#__build__:hg19 #__jars__:/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/jars #__samtools__:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin #__bedtools__:/projects/edcc_new/reference_epigenomes/housekeeping/bin/bedtools-2.26/bedtools2-2.26.0/bin hg19 /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources #__using__:CHR_BWA2UCSC_NAMES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names #__using__:CHROM_SIZES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes #__using__:TSS=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_TSS.uniq.sorted.bed.uniq #__using__:GENEBODIES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_genenames.uniq.sorted.bed #__using__:ZNF=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_Znf.uniq.sorted.bed #__using__:HOX=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/HOX_clusters.sorted.bed #__using__:ENHANCERS=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/encode_ChromHMM_enhancer_state_7.sorted.merged.bed #config hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me1 Tue.Oct.24.02.40.29.PDT.2017-bioqc06.hpc.bcgsc.ca /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me1 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.24.02.40.29.PDT.2017-bioqc06.hpc.bcgsc.ca return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig/A77342.CBKY8ANXX_5.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam", "prefix":"A77342.CBKY8ANXX_5", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig/A77342.CBKY8ANXX_5.PET.q5.F1028.PET.wig.gz.log", "wig-cmd":"/gsc/software/linux-x86_64/jre1.8.0_66/bin/java -jar -Xmx10G /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/jars/BAM2WIG.jar -bamFile /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam -F 1028 -q 5 -cp -n A77342.CBKY8ANXX_5 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig/A77342.CBKY8ANXX_5.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig/A77342.CBKY8ANXX_5.q5.F1028.PET.wig.bw", "bw-cmd":"/projects/edcc_new/reference_epigenomes/housekeeping/EDCCProd/Utils/ucsc/binaries/wigToBigWig /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig/A77342.CBKY8ANXX_5.q5.F1028.PET.wig.gz /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/wig/A77342.CBKY8ANXX_5.q5.F1028.PET.wig.bw"} return:0:0 BigWig/Wig #__DOMAIN:/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/encode_ChromHMM_enhancer_state_7.sorted.merged.bed 12161842 return:0 domainEnrichment:12161842 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.v.A77346.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary.tmp __cmd__:hg19_bwa2ucsc:['/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (17 chroms): 56 millis pass2 - checking and writing primary data (123957 records, 3 fields): 334 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bw __cmd__:hg19_ucsc2bwa:['/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/FindER.1.0.1e-A77342.CBKY8ANXX_5.v.A77346/A77342.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me1 #plotFingerprint Tue.Oct.24.03.06.52.PDT.2017-bioqc06.hpc.bcgsc.ca /projects/edcc_new/reference_epigenomes/housekeeping/bin/anaconda/envs/testenv/bin/python /projects/edcc_new/reference_epigenomes/housekeeping/deepTools/deepTools-2.5.0.1-install/bin/plotFingerprint -b /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.24.03.10.00.PDT.2017-bioqc06.hpc.bcgsc.ca #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me1 Tue.Oct.24.03.10.00.PDT.2017-bioqc06.hpc.bcgsc.ca #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77342/A77342.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me1...finished Tue.Oct.24.03.10.00.PDT.2017 #__build__:hg19 #__jars__:/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/jars #__samtools__:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin #__bedtools__:/projects/edcc_new/reference_epigenomes/housekeeping/bin/bedtools-2.26/bedtools2-2.26.0/bin hg19 /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources #__using__:CHR_BWA2UCSC_NAMES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names #__using__:CHROM_SIZES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes #__using__:TSS=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_TSS.uniq.sorted.bed.uniq #__using__:GENEBODIES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_genenames.uniq.sorted.bed #__using__:ZNF=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_Znf.uniq.sorted.bed #__using__:HOX=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/HOX_clusters.sorted.bed #__using__:ENHANCERS=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/encode_ChromHMM_enhancer_state_7.sorted.merged.bed #config hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me3 Tue.Oct.24.03.10.02.PDT.2017-bioqc06.hpc.bcgsc.ca /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me3 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.24.03.10.02.PDT.2017-bioqc06.hpc.bcgsc.ca return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig/A77343.CBKY8ANXX_5.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam", "prefix":"A77343.CBKY8ANXX_5", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig/A77343.CBKY8ANXX_5.PET.q5.F1028.PET.wig.gz.log", "wig-cmd":"/gsc/software/linux-x86_64/jre1.8.0_66/bin/java -jar -Xmx10G /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/jars/BAM2WIG.jar -bamFile /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam -F 1028 -q 5 -cp -n A77343.CBKY8ANXX_5 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig/A77343.CBKY8ANXX_5.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig/A77343.CBKY8ANXX_5.q5.F1028.PET.wig.bw", "bw-cmd":"/projects/edcc_new/reference_epigenomes/housekeeping/EDCCProd/Utils/ucsc/binaries/wigToBigWig /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig/A77343.CBKY8ANXX_5.q5.F1028.PET.wig.gz /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/wig/A77343.CBKY8ANXX_5.q5.F1028.PET.wig.bw"} return:0:0 BigWig/Wig #__DOMAIN:/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_TSS.uniq.sorted.bed.uniq 1137178 return:0 domainEnrichment:1137178 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.v.A77346.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary.tmp __cmd__:hg19_bwa2ucsc:['/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (23 chroms): 40 millis pass2 - checking and writing primary data (110034 records, 3 fields): 241 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bw __cmd__:hg19_ucsc2bwa:['/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/FindER.1.0.1e-A77343.CBKY8ANXX_5.v.A77346/A77343.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me3 #plotFingerprint Tue.Oct.24.03.39.36.PDT.2017-bioqc06.hpc.bcgsc.ca /projects/edcc_new/reference_epigenomes/housekeeping/bin/anaconda/envs/testenv/bin/python /projects/edcc_new/reference_epigenomes/housekeeping/deepTools/deepTools-2.5.0.1-install/bin/plotFingerprint -b /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam -bs 200 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.24.03.41.57.PDT.2017-bioqc06.hpc.bcgsc.ca #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me3 Tue.Oct.24.03.41.57.PDT.2017-bioqc06.hpc.bcgsc.ca #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77343/A77343.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K4me3...finished Tue.Oct.24.03.41.57.PDT.2017 #__build__:hg19 #__jars__:/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/jars #__samtools__:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin #__bedtools__:/projects/edcc_new/reference_epigenomes/housekeeping/bin/bedtools-2.26/bedtools2-2.26.0/bin hg19 /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources #__using__:CHR_BWA2UCSC_NAMES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names #__using__:CHROM_SIZES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes #__using__:TSS=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_TSS.uniq.sorted.bed.uniq #__using__:GENEBODIES=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_genenames.uniq.sorted.bed #__using__:ZNF=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/ensembl_Znf.uniq.sorted.bed #__using__:HOX=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/HOX_clusters.sorted.bed #__using__:ENHANCERS=/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/encode_ChromHMM_enhancer_state_7.sorted.merged.bed #config hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K27me3 Tue.Oct.24.03.41.57.PDT.2017-bioqc06.hpc.bcgsc.ca /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K27me3 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.24.03.41.57.PDT.2017-bioqc06.hpc.bcgsc.ca return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig/A77344.CBKY8ANXX_5.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam", "prefix":"A77344.CBKY8ANXX_5", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig/A77344.CBKY8ANXX_5.PET.q5.F1028.PET.wig.gz.log", "wig-cmd":"/gsc/software/linux-x86_64/jre1.8.0_66/bin/java -jar -Xmx10G /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/jars/BAM2WIG.jar -bamFile /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam -F 1028 -q 5 -cp -n A77344.CBKY8ANXX_5 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig/A77344.CBKY8ANXX_5.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig/A77344.CBKY8ANXX_5.q5.F1028.PET.wig.bw", "bw-cmd":"/projects/edcc_new/reference_epigenomes/housekeeping/EDCCProd/Utils/ucsc/binaries/wigToBigWig /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig/A77344.CBKY8ANXX_5.q5.F1028.PET.wig.gz /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/wig/A77344.CBKY8ANXX_5.q5.F1028.PET.wig.bw"} return:0:0 BigWig/Wig #__DOMAIN:/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/HOX_clusters.sorted.bed 36194 return:0 domainEnrichment:36194 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.v.A77346.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary.tmp __cmd__:hg19_bwa2ucsc:['/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (29 chroms): 93 millis pass2 - checking and writing primary data (226466 records, 3 fields): 594 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bw __cmd__:hg19_ucsc2bwa:['/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/FindER.1.0.1e-A77344.CBKY8ANXX_5.v.A77346/A77344.CBKY8ANXX_5.vs.A77346.CBKY8ANXX_5.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K27me3 #plotFingerprint Tue.Oct.24.04.25.49.PDT.2017-bioqc06.hpc.bcgsc.ca /projects/edcc_new/reference_epigenomes/housekeeping/bin/anaconda/envs/testenv/bin/python /projects/edcc_new/reference_epigenomes/housekeeping/deepTools/deepTools-2.5.0.1-install/bin/plotFingerprint -b /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.24.04.29.35.PDT.2017-bioqc06.hpc.bcgsc.ca #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K27me3 Tue.Oct.24.04.29.35.PDT.2017-bioqc06.hpc.bcgsc.ca #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77344/A77344.CBKY8ANXX_5.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5763/A77346/A77346.CBKY8ANXX_5.bam H3K27me3...finished Tue.Oct.24.04.29.35.PDT.2017 ..finishedOK