STAR version=STAR_2.6.1d STAR compilation time,server,dir=Fri Nov 16 17:02:31 EST 2018 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.master/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 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 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 sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic varVCFfile - waspOutputMode None quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ##### Command Line: STAR --genomeDir star --readFilesIn juvenile_1_val_1.fq.gz juvenile_2_val_2.fq.gz --runThreadN 28 --outFileNamePrefix juvenile. --sjdbGTFfile Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf --outSAMattrRGline ID:juvenile SM:juvenile --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend ##### Initial USER parameters from Command Line: outFileNamePrefix juvenile. ###### All USER parameters from Command Line: genomeDir star ~RE-DEFINED readFilesIn juvenile_1_val_1.fq.gz juvenile_2_val_2.fq.gz ~RE-DEFINED runThreadN 28 ~RE-DEFINED outFileNamePrefix juvenile. ~RE-DEFINED sjdbGTFfile Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf ~RE-DEFINED outSAMattrRGline ID:juvenile SM:juvenile ~RE-DEFINED quantMode TranscriptomeSAM ~RE-DEFINED twopassMode Basic ~RE-DEFINED outSAMtype BAM Unsorted ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED runRNGseed 0 ~RE-DEFINED outFilterMultimapNmax 20 ~RE-DEFINED alignSJDBoverhangMin 1 ~RE-DEFINED outSAMattributes NH HI AS NM MD ~RE-DEFINED quantTranscriptomeBan Singleend ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 28 runRNGseed 0 genomeDir star readFilesIn juvenile_1_val_1.fq.gz juvenile_2_val_2.fq.gz readFilesCommand zcat outFileNamePrefix juvenile. outSAMtype BAM Unsorted outSAMattributes NH HI AS NM MD outSAMattrRGline ID:juvenile SM:juvenile outFilterMultimapNmax 20 alignSJDBoverhangMin 1 sjdbGTFfile Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf quantMode TranscriptomeSAM quantTranscriptomeBan Singleend twopassMode Basic ------------------------------- ##### Final effective command line: STAR --runThreadN 28 --runRNGseed 0 --genomeDir star --readFilesIn juvenile_1_val_1.fq.gz juvenile_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix juvenile. --outSAMtype BAM Unsorted --outSAMattributes NH HI AS NM MD --outSAMattrRGline ID:juvenile SM:juvenile --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --sjdbGTFfile Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf --quantMode TranscriptomeSAM --quantTranscriptomeBan Singleend --twopassMode Basic ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 28 runDirPerm User_RWX runRNGseed 0 genomeDir star genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 genomeConsensusFile - readFilesType Fastx readFilesIn juvenile_1_val_1.fq.gz juvenile_2_val_2.fq.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 outFileNamePrefix juvenile. outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM Unsorted outSAMmode Full outSAMstrandField None outSAMattributes NH HI AS NM MD outSAMunmapped None outSAMorder Paired outSAMprimaryFlag OneBestScore outSAMreadID Standard outSAMmapqUnique 255 outSAMflagOR 0 outSAMflagAND 65535 outSAMattrRGline ID:juvenile SM:juvenile 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 20 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 1 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 Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic varVCFfile - waspOutputMode None quantMode TranscriptomeSAM quantTranscriptomeBAMcompression 1 quantTranscriptomeBan Singleend twopass1readsN 18446744073709551615 twopassMode Basic ---------------------------------------- Input read files for mate 1, from input string juvenile_1_val_1.fq.gz -rw-r--r-- 1 samwhite hyak-coe 27860510904 Mar 24 16:07 juvenile_1_val_1.fq.gz readsCommandsFile: exec > "juvenile._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "juvenile_1_val_1.fq.gz" Input read files for mate 2, from input string juvenile_2_val_2.fq.gz -rw-r--r-- 1 samwhite hyak-coe 26932397772 Mar 24 16:07 juvenile_2_val_2.fq.gz readsCommandsFile: exec > "juvenile._STARtmp/tmp.fifo.read2" echo FILE 0 zcat "juvenile_2_val_2.fq.gz" WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute Finished loading and checking parameters Reading genome generation parameters: ### STAR --runMode genomeGenerate --runThreadN 28 --genomeDir star/ --genomeFastaFiles Panopea-generosa-v1.0.fa --genomeSAindexNbases 14 --limitGenomeGenerateRAM 536770912000 --sjdbGTFfile Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf ### GstrandBit=32 versionGenome 20201 ~RE-DEFINED genomeFastaFiles Panopea-generosa-v1.0.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 976231918 6725009498 ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 18 1 Scaffold_01 89643857 0 2 Scaffold_02 69596280 89653248 3 Scaffold_03 57743597 159383552 4 Scaffold_04 65288255 217317376 5 Scaffold_05 67248332 282853376 6 Scaffold_06 61759565 350224384 7 Scaffold_07 43120122 412090368 8 Scaffold_08 61151155 455344128 9 Scaffold_09 38581958 516685824 10 Scaffold_10 53961475 555483136 11 Scaffold_11 51449921 609484800 12 Scaffold_12 50438331 661127168 13 Scaffold_13 44396874 711720960 14 Scaffold_14 45393038 756285440 15 Scaffold_15 47938513 801898496 16 Scaffold_16 31980953 849870848 17 Scaffold_17 34923512 881852416 18 Scaffold_18 27737463 916979712 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Thu Mar 24 21:05:59 2022 Genome: size given as a parameter = 976231918 SA: size given as a parameter = 6725009498 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=976231918; nSAbyte=6725009498 GstrandBit=32 SA number of indices=1630305332 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 976231918 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 976231918 bytes SA file size: 6725009498 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 6725009498 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Thu Mar 24 21:06:14 2022 Processing splice junctions database sjdbN=156542, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Mar 24 21:06:15 Loaded database junctions from the generated genome star/sjdbList.out.tab: 156542 total junctions Mar 24 21:06:15 ..... processing annotations GTF Processing pGe.sjdbGTFfile=Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf, found: 38326 transcripts 236960 exons (non-collapsed) 156542 collapsed junctions Mar 24 21:06:17 ..... finished GTF processing Mar 24 21:06:17 Loaded database junctions from the GTF file: Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.gtf: 313084 total junctions Mar 24 21:06:17 Finished preparing junctions Mar 24 21:06:17 ..... inserting junctions into the genome indices Mar 24 21:06:18 Finished SA search: number of new junctions=0, old junctions=156542 Mar 24 21:06:18 Finished sorting SA indicesL nInd=0 Genome size with junctions=976231918 944766976 31464942 GstrandBit1=32 GstrandBit=32 Mar 24 21:06:40 Finished inserting junction indices Mar 24 21:06:43 Finished SAi Mar 24 21:06:43 ..... finished inserting junctions into genome Created thread # 1 Created thread # 2 Starting to map file # 0 mate 1: juvenile_1_val_1.fq.gz mate 2: juvenile_2_val_2.fq.gz Created thread # 3 Created thread # 4 Created thread # 5 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 Created thread # 16 Created thread # 17 Created thread # 18 Created thread # 19 Created thread # 20 Created thread # 21 Created thread # 22 Created thread # 23 Created thread # 24 Created thread # 25 Created thread # 26 Created thread # 27 Thread #5 end of input stream, nextChar=-1 Completed: thread #27 Completed: thread #21 Completed: thread #26 Completed: thread #19 Completed: thread #10 Completed: thread #25 Completed: thread #8 Completed: thread #0 Completed: thread #16 Completed: thread #9 Completed: thread #2 Completed: thread #17 Completed: thread #3 Completed: thread #23 Completed: thread #18 Completed: thread #1 Joined thread # 1 Joined thread # 2 Joined thread # 3 Completed: thread #14 Completed: thread #12 Completed: thread #20 Completed: thread #7 Completed: thread #5 Completed: thread #4 Joined thread # 4 Joined thread # 5 Completed: thread #22 Completed: thread #24 Completed: thread #13 Completed: thread #11 Completed: thread #15 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 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Joined thread # 20 Joined thread # 21 Joined thread # 22 Joined thread # 23 Joined thread # 24 Joined thread # 25 Joined thread # 26 Joined thread # 27 Mar 24 22:40:20 Loaded database junctions from the 1st pass file: juvenile._STARpass1//SJ.out.tab: 679206 total junctions Mar 24 22:40:20 Finished preparing junctions Mar 24 22:40:20 ..... inserting junctions into the genome indices Mar 24 22:40:29 Finished SA search: number of new junctions=237874, old junctions=156542 Mar 24 22:41:02 Finished sorting SA indicesL nInd=94582606 Genome size with junctions=1024044592 944766976 79277616 GstrandBit1=32 GstrandBit=32 Mar 24 22:41:25 Finished inserting junction indices Mar 24 22:41:39 Finished SAi Mar 24 22:41:39 ..... finished inserting junctions into genome Input read files for mate 1, from input string juvenile_1_val_1.fq.gz -rw-r--r-- 1 samwhite hyak-coe 27860510904 Mar 24 16:07 juvenile_1_val_1.fq.gz readsCommandsFile: exec > "juvenile._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "juvenile_1_val_1.fq.gz" Input read files for mate 2, from input string juvenile_2_val_2.fq.gz -rw-r--r-- 1 samwhite hyak-coe 26932397772 Mar 24 16:07 juvenile_2_val_2.fq.gz readsCommandsFile: exec > "juvenile._STARtmp/tmp.fifo.read2" echo FILE 0 zcat "juvenile_2_val_2.fq.gz" Loaded transcript database, nTr=38326 Loaded exon database, nEx=236960 Created thread # 1 Starting to map file # 0 mate 1: juvenile_1_val_1.fq.gz mate 2: juvenile_2_val_2.fq.gz Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 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 Created thread # 16 Created thread # 17 Created thread # 18 Created thread # 19 Created thread # 20 Created thread # 21 Created thread # 22 Created thread # 23 Created thread # 24 Created thread # 25 Created thread # 26 Created thread # 27 Thread #14 end of input stream, nextChar=-1 Completed: thread #19 Completed: thread #0 Completed: thread #20 Completed: thread #16 Completed: thread #7 Completed: thread #6 Completed: thread #13 Completed: thread #5 Completed: thread #27 Completed: thread #22 Completed: thread #18 Completed: thread #9 Completed: thread #4 Completed: thread #12 Completed: thread #10 Completed: thread #1 Joined thread # 1 Completed: thread #24 Completed: thread #25 Completed: thread #2 Joined thread # 2 Completed: thread #11 Completed: thread #14 Completed: thread #26 Completed: thread #3 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Completed: thread #21 Completed: thread #17 Completed: thread #15 Completed: thread #8 Joined thread # 8 Joined thread # 9 Joined thread # 10 Joined thread # 11 Joined thread # 12 Joined thread # 13 Joined thread # 14 Joined thread # 15 Joined thread # 16 Joined thread # 17 Joined thread # 18 Joined thread # 19 Joined thread # 20 Joined thread # 21 Joined thread # 22 Completed: thread #23 Joined thread # 23 Joined thread # 24 Joined thread # 25 Joined thread # 26 Joined thread # 27 ALL DONE!