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 --genomeDir /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/StarIndex --readFilesIn data/fastq/D0-1_R1.fastq.gz data/fastq/D0-1_R2.fastq.gz --runThreadN 12 --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --twopass1readsN -1 --sjdbOverhang 149 --outFileNamePrefix NoExisitingAnnotation ##### Initial USER parameters from Command Line: outFileNamePrefix NoExisitingAnnotation ###### All USER parameters from Command Line: genomeDir /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/StarIndex ~RE-DEFINED readFilesIn data/fastq/D0-1_R1.fastq.gz data/fastq/D0-1_R2.fastq.gz ~RE-DEFINED runThreadN 12 ~RE-DEFINED genomeLoad NoSharedMemory ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED twopass1readsN 18446744073709551615 ~RE-DEFINED sjdbOverhang 149 ~RE-DEFINED outFileNamePrefix NoExisitingAnnotation ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 12 genomeDir /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/StarIndex genomeLoad NoSharedMemory readFilesIn data/fastq/D0-1_R1.fastq.gz data/fastq/D0-1_R2.fastq.gz readFilesCommand zcat outFileNamePrefix NoExisitingAnnotation outSAMtype BAM SortedByCoordinate sjdbOverhang 149 twopass1readsN 18446744073709551615 ------------------------------- ##### Final effective command line: STAR --runThreadN 12 --genomeDir /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/StarIndex --genomeLoad NoSharedMemory --readFilesIn data/fastq/D0-1_R1.fastq.gz data/fastq/D0-1_R2.fastq.gz --readFilesCommand zcat --outFileNamePrefix NoExisitingAnnotation --outSAMtype BAM SortedByCoordinate --sjdbOverhang 149 --twopass1readsN 18446744073709551615 ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 12 genomeDir /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/StarIndex genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 readFilesIn data/fastq/D0-1_R1.fastq.gz data/fastq/D0-1_R2.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 NoExisitingAnnotation 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 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 149 sjdbScore 2 quantMode - quantTranscriptomeBAMcompression 1 twopass1readsN 18446744073709551615 twopassSJlimit 1000000 ---------------------------------------- Input read files for mate 1, from input string data/fastq/D0-1_R1.fastq.gz -rw-r--r-- 1 guttea emea 457698758 Jan 22 11:10 data/fastq/D0-1_R1.fastq.gz readsCommandsFile: exec > "NoExisitingAnnotation_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "data/fastq/D0-1_R1.fastq.gz" Input read files for mate 2, from input string data/fastq/D0-1_R2.fastq.gz -rw-r--r-- 1 guttea emea 458784461 Jan 22 11:10 data/fastq/D0-1_R2.fastq.gz readsCommandsFile: exec > "NoExisitingAnnotation_STARtmp/tmp.fifo.read2" echo FILE 0 zcat "data/fastq/D0-1_R2.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 /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/10.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/11.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/12.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/13.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/14.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/15.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/16.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/17.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/18.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/19.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/1.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/20.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/21.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/22.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/2.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/3.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/4.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/5.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/6.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/7.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/8.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/9.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/MT.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/X.fa /mnt/nas_omics/shared_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/Y.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED Genome version is compatible with current STAR version Started loading the genome: Fri Jan 30 16:06:01 2015 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 Genome file size: 3166586127 bytes; state: good=1 eof=0 fail=0 bad=0 SA file size: 24136180646 bytes; state: good=1 eof=0 fail=0 bad=0 nGenome=3166586127; nSAbyte=24136180646 GstrandBit=32 SA number of indices=5851195308 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3166586127 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3166586127 bytes SA file size: 24136180646 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24136180646 bytes Loading SAindex ... done: 1565873616 bytes Finished loading the genome: Fri Jan 30 16:06:15 2015 Number of real (reference) chromosmes= 25 1 10 135534747 0 2 11 135006516 135790592 3 12 133851895 271056896 4 13 115169878 405012480 5 14 107349540 520355840 6 15 102531392 627834880 7 16 90354753 730595328 8 17 81195210 821035008 9 18 78077248 902299648 10 19 59128983 980418560 11 1 249250621 1039663104 12 20 63025520 1288962048 13 21 48129895 1352138752 14 22 51304566 1400373248 15 2 243199373 1451753472 16 3 198022430 1695023104 17 4 191154276 1893203968 18 5 180915260 2084569088 19 6 171115067 2265710592 20 7 159138663 2436890624 21 8 146364022 2596274176 22 9 141213431 2742812672 23 MT 16569 2884108288 24 X 155270560 2884370432 25 Y 59373566 3039821824 Processing splice junctions database sjdbN=334615, sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: data/fastq/D0-1_R1.fastq.gz mate 2: data/fastq/D0-1_R2.fastq.gz Created thread # 6 Created thread # 7 Created thread # 8 Created thread # 9 Created thread # 10 Created thread # 11 Thread #3 end of input stream, nextChar=-1 Completed: thread #0 Completed: thread #8 Completed: thread #11 Completed: thread #10 Completed: thread #3 Completed: thread #1 Joined thread # 1 Completed: thread #2 Joined thread # 2 Joined thread # 3 Completed: thread #4 Joined thread # 4 Completed: thread #7 Completed: thread #5 Joined thread # 5 Completed: thread #6 Joined thread # 6 Joined thread # 7 Joined thread # 8 Completed: thread #9 Joined thread # 9 Joined thread # 10 Joined thread # 11 Jan 30 16:07:19 Loaded database junctions from the 1st pass file: NoExisitingAnnotation_STARpass1//SJ.out.tab: 181026 junctions Jan 30 16:07:19 Finished preparing junctions Jan 30 16:07:23 Finished SA search