STAR version= STAR_2.5.1b STAR compilation time,server,dir=Wed May 8 16:13:25 PDT 2019 :/mnt/home/jenkins/workspace/module-STAR-5dda596---latest/sake/modules/STAR/5dda596/source ##### DEFAULT parameters: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outFileNamePrefix ./ outTmpDir - 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 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 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 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 alignSJstitchMismatchNmax 0 -1 0 0 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 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ##### Command Line: STAR --runMode genomeGenerate --genomeDir /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star --runThreadN 1 --genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa --sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf --limitGenomeGenerateRAM 17179869184 --genomeSAsparseD 1 --genomeSAindexNbases 7 --genomeChrBinNbits 9 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: runMode genomeGenerate ~RE-DEFINED genomeDir /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star ~RE-DEFINED runThreadN 1 ~RE-DEFINED genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa ~RE-DEFINED sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf ~RE-DEFINED limitGenomeGenerateRAM 17179869184 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED genomeSAindexNbases 7 ~RE-DEFINED genomeChrBinNbits 9 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runMode genomeGenerate runThreadN 1 genomeDir /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa genomeSAindexNbases 7 genomeChrBinNbits 9 genomeSAsparseD 1 limitGenomeGenerateRAM 17179869184 sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf ------------------------------- ##### Final effective command line: STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star --genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa --genomeSAindexNbases 7 --genomeChrBinNbits 9 --genomeSAsparseD 1 --limitGenomeGenerateRAM 17179869184 --sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode genomeGenerate runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star genomeLoad NoSharedMemory genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa genomeSAindexNbases 7 genomeChrBinNbits 9 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 17179869184 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outFileNamePrefix ./ outTmpDir - 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 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 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 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 alignSJstitchMismatchNmax 0 -1 0 0 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 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Finished loading and checking parameters Sep 18 12:03:55 ... Starting to generate Genome files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 0 "ERCC-00002" chrStart: 0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 1 "ERCC-00003" chrStart: 1536 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 2 "ERCC-00004" chrStart: 3072 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 3 "ERCC-00009" chrStart: 4096 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 4 "ERCC-00012" chrStart: 5120 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 5 "ERCC-00013" chrStart: 6144 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 6 "ERCC-00014" chrStart: 7168 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 7 "ERCC-00016" chrStart: 9216 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 8 "ERCC-00017" chrStart: 10240 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 9 "ERCC-00019" chrStart: 11776 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 10 "ERCC-00022" chrStart: 12800 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 11 "ERCC-00024" chrStart: 13824 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 12 "ERCC-00025" chrStart: 14848 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 13 "ERCC-00028" chrStart: 16896 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 14 "ERCC-00031" chrStart: 18432 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 15 "ERCC-00033" chrStart: 19968 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 16 "ERCC-00034" chrStart: 22016 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 17 "ERCC-00035" chrStart: 23040 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 18 "ERCC-00039" chrStart: 24576 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 19 "ERCC-00040" chrStart: 25600 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 20 "ERCC-00041" chrStart: 26624 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 21 "ERCC-00042" chrStart: 28160 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 22 "ERCC-00043" chrStart: 29696 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 23 "ERCC-00044" chrStart: 31232 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 24 "ERCC-00046" chrStart: 32768 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 25 "ERCC-00048" chrStart: 33792 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 26 "ERCC-00051" chrStart: 34816 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 27 "ERCC-00053" chrStart: 35328 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 28 "ERCC-00054" chrStart: 36864 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 29 "ERCC-00057" chrStart: 37376 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 30 "ERCC-00058" chrStart: 38400 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 31 "ERCC-00059" chrStart: 39936 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 32 "ERCC-00060" chrStart: 40960 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 33 "ERCC-00061" chrStart: 41984 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 34 "ERCC-00062" chrStart: 43520 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 35 "ERCC-00067" chrStart: 45056 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 36 "ERCC-00069" chrStart: 46080 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 37 "ERCC-00071" chrStart: 47616 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 38 "ERCC-00073" chrStart: 48640 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 39 "ERCC-00074" chrStart: 49664 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 40 "ERCC-00075" chrStart: 50688 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 41 "ERCC-00076" chrStart: 52224 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 42 "ERCC-00077" chrStart: 53248 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 43 "ERCC-00078" chrStart: 53760 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 44 "ERCC-00079" chrStart: 54784 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 45 "ERCC-00081" chrStart: 55808 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 46 "ERCC-00083" chrStart: 56832 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 47 "ERCC-00084" chrStart: 57856 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 48 "ERCC-00085" chrStart: 58880 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 49 "ERCC-00086" chrStart: 59904 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 50 "ERCC-00092" chrStart: 60928 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 51 "ERCC-00095" chrStart: 62464 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 52 "ERCC-00096" chrStart: 63488 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 53 "ERCC-00097" chrStart: 65024 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 54 "ERCC-00098" chrStart: 66048 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 55 "ERCC-00099" chrStart: 67584 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 56 "ERCC-00104" chrStart: 69120 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 57 "ERCC-00108" chrStart: 71168 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 58 "ERCC-00109" chrStart: 72192 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 59 "ERCC-00111" chrStart: 73216 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 60 "ERCC-00112" chrStart: 74240 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 61 "ERCC-00113" chrStart: 75776 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 62 "ERCC-00116" chrStart: 76800 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 63 "ERCC-00117" chrStart: 78848 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 64 "ERCC-00120" chrStart: 80384 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 65 "ERCC-00123" chrStart: 81408 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 66 "ERCC-00126" chrStart: 82432 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 67 "ERCC-00130" chrStart: 83968 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 68 "ERCC-00131" chrStart: 85504 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 69 "ERCC-00134" chrStart: 86528 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 70 "ERCC-00136" chrStart: 87040 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 71 "ERCC-00137" chrStart: 88576 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 72 "ERCC-00138" chrStart: 89600 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 73 "ERCC-00142" chrStart: 91136 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 74 "ERCC-00143" chrStart: 91648 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 75 "ERCC-00144" chrStart: 92672 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 76 "ERCC-00145" chrStart: 93696 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 77 "ERCC-00147" chrStart: 95232 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 78 "ERCC-00148" chrStart: 96768 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 79 "ERCC-00150" chrStart: 97280 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 80 "ERCC-00154" chrStart: 98304 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 81 "ERCC-00156" chrStart: 99328 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 82 "ERCC-00157" chrStart: 99840 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 83 "ERCC-00158" chrStart: 100864 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 84 "ERCC-00160" chrStart: 102400 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 85 "ERCC-00162" chrStart: 103424 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 86 "ERCC-00163" chrStart: 104448 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 87 "ERCC-00164" chrStart: 105472 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 88 "ERCC-00165" chrStart: 106496 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 89 "ERCC-00168" chrStart: 107520 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 90 "ERCC-00170" chrStart: 109056 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 91 "ERCC-00171" chrStart: 110592 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 92 "AAV8-mCherry" chrStart: 111104 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 93 "dSaCas9" chrStart: 112128 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/fasta/genome.fa : chr # 94 "KRAB" chrStart: 115712 Number of SA indices: 173628 Sep 18 12:03:56 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 1; chunks size limit: 10307770040 bytes Sep 18 12:03:56 ... sorting Suffix Array chunks and saving them to disk... Writing 1389024 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star/SA_0 ; empty space on disk = 25024965640192 bytes ... done Sep 18 12:03:56 ... loading chunks from disk, packing SA... Sep 18 12:03:56 ... Finished generating suffix array Sep 18 12:03:56 ... Generating Suffix Array index Sep 18 12:03:56 ... Completed Suffix Array index Sep 18 12:03:56 ..... Processing annotations GTF WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf: chromosome 'AAV8-mcherry' not found in Genome fasta files for line: AAV8-mcherry crispr exon 1 708 . + . gene_id "AAV8-mcherry"; transcript_id "AAV8-mcherry" Processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf, found: 93 transcripts 93 exons (non-collapsed) 0 collapsed junctions Sep 18 12:03:56 ..... Finished GTF processing Sep 18 12:03:56 Loaded database junctions from the GTF file: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/genes/genes.gtf: 0 total junctions Sep 18 12:03:56 Finished preparing junctions Sep 18 12:03:56 ..... Finished inserting junctions into genome Sep 18 12:03:56 ... writing Genome to disk ... Writing 116224 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star/Genome ; empty space on disk = 25024965640192 bytes ... done SA size in bytes: 716219 Sep 18 12:03:56 ... writing Suffix Array to disk ... Writing 716219 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star/SA ; empty space on disk = 25024965640192 bytes ... done Sep 18 12:03:56 ... writing SAindex to disk Writing 8 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star/SAindex ; empty space on disk = 25024964591616 bytes ... done Writing 64 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star/SAindex ; empty space on disk = 25024964591616 bytes ... done Writing 95571 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/ERCC/mm10_ERCC_mcherry_dcas9_KRAB/star/SAindex ; empty space on disk = 25024964591616 bytes ... done Sep 18 12:03:56 ..... Finished successfully DONE: Genome generation, EXITING