[2019-10-03 11:47:36,733] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/python-2.7-venv/lib/python2.7/site-packages/multiqc_config.yaml [2019-10-03 11:47:36,734] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/.multiqc_config.yaml [2019-10-03 11:47:36,734] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-10-03 11:47:36,734] multiqc [DEBUG ] Command used: /home/rcorbett/python-2.7-venv/bin/multiqc -f -v . [2019-10-03 11:47:37,600] multiqc [DEBUG ] Latest MultiQC version is v1.7 [2019-10-03 11:47:37,600] multiqc [INFO ] This is MultiQC v1.7 [2019-10-03 11:47:37,600] multiqc [DEBUG ] Command : /home/rcorbett/python-2.7-venv/bin/multiqc -f -v . [2019-10-03 11:47:37,600] multiqc [DEBUG ] Working dir : /projects/rcorbettprj2/silent [2019-10-03 11:47:37,601] multiqc [INFO ] Template : default [2019-10-03 11:47:37,601] multiqc [INFO ] Searching '.' [2019-10-03 11:47:37,602] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, dedup, damageprofiler, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, longranger, stacks, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, minionqc, clusterflow, bcl2fastq, interop, flash [2019-10-03 11:47:37,604] multiqc [DEBUG ] Using temporary directory for creating report: /projects/bioSCRATCH/rcorbett/tmpH4_EXg [2019-10-03 11:47:37,816] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ./multiqc_data [2019-10-03 11:47:37,959] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: B34972_2_lanes_dupsFlagged.bam [2019-10-03 11:47:37,959] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: B34972_2_lanes_dupsFlagged.bam.bai [2019-10-03 11:47:39,002] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: unmapped.bam [2019-10-03 11:47:39,002] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round1.bam [2019-10-03 11:47:39,002] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round1.bam.bai [2019-10-03 11:47:39,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round2.bam [2019-10-03 11:47:39,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round2.bam.bai [2019-10-03 11:47:40,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round3.bam [2019-10-03 11:47:40,709] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round3.bam.bai [2019-10-03 11:47:41,498] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round1.bam [2019-10-03 11:47:41,499] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round1.bam.bai [2019-10-03 11:47:42,191] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round2.bam [2019-10-03 11:47:42,191] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round2.bam.bai [2019-10-03 11:47:42,812] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round3.bam [2019-10-03 11:47:42,812] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round3.bam.bai [2019-10-03 11:47:43,506] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round1.bam [2019-10-03 11:47:43,506] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round1.bam.bai [2019-10-03 11:47:44,192] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round2.bam [2019-10-03 11:47:44,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round2.bam.bai [2019-10-03 11:47:45,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round3.bam [2019-10-03 11:47:45,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round3.bam.bai [2019-10-03 11:47:45,670] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: multiqc_report.html [2019-10-03 11:47:45,685] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:47:48,540] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:47:51,449] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:47:54,266] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:47:57,101] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:47:59,927] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:48:02,914] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:48:06,086] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:48:09,212] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:48:12,364] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-10-03 11:48:16,003] multiqc [DEBUG ] No samples found: custom_content [2019-10-03 11:48:16,014] multiqc [DEBUG ] No samples found: conpair [2019-10-03 11:48:16,024] multiqc [DEBUG ] No samples found: peddy [2019-10-03 11:48:16,034] multiqc [DEBUG ] No samples found: methylQA [2019-10-03 11:48:16,045] multiqc [DEBUG ] No samples found: phantompeakqualtools [2019-10-03 11:48:17,494] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-10-03 11:48:18,047] multiqc.modules.qualimap.qualimap [INFO ] Found 10 BamQC reports [2019-10-03 11:48:18,053] multiqc [DEBUG ] No samples found: preseq [2019-10-03 11:48:18,063] multiqc [DEBUG ] No samples found: quast [2019-10-03 11:48:18,072] multiqc [DEBUG ] No samples found: qorts [2019-10-03 11:48:18,081] multiqc [DEBUG ] No samples found: rna_seqc [2019-10-03 11:48:18,090] multiqc [DEBUG ] No samples found: rsem [2019-10-03 11:48:18,108] multiqc [DEBUG ] No samples found: rseqc [2019-10-03 11:48:18,117] multiqc [DEBUG ] No samples found: busco [2019-10-03 11:48:18,127] multiqc [DEBUG ] No samples found: goleft_indexcov [2019-10-03 11:48:18,136] multiqc [DEBUG ] No samples found: disambiguate [2019-10-03 11:48:18,147] multiqc [DEBUG ] No samples found: supernova [2019-10-03 11:48:18,165] multiqc [DEBUG ] No samples found: deeptools [2019-10-03 11:48:18,175] multiqc [DEBUG ] No samples found: sargasso [2019-10-03 11:48:18,184] multiqc [DEBUG ] No samples found: verifybamid [2019-10-03 11:48:18,194] multiqc [DEBUG ] No samples found: mirtrace [2019-10-03 11:48:18,205] multiqc [DEBUG ] No samples found: happy [2019-10-03 11:48:18,217] multiqc [DEBUG ] No samples found: homer [2019-10-03 11:48:18,227] multiqc [DEBUG ] No samples found: macs2 [2019-10-03 11:48:18,237] multiqc [DEBUG ] No samples found: theta2 [2019-10-03 11:48:18,247] multiqc [DEBUG ] No samples found: snpeff [2019-10-03 11:48:18,259] multiqc [DEBUG ] No samples found: gatk [2019-10-03 11:48:18,270] multiqc [DEBUG ] No samples found: htseq [2019-10-03 11:48:18,281] multiqc [DEBUG ] No samples found: bcftools [2019-10-03 11:48:18,290] multiqc [DEBUG ] No samples found: featureCounts [2019-10-03 11:48:18,300] multiqc [DEBUG ] No samples found: dedup [2019-10-03 11:48:18,309] multiqc [DEBUG ] No samples found: damageprofiler [2019-10-03 11:48:18,341] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in B34972_2_lanes_dupsFlagged.bam.gc.summary.txt! Overwriting: B34972_2_lanes_dupsFlagged [2019-10-03 11:48:18,346] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round1 [2019-10-03 11:48:18,351] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round2 [2019-10-03 11:48:18,356] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round3 [2019-10-03 11:48:18,361] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round1 [2019-10-03 11:48:18,366] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round2 [2019-10-03 11:48:18,371] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round3 [2019-10-03 11:48:18,376] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round1 [2019-10-03 11:48:18,381] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round2 [2019-10-03 11:48:18,387] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round3 [2019-10-03 11:48:18,402] multiqc.modules.picard.picard [INFO ] Found 10 GcBiasMetrics reports [2019-10-03 11:48:18,413] multiqc [DEBUG ] No samples found: prokka [2019-10-03 11:48:18,422] multiqc [DEBUG ] No samples found: samblaster [2019-10-03 11:48:18,583] multiqc.modules.samtools.samtools [INFO ] Found 10 stats reports [2019-10-03 11:48:18,594] multiqc [DEBUG ] No samples found: bamtools [2019-10-03 11:48:18,605] multiqc [DEBUG ] No samples found: jellyfish [2019-10-03 11:48:18,618] multiqc [DEBUG ] No samples found: vcftools [2019-10-03 11:48:18,628] multiqc [DEBUG ] No samples found: longranger [2019-10-03 11:48:18,639] multiqc [DEBUG ] No samples found: stacks [2019-10-03 11:48:18,661] multiqc [DEBUG ] No samples found: bbmap [2019-10-03 11:48:18,672] multiqc [DEBUG ] No samples found: bismark [2019-10-03 11:48:18,682] multiqc [DEBUG ] No samples found: biscuit [2019-10-03 11:48:18,692] multiqc [DEBUG ] No samples found: hicexplorer [2019-10-03 11:48:18,702] multiqc [DEBUG ] No samples found: hicup [2019-10-03 11:48:18,712] multiqc [DEBUG ] No samples found: hicpro [2019-10-03 11:48:18,722] multiqc [DEBUG ] No samples found: salmon [2019-10-03 11:48:18,732] multiqc [DEBUG ] No samples found: kallisto [2019-10-03 11:48:18,742] multiqc [DEBUG ] No samples found: slamdunk [2019-10-03 11:48:18,752] multiqc [DEBUG ] No samples found: star [2019-10-03 11:48:18,762] multiqc [DEBUG ] No samples found: hisat2 [2019-10-03 11:48:18,772] multiqc [DEBUG ] No samples found: tophat [2019-10-03 11:48:18,782] multiqc [DEBUG ] No samples found: bowtie2 [2019-10-03 11:48:18,792] multiqc [DEBUG ] No samples found: bowtie1 [2019-10-03 11:48:18,802] multiqc [DEBUG ] No samples found: kat [2019-10-03 11:48:18,811] multiqc [DEBUG ] No samples found: leehom [2019-10-03 11:48:18,822] multiqc [DEBUG ] No samples found: adapterRemoval [2019-10-03 11:48:18,832] multiqc [DEBUG ] No samples found: clipandmerge [2019-10-03 11:48:18,842] multiqc [DEBUG ] No samples found: cutadapt [2019-10-03 11:48:18,853] multiqc [DEBUG ] No samples found: flexbar [2019-10-03 11:48:18,864] multiqc [DEBUG ] No samples found: trimmomatic [2019-10-03 11:48:18,875] multiqc [DEBUG ] No samples found: skewer [2019-10-03 11:48:18,887] multiqc [DEBUG ] No samples found: sortmerna [2019-10-03 11:48:18,898] multiqc [DEBUG ] No samples found: biobloomtools [2019-10-03 11:48:18,909] multiqc [DEBUG ] No samples found: fastq_screen [2019-10-03 11:48:18,920] multiqc [DEBUG ] No samples found: afterqc [2019-10-03 11:48:18,931] multiqc [DEBUG ] No samples found: fastp [2019-10-03 11:48:18,942] multiqc [DEBUG ] No samples found: fastqc [2019-10-03 11:48:18,953] multiqc [DEBUG ] No samples found: minionqc [2019-10-03 11:48:18,963] multiqc [DEBUG ] No samples found: clusterflow [2019-10-03 11:48:18,973] multiqc [DEBUG ] No samples found: bcl2fastq [2019-10-03 11:48:18,983] multiqc [DEBUG ] No samples found: interop [2019-10-03 11:48:18,993] multiqc [DEBUG ] No samples found: flash [2019-10-03 11:48:19,120] multiqc [INFO ] Compressing plot data [2019-10-03 11:48:20,984] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-10-03 11:48:20,987] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-10-03 11:48:21,007] multiqc [INFO ] Report : multiqc_report.html [2019-10-03 11:48:21,007] multiqc [INFO ] Data : multiqc_data [2019-10-03 11:48:21,012] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpH4_EXg/multiqc_data/multiqc_picard_gcbias.txt' to '/projects/rcorbettprj2/silent/multiqc_data' [2019-10-03 11:48:21,027] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpH4_EXg/multiqc_data/multiqc_samtools_stats.txt' to '/projects/rcorbettprj2/silent/multiqc_data' [2019-10-03 11:48:21,038] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpH4_EXg/multiqc_data/multiqc_general_stats.txt' to '/projects/rcorbettprj2/silent/multiqc_data' [2019-10-03 11:48:21,048] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpH4_EXg/multiqc_data/multiqc_sources.txt' to '/projects/rcorbettprj2/silent/multiqc_data' [2019-10-03 11:48:21,063] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpH4_EXg/multiqc_data/multiqc_data.json' to '/projects/rcorbettprj2/silent/multiqc_data' [2019-10-03 11:48:21,830] multiqc [INFO ] MultiQC complete