STAR svn revision compiled=STAR_2.3.0e_r291 STAR compilation time,server,dir=Fri Jan 3 21:22:30 PST 2014 hpc-login2:/home/rcf-13/acolombo/STAR_2.3.0e ##### DEFAULT parameters: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - runMode alignReads runThreadN 1 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 outFileNamePrefix ./ outStd Log outSAMmode Full outSAMstrandField None outSAMattributes Standard outSAMunmapped None outReadsUnmapped None outQSconversionAdd 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 outFilterType Normal outFilterMultimapNmax 10 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.3 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 chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimJunctionOverhangMin 20 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbOverhang 0 sjdbScore 2 swMode 0 swWinCoverageMinP 50 ##### Command Line: /auto/rcf-proj/sa1/software/STAR_2.3.0e/STAR --runMode genomeGenerate --genomeDir /auto/rcf-proj/sa1/data/STAR/hg19/Sequence --genomeFastaFiles /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa --runThreadN 1 --sjdbFileChrStartEnd /auto/rcf-proj/sa1/data/Junctions_Annotations --sjdbOverhang 1 genomeChrBinNbits 6 --genomeSAindexNbases 4 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: runMode genomeGenerate " RE-DEFINED genomeDir /auto/rcf-proj/sa1/data/STAR/hg19/Sequence " RE-DEFINED genomeFastaFiles /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa " RE-DEFINED runThreadN 1 " RE-DEFINED sjdbFileChrStartEnd /auto/rcf-proj/sa1/data/Junctions_Annotations " RE-DEFINED sjdbOverhang 1 " RE-DEFINED genomeSAindexNbases 4 " RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runMode genomeGenerate runThreadN 1 genomeDir /auto/rcf-proj/sa1/data/STAR/hg19/Sequence genomeFastaFiles /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa genomeSAindexNbases 4 sjdbFileChrStartEnd /auto/rcf-proj/sa1/data/Junctions_Annotations sjdbOverhang 1 ------------------------------- ##### Final effective command line: /auto/rcf-proj/sa1/software/STAR_2.3.0e/STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /auto/rcf-proj/sa1/data/STAR/hg19/Sequence --genomeFastaFiles /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa --genomeSAindexNbases 4 --sjdbFileChrStartEnd /auto/rcf-proj/sa1/data/Junctions_Annotations --sjdbOverhang 1 ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - runMode genomeGenerate runThreadN 1 genomeDir /auto/rcf-proj/sa1/data/STAR/hg19/Sequence genomeLoad NoSharedMemory genomeFastaFiles /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa genomeSAindexNbases 4 genomeChrBinNbits 18 genomeSAsparseD 1 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 outFileNamePrefix ./ outStd Log outSAMmode Full outSAMstrandField None outSAMattributes Standard outSAMunmapped None outReadsUnmapped None outQSconversionAdd 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 outFilterType Normal outFilterMultimapNmax 10 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.3 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 chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimJunctionOverhangMin 20 sjdbFileChrStartEnd /auto/rcf-proj/sa1/data/Junctions_Annotations sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbOverhang 1 sjdbScore 2 swMode 0 swWinCoverageMinP 50 ---------------------------------------- Finished loading and checking parameters Jan 07 12:56:45 ... Starting to generate Genome files Loaded database junctions from file: /auto/rcf-proj/sa1/data/Junctions_Annotations: 311758 junctions /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 0 "chrM" chrStart: 0 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 1 "chr1" chrStart: 262144 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 2 "chr2" chrStart: 249561088 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 3 "chr3" chrStart: 492830720 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 4 "chr4" chrStart: 691011584 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 5 "chr5" chrStart: 882376704 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 6 "chr6" chrStart: 1063518208 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 7 "chr7" chrStart: 1234698240 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 8 "chr8" chrStart: 1394081792 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 9 "chr9" chrStart: 1540620288 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 10 "chr10" chrStart: 1681915904 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 11 "chr11" chrStart: 1817706496 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 12 "chr12" chrStart: 1952972800 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 13 "chr13" chrStart: 2086928384 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 14 "chr14" chrStart: 2202271744 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 15 "chr15" chrStart: 2309750784 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 16 "chr16" chrStart: 2412511232 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 17 "chr17" chrStart: 2502950912 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 18 "chr18" chrStart: 2584215552 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 19 "chr19" chrStart: 2662334464 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 20 "chr20" chrStart: 2721579008 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 21 "chr21" chrStart: 2784755712 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 22 "chr22" chrStart: 2832990208 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 23 "chrX" chrStart: 2884370432 /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa : chr # 24 "chrY" chrStart: 3039821824 Jan 07 12:58:03 ... finished processing splice junctions database ... Writing genome to disk... done. Number of SA indices: 5723934032 SA size in bytes: 23611227883 Jan 07 12:58:48 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 4; chunks size limit: 14879671448 bytes Jan 07 12:59:12 ... sorting Suffix Array chunks and saving them to disk... Jan 07 14:20:58 ... loading chunks from disk, packing SA... EXITING because of FATAL problem while generating the suffix array The number of indices read from chunks = 5502539551 is not equal to expected nSA=5723934032 SOLUTION: try to re-run suffix array generation, if it still does not work, report this problem to the author Jan 07 14:25:34 ...... FATAL ERROR, exiting