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 outFileNamePrefix ./ 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 /hpc/grid/shared/ngsdb/STAR/hg19_gencode19 --readFilesIn /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz --readFilesCommand zcat --runThreadN 8 --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90 --alignIntronMax 1000000 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: genomeDir /hpc/grid/shared/ngsdb/STAR/hg19_gencode19 ~RE-DEFINED readFilesIn /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED runThreadN 8 ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED alignSJDBoverhangMin 1 ~RE-DEFINED outFilterMismatchNoverLmax 0.05 ~RE-DEFINED outFilterScoreMinOverLread 0.9 ~RE-DEFINED outFilterMatchNminOverLread 0.9 ~RE-DEFINED alignIntronMax 1000000 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 8 genomeDir /hpc/grid/shared/ngsdb/STAR/hg19_gencode19 readFilesIn /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz readFilesCommand zcat outSAMtype BAM SortedByCoordinate outFilterScoreMinOverLread 0.9 outFilterMatchNminOverLread 0.9 outFilterMismatchNoverLmax 0.05 alignIntronMax 1000000 alignSJDBoverhangMin 1 ------------------------------- ##### Final effective command line: STAR --runThreadN 8 --genomeDir /hpc/grid/shared/ngsdb/STAR/hg19_gencode19 --readFilesIn /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMismatchNoverLmax 0.05 --alignIntronMax 1000000 --alignSJDBoverhangMin 1 ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 8 runDirPerm User_RWX runRNGseed 777 genomeDir /hpc/grid/shared/ngsdb/STAR/hg19_gencode19 genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.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 ./ outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM SortedByCoordinate 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 0.9 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.9 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.05 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 1000000 alignMatesGapMax 0 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 5 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 - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Input read files for mate 1, from input string /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz -rw-r--r-- 1 rnaseq tbi 1149268880 Jul 20 21:25 /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz readsCommandsFile: exec > "./_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz" WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles /hpc/grid/shared/ngsdb/bowtie2/hg19.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /hpc/grid/shared/ngsdb/annotation/gencode/hg19.gencode.v19.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 25 1 chr1 249250621 0 2 chr2 243199373 249298944 3 chr3 198022430 492568576 4 chr4 191154276 690749440 5 chr5 180915260 882114560 6 chr6 171115067 1063256064 7 chr7 159138663 1234436096 8 chr8 146364022 1393819648 9 chr9 141213431 1540358144 10 chrM 16571 1681653760 11 chrX 155270560 1681915904 12 chrY 59373566 1837367296 13 chr10 135534747 1896873984 14 chr11 135006516 2032664576 15 chr12 133851895 2167930880 16 chr13 115169878 2301886464 17 chr14 107349540 2417229824 18 chr15 102531392 2524708864 19 chr16 90354753 2627469312 20 chr17 81195210 2717908992 21 chr18 78077248 2799173632 22 chr19 59128983 2877292544 23 chr20 63025520 2936537088 24 chr21 48129895 2999713792 25 chr22 51304566 3047948288 --sjdbOverhang = 99 taken from the generated genome Started loading the genome: Fri Aug 3 09:08:29 2018 Checking Genome sizefile size: 3167899932 bytes; state: good=1 eof=0 fail=0 bad=0 Checking SA sizefile size: 24168956312 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=3167899932; nSAbyte=24168956312 GstrandBit=32 SA number of indices=5859140924 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3167899932 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3167899932 bytes SA file size: 24168956315 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=0 eof=1 fail=1 bad=0; loaded 24168956312 bytes Loading SAindex ... done: 1565873616 bytes Finished loading the genome: Fri Aug 3 09:10:22 2018 Processing splice junctions database sjdbN=344580, sjdbOverhang=99 To accomodate alignIntronMax=1000000 redefined winBinNbits=18 To accomodate alignIntronMax=1000000 and alignMatesGapMax=0, redefined winFlankNbins=4 and winAnchorDistNbins=8 Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: /hpc/grid/omics_data04/rnaseq/quickrnaseq/Epiderm_fastq/DC-180221-00042.fastq.gz Created thread # 6 Created thread # 7 BAM sorting: 262526 mapped reads BAM sorting bins genomic start loci: 1 0 152283872 2 1 44187701 3 2 33099741 4 4 55240736 5 5 62284079 6 6 98957306 7 8 130211932 8 10 100853352 9 13 47256934 10 14 52841641 11 14 91539751 12 17 33026062 13 19 975936 14 19 39777963 15 21 1434919 16 22 628353 Thread #0 end of input stream, nextChar=-1 Completed: thread #5 Completed: thread #4 Completed: thread #7 Completed: thread #0 Completed: thread #2 Completed: thread #3 Completed: thread #1 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Completed: thread #6 Joined thread # 6 Joined thread # 7 Aug 03 09:11:32 ..... started sorting BAM Max memory needed for sorting = 399840834 EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: 349881844 235742526 16 Aug 03 09:12:51 ...... FATAL ERROR, exiting