[2020-01-03 17:06:31,040] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/python-2.7-venv/lib/python2.7/site-packages/multiqc_config.yaml [2020-01-03 17:06:31,040] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/.multiqc_config.yaml [2020-01-03 17:06:31,041] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-01-03 17:06:31,041] multiqc [DEBUG ] Command used: /home/rcorbett/python-2.7-venv/bin/multiqc -f -v --sample-names sample_names.txt . [2020-01-03 17:06:32,145] multiqc [DEBUG ] Latest MultiQC version is v1.8 [2020-01-03 17:06:32,147] multiqc [DEBUG ] Loading sample renaming config settings from: sample_names.txt [2020-01-03 17:06:32,148] multiqc [DEBUG ] Found 2 sample renaming patterns [2020-01-03 17:06:32,148] multiqc [INFO ] This is MultiQC v1.8 [2020-01-03 17:06:32,148] multiqc [DEBUG ] Command : /home/rcorbett/python-2.7-venv/bin/multiqc -f -v --sample-names sample_names.txt . [2020-01-03 17:06:32,148] multiqc [DEBUG ] Working dir : /projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting [2020-01-03 17:06:32,149] multiqc [INFO ] Template : default [2020-01-03 17:06:32,149] multiqc [WARNING] You are running MultiQC with Python 2.7.11 [2020-01-03 17:06:32,149] multiqc [WARNING] Please upgrade! MultiQC will soon drop support for Python < 3.6 [2020-01-03 17:06:32,149] multiqc [INFO ] Searching : /projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting [2020-01-03 17:06:32,150] 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, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, 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, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean [2020-01-03 17:06:32,154] multiqc [DEBUG ] Using temporary directory for creating report: /projects/bioSCRATCH/rcorbett/tmpUzUjJY [2020-01-03 17:06:32,481] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ./multiqc_data [2020-01-03 17:06:32,821] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: V300032060_L01_R1_150bp_250514_paired.sorted.bam [2020-01-03 17:06:32,822] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: V300032074_L01_R1_150bp_250511_paired.sorted.bam [2020-01-03 17:06:32,822] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: V300032060_L02_R1_150bp_250515_paired.sorted.bam [2020-01-03 17:06:32,822] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: V300032074_L02_R1_150bp_250512_paired.sorted.bam [2020-01-03 17:06:32,822] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: V300032060_L03_R1_150bp_250516_paired.sorted.bam [2020-01-03 17:06:32,823] multiqc [DEBUG ] Ignoring file as matched an 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because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:06:53,465] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:06:53,604] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2020-01-03 17:06:53,643] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:06:53,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:06:53,833] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:06:53,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:06:54,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded 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pattern: qualimapReport.html [2020-01-03 17:06:56,410] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:06:56,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:06:56,587] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:06:56,629] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:06:56,797] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:06:56,837] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:06:56,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js [2020-01-03 17:06:57,008] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: jquery.js [2020-01-03 17:06:57,172] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: pygments.css [2020-01-03 17:06:57,372] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: searchtools.js [2020-01-03 17:06:57,413] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: searchtools.js [2020-01-03 17:06:57,573] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: underscore.js [2020-01-03 17:06:57,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: underscore.js [2020-01-03 17:06:57,691] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: websupport.js [2020-01-03 17:06:57,728] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: websupport.js [2020-01-03 17:06:57,927] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: coverage_across_reference.txt [2020-01-03 17:06:57,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt [2020-01-03 17:06:58,272] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:06:58,314] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:06:58,465] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt [2020-01-03 17:06:58,667] multiqc [DEBUG ] File ignored by 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because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:02,042] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:02,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2020-01-03 17:07:02,216] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:02,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:02,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:02,453] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:02,644] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded 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pattern: qualimapReport.html [2020-01-03 17:07:05,121] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:05,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:05,300] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:05,339] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:05,506] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:07:05,550] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:07:05,649] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js [2020-01-03 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by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt [2020-01-03 17:07:09,841] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:07:09,885] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:07:10,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt [2020-01-03 17:07:10,313] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt [2020-01-03 17:07:10,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt [2020-01-03 17:07:10,614] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:10,651] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:10,803] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2020-01-03 17:07:10,843] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:10,885] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:11,036] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:11,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:11,241] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:07:11,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:07:11,394] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js [2020-01-03 17:07:11,435] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: jquery.js [2020-01-03 17:07:11,584] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: pygments.css [2020-01-03 17:07:11,794] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: searchtools.js [2020-01-03 17:07:11,838] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: searchtools.js [2020-01-03 17:07:12,004] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: underscore.js [2020-01-03 17:07:12,045] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: underscore.js [2020-01-03 17:07:12,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: websupport.js [2020-01-03 17:07:12,175] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: websupport.js [2020-01-03 17:07:12,388] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: coverage_across_reference.txt [2020-01-03 17:07:12,425] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt [2020-01-03 17:07:12,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:07:12,730] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:07:12,878] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt [2020-01-03 17:07:13,092] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt [2020-01-03 17:07:13,131] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt [2020-01-03 17:07:13,399] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:13,453] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:13,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2020-01-03 17:07:13,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:13,742] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css [2020-01-03 17:07:13,869] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:13,919] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css [2020-01-03 17:07:14,098] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:07:14,138] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js [2020-01-03 17:07:14,256] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js [2020-01-03 17:07:14,297] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: jquery.js [2020-01-03 17:07:14,470] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: pygments.css [2020-01-03 17:07:14,674] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: searchtools.js [2020-01-03 17:07:14,716] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: searchtools.js [2020-01-03 17:07:14,888] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: underscore.js [2020-01-03 17:07:14,938] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: underscore.js [2020-01-03 17:07:15,036] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: websupport.js [2020-01-03 17:07:15,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: websupport.js [2020-01-03 17:07:15,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: coverage_across_reference.txt [2020-01-03 17:07:15,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt [2020-01-03 17:07:15,639] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:07:15,683] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt [2020-01-03 17:07:15,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt [2020-01-03 17:07:16,087] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt [2020-01-03 17:07:16,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt [2020-01-03 17:07:16,413] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:16,457] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt [2020-01-03 17:07:17,067] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.3 [2020-01-03 17:07:17,069] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.3 [2020-01-03 17:07:17,072] multiqc [DEBUG ] No samples found: custom_content [2020-01-03 17:07:17,081] multiqc [DEBUG ] No samples found: conpair [2020-01-03 17:07:17,091] multiqc [DEBUG ] No samples found: peddy [2020-01-03 17:07:17,101] multiqc [DEBUG ] No samples found: methylQA [2020-01-03 17:07:17,111] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-01-03 17:07:19,169] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-01-03 17:07:20,314] multiqc.modules.qualimap.qualimap [INFO ] Found 10 BamQC reports [2020-01-03 17:07:20,321] multiqc [DEBUG ] No samples found: preseq [2020-01-03 17:07:20,327] multiqc [DEBUG ] No samples found: quast [2020-01-03 17:07:20,333] multiqc [DEBUG ] No samples found: qorts [2020-01-03 17:07:20,340] multiqc [DEBUG ] No samples found: rna_seqc [2020-01-03 17:07:20,348] multiqc [DEBUG ] No samples found: rsem [2020-01-03 17:07:20,365] multiqc [DEBUG ] No samples found: rseqc [2020-01-03 17:07:20,373] multiqc [DEBUG ] No samples found: busco [2020-01-03 17:07:20,381] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-01-03 17:07:20,390] multiqc [DEBUG ] No samples found: disambiguate [2020-01-03 17:07:20,398] multiqc [DEBUG ] No samples found: supernova [2020-01-03 17:07:20,416] multiqc [DEBUG ] No samples found: deeptools [2020-01-03 17:07:20,426] multiqc [DEBUG ] No samples found: sargasso [2020-01-03 17:07:20,436] multiqc [DEBUG ] No samples found: verifybamid [2020-01-03 17:07:20,446] multiqc [DEBUG ] No samples found: mirtrace [2020-01-03 17:07:20,456] multiqc [DEBUG ] No samples found: happy [2020-01-03 17:07:20,469] multiqc [DEBUG ] No samples found: homer [2020-01-03 17:07:20,479] multiqc [DEBUG ] No samples found: macs2 [2020-01-03 17:07:20,490] multiqc [DEBUG ] No samples found: theta2 [2020-01-03 17:07:20,500] multiqc [DEBUG ] No samples found: snpeff [2020-01-03 17:07:20,513] multiqc [DEBUG ] No samples found: gatk [2020-01-03 17:07:20,524] multiqc [DEBUG ] No samples found: htseq [2020-01-03 17:07:20,536] multiqc [DEBUG ] No samples found: bcftools [2020-01-03 17:07:20,546] multiqc [DEBUG ] No samples found: featureCounts [2020-01-03 17:07:20,556] multiqc [DEBUG ] No samples found: fgbio [2020-01-03 17:07:20,565] multiqc [DEBUG ] No samples found: dedup [2020-01-03 17:07:20,574] multiqc [DEBUG ] No samples found: damageprofiler [2020-01-03 17:07:20,601] multiqc [DEBUG ] No samples found: biobambam2 [2020-01-03 17:07:20,612] multiqc [DEBUG ] No samples found: mtnucratio [2020-01-03 17:07:20,699] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in POG1047_N_1_lane.bam.gc.summary.txt! Overwriting: POG1047_N_1_lane [2020-01-03 17:07:20,704] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in POG1047_N_illumina.bam.gc.summary.txt! Overwriting: POG1047_N_illumina [2020-01-03 17:07:20,708] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032074_L03_R1_150bp_250513_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032074_L03_R1_150bp_250513_paired [2020-01-03 17:07:20,713] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032074_L04_R1_150bp_250518_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032074_L04_R1_150bp_250518_paired [2020-01-03 17:07:20,717] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032060_L03_R1_150bp_250516_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032060_L03_R1_150bp_250516_paired [2020-01-03 17:07:20,722] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032074_L02_R1_150bp_250512_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032074_L02_R1_150bp_250512_paired [2020-01-03 17:07:20,727] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032074_L01_R1_150bp_250511_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032074_L01_R1_150bp_250511_paired [2020-01-03 17:07:20,731] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032060_L02_R1_150bp_250515_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032060_L02_R1_150bp_250515_paired [2020-01-03 17:07:20,735] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032060_L04_R1_150bp_250517_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032060_L04_R1_150bp_250517_paired [2020-01-03 17:07:20,740] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in V300032060_L01_R1_150bp_250514_paired.sorted.bam.dupmark055.bam.gc2.summary.txt! Overwriting: V300032060_L01_R1_150bp_250514_paired [2020-01-03 17:07:20,753] multiqc.modules.picard.picard [INFO ] Found 10 GcBiasMetrics reports [2020-01-03 17:07:20,763] multiqc [DEBUG ] No samples found: prokka [2020-01-03 17:07:20,773] multiqc [DEBUG ] No samples found: samblaster [2020-01-03 17:07:20,891] multiqc.modules.samtools.samtools [INFO ] Found 10 stats reports [2020-01-03 17:07:20,901] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-01-03 17:07:20,909] multiqc [DEBUG ] No samples found: bamtools [2020-01-03 17:07:20,917] multiqc [DEBUG ] No samples found: jellyfish [2020-01-03 17:07:20,951] multiqc [DEBUG ] No samples found: vcftools [2020-01-03 17:07:20,977] multiqc [DEBUG ] No samples found: longranger [2020-01-03 17:07:21,004] multiqc [DEBUG ] No samples found: stacks [2020-01-03 17:07:21,041] multiqc [DEBUG ] No samples found: bbmap [2020-01-03 17:07:21,053] multiqc [DEBUG ] No samples found: bismark [2020-01-03 17:07:21,066] multiqc [DEBUG ] No samples found: biscuit [2020-01-03 17:07:21,079] multiqc [DEBUG ] No samples found: hicexplorer [2020-01-03 17:07:21,090] multiqc [DEBUG ] No samples found: hicup [2020-01-03 17:07:21,102] multiqc [DEBUG ] No samples found: hicpro [2020-01-03 17:07:21,113] multiqc [DEBUG ] No samples found: salmon [2020-01-03 17:07:21,125] multiqc [DEBUG ] No samples found: kallisto [2020-01-03 17:07:21,137] multiqc [DEBUG ] No samples found: slamdunk [2020-01-03 17:07:21,149] multiqc [DEBUG ] No samples found: star [2020-01-03 17:07:21,161] multiqc [DEBUG ] No samples found: hisat2 [2020-01-03 17:07:21,174] multiqc [DEBUG ] No samples found: tophat [2020-01-03 17:07:21,186] multiqc [DEBUG ] No samples found: bowtie2 [2020-01-03 17:07:21,197] multiqc [DEBUG ] No samples found: bowtie1 [2020-01-03 17:07:21,209] multiqc [DEBUG ] No samples found: kat [2020-01-03 17:07:21,221] multiqc [DEBUG ] No samples found: leehom [2020-01-03 17:07:21,233] multiqc [DEBUG ] No samples found: adapterRemoval [2020-01-03 17:07:21,245] multiqc [DEBUG ] No samples found: clipandmerge [2020-01-03 17:07:21,257] multiqc [DEBUG ] No samples found: cutadapt [2020-01-03 17:07:21,268] multiqc [DEBUG ] No samples found: flexbar [2020-01-03 17:07:21,279] multiqc [DEBUG ] No samples found: trimmomatic [2020-01-03 17:07:21,289] multiqc [DEBUG ] No samples found: skewer [2020-01-03 17:07:21,300] multiqc [DEBUG ] No samples found: sortmerna [2020-01-03 17:07:21,311] multiqc [DEBUG ] No samples found: biobloomtools [2020-01-03 17:07:21,321] multiqc [DEBUG ] No samples found: fastq_screen [2020-01-03 17:07:21,332] multiqc [DEBUG ] No samples found: afterqc [2020-01-03 17:07:21,343] multiqc [DEBUG ] No samples found: fastp [2020-01-03 17:07:21,351] multiqc [DEBUG ] No samples found: fastqc [2020-01-03 17:07:21,359] multiqc [DEBUG ] No samples found: minionqc [2020-01-03 17:07:21,366] multiqc [DEBUG ] No samples found: mosdepth [2020-01-03 17:07:21,376] multiqc [DEBUG ] No samples found: clusterflow [2020-01-03 17:07:21,384] multiqc [DEBUG ] No samples found: bcl2fastq [2020-01-03 17:07:21,394] multiqc [DEBUG ] No samples found: interop [2020-01-03 17:07:21,405] multiqc [DEBUG ] No samples found: flash [2020-01-03 17:07:21,416] multiqc [DEBUG ] No samples found: seqyclean [2020-01-03 17:07:21,557] multiqc [INFO ] Compressing plot data [2020-01-03 17:07:24,433] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2020-01-03 17:07:24,439] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2020-01-03 17:07:24,480] multiqc [INFO ] Report : multiqc_report.html [2020-01-03 17:07:24,480] multiqc [INFO ] Data : multiqc_data [2020-01-03 17:07:24,486] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpUzUjJY/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting/multiqc_data' [2020-01-03 17:07:24,518] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpUzUjJY/multiqc_data/multiqc_picard_gcbias.txt' to '/projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting/multiqc_data' [2020-01-03 17:07:24,538] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpUzUjJY/multiqc_data/multiqc_samtools_stats.txt' to '/projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting/multiqc_data' [2020-01-03 17:07:24,560] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpUzUjJY/multiqc_data/multiqc_general_stats.txt' to '/projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting/multiqc_data' [2020-01-03 17:07:24,590] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpUzUjJY/multiqc_data/multiqc_sources.txt' to '/projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting/multiqc_data' [2020-01-03 17:07:24,612] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpUzUjJY/multiqc_data/multiqc_data.json' to '/projects/rcorbettprj2/TechD/MGI/germline_retest/LIMS_waiting/multiqc_data' [2020-01-03 17:07:25,944] multiqc [INFO ] MultiQC complete