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/hg20/gencode/gencode_v26/STAR/ --outFileNamePrefix NC_IP-STAR-2.5.3a/STAR-2.5.3a- --readFilesIn NC_IP.end1.5p10bp-trimmed.fastq.gz --sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.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 --quantMode TranscriptomeSAM --twopassMode Basic --twopass1readsN -1 --limitBAMsortRAM 500000000000 ##### Initial USER parameters from Command Line: outFileNamePrefix NC_IP-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/hg20/gencode/gencode_v26/STAR/ ~RE-DEFINED outFileNamePrefix NC_IP-STAR-2.5.3a/STAR-2.5.3a- ~RE-DEFINED readFilesIn NC_IP.end1.5p10bp-trimmed.fastq.gz ~RE-DEFINED sjdbGTFfile /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.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 quantMode TranscriptomeSAM ~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/hg20/gencode/gencode_v26/STAR/ readFilesIn NC_IP.end1.5p10bp-trimmed.fastq.gz readFilesCommand zcat limitBAMsortRAM 500000000000 limitSjdbInsertNsj 10000000 outFileNamePrefix NC_IP-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/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf sjdbScore 1 quantMode TranscriptomeSAM 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/hg20/gencode/gencode_v26/STAR/ --readFilesIn NC_IP.end1.5p10bp-trimmed.fastq.gz --readFilesCommand zcat --limitBAMsortRAM 500000000000 --limitSjdbInsertNsj 10000000 --outFileNamePrefix NC_IP-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/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --sjdbScore 1 --quantMode TranscriptomeSAM --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/hg20/gencode/gencode_v26/STAR/ genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn NC_IP.end1.5p10bp-trimmed.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 NC_IP-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/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 1 sjdbInsertSave Basic quantMode TranscriptomeSAM quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode Basic ---------------------------------------- Input read files for mate 1, from input string NC_IP.end1.5p10bp-trimmed.fastq.gz -rw-rw----+ 1 marinovg oak_akundaje 171668543 Feb 14 03:42 NC_IP.end1.5p10bp-trimmed.fastq.gz readsCommandsFile: exec > "NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "NC_IP.end1.5p10bp-trimmed.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 /home/users/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /home/users/marinovg/genomes/hg20/gencode/gencode_v26/gencode.v26.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 3208436764 24901177516 ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 194 1 chr1 248956422 0 2 chr10 133797422 249036800 3 chr11 135086622 382992384 4 chr11_KI270721v1_random 100316 518258688 5 chr12 133275309 518520832 6 chr13 114364328 651952128 7 chr14 107043718 766509056 8 chr14_GL000009v2_random 201709 873725952 9 chr14_GL000225v1_random 211173 873988096 10 chr14_KI270722v1_random 194050 874250240 11 chr14_GL000194v1_random 191469 874512384 12 chr14_KI270723v1_random 38115 874774528 13 chr14_KI270724v1_random 39555 875036672 14 chr14_KI270725v1_random 172810 875298816 15 chr14_KI270726v1_random 43739 875560960 16 chr15 101991189 875823104 17 chr15_KI270727v1_random 448248 978059264 18 chr16 90338345 978583552 19 chr16_KI270728v1_random 1872759 1069023232 20 chr17 83257441 1071120384 21 chr17_GL000205v2_random 185591 1154482176 22 chr17_KI270729v1_random 280839 1154744320 23 chr17_KI270730v1_random 112551 1155268608 24 chr18 80373285 1155530752 25 chr19 58617616 1236008960 26 chr1_KI270706v1_random 175055 1294729216 27 chr1_KI270707v1_random 32032 1294991360 28 chr1_KI270708v1_random 127682 1295253504 29 chr1_KI270709v1_random 66860 1295515648 30 chr1_KI270710v1_random 40176 1295777792 31 chr1_KI270711v1_random 42210 1296039936 32 chr1_KI270712v1_random 176043 1296302080 33 chr1_KI270713v1_random 40745 1296564224 34 chr1_KI270714v1_random 41717 1296826368 35 chr2 242193529 1297088512 36 chr20 64444167 1539309568 37 chr21 46709983 1603796992 38 chr22 50818468 1650720768 39 chr22_KI270731v1_random 150754 1701576704 40 chr22_KI270732v1_random 41543 1701838848 41 chr22_KI270733v1_random 179772 1702100992 42 chr22_KI270734v1_random 165050 1702363136 43 chr22_KI270735v1_random 42811 1702625280 44 chr22_KI270736v1_random 181920 1702887424 45 chr22_KI270737v1_random 103838 1703149568 46 chr22_KI270738v1_random 99375 1703411712 47 chr22_KI270739v1_random 73985 1703673856 48 chr2_KI270715v1_random 161471 1703936000 49 chr2_KI270716v1_random 153799 1704198144 50 chr3 198295559 1704460288 51 chr3_GL000221v1_random 155397 1902903296 52 chr4 190214555 1903165440 53 chr4_GL000008v2_random 209709 2093481984 54 chr5 181538259 2093744128 55 chr5_GL000208v1_random 92689 2275409920 56 chr6 170805979 2275672064 57 chr7 159345973 2446589952 58 chr8 145138636 2605973504 59 chr9 138394717 2751201280 60 chr9_KI270717v1_random 40062 2889613312 61 chr9_KI270718v1_random 38054 2889875456 62 chr9_KI270719v1_random 176845 2890137600 63 chr9_KI270720v1_random 39050 2890399744 64 chrM 16569 2890661888 65 chrUn_KI270302v1 2274 2890924032 66 chrUn_KI270304v1 2165 2891186176 67 chrUn_KI270303v1 1942 2891448320 68 chrUn_KI270305v1 1472 2891710464 69 chrUn_KI270322v1 21476 2891972608 70 chrUn_KI270320v1 4416 2892234752 71 chrUn_KI270310v1 1201 2892496896 72 chrUn_KI270316v1 1444 2892759040 73 chrUn_KI270315v1 2276 2893021184 74 chrUn_KI270312v1 998 2893283328 75 chrUn_KI270311v1 12399 2893545472 76 chrUn_KI270317v1 37690 2893807616 77 chrUn_KI270412v1 1179 2894069760 78 chrUn_KI270411v1 2646 2894331904 79 chrUn_KI270414v1 2489 2894594048 80 chrUn_KI270419v1 1029 2894856192 81 chrUn_KI270418v1 2145 2895118336 82 chrUn_KI270420v1 2321 2895380480 83 chrUn_KI270424v1 2140 2895642624 84 chrUn_KI270417v1 2043 2895904768 85 chrUn_KI270422v1 1445 2896166912 86 chrUn_KI270423v1 981 2896429056 87 chrUn_KI270425v1 1884 2896691200 88 chrUn_KI270429v1 1361 2896953344 89 chrUn_KI270442v1 392061 2897215488 90 chrUn_KI270466v1 1233 2897739776 91 chrUn_KI270465v1 1774 2898001920 92 chrUn_KI270467v1 3920 2898264064 93 chrUn_KI270435v1 92983 2898526208 94 chrUn_KI270438v1 112505 2898788352 95 chrUn_KI270468v1 4055 2899050496 96 chrUn_KI270510v1 2415 2899312640 97 chrUn_KI270509v1 2318 2899574784 98 chrUn_KI270518v1 2186 2899836928 99 chrUn_KI270508v1 1951 2900099072 100 chrUn_KI270516v1 1300 2900361216 101 chrUn_KI270512v1 22689 2900623360 102 chrUn_KI270519v1 138126 2900885504 103 chrUn_KI270522v1 5674 2901147648 104 chrUn_KI270511v1 8127 2901409792 105 chrUn_KI270515v1 6361 2901671936 106 chrUn_KI270507v1 5353 2901934080 107 chrUn_KI270517v1 3253 2902196224 108 chrUn_KI270529v1 1899 2902458368 109 chrUn_KI270528v1 2983 2902720512 110 chrUn_KI270530v1 2168 2902982656 111 chrUn_KI270539v1 993 2903244800 112 chrUn_KI270538v1 91309 2903506944 113 chrUn_KI270544v1 1202 2903769088 114 chrUn_KI270548v1 1599 2904031232 115 chrUn_KI270583v1 1400 2904293376 116 chrUn_KI270587v1 2969 2904555520 117 chrUn_KI270580v1 1553 2904817664 118 chrUn_KI270581v1 7046 2905079808 119 chrUn_KI270579v1 31033 2905341952 120 chrUn_KI270589v1 44474 2905604096 121 chrUn_KI270590v1 4685 2905866240 122 chrUn_KI270584v1 4513 2906128384 123 chrUn_KI270582v1 6504 2906390528 124 chrUn_KI270588v1 6158 2906652672 125 chrUn_KI270593v1 3041 2906914816 126 chrUn_KI270591v1 5796 2907176960 127 chrUn_KI270330v1 1652 2907439104 128 chrUn_KI270329v1 1040 2907701248 129 chrUn_KI270334v1 1368 2907963392 130 chrUn_KI270333v1 2699 2908225536 131 chrUn_KI270335v1 1048 2908487680 132 chrUn_KI270338v1 1428 2908749824 133 chrUn_KI270340v1 1428 2909011968 134 chrUn_KI270336v1 1026 2909274112 135 chrUn_KI270337v1 1121 2909536256 136 chrUn_KI270363v1 1803 2909798400 137 chrUn_KI270364v1 2855 2910060544 138 chrUn_KI270362v1 3530 2910322688 139 chrUn_KI270366v1 8320 2910584832 140 chrUn_KI270378v1 1048 2910846976 141 chrUn_KI270379v1 1045 2911109120 142 chrUn_KI270389v1 1298 2911371264 143 chrUn_KI270390v1 2387 2911633408 144 chrUn_KI270387v1 1537 2911895552 145 chrUn_KI270395v1 1143 2912157696 146 chrUn_KI270396v1 1880 2912419840 147 chrUn_KI270388v1 1216 2912681984 148 chrUn_KI270394v1 970 2912944128 149 chrUn_KI270386v1 1788 2913206272 150 chrUn_KI270391v1 1484 2913468416 151 chrUn_KI270383v1 1750 2913730560 152 chrUn_KI270393v1 1308 2913992704 153 chrUn_KI270384v1 1658 2914254848 154 chrUn_KI270392v1 971 2914516992 155 chrUn_KI270381v1 1930 2914779136 156 chrUn_KI270385v1 990 2915041280 157 chrUn_KI270382v1 4215 2915303424 158 chrUn_KI270376v1 1136 2915565568 159 chrUn_KI270374v1 2656 2915827712 160 chrUn_KI270372v1 1650 2916089856 161 chrUn_KI270373v1 1451 2916352000 162 chrUn_KI270375v1 2378 2916614144 163 chrUn_KI270371v1 2805 2916876288 164 chrUn_KI270448v1 7992 2917138432 165 chrUn_KI270521v1 7642 2917400576 166 chrUn_GL000195v1 182896 2917662720 167 chrUn_GL000219v1 179198 2917924864 168 chrUn_GL000220v1 161802 2918187008 169 chrUn_GL000224v1 179693 2918449152 170 chrUn_KI270741v1 157432 2918711296 171 chrUn_GL000226v1 15008 2918973440 172 chrUn_GL000213v1 164239 2919235584 173 chrUn_KI270743v1 210658 2919497728 174 chrUn_KI270744v1 168472 2919759872 175 chrUn_KI270745v1 41891 2920022016 176 chrUn_KI270746v1 66486 2920284160 177 chrUn_KI270747v1 198735 2920546304 178 chrUn_KI270748v1 93321 2920808448 179 chrUn_KI270749v1 158759 2921070592 180 chrUn_KI270750v1 148850 2921332736 181 chrUn_KI270751v1 150742 2921594880 182 chrUn_KI270752v1 27745 2921857024 183 chrUn_KI270753v1 62944 2922119168 184 chrUn_KI270754v1 40191 2922381312 185 chrUn_KI270755v1 36723 2922643456 186 chrUn_KI270756v1 79590 2922905600 187 chrUn_KI270757v1 71251 2923167744 188 chrUn_GL000214v1 137718 2923429888 189 chrUn_KI270742v1 186739 2923692032 190 chrUn_GL000216v2 176608 2923954176 191 chrUn_GL000218v1 161147 2924216320 192 chrX 156040895 2924478464 193 chrY 57227415 3080716288 194 chrY_KI270740v1_random 37240 3138125824 --sjdbOverhang = 99 taken from the generated genome Started loading the genome: Sat Feb 14 04:07:32 2026 Genome: size given as a parameter = 3208436764 SA: size given as a parameter = 24901177516 /SAindex: size given as a parameter = 1 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=3208436764; nSAbyte=24901177516 GstrandBit=32 SA number of indices=6036649094 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3208436764 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3208436764 bytes SA file size: 24901177516 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24901177516 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Sat Feb 14 04:09:39 2026 Processing splice junctions database sjdbN=352004, sjdbOverhang=99 To accomodate alignIntronMax=1000000 redefined winBinNbits=18 To accomodate alignIntronMax=1000000 and alignMatesGapMax=1000000, redefined winFlankNbins=4 and winAnchorDistNbins=8 Feb 14 04:09:40 Loaded database junctions from the generated genome /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v26/STAR//sjdbList.out.tab: 352004 total junctions Feb 14 04:09:40 ..... processing annotations GTF Processing sjdbGTFfile=/oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf, found: 198093 transcripts 1182765 exons (non-collapsed) 350863 collapsed junctions Feb 14 04:10:20 ..... finished GTF processing Feb 14 04:10:20 Loaded database junctions from the GTF file: /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf: 702867 total junctions WARNING: long repeat for junction # 116453 : chr15 88855522 88855578; left shift = 14; right shift = 255 WARNING: long repeat for junction # 468048 : chr15 88855522 88855578; left shift = 14; right shift = 255 Feb 14 04:10:22 Finished preparing junctions Feb 14 04:10:22 ..... inserting junctions into the genome indices Feb 14 04:10:23 Finished SA search: number of new junctions=591, old junctions=352004 Feb 14 04:10:23 Finished sorting SA indicesL nInd=234036 Feb 14 04:11:34 Finished inserting junction indices Feb 14 04:11:38 Finished SAi Feb 14 04:11:38 ..... finished inserting junctions into genome Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread8 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread9 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread10 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread11 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread12 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread13 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread14 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread15 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread16 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread17 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread18 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread19 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Starting to map file # 0 mate 1: NC_IP.end1.5p10bp-trimmed.fastq.gz 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 Thread #13 end of input stream, nextChar=-1 Completed: thread #0 Completed: thread #4 Completed: thread #3 Completed: thread #2 Completed: thread #7 Completed: thread #8 Completed: thread #6 Completed: thread #11 Completed: thread #12 Completed: thread #13 Completed: thread #10 Completed: thread #1 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Completed: thread #15 Completed: thread #9 Completed: thread #5 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 Completed: thread #19 Completed: thread #17 Completed: thread #16 Completed: thread #14 Joined thread # 14 Joined thread # 15 Joined thread # 16 Joined thread # 17 Completed: thread #18 Joined thread # 18 Joined thread # 19 Feb 14 04:12:00 Loaded database junctions from the 1st pass file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARpass1//SJ.out.tab: 704075 total junctions WARNING: long repeat for junction # 116453 : chr15 88855522 88855578; left shift = 14; right shift = 255 WARNING: long repeat for junction # 468048 : chr15 88855522 88855578; left shift = 14; right shift = 255 Feb 14 04:12:00 Finished preparing junctions Feb 14 04:12:00 ..... inserting junctions into the genome indices Feb 14 04:12:01 Finished SA search: number of new junctions=86, old junctions=352595 Feb 14 04:12:02 Finished sorting SA indicesL nInd=34056 Feb 14 04:13:13 Finished inserting junction indices Feb 14 04:13:16 Finished SAi Feb 14 04:13:16 ..... finished inserting junctions into genome Input read files for mate 1, from input string NC_IP.end1.5p10bp-trimmed.fastq.gz -rw-rw----+ 1 marinovg oak_akundaje 171668543 Feb 14 03:42 NC_IP.end1.5p10bp-trimmed.fastq.gz readsCommandsFile: exec > "NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "NC_IP.end1.5p10bp-trimmed.fastq.gz" Loaded transcript database, nTr=198093 Loaded exon database, nEx=1182765 Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread8 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread9 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread10 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread11 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread12 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread13 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread14 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread15 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread16 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread17 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread18 ... ok Opening the file: NC_IP-STAR-2.5.3a/STAR-2.5.3a-_STARtmp//FilterBySJoutFiles.mate1.thread19 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Starting to map file # 0 mate 1: NC_IP.end1.5p10bp-trimmed.fastq.gz 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 Thread #3 end of input stream, nextChar=-1 Completed: thread #16 Completed: thread #14 Completed: thread #1 Completed: thread #6 Completed: thread #2 Completed: thread #3 Completed: thread #10 Completed: thread #9 Completed: thread #11 Completed: thread #4 Completed: thread #7 Completed: thread #15 Completed: thread #18 Completed: thread #8 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Completed: thread #13 Completed: thread #17 Completed: thread #19 Completed: thread #12 Completed: thread #5 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 Completed stage 1 mapping of outFilterBySJout mapping Detected 8 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 BAM sorting: 178382 mapped reads BAM sorting bins genomic start loci: 1 17 26158591 2 36 8210039 3 36 8217727 4 36 8255029 5 36 8393412 6 36 8401396 7 36 8442761 8 36 8988578 9 40 126347 10 40 134072 11 40 171457 12 40 179173 13 57 69690220 14 167 109515 15 167 117227 16 167 154242 Completed: thread #14 Completed: thread #16 Completed: thread #19 Completed: thread #12 Completed: thread #15 Completed: thread #17 Completed: thread #9 Completed: thread #3 Completed: thread #1 Completed: thread #2 Completed: thread #4 Completed: thread #7 Completed: thread #6 Completed: thread #8 Completed: thread #5 Completed: thread #10 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 Completed: thread #13 Completed: thread #11 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 Joined thread # 16 Joined thread # 17 Completed: thread #18 Joined thread # 18 Joined thread # 19 Feb 14 04:13:47 ..... started sorting BAM Max memory needed for sorting = 55182528 ALL DONE!