STAR version=2.7.1a STAR compilation time,server,dir=vie jun 21 18:03:03 CEST 2019 ant-login8.linux.crg.es:/software/mi/el7.2/software/STAR-2.7.1a/source ##### DEFAULT parameters: versionGenome 2.7.1a 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 genomeConsensusFile - readFilesType Fastx readFilesIn Read1 Read2 readFilesPrefix - readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 limitNreadsSoft 18446744073709551615 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 outBAMsortingBinsN 50 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 1 outSAMtlen 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 outFilterIntronStrands RemoveInconsistentStrands 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 seedSplitMin 12 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 alignInsertionFlush None peOverlapNbasesMin 0 peOverlapMMp 0.01 chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimMainSegmentMultNmax 10 chimJunctionOverhangMin 20 chimOutType Junctions chimFilter banGenomicN chimSegmentReadGapMax 0 chimMultimapNmax 0 chimMultimapScoreRange 1 chimNonchimScoreDropMin 20 chimOutJunctionFormat 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbGTFtagExonParentGeneName gene_name sjdbGTFtagExonParentGeneType gene_type gene_biotype sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic varVCFfile - waspOutputMode None quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None soloType None soloCBstart 1 soloUMIstart 17 soloCBlen 16 soloUMIlen 10 soloBarcodeReadLength 1 soloCBwhitelist - soloStrand Forward soloOutFileNames Solo.out/ genes.tsv barcodes.tsv matrix.mtx matrixSJ.mtx matrixGeneFull.mtx soloFeatures Gene soloUMIdedup 1MM_All ##### Command Line: STAR --genomeDir /no_backup/jvalcarcel/emancini/anieto/02_INDEX/GRCm38 ––outSJfilterReads Unique --outSAMtype BAM SortedByCoordinate --runThreadN 10 --outFileNamePrefix SRR5264060 ––outFilterMismatchNoverReadLmax 0.04 ––outFilterMismatchNmax 999 ––outFilterMultimapNmax 1 ––alignEndsType Extend5pOfRead1 --outReadsUnmapped Fastx --quantMode GeneCounts --readFilesCommand zcat --readFilesIn SRR5264060_1.fastq.gz SRR5264060_2.fastq.gz ##### Initial USER parameters from Command Line: outFileNamePrefix SRR5264060 ###### All USER parameters from Command Line: genomeDir /no_backup/jvalcarcel/emancini/anieto/02_INDEX/GRCm38 ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED runThreadN 10 ~RE-DEFINED outFileNamePrefix SRR5264060 ~RE-DEFINED outReadsUnmapped Fastx ~RE-DEFINED quantMode GeneCounts ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED readFilesIn SRR5264060_1.fastq.gz SRR5264060_2.fastq.gz ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 10 genomeDir /no_backup/jvalcarcel/emancini/anieto/02_INDEX/GRCm38 readFilesIn SRR5264060_1.fastq.gz SRR5264060_2.fastq.gz readFilesCommand zcat outFileNamePrefix SRR5264060 outReadsUnmapped Fastx outSAMtype BAM SortedByCoordinate quantMode GeneCounts ------------------------------- ##### Final effective command line: STAR --runThreadN 10 --genomeDir /no_backup/jvalcarcel/emancini/anieto/02_INDEX/GRCm38 --readFilesIn SRR5264060_1.fastq.gz SRR5264060_2.fastq.gz --readFilesCommand zcat --outFileNamePrefix SRR5264060 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts ##### Final parameters after user input--------------------------------: versionGenome 2.7.1a parametersFiles - sysShell - runMode alignReads runThreadN 10 runDirPerm User_RWX runRNGseed 777 genomeDir /no_backup/jvalcarcel/emancini/anieto/02_INDEX/GRCm38 genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 genomeConsensusFile - readFilesType Fastx readFilesIn SRR5264060_1.fastq.gz SRR5264060_2.fastq.gz readFilesPrefix - 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 limitNreadsSoft 18446744073709551615 outFileNamePrefix SRR5264060 outTmpDir - outTmpKeep None outStd Log outReadsUnmapped Fastx 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 outBAMsortingBinsN 50 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 1 outSAMtlen 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 outFilterIntronStrands RemoveInconsistentStrands 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 seedSplitMin 12 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 alignInsertionFlush None peOverlapNbasesMin 0 peOverlapMMp 0.01 chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimMainSegmentMultNmax 10 chimJunctionOverhangMin 20 chimOutType Junctions chimFilter banGenomicN chimSegmentReadGapMax 0 chimMultimapNmax 0 chimMultimapScoreRange 1 chimNonchimScoreDropMin 20 chimOutJunctionFormat 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbGTFtagExonParentGeneName gene_name sjdbGTFtagExonParentGeneType gene_type gene_biotype sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic varVCFfile - waspOutputMode None quantMode GeneCounts quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None soloType None soloCBstart 1 soloUMIstart 17 soloCBlen 16 soloUMIlen 10 soloBarcodeReadLength 1 soloCBwhitelist - soloStrand Forward soloOutFileNames Solo.out/ genes.tsv barcodes.tsv matrix.mtx matrixSJ.mtx matrixGeneFull.mtx soloFeatures Gene soloUMIdedup 1MM_All ---------------------------------------- Input read files for mate 1, from input string SRR5264060_1.fastq.gz -rw-r--r-- 1 emancini CRG_Lab_Juan_Valcarcel 1633391203 ene 29 14:16 SRR5264060_1.fastq.gz readsCommandsFile: exec > "SRR5264060_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "SRR5264060_1.fastq.gz" Input read files for mate 2, from input string SRR5264060_2.fastq.gz -rw-r--r-- 1 emancini CRG_Lab_Juan_Valcarcel 1687602007 ene 29 14:16 SRR5264060_2.fastq.gz readsCommandsFile: exec > "SRR5264060_STARtmp/tmp.fifo.read2" echo FILE 0 zcat "SRR5264060_2.fastq.gz" WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters: ### STAR --runMode genomeGenerate --runThreadN 10 --genomeDir GRCm38 --genomeFastaFiles genome.fa --outFileNamePrefix GRCm38 --sjdbGTFfile genes.gtf --sjdbOverhang 99 ### GstrandBit=32 versionGenome 2.7.1a ~RE-DEFINED genomeFastaFiles genome.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile genes.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 2776514406 22235024810 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 22 1 10 130694993 0 2 11 122082543 130809856 3 12 120129022 252968960 4 13 120421639 373293056 5 14 124902244 493879296 6 15 104043685 618921984 7 16 98207768 722993152 8 17 94987271 821297152 9 18 90702639 916455424 10 19 61431566 1007419392 11 1 195471971 1069023232 12 2 182113224 1264582656 13 3 160039680 1446772736 14 4 156508116 1606942720 15 5 151834684 1763704832 16 6 149736546 1915748352 17 7 145441459 2065694720 18 8 129401213 2211184640 19 9 124595110 2340683776 20 MT 16299 2465464320 21 X 171031299 2465726464 22 Y 91744698 2636906496 --sjdbOverhang = 99 taken from the generated genome Started loading the genome: Wed Feb 9 16:42:22 2022 Genome: size given as a parameter = 2776514406 SA: size given as a parameter = 22235024810 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=2776514406; nSAbyte=22235024810 GstrandBit=32 SA number of indices=5390309044 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 2776514406 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2776514406 bytes SA file size: 22235024810 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 22235024810 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Wed Feb 9 16:42:48 2022 Processing splice junctions database sjdbN=240490, pGe.sjdbOverhang=99 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread0 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread0 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread1 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread1 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread2 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread2 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread3 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread3 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread4 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread4 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread5 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread5 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread6 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread6 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread7 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread7 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread8 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread8 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate1.thread9 ... ok Opening the file: SRR5264060_STARtmp//Unmapped.out.mate2.thread9 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Starting to map file # 0 mate 1: SRR5264060_1.fastq.gz mate 2: SRR5264060_2.fastq.gz Created thread # 7 Created thread # 8 Created thread # 9 BAM sorting: 254562 mapped reads BAM sorting bins genomic start loci: 1 0 81049877 2 1 5067961 3 1 61523471 4 1 87117792 5 1 115523761 6 2 49385055 7 2 98435207 8 3 29015805 9 3 99423782 10 4 46808478 11 5 4026670 12 5 84987122 13 5 99037856 14 6 40466223 15 7 12920858 16 7 35864842 17 7 39847036 18 7 39847664 19 7 57080697 20 8 36789201 21 9 5275158 22 9 44306471 23 10 44163895 24 10 125394047 25 10 183322664 26 11 44830396 27 11 115949322 28 11 157901798 29 12 36568697 30 12 95234352 31 13 11545969 32 13 101658773 33 13 134470172 34 14 24138043 35 14 101895817 36 14 135736129 37 15 6816256 38 15 77279093 39 15 127141347 40 16 42106554 41 16 111075213 42 17 20148248 43 17 84974123 44 18 21074304 45 18 59586633 46 18 108572589 47 19 7184 48 20 74335773 Thread #8 end of input stream, nextChar=-1 Completed: thread #8 Completed: thread #7 Completed: thread #1 Completed: thread #0 Joined thread # 1 Completed: thread #5 Completed: thread #9 Completed: thread #3 Completed: thread #2 Joined thread # 2 Joined thread # 3 Completed: thread #4 Joined thread # 4 Joined thread # 5 Completed: thread #6 Joined thread # 6 Joined thread # 7 Joined thread # 8 Joined thread # 9 Feb 09 16:47:29 ..... started sorting BAM Max memory needed for sorting = 186412207 ALL DONE!