113344 37 GL456210.1 169725 2733375488 38 JH584303.1 158099 2733637632 39 JH584302.1 155838 2733899776 40 GL456212.1 153618 2734161920 41 JH584304.1 114452 2734424064 42 GL456379.1 72385 2734686208 43 GL456216.1 66673 2734948352 44 GL456393.1 55711 2735210496 45 GL456366.1 47073 2735472640 46 GL456367.1 42057 2735734784 47 GL456239.1 40056 2735996928 48 GL456213.1 39340 2736259072 49 GL456383.1 38659 2736521216 50 GL456385.1 35240 2736783360 51 GL456360.1 31704 2737045504 52 GL456378.1 31602 2737307648 53 GL456389.1 28772 2737569792 54 GL456372.1 28664 2737831936 55 GL456370.1 26764 2738094080 56 GL456381.1 25871 2738356224 57 GL456387.1 24685 2738618368 58 GL456390.1 24668 2738880512 59 GL456394.1 24323 2739142656 60 GL456392.1 23629 2739404800 61 GL456382.1 23158 2739666944 62 GL456359.1 22974 2739929088 63 GL456396.1 21240 2740191232 64 GL456368.1 20208 2740453376 65 JH584292.1 14945 2740715520 66 JH584295.1 1976 2740977664 Processing splice junctions database sjdbN=249916, sjdbOverhang=48 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Thread #0 end of input stream, nextChar=-1 Completed: thread #0 --genomeLoad=NoSharedMemory . Mar 31 22:35:37 ..... Started sorting BAM Max memory needed for sorting = 2214009778