#__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/IX5776/A77362/A77362.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me1 Tue.Oct.31.13.12.47.PDT.2017-bioqc01 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me1 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.13.12.47.PDT.2017-bioqc01 return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/wig/A77362.CBTEAANXX_2.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam", "prefix":"A77362.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/wig/A77362.CBTEAANXX_2.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/IX5776/A77362/A77362.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77362.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/wig/A77362.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/wig/A77362.CBTEAANXX_2.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/IX5776/A77362/wig/A77362.CBTEAANXX_2.q5.F1028.PET.wig.gz /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/wig/A77362.CBTEAANXX_2.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 11718957 return:0 domainEnrichment:11718957 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.v.A77366.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.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/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (22 chroms): 47 millis pass2 - checking and writing primary data (217190 records, 3 fields): 265 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.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/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/FindER.1.0.1e-A77362.CBTEAANXX_2.v.A77366/A77362.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me1 #plotFingerprint Tue.Oct.31.13.33.06.PDT.2017-bioqc01 /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/IX5776/A77362/A77362.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.31.13.36.12.PDT.2017-bioqc01 #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me1 Tue.Oct.31.13.36.12.PDT.2017-bioqc01 #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77362/A77362.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me1...finished Tue.Oct.31.13.36.12.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/IX5776/A77363/A77363.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me3 Tue.Oct.31.13.36.12.PDT.2017-bioqc01 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me3 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.13.36.12.PDT.2017-bioqc01 return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/wig/A77363.CBTEAANXX_2.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam", "prefix":"A77363.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/wig/A77363.CBTEAANXX_2.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/IX5776/A77363/A77363.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77363.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/wig/A77363.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/wig/A77363.CBTEAANXX_2.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/IX5776/A77363/wig/A77363.CBTEAANXX_2.q5.F1028.PET.wig.gz /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/wig/A77363.CBTEAANXX_2.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 1331402 return:0 domainEnrichment:1331402 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.v.A77366.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.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/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (27 chroms): 36 millis pass2 - checking and writing primary data (160818 records, 3 fields): 194 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.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/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/FindER.1.0.1e-A77363.CBTEAANXX_2.v.A77366/A77363.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me3 #plotFingerprint Tue.Oct.31.13.58.32.PDT.2017-bioqc01 /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/IX5776/A77363/A77363.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam -bs 200 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.31.14.00.57.PDT.2017-bioqc01 #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me3 Tue.Oct.31.14.00.57.PDT.2017-bioqc01 #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77363/A77363.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K4me3...finished Tue.Oct.31.14.00.57.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/IX5776/A77364/A77364.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K27me3 Tue.Oct.31.14.00.57.PDT.2017-bioqc01 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K27me3 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.14.00.57.PDT.2017-bioqc01 return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/wig/A77364.CBTEAANXX_2.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam", "prefix":"A77364.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/wig/A77364.CBTEAANXX_2.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/IX5776/A77364/A77364.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77364.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/wig/A77364.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/wig/A77364.CBTEAANXX_2.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/IX5776/A77364/wig/A77364.CBTEAANXX_2.q5.F1028.PET.wig.gz /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.chrom.sizes /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/wig/A77364.CBTEAANXX_2.q5.F1028.PET.wig.bw"} return:0:0 BigWig/Wig #__DOMAIN:/projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19/HOX_clusters.sorted.bed 71742 return:0 domainEnrichment:71742 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.v.A77366.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.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/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (27 chroms): 59 millis pass2 - checking and writing primary data (272313 records, 3 fields): 328 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.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/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/FindER.1.0.1e-A77364.CBTEAANXX_2.v.A77366/A77364.CBTEAANXX_2.vs.A77366.CBTEAANXX_2.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K27me3 #plotFingerprint Tue.Oct.31.14.36.29.PDT.2017-bioqc01 /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/IX5776/A77364/A77364.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.31.14.40.15.PDT.2017-bioqc01 #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K27me3 Tue.Oct.31.14.40.15.PDT.2017-bioqc01 #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77364/A77364.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77366/A77366.CBTEAANXX_2.bam H3K27me3...finished Tue.Oct.31.14.40.15.PDT.2017 ..finishedOK