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/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star --runThreadN 1 --genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa --sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf --limitGenomeGenerateRAM 17179869184 --genomeSAsparseD 3 --genomeSAindexNbases 14 --genomeChrBinNbits 18 ##### 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/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star ~RE-DEFINED runThreadN 1 ~RE-DEFINED genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa ~RE-DEFINED sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf ~RE-DEFINED limitGenomeGenerateRAM 17179869184 ~RE-DEFINED genomeSAsparseD 3 ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~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/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 3 limitGenomeGenerateRAM 17179869184 sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf ------------------------------- ##### Final effective command line: STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star --genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa --genomeSAindexNbases 14 --genomeChrBinNbits 18 --genomeSAsparseD 3 --limitGenomeGenerateRAM 17179869184 --sjdbGTFfile /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/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/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star genomeLoad NoSharedMemory genomeFastaFiles /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 3 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/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/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 Jul 06 22:38:15 ... Starting to generate Genome files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 0 "1" chrStart: 0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 1 "10" chrStart: 195559424 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 2 "11" chrStart: 326369280 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 3 "12" chrStart: 448528384 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 4 "13" chrStart: 568852480 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 5 "14" chrStart: 689438720 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 6 "15" chrStart: 814481408 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 7 "16" chrStart: 918552576 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 8 "17" chrStart: 1016856576 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 9 "18" chrStart: 1112014848 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 10 "19" chrStart: 1202978816 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 11 "2" chrStart: 1264582656 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 12 "3" chrStart: 1446772736 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 13 "4" chrStart: 1606942720 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 14 "5" chrStart: 1763704832 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 15 "6" chrStart: 1915748352 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 16 "7" chrStart: 2065694720 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 17 "8" chrStart: 2211184640 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 18 "9" chrStart: 2340683776 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 19 "MT" chrStart: 2465464320 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 20 "X" chrStart: 2465726464 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 21 "Y" chrStart: 2636906496 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 22 "JH584299.1" chrStart: 2728656896 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 23 "GL456233.1" chrStart: 2729705472 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 24 "JH584301.1" chrStart: 2730229760 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 25 "GL456211.1" chrStart: 2730491904 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 26 "GL456350.1" chrStart: 2730754048 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 27 "JH584293.1" chrStart: 2731016192 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 28 "GL456221.1" chrStart: 2731278336 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 29 "JH584297.1" chrStart: 2731540480 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 30 "JH584296.1" chrStart: 2731802624 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 31 "GL456354.1" chrStart: 2732064768 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 32 "JH584294.1" chrStart: 2732326912 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 33 "JH584298.1" chrStart: 2732589056 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 34 "JH584300.1" chrStart: 2732851200 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 35 "GL456219.1" chrStart: 2733113344 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 36 "GL456210.1" chrStart: 2733375488 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 37 "JH584303.1" chrStart: 2733637632 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 38 "JH584302.1" chrStart: 2733899776 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 39 "GL456212.1" chrStart: 2734161920 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 40 "JH584304.1" chrStart: 2734424064 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 41 "GL456379.1" chrStart: 2734686208 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 42 "GL456216.1" chrStart: 2734948352 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 43 "GL456393.1" chrStart: 2735210496 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 44 "GL456366.1" chrStart: 2735472640 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 45 "GL456367.1" chrStart: 2735734784 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 46 "GL456239.1" chrStart: 2735996928 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 47 "GL456213.1" chrStart: 2736259072 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 48 "GL456383.1" chrStart: 2736521216 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 49 "GL456385.1" chrStart: 2736783360 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 50 "GL456360.1" chrStart: 2737045504 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 51 "GL456378.1" chrStart: 2737307648 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 52 "GL456389.1" chrStart: 2737569792 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 53 "GL456372.1" chrStart: 2737831936 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 54 "GL456370.1" chrStart: 2738094080 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 55 "GL456381.1" chrStart: 2738356224 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 56 "GL456387.1" chrStart: 2738618368 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 57 "GL456390.1" chrStart: 2738880512 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 58 "GL456394.1" chrStart: 2739142656 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 59 "GL456392.1" chrStart: 2739404800 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 60 "GL456382.1" chrStart: 2739666944 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 61 "GL456359.1" chrStart: 2739929088 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 62 "GL456396.1" chrStart: 2740191232 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 63 "GL456368.1" chrStart: 2740453376 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 64 "JH584292.1" chrStart: 2740715520 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 65 "JH584295.1" chrStart: 2740977664 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 66 "ERCC-00002" chrStart: 2741239808 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 67 "ERCC-00003" chrStart: 2741501952 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 68 "ERCC-00004" chrStart: 2741764096 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 69 "ERCC-00009" chrStart: 2742026240 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 70 "ERCC-00012" chrStart: 2742288384 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 71 "ERCC-00013" chrStart: 2742550528 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 72 "ERCC-00014" chrStart: 2742812672 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 73 "ERCC-00016" chrStart: 2743074816 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 74 "ERCC-00017" chrStart: 2743336960 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 75 "ERCC-00019" chrStart: 2743599104 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 76 "ERCC-00022" chrStart: 2743861248 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 77 "ERCC-00024" chrStart: 2744123392 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 78 "ERCC-00025" chrStart: 2744385536 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 79 "ERCC-00028" chrStart: 2744647680 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 80 "ERCC-00031" chrStart: 2744909824 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 81 "ERCC-00033" chrStart: 2745171968 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 82 "ERCC-00034" chrStart: 2745434112 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 83 "ERCC-00035" chrStart: 2745696256 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 84 "ERCC-00039" chrStart: 2745958400 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 85 "ERCC-00040" chrStart: 2746220544 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 86 "ERCC-00041" chrStart: 2746482688 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 87 "ERCC-00042" chrStart: 2746744832 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 88 "ERCC-00043" chrStart: 2747006976 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 89 "ERCC-00044" chrStart: 2747269120 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 90 "ERCC-00046" chrStart: 2747531264 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 91 "ERCC-00048" chrStart: 2747793408 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 92 "ERCC-00051" chrStart: 2748055552 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 93 "ERCC-00053" chrStart: 2748317696 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 94 "ERCC-00054" chrStart: 2748579840 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 95 "ERCC-00057" chrStart: 2748841984 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 96 "ERCC-00058" chrStart: 2749104128 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 97 "ERCC-00059" chrStart: 2749366272 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 98 "ERCC-00060" chrStart: 2749628416 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 99 "ERCC-00061" chrStart: 2749890560 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 100 "ERCC-00062" chrStart: 2750152704 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 101 "ERCC-00067" chrStart: 2750414848 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 102 "ERCC-00069" chrStart: 2750676992 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 103 "ERCC-00071" chrStart: 2750939136 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 104 "ERCC-00073" chrStart: 2751201280 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 105 "ERCC-00074" chrStart: 2751463424 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 106 "ERCC-00075" chrStart: 2751725568 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 107 "ERCC-00076" chrStart: 2751987712 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 108 "ERCC-00077" chrStart: 2752249856 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 109 "ERCC-00078" chrStart: 2752512000 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 110 "ERCC-00079" chrStart: 2752774144 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 111 "ERCC-00081" chrStart: 2753036288 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 112 "ERCC-00083" chrStart: 2753298432 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 113 "ERCC-00084" chrStart: 2753560576 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 114 "ERCC-00085" chrStart: 2753822720 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 115 "ERCC-00086" chrStart: 2754084864 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 116 "ERCC-00092" chrStart: 2754347008 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 117 "ERCC-00095" chrStart: 2754609152 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 118 "ERCC-00096" chrStart: 2754871296 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 119 "ERCC-00097" chrStart: 2755133440 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 120 "ERCC-00098" chrStart: 2755395584 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 121 "ERCC-00099" chrStart: 2755657728 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 122 "ERCC-00104" chrStart: 2755919872 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 123 "ERCC-00108" chrStart: 2756182016 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 124 "ERCC-00109" chrStart: 2756444160 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 125 "ERCC-00111" chrStart: 2756706304 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 126 "ERCC-00112" chrStart: 2756968448 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 127 "ERCC-00113" chrStart: 2757230592 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 128 "ERCC-00116" chrStart: 2757492736 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 129 "ERCC-00117" chrStart: 2757754880 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 130 "ERCC-00120" chrStart: 2758017024 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 131 "ERCC-00123" chrStart: 2758279168 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 132 "ERCC-00126" chrStart: 2758541312 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 133 "ERCC-00130" chrStart: 2758803456 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 134 "ERCC-00131" chrStart: 2759065600 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 135 "ERCC-00134" chrStart: 2759327744 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 136 "ERCC-00136" chrStart: 2759589888 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 137 "ERCC-00137" chrStart: 2759852032 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 138 "ERCC-00138" chrStart: 2760114176 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 139 "ERCC-00142" chrStart: 2760376320 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 140 "ERCC-00143" chrStart: 2760638464 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 141 "ERCC-00144" chrStart: 2760900608 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 142 "ERCC-00145" chrStart: 2761162752 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 143 "ERCC-00147" chrStart: 2761424896 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 144 "ERCC-00148" chrStart: 2761687040 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 145 "ERCC-00150" chrStart: 2761949184 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 146 "ERCC-00154" chrStart: 2762211328 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 147 "ERCC-00156" chrStart: 2762473472 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 148 "ERCC-00157" chrStart: 2762735616 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 149 "ERCC-00158" chrStart: 2762997760 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 150 "ERCC-00160" chrStart: 2763259904 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 151 "ERCC-00162" chrStart: 2763522048 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 152 "ERCC-00163" chrStart: 2763784192 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 153 "ERCC-00164" chrStart: 2764046336 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 154 "ERCC-00165" chrStart: 2764308480 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 155 "ERCC-00168" chrStart: 2764570624 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 156 "ERCC-00170" chrStart: 2764832768 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 157 "ERCC-00171" chrStart: 2765094912 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 158 "AAV8-mCherry" chrStart: 2765357056 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 159 "dSaCas9" chrStart: 2765619200 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/fasta/genome.fa : chr # 160 "KRAB" chrStart: 2765881344 Number of SA indices: 1768580199 Jul 06 22:39:35 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 3; chunks size limit: 6988537320 bytes Jul 06 22:39:42 ... sorting Suffix Array chunks and saving them to disk... Writing 6970675096 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/SA_0 ; empty space on disk = 5048748736512 bytes ... done Writing 6910913112 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/SA_1 ; empty space on disk = 5029325963264 bytes ... done Writing 267053384 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/SA_2 ; empty space on disk = 5022415847424 bytes ... done Jul 06 23:19:10 ... loading chunks from disk, packing SA... Jul 06 23:19:35 ... Finished generating suffix array Jul 06 23:19:35 ... Generating Suffix Array index Jul 06 23:21:31 ... Completed Suffix Array index Jul 06 23:21:31 ..... Processing annotations GTF WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'Un_JH584304' not found in Genome fasta files for line: Un_JH584304 mm10_ct_ExonicOnly29kMultiOnly_4314 exon 52674 54479 1000 - . gene_id "Pisd-ps3"; transcript_id "Pisd-ps3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'Un_JH584304' not found in Genome fasta files for line: Un_JH584304 mm10_ct_ExonicOnly29kMultiOnly_4314 exon 54721 54867 1000 - . gene_id "Pisd-ps3"; transcript_id "Pisd-ps3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'Un_JH584304' not found in Genome fasta files for line: Un_JH584304 mm10_ct_ExonicOnly29kMultiOnly_4314 exon 55112 55248 1000 - . gene_id "Pisd-ps3"; transcript_id "Pisd-ps3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'Un_JH584304' not found in Genome fasta files for line: Un_JH584304 mm10_ct_ExonicOnly29kMultiOnly_4314 exon 55465 55701 1000 - . gene_id "Pisd-ps3"; transcript_id "Pisd-ps3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'Un_JH584304' not found in Genome fasta files for line: Un_JH584304 mm10_ct_ExonicOnly29kMultiOnly_4314 exon 56986 57151 1000 - . gene_id "Pisd-ps3"; transcript_id "Pisd-ps3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'Un_JH584304' not found in Genome fasta files for line: Un_JH584304 mm10_ct_ExonicOnly29kMultiOnly_4314 exon 58564 58835 1000 - . gene_id "Pisd-ps3"; transcript_id "Pisd-ps3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'Un_JH584304' not found in Genome fasta files for line: Un_JH584304 mm10_ct_ExonicOnly29kMultiOnly_4314 exon 59592 59689 1000 - . gene_id "Pisd-ps3"; transcript_id "Pisd-ps3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 145347 145401 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 145844 145945 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 149724 149791 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 151103 151252 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 152414 152494 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 153661 153738 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 155312 155389 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 157664 157930 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 160515 160683 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 162258 162405 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 164967 165117 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456211_random' not found in Genome fasta files for line: 1_GL456211_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 165811 165925 1000 - . gene_id "LOC100041034"; transcript_id "LOC100041034" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 111558 114076 1000 - . gene_id "Csprs"; transcript_id "Csprs" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 162798 163011 1000 - . gene_id "Csprs"; transcript_id "Csprs" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 17591 18185 1000 - . gene_id "LOC664787"; transcript_id "LOC664787" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 21897 21965 1000 - . gene_id "LOC664787"; transcript_id "LOC664787" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 23288 23437 1000 - . gene_id "LOC664787"; transcript_id "LOC664787" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 24599 24679 1000 - . gene_id "LOC664787"; transcript_id "LOC664787" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 25845 25922 1000 - . gene_id "LOC664787"; transcript_id "LOC664787" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 27498 27575 1000 - . gene_id "LOC664787"; transcript_id "LOC664787" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '1_GL456221_random' not found in Genome fasta files for line: 1_GL456221_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 30050 30203 1000 - . gene_id "LOC664787"; transcript_id "LOC664787" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456216_random' not found in Genome fasta files for line: 4_GL456216_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 16158 16407 1000 + . gene_id "Dhrsx"; transcript_id "Dhrsx" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456216_random' not found in Genome fasta files for line: 4_GL456216_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 30699 30806 1000 + . gene_id "Dhrsx"; transcript_id "Dhrsx" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456216_random' not found in Genome fasta files for line: 4_GL456216_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 31059 31127 1000 + . gene_id "Dhrsx"; transcript_id "Dhrsx" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456216_random' not found in Genome fasta files for line: 4_GL456216_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 31370 31471 1000 + . gene_id "Dhrsx"; transcript_id "Dhrsx" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456216_random' not found in Genome fasta files for line: 4_GL456216_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 34138 34345 1000 + . gene_id "Dhrsx"; transcript_id "Dhrsx" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456216_random' not found in Genome fasta files for line: 4_GL456216_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 34624 34831 1000 + . gene_id "Dhrsx"; transcript_id "Dhrsx" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456216_random' not found in Genome fasta files for line: 4_GL456216_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 35233 36213 1000 + . gene_id "Dhrsx"; transcript_id "Dhrsx" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 144079 147895 1000 - . gene_id "Fam205a2@chr4_GL456350_random(-)"; transcript_id "Fam205a2@chr4_GL456350_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 148542 148602 1000 - . gene_id "Fam205a2@chr4_GL456350_random(-)"; transcript_id "Fam205a2@chr4_GL456350_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 149041 149086 1000 - . gene_id "Fam205a2@chr4_GL456350_random(-)"; transcript_id "Fam205a2@chr4_GL456350_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 159041 159218 1000 - . gene_id "Fam205a2@chr4_GL456350_random(-)"; transcript_id "Fam205a2@chr4_GL456350_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 144081 147895 1000 - . gene_id "Fam205a4"; transcript_id "Fam205a4" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 148542 148602 1000 - . gene_id "Fam205a4"; transcript_id "Fam205a4" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 159041 159251 1000 - . gene_id "Fam205a4"; transcript_id "Fam205a4" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 173566 173625 1000 - . gene_id "Fam205a4"; transcript_id "Fam205a4" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 211325 211748 1000 - . gene_id "Gm10591"; transcript_id "Gm10591" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 211831 212013 1000 - . gene_id "Gm10591"; transcript_id "Gm10591" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 212108 212228 1000 - . gene_id "Gm10591"; transcript_id "Gm10591" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_GL456350_random' not found in Genome fasta files for line: 4_GL456350_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 212317 212455 1000 - . gene_id "Gm10591"; transcript_id "Gm10591" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584292_random' not found in Genome fasta files for line: 4_JH584292_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3536 3826 1000 + . gene_id "Vmn2r122"; transcript_id "Vmn2r122" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584292_random' not found in Genome fasta files for line: 4_JH584292_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5658 5940 1000 + . gene_id "Vmn2r122"; transcript_id "Vmn2r122" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584292_random' not found in Genome fasta files for line: 4_JH584292_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 6318 7121 1000 + . gene_id "Vmn2r122"; transcript_id "Vmn2r122" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584292_random' not found in Genome fasta files for line: 4_JH584292_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7960 8188 1000 + . gene_id "Vmn2r122"; transcript_id "Vmn2r122" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584292_random' not found in Genome fasta files for line: 4_JH584292_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 9312 9435 1000 + . gene_id "Vmn2r122"; transcript_id "Vmn2r122" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584292_random' not found in Genome fasta files for line: 4_JH584292_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 10590 11935 1000 + . gene_id "Vmn2r122"; transcript_id "Vmn2r122" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 16836 17020 1000 - . gene_id "LOC100861978@chr4_JH584293_random(-)"; transcript_id "LOC100861978@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 17210 17342 1000 - . gene_id "LOC100861978@chr4_JH584293_random(-)"; transcript_id "LOC100861978@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 17484 17590 1000 - . gene_id "LOC100861978@chr4_JH584293_random(-)"; transcript_id "LOC100861978@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 18539 18636 1000 - . gene_id "LOC100861978@chr4_JH584293_random(-)"; transcript_id "LOC100861978@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 21506 21565 1000 - . gene_id "LOC100861978@chr4_JH584293_random(-)"; transcript_id "LOC100861978@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 21777 21843 1000 - . gene_id "LOC100861978@chr4_JH584293_random(-)"; transcript_id "LOC100861978@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 22140 22237 1000 - . gene_id "LOC100861978@chr4_JH584293_random(-)"; transcript_id "LOC100861978@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 16836 17020 1000 - . gene_id "Ccl27b@chr4_JH584293_random(-)"; transcript_id "Ccl27b@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 17210 17342 1000 - . gene_id "Ccl27b@chr4_JH584293_random(-)"; transcript_id "Ccl27b@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 18539 18932 1000 - . gene_id "Ccl27b@chr4_JH584293_random(-)"; transcript_id "Ccl27b@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 21506 21565 1000 - . gene_id "Ccl27b@chr4_JH584293_random(-)"; transcript_id "Ccl27b@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 21777 21843 1000 - . gene_id "Ccl27b@chr4_JH584293_random(-)"; transcript_id "Ccl27b@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 22140 22237 1000 - . gene_id "Ccl27b@chr4_JH584293_random(-)"; transcript_id "Ccl27b@chr4_JH584293_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 85877 89266 1000 - . gene_id "Gm7819"; transcript_id "Gm7819" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 89916 89976 1000 - . gene_id "Gm7819"; transcript_id "Gm7819" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 90409 90454 1000 - . gene_id "Gm7819"; transcript_id "Gm7819" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 120129 120214 1000 - . gene_id "Gm7819"; transcript_id "Gm7819" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584293_random' not found in Genome fasta files for line: 4_JH584293_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 120478 120530 1000 - . gene_id "Gm7819"; transcript_id "Gm7819" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 1718 2111 1000 + . gene_id "Gm2506@chr4_JH584294_random(+)"; transcript_id "Gm2506@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3308 3440 1000 + . gene_id "Gm2506@chr4_JH584294_random(+)"; transcript_id "Gm2506@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3630 3814 1000 + . gene_id "Gm2506@chr4_JH584294_random(+)"; transcript_id "Gm2506@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3060 3166 1000 + . gene_id "Gm13306@chr4_JH584294_random(+)"; transcript_id "Gm13306@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3308 3440 1000 + . gene_id "Gm13306@chr4_JH584294_random(+)"; transcript_id "Gm13306@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3630 3814 1000 + . gene_id "Gm13306@chr4_JH584294_random(+)"; transcript_id "Gm13306@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3060 3166 1000 + . gene_id "Ccl27b@chr4_JH584294_random(+)"; transcript_id "Ccl27b@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3308 3440 1000 + . gene_id "Ccl27b@chr4_JH584294_random(+)"; transcript_id "Ccl27b@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3630 3814 1000 + . gene_id "Ccl27b@chr4_JH584294_random(+)"; transcript_id "Ccl27b@chr4_JH584294_random(+)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3084 4204 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 4717 4799 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5027 5123 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5221 5346 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5692 5833 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7010 7173 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7730 7896 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7975 8007 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 8161 8275 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 8404 8573 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 9399 9459 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 9603 9702 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 10698 10869 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 13444 13572 1000 - . gene_id "Gm2002"; transcript_id "Gm2002" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 3810 4204 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 4717 4799 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5027 5123 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5221 5346 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5692 5833 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7010 7173 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7730 7896 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7975 8007 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 8161 8275 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 8404 8573 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 9399 9459 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 9603 9702 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 10698 10869 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '4_JH584294_random' not found in Genome fasta files for line: 4_JH584294_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 13444 13571 1000 - . gene_id "Gm13305"; transcript_id "Gm13305" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_GL456354_random' not found in Genome fasta files for line: 5_GL456354_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 5185 5258 1000 + . gene_id "A430089I19Rik"; transcript_id "A430089I19Rik" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_GL456354_random' not found in Genome fasta files for line: 5_GL456354_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 6339 6652 1000 + . gene_id "A430089I19Rik"; transcript_id "A430089I19Rik" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_GL456354_random' not found in Genome fasta files for line: 5_GL456354_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 7107 7697 1000 + . gene_id "A430089I19Rik"; transcript_id "A430089I19Rik" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_GL456354_random' not found in Genome fasta files for line: 5_GL456354_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 8594 9462 1000 + . gene_id "A430089I19Rik"; transcript_id "A430089I19Rik" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584296_random' not found in Genome fasta files for line: 5_JH584296_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 40899 41905 1000 - . gene_id "Gm3139@chr5_JH584296_random(-)"; transcript_id "Gm3139@chr5_JH584296_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584296_random' not found in Genome fasta files for line: 5_JH584296_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 42876 43466 1000 - . gene_id "Gm3139@chr5_JH584296_random(-)"; transcript_id "Gm3139@chr5_JH584296_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584296_random' not found in Genome fasta files for line: 5_JH584296_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 44131 44444 1000 - . gene_id "Gm3139@chr5_JH584296_random(-)"; transcript_id "Gm3139@chr5_JH584296_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584296_random' not found in Genome fasta files for line: 5_JH584296_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 52831 52982 1000 - . gene_id "Gm3139@chr5_JH584296_random(-)"; transcript_id "Gm3139@chr5_JH584296_random(-)" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584299_random' not found in Genome fasta files for line: 5_JH584299_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 829045 829165 1000 + . gene_id "Gm16367"; transcript_id "Gm16367" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584299_random' not found in Genome fasta files for line: 5_JH584299_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 837337 837650 1000 + . gene_id "Gm16367"; transcript_id "Gm16367" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584299_random' not found in Genome fasta files for line: 5_JH584299_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 838318 838908 1000 + . gene_id "Gm16367"; transcript_id "Gm16367" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome '5_JH584299_random' not found in Genome fasta files for line: 5_JH584299_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 839884 840894 1000 + . gene_id "Gm16367"; transcript_id "Gm16367" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 159645 159773 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 216736 216917 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 258247 258423 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 272714 272993 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 285396 285515 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 326114 326350 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 332450 332588 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 333195 334187 1000 + . gene_id "Tmlhe"; transcript_id "Tmlhe" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 10737 12544 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 14075 14167 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 21628 21695 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 24872 24962 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 28976 29113 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 30588 30645 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 32430 32584 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 39025 39191 1000 - . gene_id "Vamp7"; transcript_id "Vamp7" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 101352 105572 1000 - . gene_id "Spry3"; transcript_id "Spry3" WARNING: while processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: chromosome 'X_GL456233_random' not found in Genome fasta files for line: X_GL456233_random mm10_ct_ExonicOnly29kMultiOnly_4314 exon 106268 106392 1000 - . gene_id "Spry3"; transcript_id "Spry3" Processing sjdbGTFfile=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf, found: 29644 transcripts 252127 exons (non-collapsed) 221426 collapsed junctions Jul 06 23:21:34 ..... Finished GTF processing Jul 06 23:21:34 Loaded database junctions from the GTF file: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/genes/genes.gtf: 221426 total junctions WARNING: long repeat for junction # 121762 : 2 175192274 175322101; left shift = 80; right shift = 255 WARNING: long repeat for junction # 157026 : 5 123190235 123190960; left shift = 255; right shift = 19 WARNING: long repeat for junction # 217628 : X 125688330 125871181; left shift = 255; right shift = 255 Jul 06 23:21:34 Finished preparing junctions Jul 06 23:21:34 ..... Inserting junctions into the genome indices Jul 06 23:25:58 Finished SA search: number of new junctions=221419, old junctions=0 Jul 06 23:26:27 Finished sorting SA indicesL nInd=88567476 Jul 06 23:26:51 Finished inserting junction indices Jul 06 23:27:08 Finished SAi Jul 06 23:27:08 ..... Finished inserting junctions into genome Jul 06 23:27:08 ... writing Genome to disk ... Writing 2810648707 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/Genome ; empty space on disk = 5036266487808 bytes ... done SA size in bytes: 7660734163 Jul 06 23:27:35 ... writing Suffix Array to disk ... Writing 7660734163 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/SA ; empty space on disk = 5032101543936 bytes ... done Jul 06 23:28:49 ... writing SAindex to disk Writing 8 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/SAindex ; empty space on disk = 5023640584192 bytes ... done Writing 120 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/SAindex ; empty space on disk = 5023640584192 bytes ... done Writing 1565873491 bytes into /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic_FrBack_Exonic/ExonicOnly29K/star/SAindex ; empty space on disk = 5023640584192 bytes ... done Jul 06 23:29:06 ..... Finished successfully DONE: Genome generation, EXITING