#__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/A77372/A77372.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me1 Tue.Oct.31.16.11.50.PDT.2017-bioqc01 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me1 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.16.11.50.PDT.2017-bioqc01 return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/wig/A77372.CBTEAANXX_2.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam", "prefix":"A77372.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/wig/A77372.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/A77372/A77372.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77372.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/wig/A77372.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/wig/A77372.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/A77372/wig/A77372.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/A77372/wig/A77372.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 11117171 return:0 domainEnrichment:11117171 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.v.A77376.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.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/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (25 chroms): 12 millis pass2 - checking and writing primary data (59343 records, 3 fields): 82 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.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/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/FindER.1.0.1e-A77372.CBTEAANXX_2.v.A77376/A77372.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me1 #plotFingerprint Tue.Oct.31.16.40.11.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/A77372/A77372.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.31.16.43.41.PDT.2017-bioqc01 #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me1 Tue.Oct.31.16.43.41.PDT.2017-bioqc01 #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77372/A77372.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me1...finished Tue.Oct.31.16.43.41.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/A77373/A77373.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me3 Tue.Oct.31.16.43.41.PDT.2017-bioqc01 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me3 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.16.43.41.PDT.2017-bioqc01 return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/wig/A77373.CBTEAANXX_2.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam", "prefix":"A77373.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/wig/A77373.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/A77373/A77373.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77373.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/wig/A77373.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/wig/A77373.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/A77373/wig/A77373.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/A77373/wig/A77373.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 625217 return:0 domainEnrichment:625217 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.v.A77376.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.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/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (26 chroms): 27 millis pass2 - checking and writing primary data (110108 records, 3 fields): 138 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.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/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/FindER.1.0.1e-A77373.CBTEAANXX_2.v.A77376/A77373.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me3 #plotFingerprint Tue.Oct.31.17.09.37.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/A77373/A77373.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam -bs 200 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.31.17.12.19.PDT.2017-bioqc01 #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me3 Tue.Oct.31.17.12.19.PDT.2017-bioqc01 #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77373/A77373.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K4me3...finished Tue.Oct.31.17.12.19.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/A77374/A77374.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K27me3 Tue.Oct.31.17.12.19.PDT.2017-bioqc01 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam __mode__:3 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K27me3 #samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.17.12.19.PDT.2017-bioqc01 return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam.dedupstats return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam #__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam.bai return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam #return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/wig/A77374.CBTEAANXX_2.q5.F1028.PET.wig.bw {"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam", "prefix":"A77374.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/wig/A77374.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/A77374/A77374.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77374.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/wig/A77374.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/wig/A77374.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/A77374/wig/A77374.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/A77374/wig/A77374.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 5630 return:0 domainEnrichment:5630 #STARTING FindER (hg19) #/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.v.A77376.log return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam #__ return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.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/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary return:0 bigWig #__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col pass1 - making usageList (27 chroms): 29 millis pass2 - checking and writing primary data (118072 records, 3 fields): 148 millis return:0 bigBed #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bb #__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.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/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.FindER.bwaChr'] written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.FindER.bwaChr return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/FindER.1.0.1e-A77374.CBTEAANXX_2.v.A77376/A77374.CBTEAANXX_2.vs.A77376.CBTEAANXX_2.FDR_0.05.FindER.bed.gz OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam plotFingerprint 2.5.0.1 args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K27me3 #plotFingerprint Tue.Oct.31.17.51.56.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/A77374/A77374.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates return:0 plotFingerprint Tue.Oct.31.17.55.52.PDT.2017-bioqc01 #config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K27me3 Tue.Oct.31.17.55.52.PDT.2017-bioqc01 #BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77374/A77374.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77376/A77376.CBTEAANXX_2.bam H3K27me3...finished Tue.Oct.31.17.55.52.PDT.2017 ..finishedOK