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_erecta/STAR --outFileNamePrefix Dere_20-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn Dere_20.end1.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_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 Dere_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_erecta/STAR ~RE-DEFINED outFileNamePrefix Dere_20-STAR-2.5.3a/STAR-2.5.3a- ~RE-DEFINED readFilesIn Dere_20.end1.fastq.gz ~RE-DEFINED sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_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_erecta/STAR readFilesIn Dere_20.end1.fastq.gz readFilesCommand zcat limitBAMsortRAM 500000000000 limitSjdbInsertNsj 10000000 outFileNamePrefix Dere_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_erecta/Drosophila_erecta.dere_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_erecta/STAR --readFilesIn Dere_20.end1.fastq.gz --readFilesCommand zcat --limitBAMsortRAM 500000000000 --limitSjdbInsertNsj 10000000 --outFileNamePrefix Dere_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_erecta/Drosophila_erecta.dere_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_erecta/STAR genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn Dere_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 Dere_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_erecta/Drosophila_erecta.dere_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 Dere_20.end1.fastq.gz -rw-rw----+ 1 marinovg oak_akundaje 202539633 Dec 21 2017 Dere_20.end1.fastq.gz readsCommandsFile: exec > "Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "Dere_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_erecta/sequence/Drosophila_erecta.dere_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 1468268544 1196943160 ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 5124 1 CH959300.1 154 0 2 CH959299.1 182 262144 3 CH959298.1 202 524288 4 CH959297.1 217 786432 5 CH959296.1 244 1048576 6 CH959295.1 261 1310720 7 CH959294.1 265 1572864 8 CH959293.1 317 1835008 9 CH959292.1 344 2097152 10 CH959291.1 370 2359296 11 CH959290.1 386 2621440 12 CH959289.1 418 2883584 13 CH959288.1 436 3145728 14 CH959287.1 437 3407872 15 CH959286.1 450 3670016 16 CH959285.1 452 3932160 17 CH959284.1 455 4194304 18 CH959283.1 470 4456448 19 CH959282.1 471 4718592 20 CH959281.1 473 4980736 21 CH959280.1 476 5242880 22 CH959279.1 502 5505024 23 CH959278.1 507 5767168 24 CH959277.1 516 6029312 25 CH959276.1 524 6291456 26 CH959275.1 529 6553600 27 CH959274.1 532 6815744 28 CH959273.1 542 7077888 29 CH959272.1 582 7340032 30 CH959271.1 598 7602176 31 CH959270.1 607 7864320 32 CH959269.1 613 8126464 33 CH959268.1 615 8388608 34 CH959267.1 619 8650752 35 CH959266.1 626 8912896 36 CH959265.1 634 9175040 37 CH959264.1 637 9437184 38 CH959263.1 637 9699328 39 CH959262.1 640 9961472 40 CH959261.1 641 10223616 41 CH959260.1 645 10485760 42 CH959259.1 654 10747904 43 CH959258.1 673 11010048 44 CH959257.1 673 11272192 45 CH959256.1 677 11534336 46 CH959255.1 678 11796480 47 CH959254.1 683 12058624 48 CH959253.1 684 12320768 49 CH959252.1 685 12582912 50 CH959251.1 686 12845056 51 CH959250.1 687 13107200 52 CH959249.1 688 13369344 53 CH959248.1 692 13631488 54 CH959247.1 692 13893632 55 CH959246.1 696 14155776 56 CH959244.1 701 14417920 57 CH959245.1 701 14680064 58 CH959243.1 706 14942208 59 CH959241.1 707 15204352 60 CH959242.1 707 15466496 61 CH959240.1 708 15728640 62 CH959239.1 708 15990784 63 CH959238.1 708 16252928 64 CH959237.1 710 16515072 65 CH959235.1 712 16777216 66 CH959236.1 712 17039360 67 CH959234.1 713 17301504 68 CH959233.1 717 17563648 69 CH959231.1 718 17825792 70 CH959232.1 718 18087936 71 CH959230.1 720 18350080 72 CH959229.1 721 18612224 73 CH959228.1 724 18874368 74 CH959227.1 725 19136512 75 CH959226.1 726 19398656 76 CH959223.1 728 19660800 77 CH959225.1 728 19922944 78 CH959224.1 728 20185088 79 CH959222.1 729 20447232 80 CH959221.1 732 20709376 81 CH959219.1 734 20971520 82 CH959220.1 734 21233664 83 CH959218.1 735 21495808 84 CH959217.1 736 21757952 85 CH959216.1 737 22020096 86 CH959215.1 738 22282240 87 CH959214.1 738 22544384 88 CH959213.1 739 22806528 89 CH959212.1 741 23068672 90 CH959211.1 742 23330816 91 CH959210.1 743 23592960 92 CH959208.1 744 23855104 93 CH959209.1 744 24117248 94 CH959207.1 745 24379392 95 CH959206.1 745 24641536 96 CH959205.1 747 24903680 97 CH959204.1 750 25165824 98 CH959203.1 751 25427968 99 CH959201.1 753 25690112 100 CH959202.1 753 25952256 101 CH959199.1 754 26214400 102 CH959200.1 754 26476544 103 CH959198.1 755 26738688 104 CH959197.1 755 27000832 105 CH959196.1 755 27262976 106 CH959195.1 758 27525120 107 CH959194.1 759 27787264 108 CH959193.1 760 28049408 109 CH959192.1 760 28311552 110 CH959191.1 762 28573696 111 CH959190.1 762 28835840 112 CH959189.1 764 29097984 113 CH959188.1 765 29360128 114 CH959187.1 766 29622272 115 CH959186.1 767 29884416 116 CH959184.1 768 30146560 117 CH959183.1 768 30408704 118 CH959185.1 768 30670848 119 CH959180.1 770 30932992 120 CH959182.1 770 31195136 121 CH959181.1 770 31457280 122 CH959178.1 770 31719424 123 CH959179.1 770 31981568 124 CH959177.1 773 32243712 125 CH959174.1 776 32505856 126 CH959175.1 776 32768000 127 CH959176.1 776 33030144 128 CH959172.1 777 33292288 129 CH959173.1 777 33554432 130 CH959171.1 779 33816576 131 CH959170.1 780 34078720 132 CH959169.1 781 34340864 133 CH959168.1 784 34603008 134 CH959167.1 784 34865152 135 CH959166.1 785 35127296 136 CH959165.1 786 35389440 137 CH959164.1 787 35651584 138 CH959163.1 787 35913728 139 CH959162.1 788 36175872 140 CH959161.1 788 36438016 141 CH959159.1 789 36700160 142 CH959160.1 789 36962304 143 CH959157.1 793 37224448 144 CH959158.1 793 37486592 145 CH959156.1 794 37748736 146 CH959155.1 797 38010880 147 CH959154.1 798 38273024 148 CH959153.1 800 38535168 149 CH959152.1 801 38797312 150 CH959151.1 802 39059456 151 CH959150.1 804 39321600 152 CH959149.1 805 39583744 153 CH959147.1 807 39845888 154 CH959148.1 807 40108032 155 CH959146.1 809 40370176 156 CH959144.1 809 40632320 157 CH959145.1 809 40894464 158 CH959140.1 811 41156608 159 CH959142.1 811 41418752 160 CH959143.1 811 41680896 161 CH959141.1 811 41943040 162 CH959139.1 813 42205184 163 CH959138.1 813 42467328 164 CH959137.1 815 42729472 165 CH959136.1 816 42991616 166 CH959135.1 817 43253760 167 CH959134.1 817 43515904 168 CH959133.1 818 43778048 169 CH959132.1 819 44040192 170 CH959131.1 819 44302336 171 CH959130.1 822 44564480 172 CH959129.1 823 44826624 173 CH959128.1 827 45088768 174 CH959127.1 828 45350912 175 CH959126.1 828 45613056 176 CH959125.1 829 45875200 177 CH959123.1 831 46137344 178 CH959124.1 831 46399488 179 CH959122.1 832 46661632 180 CH959120.1 833 46923776 181 CH959121.1 833 47185920 182 CH959119.1 834 47448064 183 CH959118.1 835 47710208 184 CH959117.1 836 47972352 185 CH959116.1 838 48234496 186 CH959115.1 838 48496640 187 CH959114.1 839 48758784 188 CH959113.1 840 49020928 189 CH959112.1 843 49283072 190 CH959111.1 849 49545216 191 CH959110.1 850 49807360 192 CH959109.1 851 50069504 193 CH959108.1 852 50331648 194 CH959107.1 852 50593792 195 CH959106.1 852 50855936 196 CH959105.1 852 51118080 197 CH959104.1 854 51380224 198 CH959103.1 858 51642368 199 CH959102.1 862 51904512 200 CH959101.1 862 52166656 201 CH959100.1 863 52428800 202 CH959098.1 865 52690944 203 CH959099.1 865 52953088 204 CH959097.1 866 53215232 205 CH959096.1 867 53477376 206 CH959095.1 868 53739520 207 CH959094.1 869 54001664 208 CH959093.1 872 54263808 209 CH959092.1 873 54525952 210 CH959090.1 875 54788096 211 CH959089.1 875 55050240 212 CH959091.1 875 55312384 213 CH959088.1 877 55574528 214 CH959087.1 877 55836672 215 CH959086.1 878 56098816 216 CH959085.1 878 56360960 217 CH959084.1 880 56623104 218 CH959083.1 880 56885248 219 CH959081.1 880 57147392 220 CH959080.1 880 57409536 221 CH959082.1 880 57671680 222 CH959079.1 881 57933824 223 CH959078.1 882 58195968 224 CH959076.1 883 58458112 225 CH959077.1 883 58720256 226 CH959075.1 884 58982400 227 CH959074.1 886 59244544 228 CH959073.1 886 59506688 229 CH959072.1 888 59768832 230 CH959071.1 892 60030976 231 CH959069.1 893 60293120 232 CH959070.1 893 60555264 233 CH959067.1 894 60817408 234 CH959068.1 894 61079552 235 CH959065.1 895 61341696 236 CH959066.1 895 61603840 237 CH959064.1 896 61865984 238 CH959063.1 896 62128128 239 CH959062.1 898 62390272 240 CH959061.1 898 62652416 241 CH959060.1 899 62914560 242 CH959059.1 900 63176704 243 CH959058.1 901 63438848 244 CH959057.1 903 63700992 245 CH959056.1 903 63963136 246 CH959055.1 904 64225280 247 CH959054.1 905 64487424 248 CH959053.1 907 64749568 249 CH959052.1 909 65011712 250 CH959051.1 909 65273856 251 CH959050.1 911 65536000 252 CH959049.1 912 65798144 253 CH959048.1 912 66060288 254 CH959045.1 914 66322432 255 CH959046.1 914 66584576 256 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5076 CH954225.1 84040 1330380800 5077 CH954224.1 85266 1330642944 5078 CH954223.1 87511 1330905088 5079 CH954222.1 87629 1331167232 5080 CH954221.1 88178 1331429376 5081 CH954220.1 89879 1331691520 5082 CH954219.1 90863 1331953664 5083 CH954218.1 90951 1332215808 5084 CH954217.1 91523 1332477952 5085 CH954216.1 92376 1332740096 5086 CH954215.1 94554 1333002240 5087 CH954214.1 101947 1333264384 5088 CH954213.1 103426 1333526528 5089 CH954212.1 104115 1333788672 5090 CH954211.1 105853 1334050816 5091 CH954210.1 109464 1334312960 5092 CH954209.1 111674 1334575104 5093 CH954208.1 111971 1334837248 5094 CH954207.1 113016 1335099392 5095 CH954206.1 119159 1335361536 5096 CH954205.1 125611 1335623680 5097 CH954204.1 128025 1335885824 5098 CH954203.1 128029 1336147968 5099 CH954202.1 132001 1336410112 5100 CH954201.1 138015 1336672256 5101 CH954200.1 140085 1336934400 5102 CH954199.1 145960 1337196544 5103 CH954198.1 149445 1337458688 5104 CH954197.1 155306 1337720832 5105 CH954196.1 157145 1337982976 5106 CH954195.1 159895 1338245120 5107 CH954194.1 163109 1338507264 5108 CH954193.1 183471 1338769408 5109 CH954192.1 184191 1339031552 5110 CH954191.1 193804 1339293696 5111 CH954190.1 194427 1339555840 5112 CH954189.1 201718 1339817984 5113 CH954188.1 212294 1340080128 5114 CH954187.1 237013 1340342272 5115 CH954186.1 242605 1340604416 5116 CH954185.1 577315 1340866560 5117 CH954184.1 1286254 1341652992 5118 CH954183.1 2521924 1342963712 5119 CH954182.1 10470090 1345585152 5120 CH954181.1 17746568 1356070912 5121 CH954180.1 18748788 1373896704 5122 CH954179.1 22589142 1392771072 5123 CH954178.1 25762168 1415577600 5124 CH954177.1 26641161 1441529856 Started loading the genome: Fri Aug 1 01:45:03 2025 Genome: size given as a parameter = 1468268544 SA: size given as a parameter = 1196943160 /SAindex: size given as a parameter = 1 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=1468268544; nSAbyte=1196943160 GstrandBit=32 SA number of indices=290168038 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 1468268544 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 1468268544 bytes SA file size: 1196943160 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 1196943160 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Fri Aug 1 01:45:19 2025 To accomodate alignIntronMax=1000000 redefined winBinNbits=18 To accomodate alignIntronMax=1000000 and alignMatesGapMax=1000000, redefined winFlankNbins=4 and winAnchorDistNbins=8 Aug 01 01:45:19 ..... processing annotations GTF WARNING: while processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.gtf: overlapping or touching exons: CH954183.1 1313082 1326871 CH954183.1 1313082 1326871 WARNING: while processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.gtf: overlapping or touching exons: CH954179.1 13988028 14001508 CH954179.1 13988028 14001508 WARNING: while processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.gtf: overlapping or touching exons: CH954177.1 5206915 5220102 CH954177.1 5206915 5220102 Processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.gtf, found: 15902 transcripts 56839 exons (non-collapsed) 40923 collapsed junctions Aug 01 01:45:20 ..... finished GTF processing Aug 01 01:45:20 Loaded database junctions from the GTF file: /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Drosophila_erecta/Drosophila_erecta.dere_caf1.20.gtf: 40923 total junctions Aug 01 01:45:20 Finished preparing junctions Aug 01 01:45:20 ..... inserting junctions into the genome indices Aug 01 01:45:23 Finished SA search: number of new junctions=40923, old junctions=0 Aug 01 01:45:26 Finished sorting SA indicesL nInd=16368426 Aug 01 01:45:29 Finished inserting junction indices Aug 01 01:45:36 Finished SAi Aug 01 01:45:36 ..... finished inserting junctions into genome Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread8 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread9 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread10 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread11 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread12 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread13 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread14 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread15 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread16 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread17 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread18 ... ok Opening the file: Dere_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: Dere_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 #19 end of input stream, nextChar=-1 Completed: thread #5 Completed: thread #1 Completed: thread #11 Completed: thread #4 Completed: thread #7 Completed: thread #8 Completed: thread #6 Completed: thread #14 Completed: thread #3 Completed: thread #9 Completed: thread #13 Completed: thread #2 Completed: thread #19 Completed: thread #12 Completed: thread #10 Completed: thread #17 Completed: thread #18 Completed: thread #15 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 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 Completed: thread #16 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Aug 01 01:45:58 Loaded database junctions from the 1st pass file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARpass1//SJ.out.tab: 49716 total junctions Aug 01 01:45:58 Finished preparing junctions Aug 01 01:45:58 ..... inserting junctions into the genome indices Aug 01 01:45:59 Finished SA search: number of new junctions=5534, old junctions=40923 Aug 01 01:46:00 Finished sorting SA indicesL nInd=2212944 Aug 01 01:46:03 Finished inserting junction indices Aug 01 01:46:07 Finished SAi Aug 01 01:46:07 ..... finished inserting junctions into genome Input read files for mate 1, from input string Dere_20.end1.fastq.gz -rw-rw----+ 1 marinovg oak_akundaje 202539633 Dec 21 2017 Dere_20.end1.fastq.gz readsCommandsFile: exec > "Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "Dere_20.end1.fastq.gz" Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread8 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread9 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread10 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread11 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread12 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread13 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread14 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread15 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread16 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread17 ... ok Opening the file: Dere_20-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread18 ... ok Opening the file: Dere_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: Dere_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 #0 end of input stream, nextChar=-1 Completed: thread #19 Completed: thread #1 Completed: thread #10 Completed: thread #16 Completed: thread #7 Completed: thread #4 Completed: thread #8 Completed: thread #0 Joined thread # 1 Completed: thread #2 Joined thread # 2 Completed: thread #3 Joined thread # 3 Joined thread # 4 Completed: thread #13 Completed: thread #11 Completed: thread #5 Joined thread # 5 Completed: thread #17 Completed: thread #14 Completed: thread #12 Completed: thread #9 Completed: thread #6 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 Completed: thread #18 Completed: thread #15 Joined thread # 15 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Completed stage 1 mapping of outFilterBySJout mapping Detected 18 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 Created thread # 17 Created thread # 18 Created thread # 19 Completed: thread #19 BAM sorting: 166849 mapped reads BAM sorting bins genomic start loci: 1 3049 2164 2 4743 8956 3 5107 29210 4 5116 190574 5 5119 4317642 6 5120 4773774 7 5121 3044580 8 5121 14651081 9 5121 20999892 10 5122 4268815 11 5122 6515171 12 5122 8822447 13 5122 8825119 14 5122 16803347 15 5122 21221814 16 5123 6490505 Completed: thread #11 Completed: thread #12 Completed: thread #3 Completed: thread #1 Completed: thread #0 Joined thread # 1 Completed: thread #6 Completed: thread #9 Completed: thread #4 Completed: thread #13 Completed: thread #18 Completed: thread #8 Completed: thread #17 Completed: thread #10 Completed: thread #14 Completed: thread #16 Completed: thread #7 Completed: thread #15 Completed: thread #5 Completed: thread #2 Joined thread # 2 Joined thread # 3 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 01:46:33 ..... started sorting BAM Max memory needed for sorting = 57200216 ALL DONE!