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 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 --genomeDir STAR_index --readFilesCommand zcat --readFilesIn ./data/SRR7939025_1.fastq.gz ./data/SRR7939025_2.fastq.gz --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFileNamePrefix STAR_alignments/SRR7939025_ ##### Initial USER parameters from Command Line: outFileNamePrefix STAR_alignments/SRR7939025_ ###### All USER parameters from Command Line: genomeDir STAR_index ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED readFilesIn ./data/SRR7939025_1.fastq.gz ./data/SRR7939025_2.fastq.gz ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED quantMode GeneCounts ~RE-DEFINED outFileNamePrefix STAR_alignments/SRR7939025_ ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: genomeDir STAR_index readFilesIn ./data/SRR7939025_1.fastq.gz ./data/SRR7939025_2.fastq.gz readFilesCommand zcat outFileNamePrefix STAR_alignments/SRR7939025_ outSAMtype BAM SortedByCoordinate quantMode GeneCounts ------------------------------- ##### Final effective command line: STAR --genomeDir STAR_index --readFilesIn ./data/SRR7939025_1.fastq.gz ./data/SRR7939025_2.fastq.gz --readFilesCommand zcat --outFileNamePrefix STAR_alignments/SRR7939025_ --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir STAR_index genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn ./data/SRR7939025_1.fastq.gz ./data/SRR7939025_2.fastq.gz readFilesCommand zcat readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outFileNamePrefix STAR_alignments/SRR7939025_ 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 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 GeneCounts quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Input read files for mate 1, from input string ./data/SRR7939025_1.fastq.gz -rw-r--r-- 1 jponomarenko Bioinformatics_Unit 3352692175 May 8 17:37 ./data/SRR7939025_1.fastq.gz readsCommandsFile: exec > "STAR_alignments/SRR7939025__STARtmp/tmp.fifo.read1" echo FILE 0 zcat "./data/SRR7939025_1.fastq.gz" Input read files for mate 2, from input string ./data/SRR7939025_2.fastq.gz -rw-r--r-- 1 jponomarenko Bioinformatics_Unit 3539990673 May 8 17:37 ./data/SRR7939025_2.fastq.gz readsCommandsFile: exec > "STAR_alignments/SRR7939025__STARtmp/tmp.fifo.read2" echo FILE 0 zcat "./data/SRR7939025_2.fastq.gz" 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 annotations/GRCm38.p6.genome.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile annotations/gencode.vM21.annotation.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 2832170936 22556835010 ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 139 1 chr1 195471971 0 2 chr2 182113224 195559424 3 chr3 160039680 377749504 4 chr4 156508116 537919488 5 chr5 151834684 694681600 6 chr6 149736546 846725120 7 chr7 145441459 996671488 8 chr8 129401213 1142161408 9 chr9 124595110 1271660544 10 chr10 130694993 1396441088 11 chr11 122082543 1527250944 12 chr12 120129022 1649410048 13 chr13 120421639 1769734144 14 chr14 124902244 1890320384 15 chr15 104043685 2015363072 16 chr16 98207768 2119434240 17 chr17 94987271 2217738240 18 chr18 90702639 2312896512 19 chr19 61431566 2403860480 20 chrX 171031299 2465464320 21 chrY 91744698 2636644352 22 chrM 16299 2728394752 23 KZ289080.1 394982 2728656896 24 KZ289081.1 369973 2729181184 25 GL456210.1 169725 2729705472 26 GL456211.1 241735 2729967616 27 GL456212.1 153618 2730229760 28 GL456213.1 39340 2730491904 29 GL456216.1 66673 2730754048 30 GL456219.1 175968 2731016192 31 GL456221.1 206961 2731278336 32 GL456233.1 336933 2731540480 33 GL456239.1 40056 2732064768 34 GL456350.1 227966 2732326912 35 GL456354.1 195993 2732589056 36 GL456359.1 22974 2732851200 37 GL456360.1 31704 2733113344 38 GL456366.1 47073 2733375488 39 GL456367.1 42057 2733637632 40 GL456368.1 20208 2733899776 41 GL456370.1 26764 2734161920 42 GL456372.1 28664 2734424064 43 GL456378.1 31602 2734686208 44 GL456379.1 72385 2734948352 45 GL456381.1 25871 2735210496 46 GL456382.1 23158 2735472640 47 GL456383.1 38659 2735734784 48 GL456385.1 35240 2735996928 49 GL456387.1 24685 2736259072 50 GL456389.1 28772 2736521216 51 GL456390.1 24668 2736783360 52 GL456392.1 23629 2737045504 53 GL456393.1 55711 2737307648 54 GL456394.1 24323 2737569792 55 GL456396.1 21240 2737831936 56 JH584292.1 14945 2738094080 57 JH584293.1 207968 2738356224 58 JH584294.1 191905 2738618368 59 JH584295.1 1976 2738880512 60 JH584296.1 199368 2739142656 61 JH584297.1 205776 2739404800 62 JH584298.1 184189 2739666944 63 JH584299.1 953012 2739929088 64 JH584300.1 182347 2740977664 65 JH584301.1 259875 2741239808 66 JH584302.1 155838 2741501952 67 JH584303.1 158099 2741764096 68 JH584304.1 114452 2742026240 69 KZ289092.1 460895 2742288384 70 KQ030490.1 120154 2742812672 71 KB469738.3 210641 2743074816 72 JH792830.1 246751 2743336960 73 KV575237.1 1224174 2743599104 74 KK082442.1 154766 2744909824 75 KV575240.1 171859 2745171968 76 KV575235.1 195735 2745434112 77 KZ289088.1 328684 2745696256 78 KV575239.1 71460 2746220544 79 KQ030495.1 490000 2746482688 80 KV575238.1 414410 2747006976 81 KZ289082.1 111720 2747531264 82 KV575234.1 686942 2747793408 83 KZ289072.1 425386 2748579840 84 KQ030485.1 185548 2749104128 85 KQ030486.1 399265 2749366272 86 KQ030487.1 316842 2749890560 87 KZ289070.1 378870 2750414848 88 KZ289084.1 283434 2750939136 89 KZ289085.1 380404 2751463424 90 KZ289093.1 245130 2751987712 91 KZ289094.1 155470 2752249856 92 KZ289095.1 305464 2752512000 93 KZ289090.1 263917 2753036288 94 KZ289091.1 448905 2753560576 95 KZ289065.1 171653 2754084864 96 KZ289064.1 117769 2754347008 97 KB469739.1 331111 2754609152 98 KB469741.2 505876 2755133440 99 JH792829.1 352455 2755657728 100 KV575236.1 166096 2756182016 101 KV575233.1 266016 2756444160 102 JH792826.1 368286 2756968448 103 KZ289071.1 355613 2757492736 104 JH792828.1 473738 2758017024 105 KZ289083.1 66290 2758541312 106 KB469740.1 316140 2758803456 107 KZ289087.1 253113 2759327744 108 KZ289089.1 662433 2759589888 109 JH792832.1 544189 2760376320 110 JH792833.1 221588 2761162752 111 JH792827.1 205713 2761424896 112 JH792834.1 331480 2761687040 113 JH792831.2 203377 2762211328 114 KB469742.1 1059955 2762473472 115 KZ289067.1 583977 2763784192 116 KQ030484.1 214957 2764570624 117 KQ030494.1 506812 2764832768 118 KQ030496.1 260447 2765357056 119 KQ030497.1 219721 2765619200 120 KQ030492.1 166012 2765881344 121 KQ030493.2 423369 2766143488 122 KQ030491.1 129865 2766667776 123 KQ030488.1 45901 2766929920 124 KQ030489.1 188269 2767192064 125 KV575232.1 200008 2767454208 126 KV575241.1 211337 2767716352 127 KZ289076.1 318915 2767978496 128 KZ289068.1 532572 2768502784 129 KZ289069.1 709099 2769289216 130 KV575242.1 299789 2770075648 131 KZ289086.1 542789 2770599936 132 KZ289066.1 339234 2771386368 133 KK082441.1 456798 2771910656 134 KZ289077.1 186144 2772434944 135 KZ289078.1 390920 2772697088 136 KZ289079.1 368967 2773221376 137 KZ289073.1 215264 2773745664 138 KZ289074.1 394026 2774007808 139 KZ289075.1 322221 2774532096 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Sat May 11 12:33:11 2019 Genome: size given as a parameter = 2832170936 SA: size given as a parameter = 22556835010 /SAindex: size given as a parameter = 1 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=2832170936; nSAbyte=22556835010 GstrandBit=32 SA number of indices=5468323638 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 2832170936 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2832170936 bytes SA file size: 22556835010 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 22556835010 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Sat May 11 12:35:04 2019 Processing splice junctions database sjdbN=284152, sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Starting to map file # 0 mate 1: ./data/SRR7939025_1.fastq.gz mate 2: ./data/SRR7939025_2.fastq.gz BAM sorting: 211535 mapped reads BAM sorting bins genomic start loci: 1 1 92599927 2 3 123190986 3 5 116241447 4 7 107057111 5 10 17198723 6 11 111785315 7 15 33251505 8 19 18272017 Thread #0 end of input stream, nextChar=-1 Completed: thread #0 May 11 13:32:17 ..... started sorting BAM Max memory needed for sorting = 2902979822 ALL DONE!