STAR version=STAR_2.5.3a STAR compilation time,server,dir=Fri Mar 17 11:35:46 EDT 2017 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source ##### DEFAULT parameters: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype SAM outSAMmode Full outSAMstrandField None outSAMattributes Standard outSAMunmapped None outSAMorder Paired outSAMprimaryFlag OneBestScore outSAMreadID Standard outSAMmapqUnique 255 outSAMflagOR 0 outSAMflagAND 65535 outSAMattrRGline - outSAMheaderHD - outSAMheaderPG - outSAMheaderCommentFile - outBAMcompression 1 outBAMsortingThreadN 0 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 1 outSJfilterReads All outSJfilterCountUniqueMin 3 1 1 1 outSJfilterCountTotalMin 3 1 1 1 outSJfilterOverhangMin 30 12 12 12 outSJfilterDistToOtherSJmin 10 0 5 10 outSJfilterIntronMaxVsReadN 50000 100000 200000 outWigType None outWigStrand Stranded outWigReferencesPrefix - outWigNorm RPM outFilterType Normal outFilterMultimapNmax 10 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.3 outFilterMismatchNoverReadLmax 1 outFilterIntronMotifs None clip5pNbases 0 clip3pNbases 0 clip3pAfterAdapterNbases 0 clip3pAdapterSeq - clip3pAdapterMMp 0.1 winBinNbits 16 winAnchorDistNbins 9 winFlankNbins 4 winAnchorMultimapNmax 50 winReadCoverageRelativeMin 0.5 winReadCoverageBasesMin 0 scoreGap 0 scoreGapNoncan -8 scoreGapGCAG -4 scoreGapATAC -8 scoreStitchSJshift 1 scoreGenomicLengthLog2scale -0.25 scoreDelBase -2 scoreDelOpen -2 scoreInsOpen -2 scoreInsBase -2 seedSearchLmax 0 seedSearchStartLmax 50 seedSearchStartLmaxOverLread 1 seedPerReadNmax 1000 seedPerWindowNmax 50 seedNoneLociPerWindow 10 seedMultimapNmax 10000 alignIntronMin 21 alignIntronMax 0 alignMatesGapMax 0 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 5 alignSJDBoverhangMin 3 alignSJstitchMismatchNmax 0 -1 0 0 alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes alignEndsProtrude 0 ConcordantPair chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimMainSegmentMultNmax 10 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ##### Command Line: STAR --genomeDir /data/share/htp/zUMIs_paper/GigaDB/reference/STAR5idx_noGTF --runThreadN 16 --readFilesCommand zcat --sjdbGTFfile /data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf --outFileNamePrefix /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK. --outSAMtype BAM Unsorted --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --sjdbOverhang 49 --twopassMode Basic --readFilesIn /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz ##### Initial USER parameters from Command Line: outFileNamePrefix /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK. ###### All USER parameters from Command Line: genomeDir /data/share/htp/zUMIs_paper/GigaDB/reference/STAR5idx_noGTF ~RE-DEFINED runThreadN 16 ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED sjdbGTFfile /data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf ~RE-DEFINED outFileNamePrefix /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK. ~RE-DEFINED outSAMtype BAM Unsorted ~RE-DEFINED outSAMmultNmax 1 ~RE-DEFINED outFilterMultimapNmax 50 ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED sjdbOverhang 49 ~RE-DEFINED twopassMode Basic ~RE-DEFINED readFilesIn /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 16 genomeDir /data/share/htp/zUMIs_paper/GigaDB/reference/STAR5idx_noGTF readFilesIn /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz readFilesCommand zcat outFileNamePrefix /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK. outSAMtype BAM Unsorted outSAMunmapped Within outSAMmultNmax 1 outFilterMultimapNmax 50 sjdbGTFfile /data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf sjdbOverhang 49 twopassMode Basic ------------------------------- ##### Final effective command line: STAR --runThreadN 16 --genomeDir /data/share/htp/zUMIs_paper/GigaDB/reference/STAR5idx_noGTF --readFilesIn /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz --readFilesCommand zcat --outFileNamePrefix /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK. --outSAMtype BAM Unsorted --outSAMunmapped Within --outSAMmultNmax 1 --outFilterMultimapNmax 50 --sjdbGTFfile /data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf --sjdbOverhang 49 --twopassMode Basic ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 16 runDirPerm User_RWX runRNGseed 777 genomeDir /data/share/htp/zUMIs_paper/GigaDB/reference/STAR5idx_noGTF genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz readFilesCommand zcat readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outFileNamePrefix /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK. outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM Unsorted outSAMmode Full outSAMstrandField None outSAMattributes Standard 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 1 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 50 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 /data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 49 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode Basic ---------------------------------------- Input read files for mate 1, from input string /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz -rw-r--r-- 1 ziegenhain ngs 8439509463 Apr 22 15:53 /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz readsCommandsFile: exec > "/data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz" Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles /data/share/ngs/genomes/Human/hg38/hg38.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 Genome version is compatible with current STAR version Number of real (reference) chromosomes= 455 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 chr1_KI270762v1_alt 354444 2890661888 65 chr1_KI270766v1_alt 256271 2891186176 66 chr1_KI270760v1_alt 109528 2891448320 67 chr1_KI270765v1_alt 185285 2891710464 68 chr1_GL383518v1_alt 182439 2891972608 69 chr1_GL383519v1_alt 110268 2892234752 70 chr1_GL383520v2_alt 366580 2892496896 71 chr1_KI270764v1_alt 50258 2893021184 72 chr1_KI270763v1_alt 911658 2893283328 73 chr1_KI270759v1_alt 425601 2894331904 74 chr1_KI270761v1_alt 165834 2894856192 75 chr2_KI270770v1_alt 136240 2895118336 76 chr2_KI270773v1_alt 70887 2895380480 77 chr2_KI270774v1_alt 223625 2895642624 78 chr2_KI270769v1_alt 120616 2895904768 79 chr2_GL383521v1_alt 143390 2896166912 80 chr2_KI270772v1_alt 133041 2896429056 81 chr2_KI270775v1_alt 138019 2896691200 82 chr2_KI270771v1_alt 110395 2896953344 83 chr2_KI270768v1_alt 110099 2897215488 84 chr2_GL582966v2_alt 96131 2897477632 85 chr2_GL383522v1_alt 123821 2897739776 86 chr2_KI270776v1_alt 174166 2898001920 87 chr2_KI270767v1_alt 161578 2898264064 88 chr3_JH636055v2_alt 173151 2898526208 89 chr3_KI270783v1_alt 109187 2898788352 90 chr3_KI270780v1_alt 224108 2899050496 91 chr3_GL383526v1_alt 180671 2899312640 92 chr3_KI270777v1_alt 173649 2899574784 93 chr3_KI270778v1_alt 248252 2899836928 94 chr3_KI270781v1_alt 113034 2900099072 95 chr3_KI270779v1_alt 205312 2900361216 96 chr3_KI270782v1_alt 162429 2900623360 97 chr3_KI270784v1_alt 184404 2900885504 98 chr4_KI270790v1_alt 220246 2901147648 99 chr4_GL383528v1_alt 376187 2901409792 100 chr4_KI270787v1_alt 111943 2901934080 101 chr4_GL000257v2_alt 586476 2902196224 102 chr4_KI270788v1_alt 158965 2902982656 103 chr4_GL383527v1_alt 164536 2903244800 104 chr4_KI270785v1_alt 119912 2903506944 105 chr4_KI270789v1_alt 205944 2903769088 106 chr4_KI270786v1_alt 244096 2904031232 107 chr5_KI270793v1_alt 126136 2904293376 108 chr5_KI270792v1_alt 179043 2904555520 109 chr5_KI270791v1_alt 195710 2904817664 110 chr5_GL383532v1_alt 82728 2905079808 111 chr5_GL949742v1_alt 226852 2905341952 112 chr5_KI270794v1_alt 164558 2905604096 113 chr5_GL339449v2_alt 1612928 2905866240 114 chr5_GL383530v1_alt 101241 2907701248 115 chr5_KI270796v1_alt 172708 2907963392 116 chr5_GL383531v1_alt 173459 2908225536 117 chr5_KI270795v1_alt 131892 2908487680 118 chr6_GL000250v2_alt 4672374 2908749824 119 chr6_KI270800v1_alt 175808 2913468416 120 chr6_KI270799v1_alt 152148 2913730560 121 chr6_GL383533v1_alt 124736 2913992704 122 chr6_KI270801v1_alt 870480 2914254848 123 chr6_KI270802v1_alt 75005 2915303424 124 chr6_KB021644v2_alt 185823 2915565568 125 chr6_KI270797v1_alt 197536 2915827712 126 chr6_KI270798v1_alt 271782 2916089856 127 chr7_KI270804v1_alt 157952 2916614144 128 chr7_KI270809v1_alt 209586 2916876288 129 chr7_KI270806v1_alt 158166 2917138432 130 chr7_GL383534v2_alt 119183 2917400576 131 chr7_KI270803v1_alt 1111570 2917662720 132 chr7_KI270808v1_alt 271455 2918973440 133 chr7_KI270807v1_alt 126434 2919497728 134 chr7_KI270805v1_alt 209988 2919759872 135 chr8_KI270818v1_alt 145606 2920022016 136 chr8_KI270812v1_alt 282736 2920284160 137 chr8_KI270811v1_alt 292436 2920808448 138 chr8_KI270821v1_alt 985506 2921332736 139 chr8_KI270813v1_alt 300230 2922381312 140 chr8_KI270822v1_alt 624492 2922905600 141 chr8_KI270814v1_alt 141812 2923692032 142 chr8_KI270810v1_alt 374415 2923954176 143 chr8_KI270819v1_alt 133535 2924478464 144 chr8_KI270820v1_alt 36640 2924740608 145 chr8_KI270817v1_alt 158983 2925002752 146 chr8_KI270816v1_alt 305841 2925264896 147 chr8_KI270815v1_alt 132244 2925789184 148 chr9_GL383539v1_alt 162988 2926051328 149 chr9_GL383540v1_alt 71551 2926313472 150 chr9_GL383541v1_alt 171286 2926575616 151 chr9_GL383542v1_alt 60032 2926837760 152 chr9_KI270823v1_alt 439082 2927099904 153 chr10_GL383545v1_alt 179254 2927624192 154 chr10_KI270824v1_alt 181496 2927886336 155 chr10_GL383546v1_alt 309802 2928148480 156 chr10_KI270825v1_alt 188315 2928672768 157 chr11_KI270832v1_alt 210133 2928934912 158 chr11_KI270830v1_alt 177092 2929197056 159 chr11_KI270831v1_alt 296895 2929459200 160 chr11_KI270829v1_alt 204059 2929983488 161 chr11_GL383547v1_alt 154407 2930245632 162 chr11_JH159136v1_alt 200998 2930507776 163 chr11_JH159137v1_alt 191409 2930769920 164 chr11_KI270827v1_alt 67707 2931032064 165 chr11_KI270826v1_alt 186169 2931294208 166 chr12_GL877875v1_alt 167313 2931556352 167 chr12_GL877876v1_alt 408271 2931818496 168 chr12_KI270837v1_alt 40090 2932342784 169 chr12_GL383549v1_alt 120804 2932604928 170 chr12_KI270835v1_alt 238139 2932867072 171 chr12_GL383550v2_alt 169178 2933129216 172 chr12_GL383552v1_alt 138655 2933391360 173 chr12_GL383553v2_alt 152874 2933653504 174 chr12_KI270834v1_alt 119498 2933915648 175 chr12_GL383551v1_alt 184319 2934177792 176 chr12_KI270833v1_alt 76061 2934439936 177 chr12_KI270836v1_alt 56134 2934702080 178 chr13_KI270840v1_alt 191684 2934964224 179 chr13_KI270839v1_alt 180306 2935226368 180 chr13_KI270843v1_alt 103832 2935488512 181 chr13_KI270841v1_alt 169134 2935750656 182 chr13_KI270838v1_alt 306913 2936012800 183 chr13_KI270842v1_alt 37287 2936537088 184 chr14_KI270844v1_alt 322166 2936799232 185 chr14_KI270847v1_alt 1511111 2937323520 186 chr14_KI270845v1_alt 180703 2938896384 187 chr14_KI270846v1_alt 1351393 2939158528 188 chr15_KI270852v1_alt 478999 2940731392 189 chr15_KI270851v1_alt 263054 2941255680 190 chr15_KI270848v1_alt 327382 2941779968 191 chr15_GL383554v1_alt 296527 2942304256 192 chr15_KI270849v1_alt 244917 2942828544 193 chr15_GL383555v2_alt 388773 2943090688 194 chr15_KI270850v1_alt 430880 2943614976 195 chr16_KI270854v1_alt 134193 2944139264 196 chr16_KI270856v1_alt 63982 2944401408 197 chr16_KI270855v1_alt 232857 2944663552 198 chr16_KI270853v1_alt 2659700 2944925696 199 chr16_GL383556v1_alt 192462 2947809280 200 chr16_GL383557v1_alt 89672 2948071424 201 chr17_GL383563v3_alt 375691 2948333568 202 chr17_KI270862v1_alt 391357 2948857856 203 chr17_KI270861v1_alt 196688 2949382144 204 chr17_KI270857v1_alt 2877074 2949644288 205 chr17_JH159146v1_alt 278131 2952527872 206 chr17_JH159147v1_alt 70345 2953052160 207 chr17_GL383564v2_alt 133151 2953314304 208 chr17_GL000258v2_alt 1821992 2953576448 209 chr17_GL383565v1_alt 223995 2955411456 210 chr17_KI270858v1_alt 235827 2955673600 211 chr17_KI270859v1_alt 108763 2955935744 212 chr17_GL383566v1_alt 90219 2956197888 213 chr17_KI270860v1_alt 178921 2956460032 214 chr18_KI270864v1_alt 111737 2956722176 215 chr18_GL383567v1_alt 289831 2956984320 216 chr18_GL383570v1_alt 164789 2957508608 217 chr18_GL383571v1_alt 198278 2957770752 218 chr18_GL383568v1_alt 104552 2958032896 219 chr18_GL383569v1_alt 167950 2958295040 220 chr18_GL383572v1_alt 159547 2958557184 221 chr18_KI270863v1_alt 167999 2958819328 222 chr19_KI270868v1_alt 61734 2959081472 223 chr19_KI270865v1_alt 52969 2959343616 224 chr19_GL383573v1_alt 385657 2959605760 225 chr19_GL383575v2_alt 170222 2960130048 226 chr19_GL383576v1_alt 188024 2960392192 227 chr19_GL383574v1_alt 155864 2960654336 228 chr19_KI270866v1_alt 43156 2960916480 229 chr19_KI270867v1_alt 233762 2961178624 230 chr19_GL949746v1_alt 987716 2961440768 231 chr20_GL383577v2_alt 128386 2962489344 232 chr20_KI270869v1_alt 118774 2962751488 233 chr20_KI270871v1_alt 58661 2963013632 234 chr20_KI270870v1_alt 183433 2963275776 235 chr21_GL383578v2_alt 63917 2963537920 236 chr21_KI270874v1_alt 166743 2963800064 237 chr21_KI270873v1_alt 143900 2964062208 238 chr21_GL383579v2_alt 201197 2964324352 239 chr21_GL383580v2_alt 74653 2964586496 240 chr21_GL383581v2_alt 116689 2964848640 241 chr21_KI270872v1_alt 82692 2965110784 242 chr22_KI270875v1_alt 259914 2965372928 243 chr22_KI270878v1_alt 186262 2965635072 244 chr22_KI270879v1_alt 304135 2965897216 245 chr22_KI270876v1_alt 263666 2966421504 246 chr22_KI270877v1_alt 101331 2966945792 247 chr22_GL383583v2_alt 96924 2967207936 248 chr22_GL383582v2_alt 162811 2967470080 249 chrX_KI270880v1_alt 284869 2967732224 250 chrX_KI270881v1_alt 144206 2968256512 251 chr19_KI270882v1_alt 248807 2968518656 252 chr19_KI270883v1_alt 170399 2968780800 253 chr19_KI270884v1_alt 157053 2969042944 254 chr19_KI270885v1_alt 171027 2969305088 255 chr19_KI270886v1_alt 204239 2969567232 256 chr19_KI270887v1_alt 209512 2969829376 257 chr19_KI270888v1_alt 155532 2970091520 258 chr19_KI270889v1_alt 170698 2970353664 259 chr19_KI270890v1_alt 184499 2970615808 260 chr19_KI270891v1_alt 170680 2970877952 261 chr1_KI270892v1_alt 162212 2971140096 262 chr2_KI270894v1_alt 214158 2971402240 263 chr2_KI270893v1_alt 161218 2971664384 264 chr3_KI270895v1_alt 162896 2971926528 265 chr4_KI270896v1_alt 378547 2972188672 266 chr5_KI270897v1_alt 1144418 2972712960 267 chr5_KI270898v1_alt 130957 2974023680 268 chr6_GL000251v2_alt 4795265 2974285824 269 chr7_KI270899v1_alt 190869 2979266560 270 chr8_KI270901v1_alt 136959 2979528704 271 chr8_KI270900v1_alt 318687 2979790848 272 chr11_KI270902v1_alt 106711 2980315136 273 chr11_KI270903v1_alt 214625 2980577280 274 chr12_KI270904v1_alt 572349 2980839424 275 chr15_KI270906v1_alt 196384 2981625856 276 chr15_KI270905v1_alt 5161414 2981888000 277 chr17_KI270907v1_alt 137721 2987130880 278 chr17_KI270910v1_alt 157099 2987393024 279 chr17_KI270909v1_alt 325800 2987655168 280 chr17_JH159148v1_alt 88070 2988179456 281 chr17_KI270908v1_alt 1423190 2988441600 282 chr18_KI270912v1_alt 174061 2990014464 283 chr18_KI270911v1_alt 157710 2990276608 284 chr19_GL949747v2_alt 729520 2990538752 285 chr22_KB663609v1_alt 74013 2991325184 286 chrX_KI270913v1_alt 274009 2991587328 287 chr19_KI270914v1_alt 205194 2992111616 288 chr19_KI270915v1_alt 170665 2992373760 289 chr19_KI270916v1_alt 184516 2992635904 290 chr19_KI270917v1_alt 190932 2992898048 291 chr19_KI270918v1_alt 123111 2993160192 292 chr19_KI270919v1_alt 170701 2993422336 293 chr19_KI270920v1_alt 198005 2993684480 294 chr19_KI270921v1_alt 282224 2993946624 295 chr19_KI270922v1_alt 187935 2994470912 296 chr19_KI270923v1_alt 189352 2994733056 297 chr3_KI270924v1_alt 166540 2994995200 298 chr4_KI270925v1_alt 555799 2995257344 299 chr6_GL000252v2_alt 4604811 2996043776 300 chr8_KI270926v1_alt 229282 3000762368 301 chr11_KI270927v1_alt 218612 3001024512 302 chr19_GL949748v2_alt 1064304 3001286656 303 chr22_KI270928v1_alt 176103 3002597376 304 chr19_KI270929v1_alt 186203 3002859520 305 chr19_KI270930v1_alt 200773 3003121664 306 chr19_KI270931v1_alt 170148 3003383808 307 chr19_KI270932v1_alt 215732 3003645952 308 chr19_KI270933v1_alt 170537 3003908096 309 chr19_GL000209v2_alt 177381 3004170240 310 chr3_KI270934v1_alt 163458 3004432384 311 chr6_GL000253v2_alt 4677643 3004694528 312 chr19_GL949749v2_alt 1091841 3009413120 313 chr3_KI270935v1_alt 197351 3010723840 314 chr6_GL000254v2_alt 4827813 3010985984 315 chr19_GL949750v2_alt 1066390 3015966720 316 chr3_KI270936v1_alt 164170 3017277440 317 chr6_GL000255v2_alt 4606388 3017539584 318 chr19_GL949751v2_alt 1002683 3022258176 319 chr3_KI270937v1_alt 165607 3023306752 320 chr6_GL000256v2_alt 4929269 3023568896 321 chr19_GL949752v1_alt 987100 3028549632 322 chr6_KI270758v1_alt 76752 3029598208 323 chr19_GL949753v2_alt 796479 3029860352 324 chr19_KI270938v1_alt 1066800 3030908928 325 chrM 16569 3032219648 326 chrUn_KI270302v1 2274 3032481792 327 chrUn_KI270304v1 2165 3032743936 328 chrUn_KI270303v1 1942 3033006080 329 chrUn_KI270305v1 1472 3033268224 330 chrUn_KI270322v1 21476 3033530368 331 chrUn_KI270320v1 4416 3033792512 332 chrUn_KI270310v1 1201 3034054656 333 chrUn_KI270316v1 1444 3034316800 334 chrUn_KI270315v1 2276 3034578944 335 chrUn_KI270312v1 998 3034841088 336 chrUn_KI270311v1 12399 3035103232 337 chrUn_KI270317v1 37690 3035365376 338 chrUn_KI270412v1 1179 3035627520 339 chrUn_KI270411v1 2646 3035889664 340 chrUn_KI270414v1 2489 3036151808 341 chrUn_KI270419v1 1029 3036413952 342 chrUn_KI270418v1 2145 3036676096 343 chrUn_KI270420v1 2321 3036938240 344 chrUn_KI270424v1 2140 3037200384 345 chrUn_KI270417v1 2043 3037462528 346 chrUn_KI270422v1 1445 3037724672 347 chrUn_KI270423v1 981 3037986816 348 chrUn_KI270425v1 1884 3038248960 349 chrUn_KI270429v1 1361 3038511104 350 chrUn_KI270442v1 392061 3038773248 351 chrUn_KI270466v1 1233 3039297536 352 chrUn_KI270465v1 1774 3039559680 353 chrUn_KI270467v1 3920 3039821824 354 chrUn_KI270435v1 92983 3040083968 355 chrUn_KI270438v1 112505 3040346112 356 chrUn_KI270468v1 4055 3040608256 357 chrUn_KI270510v1 2415 3040870400 358 chrUn_KI270509v1 2318 3041132544 359 chrUn_KI270518v1 2186 3041394688 360 chrUn_KI270508v1 1951 3041656832 361 chrUn_KI270516v1 1300 3041918976 362 chrUn_KI270512v1 22689 3042181120 363 chrUn_KI270519v1 138126 3042443264 364 chrUn_KI270522v1 5674 3042705408 365 chrUn_KI270511v1 8127 3042967552 366 chrUn_KI270515v1 6361 3043229696 367 chrUn_KI270507v1 5353 3043491840 368 chrUn_KI270517v1 3253 3043753984 369 chrUn_KI270529v1 1899 3044016128 370 chrUn_KI270528v1 2983 3044278272 371 chrUn_KI270530v1 2168 3044540416 372 chrUn_KI270539v1 993 3044802560 373 chrUn_KI270538v1 91309 3045064704 374 chrUn_KI270544v1 1202 3045326848 375 chrUn_KI270548v1 1599 3045588992 376 chrUn_KI270583v1 1400 3045851136 377 chrUn_KI270587v1 2969 3046113280 378 chrUn_KI270580v1 1553 3046375424 379 chrUn_KI270581v1 7046 3046637568 380 chrUn_KI270579v1 31033 3046899712 381 chrUn_KI270589v1 44474 3047161856 382 chrUn_KI270590v1 4685 3047424000 383 chrUn_KI270584v1 4513 3047686144 384 chrUn_KI270582v1 6504 3047948288 385 chrUn_KI270588v1 6158 3048210432 386 chrUn_KI270593v1 3041 3048472576 387 chrUn_KI270591v1 5796 3048734720 388 chrUn_KI270330v1 1652 3048996864 389 chrUn_KI270329v1 1040 3049259008 390 chrUn_KI270334v1 1368 3049521152 391 chrUn_KI270333v1 2699 3049783296 392 chrUn_KI270335v1 1048 3050045440 393 chrUn_KI270338v1 1428 3050307584 394 chrUn_KI270340v1 1428 3050569728 395 chrUn_KI270336v1 1026 3050831872 396 chrUn_KI270337v1 1121 3051094016 397 chrUn_KI270363v1 1803 3051356160 398 chrUn_KI270364v1 2855 3051618304 399 chrUn_KI270362v1 3530 3051880448 400 chrUn_KI270366v1 8320 3052142592 401 chrUn_KI270378v1 1048 3052404736 402 chrUn_KI270379v1 1045 3052666880 403 chrUn_KI270389v1 1298 3052929024 404 chrUn_KI270390v1 2387 3053191168 405 chrUn_KI270387v1 1537 3053453312 406 chrUn_KI270395v1 1143 3053715456 407 chrUn_KI270396v1 1880 3053977600 408 chrUn_KI270388v1 1216 3054239744 409 chrUn_KI270394v1 970 3054501888 410 chrUn_KI270386v1 1788 3054764032 411 chrUn_KI270391v1 1484 3055026176 412 chrUn_KI270383v1 1750 3055288320 413 chrUn_KI270393v1 1308 3055550464 414 chrUn_KI270384v1 1658 3055812608 415 chrUn_KI270392v1 971 3056074752 416 chrUn_KI270381v1 1930 3056336896 417 chrUn_KI270385v1 990 3056599040 418 chrUn_KI270382v1 4215 3056861184 419 chrUn_KI270376v1 1136 3057123328 420 chrUn_KI270374v1 2656 3057385472 421 chrUn_KI270372v1 1650 3057647616 422 chrUn_KI270373v1 1451 3057909760 423 chrUn_KI270375v1 2378 3058171904 424 chrUn_KI270371v1 2805 3058434048 425 chrUn_KI270448v1 7992 3058696192 426 chrUn_KI270521v1 7642 3058958336 427 chrUn_GL000195v1 182896 3059220480 428 chrUn_GL000219v1 179198 3059482624 429 chrUn_GL000220v1 161802 3059744768 430 chrUn_GL000224v1 179693 3060006912 431 chrUn_KI270741v1 157432 3060269056 432 chrUn_GL000226v1 15008 3060531200 433 chrUn_GL000213v1 164239 3060793344 434 chrUn_KI270743v1 210658 3061055488 435 chrUn_KI270744v1 168472 3061317632 436 chrUn_KI270745v1 41891 3061579776 437 chrUn_KI270746v1 66486 3061841920 438 chrUn_KI270747v1 198735 3062104064 439 chrUn_KI270748v1 93321 3062366208 440 chrUn_KI270749v1 158759 3062628352 441 chrUn_KI270750v1 148850 3062890496 442 chrUn_KI270751v1 150742 3063152640 443 chrUn_KI270752v1 27745 3063414784 444 chrUn_KI270753v1 62944 3063676928 445 chrUn_KI270754v1 40191 3063939072 446 chrUn_KI270755v1 36723 3064201216 447 chrUn_KI270756v1 79590 3064463360 448 chrUn_KI270757v1 71251 3064725504 449 chrUn_GL000214v1 137718 3064987648 450 chrUn_KI270742v1 186739 3065249792 451 chrUn_GL000216v2 176608 3065511936 452 chrUn_GL000218v1 161147 3065774080 453 chrX 156040895 3066036224 454 chrY 57227415 3222274048 455 chrY_KI270740v1_random 37240 3279683584 Started loading the genome: Sun Apr 22 16:02:50 2018 Checking Genome sizefile size: 3279945728 bytes; state: good=1 eof=0 fail=0 bad=0 Checking SA sizefile size: 25156855213 bytes; state: good=1 eof=0 fail=0 bad=0 /SAindex: size given as a parameter = 1 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=3279945728; nSAbyte=25156855213 GstrandBit=32 SA number of indices=6098631566 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3279945728 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3279945728 bytes SA file size: 25156855213 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 25156855213 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Sun Apr 22 16:04:31 2018 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Apr 22 16:04:31 ..... processing annotations GTF Processing sjdbGTFfile=/data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf, found: 199184 transcripts 1176808 exons (non-collapsed) 348697 collapsed junctions Apr 22 16:05:08 ..... finished GTF processing Apr 22 16:05:08 Loaded database junctions from the GTF file: /data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf: 348697 total junctions WARNING: long repeat for junction # 115413 : chr15 88855522 88855578; left shift = 14; right shift = 255 WARNING: long repeat for junction # 157788 : chr18 46969610 47029116; left shift = 183; right shift = 255 Apr 22 16:05:09 Finished preparing junctions Apr 22 16:05:09 ..... inserting junctions into the genome indices Apr 22 16:05:53 Finished SA search: number of new junctions=348621, old junctions=0 Apr 22 16:06:34 Finished sorting SA indicesL nInd=68329716 Apr 22 16:08:53 Finished inserting junction indices Apr 22 16:09:28 Finished SAi Apr 22 16:09:28 ..... finished inserting junctions into genome Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.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 Thread #9 end of input stream, nextChar=-1 Completed: thread #12 Completed: thread #7 Completed: thread #14 Completed: thread #1 Completed: thread #3 Completed: thread #9 Completed: thread #10 Completed: thread #15 Completed: thread #8 Completed: thread #11 Completed: thread #4 Completed: thread #2 Completed: thread #6 Completed: thread #5 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 Completed: thread #13 Joined thread # 13 Joined thread # 14 Joined thread # 15 Apr 22 16:27:19 Loaded database junctions from the 1st pass file: /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK._STARpass1//SJ.out.tab: 500222 total junctions WARNING: long repeat for junction # 115413 : chr15 88855522 88855578; left shift = 14; right shift = 255 WARNING: long repeat for junction # 157788 : chr18 46969610 47029116; left shift = 183; right shift = 255 Apr 22 16:27:20 Finished preparing junctions Apr 22 16:27:20 ..... inserting junctions into the genome indices Apr 22 16:27:27 Finished SA search: number of new junctions=52628, old junctions=348621 Apr 22 16:27:33 Finished sorting SA indicesL nInd=10314854 Apr 22 16:29:58 Finished inserting junction indices Apr 22 16:30:10 Finished SAi Apr 22 16:30:10 ..... finished inserting junctions into genome Input read files for mate 1, from input string /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz -rw-r--r-- 1 ziegenhain ngs 8439509463 Apr 22 15:53 /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz readsCommandsFile: exec > "/data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.fastq.gz" Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: /data/share/htp/zUMIs_paper/GigaDB/run_dir//HEK.cdnaread.filtered.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 Thread #8 end of input stream, nextChar=-1 Completed: thread #11 Completed: thread #2 Completed: thread #12 Completed: thread #1 Completed: thread #9 Completed: thread #5 Completed: thread #13 Completed: thread #3 Completed: thread #14 Completed: thread #4 Completed: thread #8 Completed: thread #15 Completed: thread #7 Completed: thread #10 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 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 Joined thread # 15 ALL DONE!