STAR version=STAR_2.4.0i STAR compilation time,server,dir=Wed Jan 14 18:19:54 EST 2015 modena.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/Releases/STAR_2.4.0i/source ##### DEFAULT parameters: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 outTmpDir - outStd Log outReadsUnmapped None outQSconversionAdd 0 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 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 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 alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimJunctionOverhangMin 20 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 0 sjdbScore 2 quantMode - quantTranscriptomeBAMcompression 1 twopass1readsN 0 twopassSJlimit 1000000 ##### Command Line: STAR --runThreadN 4 --genomeDir star-index --readFilesIn ../WT_rep1_1_Ch6.fastq.gz ../WT_rep1_2_Ch6.fastq.gz --readFilesCommand zcat --alignIntronMax 5000 --outFileNamePrefix ./aln_star_wt --outSAMtype BAM SortedByCoordinate ##### Initial USER parameters from Command Line: outFileNamePrefix ./aln_star_wt ###### All USER parameters from Command Line: runThreadN 4 ~RE-DEFINED genomeDir star-index ~RE-DEFINED readFilesIn ../WT_rep1_1_Ch6.fastq.gz ../WT_rep1_2_Ch6.fastq.gz ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED alignIntronMax 5000 ~RE-DEFINED outFileNamePrefix ./aln_star_wt ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 4 genomeDir star-index readFilesIn ../WT_rep1_1_Ch6.fastq.gz ../WT_rep1_2_Ch6.fastq.gz readFilesCommand zcat outFileNamePrefix ./aln_star_wt outSAMtype BAM SortedByCoordinate alignIntronMax 5000 ------------------------------- ##### Final effective command line: STAR --runThreadN 4 --genomeDir star-index --readFilesIn ../WT_rep1_1_Ch6.fastq.gz ../WT_rep1_2_Ch6.fastq.gz --readFilesCommand zcat --outFileNamePrefix ./aln_star_wt --outSAMtype BAM SortedByCoordinate --alignIntronMax 5000 ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 4 genomeDir star-index genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 readFilesIn ../WT_rep1_1_Ch6.fastq.gz ../WT_rep1_2_Ch6.fastq.gz readFilesCommand zcat readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 outFileNamePrefix ./aln_star_wt outTmpDir - outStd Log outReadsUnmapped None outQSconversionAdd 0 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 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 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 5000 alignMatesGapMax 0 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 5 alignSJDBoverhangMin 3 alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimJunctionOverhangMin 20 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 0 sjdbScore 2 quantMode - quantTranscriptomeBAMcompression 1 twopass1readsN 0 twopassSJlimit 1000000 ---------------------------------------- Input read files for mate 1, from input string ../WT_rep1_1_Ch6.fastq.gz -rw-rw-r-- 1 formation formation 106238937 Mar 26 2015 ../WT_rep1_1_Ch6.fastq.gz readsCommandsFile: exec > "./aln_star_wt_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "../WT_rep1_1_Ch6.fastq.gz" Input read files for mate 2, from input string ../WT_rep1_2_Ch6.fastq.gz -rw-rw-r-- 1 formation formation 104918284 Mar 26 2015 ../WT_rep1_2_Ch6.fastq.gz readsCommandsFile: exec > "./aln_star_wt_STARtmp/tmp.fifo.read2" echo FILE 0 zcat "../WT_rep1_2_Ch6.fastq.gz" WARNING: --limitBAMsortRAM=0, will use genome sizeas RAM linit foro BAM sorting Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles ITAG2.3_genomic_Ch6.fasta ~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 Genome version is compatible with current STAR version Started loading the genome: Mon Mar 14 16:40:53 2016 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 Genome file size: 46137344 bytes; state: good=1 eof=0 fail=0 bad=0 SA file size: 359476846 bytes; state: good=1 eof=0 fail=0 bad=0 nGenome=46137344; nSAbyte=359476846 GstrandBit=32 SA number of indices=87145902 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 46137344 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 46137344 bytes SA file size: 359476846 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 359476846 bytes Loading SAindex ... done: 1565873616 bytes Finished loading the genome: Mon Mar 14 16:40:54 2016 Number of real (reference) chromosmes= 1 1 SL2.40ch06 46041636 0 To accomodate alignIntronMax=5000 redefined winBinNbits=10 To accomodate alignIntronMax=5000 and alignMatesGapMax=0, redefined winFlankNbins=5 and winAnchorDistNbins=10 Created thread # 1 Created thread # 2 Created thread # 3 Starting to map file # 0 mate 1: ../WT_rep1_1_Ch6.fastq.gz mate 2: ../WT_rep1_2_Ch6.fastq.gz Thread #2 end of input stream, nextChar=-1 Completed: thread #2 Completed: thread #1 Completed: thread #3 Completed: thread #0 Joined thread # 1 Joined thread # 2 Joined thread # 3 Mar 14 16:41:16 ..... Started sorting BAM Max memory needed for sorting = 207145393 ALL DONE!