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===Trial 3=== ====Reorder HsGenome19.fa to karyotypic order==== csplit -f c HsGenome19.fa /'>chr9'/ /'>chr5'/ /'>chr2'/ /'>chr17'/ /'>chr14'/ /'>chr4'/ /'>chr16'/ /'>chr21'/ /'>chrM'/ /'>chr7'/ /'>chr3'/ /'>chr18'/ /'>chr12'/ /'>chrX'/ /'>chr13'/ /'>chr15'/ /'>chr8'/ /'>chr22'/ /'>chr11'/ /'>chr10'/ /'>chr20'/ /'>chr19'/ /'>chr6'/ /'>chr1'/ /'>chrY'/ cat c24 c03 c11 c06 c02 c23 c10 c17 c01 c20 c19 c13 c15 c05 c16 c07 c04 c12 c22 c21 c08 c18 c14 c25 c09 > HsGenome19_karyorder.fa rm HsGenome19.* mv HsGenome19_karyorder.fa ./HsGenome19.fa {| {{table}} | align="center" style="background:#f0f0f0;"|'''Old chr order''' | align="center" style="background:#f0f0f0;"|'''Add /''/''' | align="center" style="background:#f0f0f0;"|'''csplit output files''' | align="center" style="background:#f0f0f0;"|'''cat order''' | align="center" style="background:#f0f0f0;"|'''New chr order''' |- | >chr9||/'>chr9'/||c01||c24||chr1 |- | >chr5||/'>chr5'/||c02||c03||chr2 |- | >chr2||/'>chr2'/||c03||c11||chr3 |- | >chr17||/'>chr17'/||c04||c06||chr4 |- | >chr14||/'>chr14'/||c05||c02||chr5 |- | >chr4||/'>chr4'/||c06||c23||chr6 |- | >chr16||/'>chr16'/||c07||c10||chr7 |- | >chr21||/'>chr21'/||c08||c17||chr8 |- | >chrM||/'>chrM'/||c09||c01||chr9 |- | >chr7||/'>chr7'/||c10||c20||chr10 |- | >chr3||/'>chr3'/||c11||c19||chr11 |- | >chr18||/'>chr18'/||c12||c13||chr12 |- | >chr12||/'>chr12'/||c13||c15||chr13 |- | >chrX||/'>chrX'/||c14||c05||chr14 |- | >chr13||/'>chr13'/||c15||c16||chr15 |- | >chr15||/'>chr15'/||c16||c07||chr16 |- | >chr8||/'>chr8'/||c17||c04||chr17 |- | >chr22||/'>chr22'/||c18||c12||chr18 |- | >chr11||/'>chr11'/||c19||c22||chr19 |- | >chr10||/'>chr10'/||c20||c21||chr20 |- | >chr20||/'>chr20'/||c21||c08||chr21 |- | >chr19||/'>chr19'/||c22||c18||chr22 |- | >chr6||/'>chr6'/||c23||c14||chrX |- | >chr1||/'>chr1'/||c24||c25||chrY |- | >chrY||/'>chrY'/||c25||c09||chrM |} ====Index reference fasta and create sequence dictionary==== *samtools faidx samtools faidx ~/Genomes/HsGenome19.fa *Picard.CreateSequenceDictionary java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.79/CreateSequenceDictionary.jar REFERENCE=~/Genomes/HsGenome19.fa OUTPUT=~/Genomes/HsGenome19.dict ====Match order of contigs in Bam file to reference file==== *Picard.ReorderSam rm accepted_hits_RanHex.coorsortRGreorder.bam* java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.79/ReorderSam.jar INPUT=accepted_hits_RanHex.coorsortRG.bam OUTPUT=accepted_hits_RanHex.coorsortRGreorder.bam REFERENCE=~/Genomes/HsGenome19.fa ====Index bam file==== samtools index accepted_hits_RanHex.coorsortRGreorder.bam ====Run RNA-SeQC v1.1.7.jar==== java -jar /home/kunzhang/softwares/RNA-SeQC_v1.1.7.jar -bwa /home/kunzhang/softwares/bwa-0.7.5a/bwa -BWArRNA ~/Genomes/RNA-SeqCResources/human_all_rRNA.fasta -s ~/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_samples.txt -t ~/Genomes/RNA-SeqCResources/gencode.v7.annotation.gtf -r ~/Genomes/HsGenome19.fa -o ~/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/ -strat gc -gc ~/Genomes/RNA-SeqCResources/gencode.v7.gc.txt -singleEnd <!-- RNA-SeQC v1.1.7 05/14/12 Retriving contig names from reference contig names in reference: 25 Loading GTF for Read Counting Converting to refGene Transcript objects to RefGen format: 2 s Running IntronicExpressionReadBlock Walker .... Arguments: [-T, IntronicExpressionReadBlock, --outfile_metrics, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/RanHex.metrics.tmp.txt, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -refseq, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//refGene.txt, -l, ERROR] Finished writing /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/RanHex.metrics.tmp.txt.intronReport.txt Finished writing /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/RanHex.metrics.tmp.txt.intronReport.txt_intronOnly.txt, now creating RPKM values for introns .. GATK command result code: 0 ... GATK CoutReadMetrics Analysis DONE CountReadMetricsWalker Runtime: 0 min Counting rRNA reads with BWA and /home/mzcai/Genomes/RNA-SeqCResources/human_all_rRNA.fasta BWA on end 1 Running BWA on /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam Command: [/home/kunzhang/softwares/bwa-0.7.5a/bwa, aln, /home/mzcai/Genomes/RNA-SeqCResources/human_all_rRNA.fasta, -b0, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam] [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... Call to BWA complete Running BWA sampe Command: [/home/kunzhang/softwares/bwa-0.7.5a/bwa, samse, /home/mzcai/Genomes/RNA-SeqCResources/human_all_rRNA.fasta, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/end1.sai, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam] [fread] Unexpected end of file Call to BWA complete Counting aligned reads in /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/rRNA.sam BWA based rRNA Estimation for RanHex: 0 min Calculating library complexity for RanHex Libary Complexity Calculation Time: 0 s Stratifying Transcripts By Expression Number of expressed transcripts at this cuttoff: 3093 Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/lowexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/lowexpr Loading transcripts Preparing intervals for 1000 transcripts Interval Loading: 19 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/medexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/medexpr Loading transcripts Preparing intervals for 1000 transcripts Interval Loading: 20 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/highexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/highexpr Loading transcripts Preparing intervals for 1000 transcripts Interval Loading: 19 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/lowexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/lowexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/lowexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/lowexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 1 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/medexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/medexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/medexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/medexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/highexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/highexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/highexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/highexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/lowexpr//perBaseDoC.out: 4 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/lowexpr//perBaseDoC.out: 13 s Mapped intervals back to transcripts: 17 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/lowexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/lowexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/medexpr//perBaseDoC.out: 1 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/medexpr//perBaseDoC.out: 6 s Mapped intervals back to transcripts: 7 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/medexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/medexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/highexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//RanHex/highexpr//perBaseDoC.out: 1 s Mapped intervals back to transcripts: 2 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/highexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/RanHex/highexpr/RanHex.metrics.tmp.txt.rpkm.gct Lower Bound Z score cutoff: 0.375 Percentile: 0.03766231 Total Transcripts in this percentile: 3179 Upper Bound Z score cutoff: 0.625 Percentile: 0.090299495 Total Transcripts in this percentile: 7622 Middle Percentile: 0.8720382 Total Transcripts in this percentile: 73607 Copying transcript model in to GC stratifications Stratifying transcripts with file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/lowgc.gtf Arguments in this stratification [-bwa, /home/kunzhang/softwares/bwa-0.7.5a/bwa, -BWArRNA, /home/mzcai/Genomes/RNA-SeqCResources/human_all_rRNA.fasta, -s, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_samples.txt, -t, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/lowgc.gtf, -r, /home/mzcai/Genomes/HsGenome19.fa, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low, -strat, none, -gc, /home/mzcai/Genomes/RNA-SeqCResources/gencode.v7.gc.txt, -singleEnd, -noReadCounting, -rRNA, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//rRNA_intervals.list, -expr, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//exons.rpkm.gct] RNA-SeQC v1.1.7 05/14/12 Suppressing Read Count Metrics within Recursive Call. Retriving contig names from reference contig names in reference: 25 Loading GTF for Read Counting Converting to refGene Transcript objects to RefGen format: 0 s Filtering GTF file to correspond to GCT file. Metrics suppressed Stratifying Transcripts By Expression Number of expressed transcripts at this cuttoff: 103 Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/lowexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/lowexpr Loading transcripts Preparing intervals for 103 transcripts Interval Loading: 0 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/medexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/medexpr Loading transcripts Preparing intervals for 103 transcripts Interval Loading: 0 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/highexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/highexpr Loading transcripts Preparing intervals for 103 transcripts Interval Loading: 0 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/lowexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/lowexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/lowexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/lowexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/medexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/medexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/medexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/medexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/highexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/highexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/highexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/highexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/lowexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/lowexpr//perBaseDoC.out: 0 s Mapped intervals back to transcripts: 1 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/lowexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/lowexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/medexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/medexpr//perBaseDoC.out: 0 s Mapped intervals back to transcripts: 1 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/medexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/medexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/highexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/low/RanHex/highexpr//perBaseDoC.out: 0 s Mapped intervals back to transcripts: 1 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/highexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/low/RanHex/highexpr/RanHex.metrics.tmp.txt.rpkm.gct Stratifying transcripts with file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/medgc.gtf Arguments in this stratification [-bwa, /home/kunzhang/softwares/bwa-0.7.5a/bwa, -BWArRNA, /home/mzcai/Genomes/RNA-SeqCResources/human_all_rRNA.fasta, -s, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_samples.txt, -t, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/medgc.gtf, -r, /home/mzcai/Genomes/HsGenome19.fa, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid, -strat, none, -gc, /home/mzcai/Genomes/RNA-SeqCResources/gencode.v7.gc.txt, -singleEnd, -noReadCounting, -rRNA, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//rRNA_intervals.list, -expr, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//exons.rpkm.gct] RNA-SeQC v1.1.7 05/14/12 Suppressing Read Count Metrics within Recursive Call. Retriving contig names from reference contig names in reference: 25 Loading GTF for Read Counting Converting to refGene Transcript objects to RefGen format: 0 s Filtering GTF file to correspond to GCT file. Metrics suppressed Stratifying Transcripts By Expression Number of expressed transcripts at this cuttoff: 2327 Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/lowexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/lowexpr Loading transcripts Preparing intervals for 1000 transcripts Interval Loading: 13 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/medexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/medexpr Loading transcripts Preparing intervals for 1000 transcripts Interval Loading: 13 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/highexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/highexpr Loading transcripts Preparing intervals for 1000 transcripts Interval Loading: 13 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/lowexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/lowexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/lowexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/lowexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 1 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/medexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/medexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/medexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/medexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/highexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/highexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/highexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/highexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/lowexpr//perBaseDoC.out: 2 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/lowexpr//perBaseDoC.out: 13 s Mapped intervals back to transcripts: 16 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/lowexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/lowexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/medexpr//perBaseDoC.out: 1 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/medexpr//perBaseDoC.out: 7 s Mapped intervals back to transcripts: 8 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/medexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/medexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/highexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/mid/RanHex/highexpr//perBaseDoC.out: 2 s Mapped intervals back to transcripts: 3 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/highexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/mid/RanHex/highexpr/RanHex.metrics.tmp.txt.rpkm.gct Stratifying transcripts with file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/highgc.gtf Arguments in this stratification [-bwa, /home/kunzhang/softwares/bwa-0.7.5a/bwa, -BWArRNA, /home/mzcai/Genomes/RNA-SeqCResources/human_all_rRNA.fasta, -s, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_samples.txt, -t, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/highgc.gtf, -r, /home/mzcai/Genomes/HsGenome19.fa, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high, -strat, none, -gc, /home/mzcai/Genomes/RNA-SeqCResources/gencode.v7.gc.txt, -singleEnd, -noReadCounting, -rRNA, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//rRNA_intervals.list, -expr, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//exons.rpkm.gct] RNA-SeQC v1.1.7 05/14/12 Suppressing Read Count Metrics within Recursive Call. Retriving contig names from reference contig names in reference: 25 Loading GTF for Read Counting Converting to refGene Transcript objects to RefGen format: 0 s Filtering GTF file to correspond to GCT file. Metrics suppressed Stratifying Transcripts By Expression Number of expressed transcripts at this cuttoff: 35 Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/lowexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/lowexpr Loading transcripts Preparing intervals for 35 transcripts Interval Loading: 1 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/medexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/medexpr Loading transcripts Preparing intervals for 35 transcripts Interval Loading: 1 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Expression file for DoC: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/highexpr/RanHex.transcripts.list Writing DoC per gene into: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/highexpr Loading transcripts Preparing intervals for 35 transcripts Interval Loading: 1 s Creating interval list Writing intervals from transcript objects Transcript objects to interval list conversion: 0 s Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/lowexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/lowexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/lowexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/lowexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/medexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/medexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/medexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/medexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R /home/mzcai/Genomes/HsGenome19.fa -I /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam -o /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/highexpr//perBaseDoC.out -L /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/highexpr/intervals.list -l ERROR Arguments Array: [-T, DepthOfCoverage, -R, /home/mzcai/Genomes/HsGenome19.fa, -I, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/accepted_hits_RanHex.coorsortRGreorder.bam, -o, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/highexpr//perBaseDoC.out, -L, /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/highexpr/intervals.list, -l, ERROR] GATK command result code: 0 Depth of Coverage run time: 0 min ... GATK Depth of Coverage Analysis DONE Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/lowexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/lowexpr//perBaseDoC.out: 0 s Mapped intervals back to transcripts: 0 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/lowexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/lowexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/medexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/medexpr//perBaseDoC.out: 0 s Mapped intervals back to transcripts: 0 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/medexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/medexpr/RanHex.metrics.tmp.txt.rpkm.gct Loading transcripts Splitting intervals into transcript-oriented DoC files Indexing DoC result file: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/highexpr//perBaseDoC.out: 0 s Finding DoC results per transcript DoC Results by interval have been mapped back to the transcripts: /home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output//gc/high/RanHex/highexpr//perBaseDoC.out: 0 s Mapped intervals back to transcripts: 0 s Library size link path/home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/highexpr/.. Absolute path to metrics.tmp.txt/media/Ext12T/MC_Ext12T/RanHex_EnrichmRNA/inVitroRTSeq/tophat_hg19unmask_Indx26_RanHex/../home/mzcai/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/gc/high/RanHex/highexpr/RanHex.metrics.tmp.txt.rpkm.gct Finished Successfully. RNA-SeQC Total Runtime: 12 min-->
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