[2019-11-01 14:44:14,493] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/python-2.7-venv/lib/python2.7/site-packages/multiqc_config.yaml [2019-11-01 14:44:14,494] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/.multiqc_config.yaml [2019-11-01 14:44:14,495] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-11-01 14:44:14,495] multiqc [DEBUG ] Command used: /home/rcorbett/python-2.7-venv/bin/multiqc -f -v . [2019-11-01 14:44:15,513] multiqc [DEBUG ] Latest MultiQC version is v1.7 [2019-11-01 14:44:15,513] multiqc [INFO ] This is MultiQC v1.7 [2019-11-01 14:44:15,513] multiqc [DEBUG ] Command : /home/rcorbett/python-2.7-venv/bin/multiqc -f -v . [2019-11-01 14:44:15,513] multiqc [DEBUG ] Working dir : /projects/rcorbettprj2/TechD/MGI/round2 [2019-11-01 14:44:15,513] multiqc [INFO ] Template : default [2019-11-01 14:44:15,514] multiqc [INFO ] Searching '.' [2019-11-01 14:44:15,515] 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 [2019-11-01 14:44:15,519] multiqc [DEBUG ] Using temporary directory for creating report: /projects/bioSCRATCH/rcorbett/tmpmdhIJE [2019-11-01 14:44:15,798] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ./multiqc_data [2019-11-01 14:44:16,830] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_3_lanes.bam.bai [2019-11-01 14:44:16,830] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_N_1_lane.bam [2019-11-01 14:44:16,831] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_N_1_lane.bam.bai [2019-11-01 14:44:16,831] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_3_lanes.bam [2019-11-01 14:44:17,952] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: multiqc_report.html [2019-11-01 14:44:17,953] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_1_lane2.bam [2019-11-01 14:44:17,953] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_1_lane2.bam.bai [2019-11-01 14:44:17,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_1_lane3.bam [2019-11-01 14:44:17,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_1_lane3.bam.bai [2019-11-01 14:44:17,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_1_lane4.bam [2019-11-01 14:44:17,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: POG1047_T_1_lane4.bam.bai [2019-11-01 14:44:21,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: K003446-K003447-K003448-K003449_4_lanes_dupsFlagged.bam [2019-11-01 14:44:21,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: K003446-K003447-K003448-K003449_4_lanes_dupsFlagged.bam.bai [2019-11-01 14:44:21,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: K003446-K003447-K003448-K003449_4_lanes_dupsFlagged.bam.pdf [2019-11-01 14:44:22,442] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: K003450-K003451-K003452-K003453_4_lanes_dupsFlagged.bam [2019-11-01 14:44:22,442] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: K003450-K003451-K003452-K003453_4_lanes_dupsFlagged.bam.bai [2019-11-01 14:44:22,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: K003450-K003451-K003452-K003453_4_lanes_dupsFlagged.bam.pdf [2019-11-01 14:44:24,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: K003454-K003455-K003456-K003457_4_lanes_dupsFlagged.bam.pdf [2019-11-01 14:44:25,040] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round1.bam [2019-11-01 14:44:25,042] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round1.bam.bai [2019-11-01 14:44:45,024] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round2.bam [2019-11-01 14:44:45,025] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round2.bam.bai [2019-11-01 14:45:05,270] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round3.bam [2019-11-01 14:45:05,271] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round3.bam.bai [2019-11-01 14:45:25,950] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round1.bam [2019-11-01 14:45:25,955] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round1.bam.bai [2019-11-01 14:45:46,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round2.bam [2019-11-01 14:45:46,212] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round2.bam.bai [2019-11-01 14:46:06,612] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round3.bam [2019-11-01 14:46:06,616] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round3.bam.bai [2019-11-01 14:46:26,864] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round1.bam [2019-11-01 14:46:26,869] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round1.bam.bai [2019-11-01 14:46:47,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round2.bam [2019-11-01 14:46:47,156] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round2.bam.bai [2019-11-01 14:47:07,801] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round3.bam [2019-11-01 14:47:07,805] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round3.bam.bai [2019-11-01 14:47:28,664] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:32,337] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:35,896] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:39,502] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:43,349] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:46,869] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:50,389] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:54,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:47:57,744] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:01,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:05,170] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:08,739] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:12,301] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:15,855] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:19,400] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:23,040] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-11-01 14:48:28,102] multiqc [DEBUG ] No samples found: custom_content [2019-11-01 14:48:28,129] multiqc [DEBUG ] No samples found: conpair [2019-11-01 14:48:28,163] multiqc [DEBUG ] No samples found: peddy [2019-11-01 14:48:28,194] multiqc [DEBUG ] No samples found: methylQA [2019-11-01 14:48:28,221] multiqc [DEBUG ] No samples found: phantompeakqualtools [2019-11-01 14:48:30,690] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-11-01 14:48:31,931] multiqc.modules.qualimap.qualimap [INFO ] Found 16 BamQC reports [2019-11-01 14:48:31,953] multiqc [DEBUG ] No samples found: preseq [2019-11-01 14:48:31,974] multiqc [DEBUG ] No samples found: quast [2019-11-01 14:48:31,996] multiqc [DEBUG ] No samples found: qorts [2019-11-01 14:48:32,016] multiqc [DEBUG ] No samples found: rna_seqc [2019-11-01 14:48:32,039] multiqc [DEBUG ] No samples found: rsem [2019-11-01 14:48:32,105] multiqc [DEBUG ] No samples found: rseqc [2019-11-01 14:48:32,133] multiqc [DEBUG ] No samples found: busco [2019-11-01 14:48:32,158] multiqc [DEBUG ] No samples found: goleft_indexcov [2019-11-01 14:48:32,180] multiqc [DEBUG ] No samples found: disambiguate [2019-11-01 14:48:32,212] multiqc [DEBUG ] No samples found: supernova [2019-11-01 14:48:32,274] multiqc [DEBUG ] No samples found: deeptools [2019-11-01 14:48:32,296] multiqc [DEBUG ] No samples found: sargasso [2019-11-01 14:48:32,328] multiqc [DEBUG ] No samples found: verifybamid [2019-11-01 14:48:32,361] multiqc [DEBUG ] No samples found: mirtrace [2019-11-01 14:48:32,391] multiqc [DEBUG ] No samples found: happy [2019-11-01 14:48:32,429] multiqc [DEBUG ] No samples found: homer [2019-11-01 14:48:32,450] multiqc [DEBUG ] No samples found: macs2 [2019-11-01 14:48:32,471] multiqc [DEBUG ] No samples found: theta2 [2019-11-01 14:48:32,491] multiqc [DEBUG ] No samples found: snpeff [2019-11-01 14:48:32,518] multiqc [DEBUG ] No samples found: gatk [2019-11-01 14:48:32,539] multiqc [DEBUG ] No samples found: htseq [2019-11-01 14:48:32,565] multiqc [DEBUG ] No samples found: bcftools [2019-11-01 14:48:32,590] multiqc [DEBUG ] No samples found: featureCounts [2019-11-01 14:48:32,619] multiqc [DEBUG ] No samples found: dedup [2019-11-01 14:48:32,650] multiqc [DEBUG ] No samples found: damageprofiler [2019-11-01 14:48:32,746] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in POG1047_N_1_lane.bam.gc.summary.txt! Overwriting: POG1047_N_1_lane [2019-11-01 14:48:32,753] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in POG1047_T_1_lane2.bam.gc.summary.txt! Overwriting: POG1047_T_1_lane2 [2019-11-01 14:48:32,759] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in POG1047_T_1_lane4.bam.gc.summary.txt! Overwriting: POG1047_T_1_lane4 [2019-11-01 14:48:32,767] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in POG1047_T_1_lane3.bam.gc.summary.txt! Overwriting: POG1047_T_1_lane3 [2019-11-01 14:48:32,776] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in K003446-K003447-K003448-K003449_4_lanes_dupsFlagged.bam.gc.summary.txt! Overwriting: K003446-K003447-K003448-K003449_4_lanes_dupsFlagged [2019-11-01 14:48:32,783] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in K003450-K003451-K003452-K003453_4_lanes_dupsFlagged.bam.gc.summary.txt! Overwriting: K003450-K003451-K003452-K003453_4_lanes_dupsFlagged [2019-11-01 14:48:32,793] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in K003454-K003455-K003456-K003457_4_lanes_dupsFlagged.bam.gc.summary.txt! Overwriting: K003454-K003455-K003456-K003457_4_lanes_dupsFlagged [2019-11-01 14:48:32,801] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round1 [2019-11-01 14:48:32,807] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round2 [2019-11-01 14:48:32,815] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round3 [2019-11-01 14:48:32,823] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round1 [2019-11-01 14:48:32,832] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round2 [2019-11-01 14:48:32,841] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round3 [2019-11-01 14:48:32,849] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round1 [2019-11-01 14:48:32,857] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round2 [2019-11-01 14:48:32,865] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round3 [2019-11-01 14:48:32,894] multiqc.modules.picard.picard [INFO ] Found 16 GcBiasMetrics reports [2019-11-01 14:48:32,918] multiqc [DEBUG ] No samples found: prokka [2019-11-01 14:48:32,945] multiqc [DEBUG ] No samples found: samblaster [2019-11-01 14:48:33,220] multiqc.modules.samtools.samtools [INFO ] Found 16 stats reports [2019-11-01 14:48:33,246] multiqc [DEBUG ] No samples found: bamtools [2019-11-01 14:48:33,267] multiqc [DEBUG ] No samples found: jellyfish [2019-11-01 14:48:33,305] multiqc [DEBUG ] No samples found: vcftools [2019-11-01 14:48:33,333] multiqc [DEBUG ] No samples found: longranger [2019-11-01 14:48:33,360] multiqc [DEBUG ] No samples found: stacks [2019-11-01 14:48:33,427] multiqc [DEBUG ] No samples found: bbmap [2019-11-01 14:48:33,454] multiqc [DEBUG ] No samples found: bismark [2019-11-01 14:48:33,480] multiqc [DEBUG ] No samples found: biscuit [2019-11-01 14:48:33,502] multiqc [DEBUG ] No samples found: hicexplorer [2019-11-01 14:48:33,524] multiqc [DEBUG ] No samples found: hicup [2019-11-01 14:48:33,549] multiqc [DEBUG ] No samples found: hicpro [2019-11-01 14:48:33,576] multiqc [DEBUG ] No samples found: salmon [2019-11-01 14:48:33,603] multiqc [DEBUG ] No samples found: kallisto [2019-11-01 14:48:33,629] multiqc [DEBUG ] No samples found: slamdunk [2019-11-01 14:48:33,656] multiqc [DEBUG ] No samples found: star [2019-11-01 14:48:33,682] multiqc [DEBUG ] No samples found: hisat2 [2019-11-01 14:48:33,709] multiqc [DEBUG ] No samples found: tophat [2019-11-01 14:48:33,735] multiqc [DEBUG ] No samples found: bowtie2 [2019-11-01 14:48:33,760] multiqc [DEBUG ] No samples found: bowtie1 [2019-11-01 14:48:33,782] multiqc [DEBUG ] No samples found: kat [2019-11-01 14:48:33,805] multiqc [DEBUG ] No samples found: leehom [2019-11-01 14:48:33,828] multiqc [DEBUG ] No samples found: adapterRemoval [2019-11-01 14:48:33,853] multiqc [DEBUG ] No samples found: clipandmerge [2019-11-01 14:48:33,878] multiqc [DEBUG ] No samples found: cutadapt [2019-11-01 14:48:33,902] multiqc [DEBUG ] No samples found: flexbar [2019-11-01 14:48:33,928] multiqc [DEBUG ] No samples found: trimmomatic [2019-11-01 14:48:33,953] multiqc [DEBUG ] No samples found: skewer [2019-11-01 14:48:33,980] multiqc [DEBUG ] No samples found: sortmerna [2019-11-01 14:48:34,003] multiqc [DEBUG ] No samples found: biobloomtools [2019-11-01 14:48:34,030] multiqc [DEBUG ] No samples found: fastq_screen [2019-11-01 14:48:34,055] multiqc [DEBUG ] No samples found: afterqc [2019-11-01 14:48:34,080] multiqc [DEBUG ] No samples found: fastp [2019-11-01 14:48:34,112] multiqc [DEBUG ] No samples found: fastqc [2019-11-01 14:48:34,142] multiqc [DEBUG ] No samples found: minionqc [2019-11-01 14:48:34,173] multiqc [DEBUG ] No samples found: clusterflow [2019-11-01 14:48:34,204] multiqc [DEBUG ] No samples found: bcl2fastq [2019-11-01 14:48:34,233] multiqc [DEBUG ] No samples found: interop [2019-11-01 14:48:34,264] multiqc [DEBUG ] No samples found: flash [2019-11-01 14:48:34,459] multiqc [INFO ] Compressing plot data [2019-11-01 14:48:37,441] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-11-01 14:48:37,448] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-11-01 14:48:37,496] multiqc [INFO ] Report : multiqc_report.html [2019-11-01 14:48:37,496] multiqc [INFO ] Data : multiqc_data [2019-11-01 14:48:37,502] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpmdhIJE/multiqc_data/multiqc_picard_gcbias.txt' to '/projects/rcorbettprj2/TechD/MGI/round2/multiqc_data' [2019-11-01 14:48:37,531] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpmdhIJE/multiqc_data/multiqc_samtools_stats.txt' to '/projects/rcorbettprj2/TechD/MGI/round2/multiqc_data' [2019-11-01 14:48:37,558] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpmdhIJE/multiqc_data/multiqc_general_stats.txt' to '/projects/rcorbettprj2/TechD/MGI/round2/multiqc_data' [2019-11-01 14:48:37,584] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpmdhIJE/multiqc_data/multiqc_sources.txt' to '/projects/rcorbettprj2/TechD/MGI/round2/multiqc_data' [2019-11-01 14:48:37,612] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpmdhIJE/multiqc_data/multiqc_data.json' to '/projects/rcorbettprj2/TechD/MGI/round2/multiqc_data' [2019-11-01 14:48:39,663] multiqc [INFO ] MultiQC complete