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: /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --limitSjdbInsertNsj 10000000 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/STAR --outFileNamePrefix Dana_20-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Dana_20.end1.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf --runThreadN 20 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 50 --outSAMstrandField intronMotif --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigStrand Stranded --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 ##### Initial USER parameters from Command Line: outFileNamePrefix Dana_20-STAR-2.5.3a/STAR-2.5.3a- ###### All USER parameters from Command Line: limitSjdbInsertNsj 10000000 ~RE-DEFINED genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/STAR ~RE-DEFINED outFileNamePrefix Dana_20-STAR-2.5.3a/STAR-2.5.3a- ~RE-DEFINED readFilesIn Dana_20.end1.fastq.gz ~RE-DEFINED sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf ~RE-DEFINED runThreadN 20 ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED outFilterType BySJout ~RE-DEFINED outSAMattributes NH HI AS NM MD ~RE-DEFINED outFilterMultimapNmax 50 ~RE-DEFINED outSAMstrandField intronMotif ~RE-DEFINED outFilterMismatchNmax 999 ~RE-DEFINED outFilterMismatchNoverReadLmax0.04 ~RE-DEFINED alignIntronMin 10 ~RE-DEFINED alignIntronMax 1000000 ~RE-DEFINED alignMatesGapMax 1000000 ~RE-DEFINED alignSJoverhangMin 8 ~RE-DEFINED alignSJDBoverhangMin 1 ~RE-DEFINED sjdbScore 1 ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED outWigStrand Stranded ~RE-DEFINED twopassMode Basic ~RE-DEFINED twopass1readsN 18446744073709551615 ~RE-DEFINED limitBAMsortRAM 500000000000 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 20 genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/STAR readFilesIn Dana_20.end1.fastq.gz readFilesCommand zcat limitBAMsortRAM 500000000000 limitSjdbInsertNsj 10000000 outFileNamePrefix Dana_20-STAR-2.5.3a/STAR-2.5.3a- outSAMtype BAM SortedByCoordinate outSAMstrandField intronMotif outSAMattributes NH HI AS NM MD outSAMunmapped Within outWigStrand Stranded outFilterType BySJout outFilterMultimapNmax 50 outFilterMismatchNmax 999 outFilterMismatchNoverReadLmax 0.04 alignIntronMin 10 alignIntronMax 1000000 alignMatesGapMax 1000000 alignSJoverhangMin 8 alignSJDBoverhangMin 1 sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf sjdbScore 1 twopass1readsN 18446744073709551615 twopassMode Basic ------------------------------- ##### Final effective command line: /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/STAR --runThreadN 20 --genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/STAR --readFilesIn Dana_20.end1.fastq.gz --readFilesCommand zcat --limitBAMsortRAM 500000000000 --limitSjdbInsertNsj 10000000 --outFileNamePrefix Dana_20-STAR-2.5.3a/STAR-2.5.3a- --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD --outSAMunmapped Within --outWigStrand Stranded --outFilterType BySJout --outFilterMultimapNmax 50 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf --sjdbScore 1 --twopass1readsN 18446744073709551615 --twopassMode Basic ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 20 runDirPerm User_RWX runRNGseed 777 genomeDir /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/STAR genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn Dana_20.end1.fastq.gz readFilesCommand zcat readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 500000000000 limitSjdbInsertNsj 10000000 outFileNamePrefix Dana_20-STAR-2.5.3a/STAR-2.5.3a- outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM SortedByCoordinate outSAMmode Full outSAMstrandField intronMotif outSAMattributes NH HI AS NM MD outSAMunmapped Within 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 BySJout outFilterMultimapNmax 50 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 999 outFilterMismatchNoverLmax 0.3 outFilterMismatchNoverReadLmax 0.04 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 10 alignIntronMax 1000000 alignMatesGapMax 1000000 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 8 alignSJDBoverhangMin 1 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 /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 1 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode Basic ---------------------------------------- Input read files for mate 1, from input string Dana_20.end1.fastq.gz -rw-rw----+ 1 marinovg oak_akundaje 140776000 Dec 21 2017 Dana_20.end1.fastq.gz readsCommandsFile: exec > "Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "Dana_20.end1.fastq.gz" WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/sequence/Drosophila_ananassae.dana_caf1.20.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 0 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile - ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3771203584 1764830244 ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 13749 1 CH916365.1 55 0 2 CH916364.1 121 262144 3 CH916363.1 141 524288 4 CH916362.1 145 786432 5 CH916361.1 223 1048576 6 CH916360.1 254 1310720 7 CH916359.1 276 1572864 8 CH916358.1 287 1835008 9 CH916357.1 308 2097152 10 CH916356.1 327 2359296 11 CH916355.1 328 2621440 12 CH916354.1 332 2883584 13 CH916353.1 371 3145728 14 CH916352.1 392 3407872 15 CH916351.1 393 3670016 16 CH916350.1 396 3932160 17 CH916349.1 400 4194304 18 CH916348.1 419 4456448 19 CH916347.1 431 4718592 20 CH916346.1 432 4980736 21 CH916345.1 439 5242880 22 CH916344.1 441 5505024 23 CH916343.1 441 5767168 24 CH916342.1 444 6029312 25 CH916341.1 450 6291456 26 CH916340.1 463 6553600 27 CH916339.1 467 6815744 28 CH916338.1 470 7077888 29 CH916337.1 474 7340032 30 CH916336.1 482 7602176 31 CH916335.1 484 7864320 32 CH916334.1 493 8126464 33 CH916333.1 509 8388608 34 CH916332.1 510 8650752 35 CH916331.1 512 8912896 36 CH916330.1 516 9175040 37 CH916329.1 532 9437184 38 CH916328.1 534 9699328 39 CH916327.1 541 9961472 40 CH916326.1 553 10223616 41 CH916325.1 556 10485760 42 CH916324.1 557 10747904 43 CH916323.1 558 11010048 44 CH916322.1 559 11272192 45 CH916321.1 560 11534336 46 CH916320.1 562 11796480 47 CH916319.1 563 12058624 48 CH916318.1 571 12320768 49 CH916317.1 574 12582912 50 CH916316.1 577 12845056 51 CH916315.1 585 13107200 52 CH916314.1 598 13369344 53 CH916313.1 599 13631488 54 CH916312.1 600 13893632 55 CH916311.1 602 14155776 56 CH916310.1 602 14417920 57 CH916309.1 603 14680064 58 CH916308.1 609 14942208 59 CH916307.1 610 15204352 60 CH916306.1 612 15466496 61 CH916305.1 618 15728640 62 CH916304.1 621 15990784 63 CH916303.1 624 16252928 64 CH916302.1 626 16515072 65 CH916300.1 628 16777216 66 CH916301.1 628 17039360 67 CH916299.1 632 17301504 68 CH916297.1 634 17563648 69 CH916298.1 634 17825792 70 CH916296.1 636 18087936 71 CH916295.1 641 18350080 72 CH916294.1 642 18612224 73 CH916293.1 644 18874368 74 CH916292.1 647 19136512 75 CH916291.1 647 19398656 76 CH916290.1 650 19660800 77 CH916289.1 652 19922944 78 CH916288.1 653 20185088 79 CH916287.1 656 20447232 80 CH916286.1 657 20709376 81 CH916285.1 658 20971520 82 CH916284.1 660 21233664 83 CH916282.1 662 21495808 84 CH916283.1 662 21757952 85 CH916281.1 665 22020096 86 CH916280.1 666 22282240 87 CH916279.1 667 22544384 88 CH916278.1 668 22806528 89 CH916277.1 670 23068672 90 CH916276.1 670 23330816 91 CH916275.1 671 23592960 92 CH916274.1 671 23855104 93 CH916273.1 672 24117248 94 CH916272.1 673 24379392 95 CH916271.1 673 24641536 96 CH916270.1 674 24903680 97 CH916269.1 675 25165824 98 CH916268.1 676 25427968 99 CH916267.1 676 25690112 100 CH916265.1 677 25952256 101 CH916266.1 677 26214400 102 CH916264.1 678 26476544 103 CH916263.1 683 26738688 104 CH916262.1 683 27000832 105 CH916260.1 684 27262976 106 CH916259.1 684 27525120 107 CH916261.1 684 27787264 108 CH916258.1 686 28049408 109 CH916257.1 687 28311552 110 CH916256.1 689 28573696 111 CH916254.1 692 28835840 112 CH916255.1 692 29097984 113 CH916252.1 693 29360128 114 CH916253.1 693 29622272 115 CH916250.1 694 29884416 116 CH916251.1 694 30146560 117 CH916249.1 695 30408704 118 CH916248.1 695 30670848 119 CH916247.1 696 30932992 120 CH916246.1 696 31195136 121 CH916243.1 697 31457280 122 CH916244.1 697 31719424 123 CH916245.1 697 31981568 124 CH916242.1 698 32243712 125 CH916241.1 698 32505856 126 CH916238.1 701 32768000 127 CH916239.1 701 33030144 128 CH916240.1 701 33292288 129 CH916237.1 702 33554432 130 CH916236.1 703 33816576 131 CH916235.1 705 34078720 132 CH916233.1 706 34340864 133 CH916234.1 706 34603008 134 CH916232.1 707 34865152 135 CH916230.1 707 35127296 136 CH916231.1 707 35389440 137 CH916228.1 708 35651584 138 CH916229.1 708 35913728 139 CH916225.1 708 36175872 140 CH916226.1 708 36438016 141 CH916227.1 708 36700160 142 CH916224.1 709 36962304 143 CH916223.1 711 37224448 144 CH916220.1 712 37486592 145 CH916222.1 712 37748736 146 CH916219.1 712 38010880 147 CH916221.1 712 38273024 148 CH916218.1 715 38535168 149 CH916217.1 716 38797312 150 CH916215.1 717 39059456 151 CH916216.1 717 39321600 152 CH916214.1 718 39583744 153 CH916212.1 720 39845888 154 CH916213.1 720 40108032 155 CH916211.1 721 40370176 156 CH916210.1 722 40632320 157 CH916208.1 722 40894464 158 CH916209.1 722 41156608 159 CH916207.1 723 41418752 160 CH916204.1 724 41680896 161 CH916205.1 724 41943040 162 CH916206.1 724 42205184 163 CH916203.1 725 42467328 164 CH916202.1 725 42729472 165 CH916201.1 726 42991616 166 CH916200.1 726 43253760 167 CH916198.1 727 43515904 168 CH916199.1 727 43778048 169 CH916197.1 728 44040192 170 CH916196.1 729 44302336 171 CH916195.1 730 44564480 172 CH916194.1 730 44826624 173 CH916193.1 730 45088768 174 CH916192.1 731 45350912 175 CH916191.1 732 45613056 176 CH916190.1 733 45875200 177 CH916189.1 734 46137344 178 CH916188.1 734 46399488 179 CH916186.1 735 46661632 180 CH916185.1 735 46923776 181 CH916187.1 735 47185920 182 CH916184.1 736 47448064 183 CH916183.1 737 47710208 184 CH916181.1 737 47972352 185 CH916182.1 737 48234496 186 CH916178.1 738 48496640 187 CH916179.1 738 48758784 188 CH916180.1 738 49020928 189 CH916176.1 739 49283072 190 CH916177.1 739 49545216 191 CH916175.1 739 49807360 192 CH916174.1 740 50069504 193 CH916173.1 741 50331648 194 CH916171.1 742 50593792 195 CH916172.1 742 50855936 196 CH916170.1 742 51118080 197 CH916169.1 743 51380224 198 CH916168.1 743 51642368 199 CH916166.1 745 51904512 200 CH916167.1 745 52166656 201 CH916165.1 745 52428800 202 CH916164.1 745 52690944 203 CH916163.1 746 52953088 204 CH916162.1 749 53215232 205 CH916161.1 749 53477376 206 CH916159.1 750 53739520 207 CH916158.1 750 54001664 208 CH916160.1 750 54263808 209 CH916156.1 751 54525952 210 CH916155.1 751 54788096 211 CH916157.1 751 55050240 212 CH916154.1 752 55312384 213 CH916152.1 754 55574528 214 CH916153.1 754 55836672 215 CH916151.1 756 56098816 216 CH916149.1 758 56360960 217 CH916150.1 758 56623104 218 CH916146.1 759 56885248 219 CH916145.1 759 57147392 220 CH916144.1 759 57409536 221 CH916147.1 759 57671680 222 CH916148.1 759 57933824 223 CH916143.1 761 58195968 224 CH916142.1 761 58458112 225 CH916141.1 761 58720256 226 CH916140.1 762 58982400 227 CH916137.1 763 59244544 228 CH916138.1 763 59506688 229 CH916139.1 763 59768832 230 CH916135.1 764 60030976 231 CH916136.1 764 60293120 232 CH916133.1 765 60555264 233 CH916134.1 765 60817408 234 CH916132.1 766 61079552 235 CH916131.1 767 61341696 236 CH916130.1 767 61603840 237 CH916129.1 768 61865984 238 CH916128.1 768 62128128 239 CH916127.1 769 62390272 240 CH916126.1 770 62652416 241 CH916123.1 770 62914560 242 CH916124.1 770 63176704 243 CH916125.1 770 63438848 244 CH916122.1 770 63700992 245 CH916121.1 771 63963136 246 CH916120.1 772 64225280 247 CH916119.1 772 64487424 248 CH916118.1 773 64749568 249 CH916117.1 774 65011712 250 CH916115.1 774 65273856 251 CH916116.1 774 65536000 252 CH916114.1 775 65798144 253 CH916111.1 777 66060288 254 CH916110.1 777 66322432 255 CH916113.1 777 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CH902757.1 81014 3567255552 13610 CH902756.1 81109 3567517696 13611 CH902755.1 81207 3567779840 13612 CH902754.1 81556 3568041984 13613 CH902753.1 82599 3568304128 13614 CH902752.1 82930 3568566272 13615 CH902751.1 83202 3568828416 13616 CH902750.1 83613 3569090560 13617 CH902749.1 83622 3569352704 13618 CH902748.1 83628 3569614848 13619 CH902747.1 84221 3569876992 13620 CH902746.1 84503 3570139136 13621 CH902745.1 84603 3570401280 13622 CH902744.1 84862 3570663424 13623 CH902743.1 84862 3570925568 13624 CH902742.1 85085 3571187712 13625 CH902741.1 85352 3571449856 13626 CH902740.1 85546 3571712000 13627 CH902739.1 85871 3571974144 13628 CH902738.1 86653 3572236288 13629 CH902737.1 86751 3572498432 13630 CH902736.1 86947 3572760576 13631 CH902735.1 87051 3573022720 13632 CH902734.1 87073 3573284864 13633 CH902733.1 88298 3573547008 13634 CH902732.1 88368 3573809152 13635 CH902731.1 88448 3574071296 13636 CH902730.1 88615 3574333440 13637 CH902729.1 88626 3574595584 13638 CH902728.1 89734 3574857728 13639 CH902727.1 90471 3575119872 13640 CH902726.1 90911 3575382016 13641 CH902725.1 92002 3575644160 13642 CH902724.1 92214 3575906304 13643 CH902723.1 94255 3576168448 13644 CH902722.1 94449 3576430592 13645 CH902721.1 95123 3576692736 13646 CH902720.1 96234 3576954880 13647 CH902719.1 96352 3577217024 13648 CH902718.1 96668 3577479168 13649 CH902717.1 99986 3577741312 13650 CH902716.1 103667 3578003456 13651 CH902715.1 104162 3578265600 13652 CH902714.1 104732 3578527744 13653 CH902713.1 106490 3578789888 13654 CH902712.1 110321 3579052032 13655 CH902711.1 116542 3579314176 13656 CH902710.1 118864 3579576320 13657 CH902709.1 119289 3579838464 13658 CH902708.1 119555 3580100608 13659 CH902707.1 120443 3580362752 13660 CH902706.1 120443 3580624896 13661 CH902705.1 122714 3580887040 13662 CH902704.1 122800 3581149184 13663 CH902703.1 128409 3581411328 13664 CH902702.1 130031 3581673472 13665 CH902701.1 130239 3581935616 13666 CH902700.1 131564 3582197760 13667 CH902699.1 132638 3582459904 13668 CH902698.1 135327 3582722048 13669 CH902697.1 136333 3582984192 13670 CH902696.1 139307 3583246336 13671 CH902695.1 140146 3583508480 13672 CH902694.1 141129 3583770624 13673 CH902693.1 142579 3584032768 13674 CH902692.1 151219 3584294912 13675 CH902691.1 152916 3584557056 13676 CH902690.1 159719 3584819200 13677 CH902689.1 160054 3585081344 13678 CH902688.1 174884 3585343488 13679 CH902687.1 175366 3585605632 13680 CH902686.1 185238 3585867776 13681 CH902685.1 187244 3586129920 13682 CH902684.1 189693 3586392064 13683 CH902683.1 193881 3586654208 13684 CH902682.1 199132 3586916352 13685 CH902681.1 203597 3587178496 13686 CH902680.1 205772 3587440640 13687 CH902679.1 213337 3587702784 13688 CH902678.1 214038 3587964928 13689 CH902677.1 215805 3588227072 13690 CH902676.1 236354 3588489216 13691 CH902675.1 236608 3588751360 13692 CH902674.1 240082 3589013504 13693 CH902673.1 265444 3589275648 13694 CH902672.1 272910 3589799936 13695 CH902671.1 284793 3590324224 13696 CH902670.1 295132 3590848512 13697 CH902669.1 320451 3591372800 13698 CH902668.1 323522 3591897088 13699 CH902667.1 441482 3592421376 13700 CH902666.1 443544 3592945664 13701 CH902665.1 488297 3593469952 13702 CH902664.1 509009 3593994240 13703 CH902663.1 519072 3594518528 13704 CH902662.1 529493 3595042816 13705 CH902661.1 569066 3595829248 13706 CH902660.1 569613 3596615680 13707 CH902659.1 610351 3597402112 13708 CH902658.1 631617 3598188544 13709 CH902657.1 632140 3598974976 13710 CH902656.1 637250 3599761408 13711 CH902655.1 673502 3600547840 13712 CH902654.1 692136 3601334272 13713 CH902653.1 742402 3602120704 13714 CH902652.1 754457 3602907136 13715 CH902651.1 771024 3603693568 13716 CH902650.1 802071 3604480000 13717 CH902649.1 865660 3605528576 13718 CH902648.1 871550 3606577152 13719 CH902647.1 940145 3607625728 13720 CH902646.1 978470 3608674304 13721 CH902645.1 1099307 3609722880 13722 CH902644.1 1373759 3611033600 13723 CH902643.1 1428709 3612606464 13724 CH902642.1 1527837 3614179328 13725 CH902641.1 1551108 3615752192 13726 CH902640.1 1562580 3617325056 13727 CH902639.1 1574637 3618897920 13728 CH902638.1 1584923 3620732928 13729 CH902637.1 1685616 3622567936 13730 CH902636.1 1739075 3624402944 13731 CH902635.1 1816235 3626237952 13732 CH902634.1 2125536 3628072960 13733 CH902633.1 2223656 3630432256 13734 CH902632.1 3277472 3632791552 13735 CH902631.1 3324263 3636199424 13736 CH902630.1 3335858 3639607296 13737 CH902629.1 3535662 3643015168 13738 CH902628.1 3602488 3646685184 13739 CH902627.1 3919855 3650355200 13740 CH902626.1 4599533 3654287360 13741 CH902625.1 4840945 3659005952 13742 CH902624.1 5039921 3663986688 13743 CH902623.1 5364042 3669229568 13744 CH902622.1 5790199 3674734592 13745 CH902621.1 6960332 3680763904 13746 CH902620.1 16180835 3687841792 13747 CH902619.1 19884421 3704094720 13748 CH902618.1 23293914 3724017664 13749 CH902617.1 23697760 3747348480 Started loading the genome: Fri Aug 1 01:45:01 2025 Genome: size given as a parameter = 3771203584 SA: size given as a parameter = 1764830244 /SAindex: size given as a parameter = 1 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=3771203584; nSAbyte=1764830244 GstrandBit=32 SA number of indices=427837634 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3771203584 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3771203584 bytes SA file size: 1764830244 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 1764830244 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Fri Aug 1 01:45:32 2025 To accomodate alignIntronMax=1000000 redefined winBinNbits=18 To accomodate alignIntronMax=1000000 and alignMatesGapMax=1000000, redefined winFlankNbins=4 and winAnchorDistNbins=8 Aug 01 01:45:32 ..... processing annotations GTF WARNING: while processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf: overlapping or touching exons: CH902624.1 4198077 4210449 CH902624.1 4198077 4210449 WARNING: while processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf: overlapping or touching exons: CH902622.1 1774818 1788478 CH902622.1 1774818 1788478 WARNING: while processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf: overlapping or touching exons: CH902620.1 10023055 10036242 CH902620.1 10023055 10036242 Processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf, found: 16061 transcripts 57317 exons (non-collapsed) 41251 collapsed junctions Aug 01 01:45:33 ..... finished GTF processing Aug 01 01:45:33 Loaded database junctions from the GTF file: /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_ananassae/Drosophila_ananassae.dana_caf1.20.gtf: 41251 total junctions Aug 01 01:45:33 Finished preparing junctions Aug 01 01:45:33 ..... inserting junctions into the genome indices Aug 01 01:45:38 Finished SA search: number of new junctions=41251, old junctions=0 Aug 01 01:45:44 Finished sorting SA indicesL nInd=16498976 Aug 01 01:45:51 Finished inserting junction indices Aug 01 01:46:02 Finished SAi Aug 01 01:46:02 ..... finished inserting junctions into genome Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread8 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread9 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread10 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread11 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread12 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread13 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread14 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread15 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread16 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread17 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread18 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread19 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: Dana_20.end1.fastq.gz Created thread # 6 Created thread # 7 Created thread # 8 Created thread # 9 Created thread # 10 Created thread # 11 Created thread # 12 Created thread # 13 Created thread # 14 Created thread # 15 Created thread # 16 Created thread # 17 Created thread # 18 Created thread # 19 Thread #14 end of input stream, nextChar=-1 Completed: thread #15 Completed: thread #16 Completed: thread #17 Completed: thread #18 Completed: thread #0 Completed: thread #19 Completed: thread #5 Completed: thread #13 Completed: thread #1 Joined thread # 1 Completed: thread #6 Completed: thread #2 Joined thread # 2 Completed: thread #3 Joined thread # 3 Completed: thread #4 Joined thread # 4 Joined thread # 5 Joined thread # 6 Completed: thread #10 Completed: thread #7 Joined thread # 7 Completed: thread #8 Joined thread # 8 Completed: thread #11 Completed: thread #14 Completed: thread #12 Completed: thread #9 Joined thread # 9 Joined thread # 10 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Aug 01 01:46:40 Loaded database junctions from the 1st pass file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARpass1//SJ.out.tab: 51314 total junctions Aug 01 01:46:40 Finished preparing junctions Aug 01 01:46:40 ..... inserting junctions into the genome indices Aug 01 01:46:41 Finished SA search: number of new junctions=6404, old junctions=41251 Aug 01 01:46:42 Finished sorting SA indicesL nInd=2560798 Aug 01 01:46:51 Finished inserting junction indices Aug 01 01:46:59 Finished SAi Aug 01 01:46:59 ..... finished inserting junctions into genome Input read files for mate 1, from input string Dana_20.end1.fastq.gz -rw-rw----+ 1 marinovg oak_akundaje 140776000 Dec 21 2017 Dana_20.end1.fastq.gz readsCommandsFile: exec > "Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "Dana_20.end1.fastq.gz" Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread8 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread9 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread10 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread11 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread12 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread13 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread14 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread15 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread16 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread17 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread18 ... ok Opening the file: Dana_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread19 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Starting to map file # 0 mate 1: Dana_20.end1.fastq.gz Created thread # 5 Created thread # 6 Created thread # 7 Created thread # 8 Created thread # 9 Created thread # 10 Created thread # 11 Created thread # 12 Created thread # 13 Created thread # 14 Created thread # 15 Created thread # 16 Created thread # 17 Created thread # 18 Created thread # 19 Thread #13 end of input stream, nextChar=-1 Completed: thread #14 Completed: thread #15 Completed: thread #16 Completed: thread #17 Completed: thread #18 Completed: thread #0 Completed: thread #19 Completed: thread #12 Completed: thread #1 Joined thread # 1 Completed: thread #5 Completed: thread #10 Completed: thread #4 Completed: thread #3 Completed: thread #6 Completed: thread #11 Completed: thread #8 Completed: thread #2 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Completed: thread #9 Completed: thread #13 Completed: thread #7 Joined thread # 7 Joined thread # 8 Joined thread # 9 Joined thread # 10 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Completed stage 1 mapping of outFilterBySJout mapping Detected 25 novel junctions that passed filtering, will proceed to filter reads that contained unannotated junctions Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Created thread # 8 Created thread # 9 Created thread # 10 Created thread # 11 Created thread # 12 Created thread # 13 Created thread # 14 Created thread # 15 Created thread # 16 Completed: thread #14 Created thread # 17 Created thread # 18 Created thread # 19 Completed: thread #0 Completed: thread #15 Completed: thread #17 Completed: thread #19 Completed: thread #16 Completed: thread #18 BAM sorting: 171865 mapped reads BAM sorting bins genomic start loci: 1 2354 414 2 4812 932 3 6848 290 4 12041 5946 5 13646 32367 6 13695 153389 7 13735 3289098 8 13742 2380231 9 13745 2354662 10 13745 14530285 11 13746 10430459 12 13747 294102 13 13747 9625577 14 13747 20785325 15 13747 20810656 16 13748 6499351 Completed: thread #12 Completed: thread #10 Completed: thread #1 Joined thread # 1 Completed: thread #5 Completed: thread #6 Completed: thread #11 Completed: thread #3 Completed: thread #9 Completed: thread #2 Joined thread # 2 Joined thread # 3 Completed: thread #13 Completed: thread #7 Completed: thread #8 Completed: thread #4 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Joined thread # 8 Joined thread # 9 Joined thread # 10 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Aug 01 01:47:43 ..... started sorting BAM Max memory needed for sorting = 61015256 ALL DONE!