#__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/A77357/A77357.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me1  Tue.Oct.31.11.42.26.PDT.2017-bioqc01
/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam __mode__:3  /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me1
#samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.11.42.26.PDT.2017-bioqc01
return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam.dedupstats
return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam
#__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam.bai
return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam
return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam
#return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/wig/A77357.CBTEAANXX_2.q5.F1028.PET.wig.bw
{"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam", "prefix":"A77357.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/wig/A77357.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/A77357/A77357.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77357.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/wig/A77357.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/wig/A77357.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/A77357/wig/A77357.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/A77357/wig/A77357.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
9173410
return:0 domainEnrichment:9173410
#STARTING FindER (hg19)
#/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.v.A77361.log
return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam
#__  return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.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/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary']
written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary
return:0 bigWig
#__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col
pass1 - making usageList (25 chroms): 51 millis
pass2 - checking and writing primary data (227130 records, 3 fields): 271 millis
return:0 bigBed
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bb
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.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/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.FindER.bwaChr']
written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.FindER.bwaChr
return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/FindER.1.0.1e-A77357.CBTEAANXX_2.v.A77361/A77357.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz
OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam
plotFingerprint 2.5.0.1
args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me1
#plotFingerprint Tue.Oct.31.12.02.54.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/A77357/A77357.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates
return:0 plotFingerprint Tue.Oct.31.12.06.21.PDT.2017-bioqc01
#config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me1  Tue.Oct.31.12.06.21.PDT.2017-bioqc01
#BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77357/A77357.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me1...finished Tue.Oct.31.12.06.21.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/A77358/A77358.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me3  Tue.Oct.31.12.06.21.PDT.2017-bioqc01
/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam __mode__:3  /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me3
#samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.12.06.21.PDT.2017-bioqc01
return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam.dedupstats
return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam
#__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam.bai
return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam
return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam
#return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/wig/A77358.CBTEAANXX_2.q5.F1028.PET.wig.bw
{"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam", "prefix":"A77358.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/wig/A77358.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/A77358/A77358.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77358.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/wig/A77358.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/wig/A77358.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/A77358/wig/A77358.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/A77358/wig/A77358.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
976129
return:0 domainEnrichment:976129
#STARTING FindER (hg19)
#/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.v.A77361.log
return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam
#__  return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.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/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary']
written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary
return:0 bigWig
#__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col
pass1 - making usageList (28 chroms): 39 millis
pass2 - checking and writing primary data (174146 records, 3 fields): 215 millis
return:0 bigBed
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bb
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.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/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.FindER.bwaChr']
written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.FindER.bwaChr
return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/FindER.1.0.1e-A77358.CBTEAANXX_2.v.A77361/A77358.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz
OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam
plotFingerprint 2.5.0.1
args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me3
#plotFingerprint Tue.Oct.31.12.30.55.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/A77358/A77358.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam -bs 200 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates
return:0 plotFingerprint Tue.Oct.31.12.33.46.PDT.2017-bioqc01
#config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me3  Tue.Oct.31.12.33.46.PDT.2017-bioqc01
#BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77358/A77358.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K4me3...finished Tue.Oct.31.12.33.46.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/A77359/A77359.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K27me3  Tue.Oct.31.12.33.47.PDT.2017-bioqc01
/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam __mode__:3  /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K27me3
#samtools:/projects/edcc_new/reference_epigenomes/housekeeping/samtools/1.3.1/bin Tue.Oct.31.12.33.47.PDT.2017-bioqc01
return:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam.dedupstats
return:0 flagstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam
#__alreadyIndexed__:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam.bai
return:0 idxstats /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam
return:0 [md5] /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam
#return:0 indexing /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/wig/A77359.CBTEAANXX_2.q5.F1028.PET.wig.bw
{"wig-ok":0, "bam":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam", "prefix":"A77359.CBTEAANXX_2", "log":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/wig/A77359.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/A77359/A77359.CBTEAANXX_2.bam -F 1028 -q 5 -cp -n A77359.CBTEAANXX_2 -chr /projects/tab/dev/code/thirdParty/ChIPProductionPipeline/resources/hg19.bwa2ucsc.names -out /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/wig", "outdir":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/wig", "wig":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/wig/A77359.CBTEAANXX_2.q5.F1028.PET.wig.gz", "bw-ok":0, "bw":"/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/wig/A77359.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/A77359/wig/A77359.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/A77359/wig/A77359.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
15070
return:0 domainEnrichment:15070
#STARTING FindER (hg19)
#/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.v.A77361.log
return:0 FindER /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam
#__  return:0 peakcall-binary /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.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/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary.tmp', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary']
written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary
return:0 bigWig
#__ 0: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.3col
pass1 - making usageList (30 chroms): 47 millis
pass2 - checking and writing primary data (214304 records, 3 fields): 584 millis
return:0 bigBed
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bb
#__NO_WWW_SET_TRACKS_NOT_PUBLISHED:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.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/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz.binary', '/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.FindER.bwaChr']
written:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.FindER.bwaChr
return:0 PeakCallTracks /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/FindER.1.0.1e-A77359.CBTEAANXX_2.v.A77361/A77359.CBTEAANXX_2.vs.A77361.CBTEAANXX_2.FDR_0.05.FindER.bed.gz
OK:/projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam
plotFingerprint 2.5.0.1
args: /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K27me3
#plotFingerprint Tue.Oct.31.13.09.12.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/A77359/A77359.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam -bs 1000 --JSDsample /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam --outQualityMetrics /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam.pf.txt -plot /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam.pf.png -p 4 --ignoreDuplicates
return:0 plotFingerprint Tue.Oct.31.13.12.46.PDT.2017-bioqc01
#config:ok hg19 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K27me3  Tue.Oct.31.13.12.46.PDT.2017-bioqc01
#BATCH:0 /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77359/A77359.CBTEAANXX_2.bam /projects/bioqc_dev/ilitests/BQ-861/cPin/IX5776/A77361/A77361.CBTEAANXX_2.bam H3K27me3...finished Tue.Oct.31.13.12.46.PDT.2017


..finishedOK