STAR version=STAR_2.5.2b STAR compilation time,server,dir=Thu Aug 18 17:21:53 EDT 2016 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 - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 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 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: /mnt/isilon/cbmi/variome/bin/star/STAR-2.5.2b/bin/Linux_x86_64/STARlong --runThreadN 4 --genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38_no_alt --readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz --readFilesCommand zcat --outFileNamePrefix CHP134_ --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --limitBAMsortRAM 50000000000 ##### Initial USER parameters from Command Line: outFileNamePrefix CHP134_ ###### All USER parameters from Command Line: runThreadN 4 ~RE-DEFINED genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38_no_alt ~RE-DEFINED readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED outFileNamePrefix CHP134_ ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED quantMode TranscriptomeSAM ~RE-DEFINED outSAMattributes NH HI AS NM MD ~RE-DEFINED outFilterType BySJout ~RE-DEFINED outFilterMultimapNmax 20 ~RE-DEFINED outFilterMismatchNmax 999 ~RE-DEFINED outFilterMismatchNoverReadLmax0.04 ~RE-DEFINED alignIntronMin 20 ~RE-DEFINED alignIntronMax 1000000 ~RE-DEFINED alignMatesGapMax 1000000 ~RE-DEFINED alignSJoverhangMin 8 ~RE-DEFINED alignSJDBoverhangMin 1 ~RE-DEFINED sjdbScore 1 ~RE-DEFINED limitBAMsortRAM 50000000000 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 4 genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38_no_alt readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz readFilesCommand zcat limitBAMsortRAM 50000000000 outFileNamePrefix CHP134_ outSAMtype BAM SortedByCoordinate outSAMattributes NH HI AS NM MD outSAMunmapped Within outFilterType BySJout outFilterMultimapNmax 20 outFilterMismatchNmax 999 outFilterMismatchNoverReadLmax 0.04 alignIntronMin 20 alignIntronMax 1000000 alignMatesGapMax 1000000 alignSJoverhangMin 8 alignSJDBoverhangMin 1 sjdbScore 1 quantMode TranscriptomeSAM ------------------------------- ##### Final effective command line: /mnt/isilon/cbmi/variome/bin/star/STAR-2.5.2b/bin/Linux_x86_64/STARlong --runThreadN 4 --genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38_no_alt --readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz --readFilesCommand zcat --limitBAMsortRAM 50000000000 --outFileNamePrefix CHP134_ --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 4 runDirPerm User_RWX runRNGseed 777 genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38_no_alt genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz readFilesCommand zcat readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 50000000000 limitSjdbInsertNsj 1000000 outFileNamePrefix CHP134_ outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM SortedByCoordinate outSAMmode Full outSAMstrandField None 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 20 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 20 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 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 1 sjdbInsertSave Basic quantMode TranscriptomeSAM quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Input read files for mate 1, from input string CHP134_R1.fastq.gz -rw-r--r--. 1 rathik reslnusers 5144235234 Sep 26 11:08 CHP134_R1.fastq.gz readsCommandsFile: exec > "CHP134__STARtmp/tmp.fifo.read1" echo FILE 0 zcat "CHP134_R1.fastq.gz" Input read files for mate 2, from input string CHP134_R2.fastq.gz -rw-r--r--. 1 rathik reslnusers 5410305721 Sep 26 11:09 CHP134_R2.fastq.gz readsCommandsFile: exec > "CHP134__STARtmp/tmp.fifo.read2" echo FILE 0 zcat "CHP134_R2.fastq.gz" Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles /mnt/isilon/cbmi/variome/reference/hg38/hg38_no_alt.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /mnt/isilon/cbmi/variome/reference/gencode/v23/gencode.v23.annotation.gtf ~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= 195 1 chr1 248956422 0 2 chr2 242193529 249036800 3 chr3 198295559 491257856 4 chr4 190214555 689700864 5 chr5 181538259 880017408 6 chr6 170805979 1061683200 7 chr7 159345973 1232601088 8 chr8 145138636 1391984640 9 chr9 138394717 1537212416 10 chr10 133797422 1675624448 11 chr11 135086622 1809580032 12 chr12 133275309 1944846336 13 chr13 114364328 2078277632 14 chr14 107043718 2192834560 15 chr15 101991189 2300051456 16 chr16 90338345 2402287616 17 chr17 83257441 2492727296 18 chr18 80373285 2576089088 19 chr19 58617616 2656567296 20 chr20 64444167 2715287552 21 chr21 46709983 2779774976 22 chr22 50818468 2826698752 23 chrX 156040895 2877554688 24 chrY 57227415 3033792512 25 chrM 16569 3091202048 26 chr1_KI270706v1_random 175055 3091464192 27 chr1_KI270707v1_random 32032 3091726336 28 chr1_KI270708v1_random 127682 3091988480 29 chr1_KI270709v1_random 66860 3092250624 30 chr1_KI270710v1_random 40176 3092512768 31 chr1_KI270711v1_random 42210 3092774912 32 chr1_KI270712v1_random 176043 3093037056 33 chr1_KI270713v1_random 40745 3093299200 34 chr1_KI270714v1_random 41717 3093561344 35 chr2_KI270715v1_random 161471 3093823488 36 chr2_KI270716v1_random 153799 3094085632 37 chr3_GL000221v1_random 155397 3094347776 38 chr4_GL000008v2_random 209709 3094609920 39 chr5_GL000208v1_random 92689 3094872064 40 chr9_KI270717v1_random 40062 3095134208 41 chr9_KI270718v1_random 38054 3095396352 42 chr9_KI270719v1_random 176845 3095658496 43 chr9_KI270720v1_random 39050 3095920640 44 chr11_KI270721v1_random 100316 3096182784 45 chr14_GL000009v2_random 201709 3096444928 46 chr14_GL000225v1_random 211173 3096707072 47 chr14_KI270722v1_random 194050 3096969216 48 chr14_GL000194v1_random 191469 3097231360 49 chr14_KI270723v1_random 38115 3097493504 50 chr14_KI270724v1_random 39555 3097755648 51 chr14_KI270725v1_random 172810 3098017792 52 chr14_KI270726v1_random 43739 3098279936 53 chr15_KI270727v1_random 448248 3098542080 54 chr16_KI270728v1_random 1872759 3099066368 55 chr17_GL000205v2_random 185591 3101163520 56 chr17_KI270729v1_random 280839 3101425664 57 chr17_KI270730v1_random 112551 3101949952 58 chr22_KI270731v1_random 150754 3102212096 59 chr22_KI270732v1_random 41543 3102474240 60 chr22_KI270733v1_random 179772 3102736384 61 chr22_KI270734v1_random 165050 3102998528 62 chr22_KI270735v1_random 42811 3103260672 63 chr22_KI270736v1_random 181920 3103522816 64 chr22_KI270737v1_random 103838 3103784960 65 chr22_KI270738v1_random 99375 3104047104 66 chr22_KI270739v1_random 73985 3104309248 67 chrY_KI270740v1_random 37240 3104571392 68 chrUn_KI270302v1 2274 3104833536 69 chrUn_KI270304v1 2165 3105095680 70 chrUn_KI270303v1 1942 3105357824 71 chrUn_KI270305v1 1472 3105619968 72 chrUn_KI270322v1 21476 3105882112 73 chrUn_KI270320v1 4416 3106144256 74 chrUn_KI270310v1 1201 3106406400 75 chrUn_KI270316v1 1444 3106668544 76 chrUn_KI270315v1 2276 3106930688 77 chrUn_KI270312v1 998 3107192832 78 chrUn_KI270311v1 12399 3107454976 79 chrUn_KI270317v1 37690 3107717120 80 chrUn_KI270412v1 1179 3107979264 81 chrUn_KI270411v1 2646 3108241408 82 chrUn_KI270414v1 2489 3108503552 83 chrUn_KI270419v1 1029 3108765696 84 chrUn_KI270418v1 2145 3109027840 85 chrUn_KI270420v1 2321 3109289984 86 chrUn_KI270424v1 2140 3109552128 87 chrUn_KI270417v1 2043 3109814272 88 chrUn_KI270422v1 1445 3110076416 89 chrUn_KI270423v1 981 3110338560 90 chrUn_KI270425v1 1884 3110600704 91 chrUn_KI270429v1 1361 3110862848 92 chrUn_KI270442v1 392061 3111124992 93 chrUn_KI270466v1 1233 3111649280 94 chrUn_KI270465v1 1774 3111911424 95 chrUn_KI270467v1 3920 3112173568 96 chrUn_KI270435v1 92983 3112435712 97 chrUn_KI270438v1 112505 3112697856 98 chrUn_KI270468v1 4055 3112960000 99 chrUn_KI270510v1 2415 3113222144 100 chrUn_KI270509v1 2318 3113484288 101 chrUn_KI270518v1 2186 3113746432 102 chrUn_KI270508v1 1951 3114008576 103 chrUn_KI270516v1 1300 3114270720 104 chrUn_KI270512v1 22689 3114532864 105 chrUn_KI270519v1 138126 3114795008 106 chrUn_KI270522v1 5674 3115057152 107 chrUn_KI270511v1 8127 3115319296 108 chrUn_KI270515v1 6361 3115581440 109 chrUn_KI270507v1 5353 3115843584 110 chrUn_KI270517v1 3253 3116105728 111 chrUn_KI270529v1 1899 3116367872 112 chrUn_KI270528v1 2983 3116630016 113 chrUn_KI270530v1 2168 3116892160 114 chrUn_KI270539v1 993 3117154304 115 chrUn_KI270538v1 91309 3117416448 116 chrUn_KI270544v1 1202 3117678592 117 chrUn_KI270548v1 1599 3117940736 118 chrUn_KI270583v1 1400 3118202880 119 chrUn_KI270587v1 2969 3118465024 120 chrUn_KI270580v1 1553 3118727168 121 chrUn_KI270581v1 7046 3118989312 122 chrUn_KI270579v1 31033 3119251456 123 chrUn_KI270589v1 44474 3119513600 124 chrUn_KI270590v1 4685 3119775744 125 chrUn_KI270584v1 4513 3120037888 126 chrUn_KI270582v1 6504 3120300032 127 chrUn_KI270588v1 6158 3120562176 128 chrUn_KI270593v1 3041 3120824320 129 chrUn_KI270591v1 5796 3121086464 130 chrUn_KI270330v1 1652 3121348608 131 chrUn_KI270329v1 1040 3121610752 132 chrUn_KI270334v1 1368 3121872896 133 chrUn_KI270333v1 2699 3122135040 134 chrUn_KI270335v1 1048 3122397184 135 chrUn_KI270338v1 1428 3122659328 136 chrUn_KI270340v1 1428 3122921472 137 chrUn_KI270336v1 1026 3123183616 138 chrUn_KI270337v1 1121 3123445760 139 chrUn_KI270363v1 1803 3123707904 140 chrUn_KI270364v1 2855 3123970048 141 chrUn_KI270362v1 3530 3124232192 142 chrUn_KI270366v1 8320 3124494336 143 chrUn_KI270378v1 1048 3124756480 144 chrUn_KI270379v1 1045 3125018624 145 chrUn_KI270389v1 1298 3125280768 146 chrUn_KI270390v1 2387 3125542912 147 chrUn_KI270387v1 1537 3125805056 148 chrUn_KI270395v1 1143 3126067200 149 chrUn_KI270396v1 1880 3126329344 150 chrUn_KI270388v1 1216 3126591488 151 chrUn_KI270394v1 970 3126853632 152 chrUn_KI270386v1 1788 3127115776 153 chrUn_KI270391v1 1484 3127377920 154 chrUn_KI270383v1 1750 3127640064 155 chrUn_KI270393v1 1308 3127902208 156 chrUn_KI270384v1 1658 3128164352 157 chrUn_KI270392v1 971 3128426496 158 chrUn_KI270381v1 1930 3128688640 159 chrUn_KI270385v1 990 3128950784 160 chrUn_KI270382v1 4215 3129212928 161 chrUn_KI270376v1 1136 3129475072 162 chrUn_KI270374v1 2656 3129737216 163 chrUn_KI270372v1 1650 3129999360 164 chrUn_KI270373v1 1451 3130261504 165 chrUn_KI270375v1 2378 3130523648 166 chrUn_KI270371v1 2805 3130785792 167 chrUn_KI270448v1 7992 3131047936 168 chrUn_KI270521v1 7642 3131310080 169 chrUn_GL000195v1 182896 3131572224 170 chrUn_GL000219v1 179198 3131834368 171 chrUn_GL000220v1 161802 3132096512 172 chrUn_GL000224v1 179693 3132358656 173 chrUn_KI270741v1 157432 3132620800 174 chrUn_GL000226v1 15008 3132882944 175 chrUn_GL000213v1 164239 3133145088 176 chrUn_KI270743v1 210658 3133407232 177 chrUn_KI270744v1 168472 3133669376 178 chrUn_KI270745v1 41891 3133931520 179 chrUn_KI270746v1 66486 3134193664 180 chrUn_KI270747v1 198735 3134455808 181 chrUn_KI270748v1 93321 3134717952 182 chrUn_KI270749v1 158759 3134980096 183 chrUn_KI270750v1 148850 3135242240 184 chrUn_KI270751v1 150742 3135504384 185 chrUn_KI270752v1 27745 3135766528 186 chrUn_KI270753v1 62944 3136028672 187 chrUn_KI270754v1 40191 3136290816 188 chrUn_KI270755v1 36723 3136552960 189 chrUn_KI270756v1 79590 3136815104 190 chrUn_KI270757v1 71251 3137077248 191 chrUn_GL000214v1 137718 3137339392 192 chrUn_KI270742v1 186739 3137601536 193 chrUn_GL000216v2 176608 3137863680 194 chrUn_GL000218v1 161147 3138125824 195 chrEBV 171823 3138387968 --sjdbOverhang = 99 taken from the generated genome Started loading the genome: Tue Sep 27 09:56:18 2016 checking Genome sizefile size: 3207850969 bytes; state: good=1 eof=0 fail=0 bad=0 checking SA sizefile size: 24780344205 bytes; state: good=1 eof=0 fail=0 bad=0 checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=3207850969; nSAbyte=24780344205 GstrandBit=32 SA number of indices=6007356170 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3207850969 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3207850969 bytes SA file size: 24780344205 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24780344205 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Tue Sep 27 10:33:05 2016 Processing splice junctions database sjdbN=347743, sjdbOverhang=99 To accomodate alignIntronMax=1000000 redefined winBinNbits=18 To accomodate alignIntronMax=1000000 and alignMatesGapMax=1000000, redefined winFlankNbins=4 and winAnchorDistNbins=8 Loaded transcript database, nTr=198619 Loaded exon database, nEx=1173255 Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate2.thread0 ... ok Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate2.thread1 ... ok Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate2.thread2 ... ok Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: CHP134__STARtmp//FilterBySJoutFiles.mate2.thread3 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Starting to map file # 0 mate 1: CHP134_R1.fastq.gz mate 2: CHP134_R2.fastq.gz BAM sorting: 213106 mapped reads BAM sorting bins genomic start loci: 1 1 117950374 2 4 177466959 3 7 103826407 4 11 105342211 5 15 46964662 6 20 8215873 7 20 8437832 8 59 127240 9 59 134496 10 170 115048 Thread #1 end of input stream, nextChar=-1 Completed: thread #1 Completed: thread #3 Completed: thread #2 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Completed stage 1 mapping of outFilterBySJout mapping Detected 116441 novel junctions that passed filtering, will proceed to filter reads that contained unannotated junctions Created thread # 1 Created thread # 2 Created thread # 3 EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length @NB501069:27:HY32VBGXX:1:12111:11340:4339 GCGGGCGGGGAAGAGGGCACAGACGGGCGGGCGAGGGCCGGGGACCGCGAGGGCAAGGGCACCCGGGAGCCCGCAGAGGCGGCGGCTCGGGGAGAAACCTC SOLUTION: fix your fastq file Sep 27 12:44:12 ...... FATAL ERROR, exiting