[2021-10-06 23:26:15,239] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-06 23:26:15,239] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-06 23:26:15,239] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-06 23:26:15,240] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-06 23:26:15,240] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-06 23:26:15,240] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5G5CBGXK/merged [2021-10-06 23:26:16,612] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-06 23:26:16,612] multiqc [INFO ] This is MultiQC v1.9 [2021-10-06 23:26:16,612] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5G5CBGXK/merged [2021-10-06 23:26:16,612] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5G5CBGXK/merged [2021-10-06 23:26:16,612] multiqc [INFO ] Template : default [2021-10-06 23:26:16,612] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-06 23:26:16,612] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5G5CBGXK/merged [2021-10-06 23:26:16,613] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean [2021-10-06 23:26:16,613] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10636199/tmp4eau4fjx [2021-10-06 23:26:16,718] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM268_fastqc.html [2021-10-06 23:26:16,720] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_JK43_fastqc.html [2021-10-06 23:26:17,186] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_JK43_fastqc.html [2021-10-06 23:26:17,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM272_fastqc.html [2021-10-06 23:26:17,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM272_fastqc.html [2021-10-06 23:26:17,264] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM269_fastqc.html [2021-10-06 23:26:17,266] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM269_fastqc.html [2021-10-06 23:26:17,304] multiqc [DEBUG ] File ignored by hicexplorer because it 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H5G5CBGXK_n01_DO01_fastqc.html [2021-10-06 23:26:17,424] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_DO01_fastqc.html [2021-10-06 23:26:17,464] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM273_fastqc.html [2021-10-06 23:26:17,466] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM273_fastqc.html [2021-10-06 23:26:17,506] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM267_fastqc.html [2021-10-06 23:26:17,507] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM267_fastqc.html [2021-10-06 23:26:17,545] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM278_fastqc.html [2021-10-06 23:26:17,547] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM278_fastqc.html [2021-10-06 23:26:17,584] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_JK48_fastqc.html [2021-10-06 23:26:17,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_JK48_fastqc.html [2021-10-06 23:26:17,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_JK45_fastqc.html [2021-10-06 23:26:17,626] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_JK45_fastqc.html [2021-10-06 23:26:17,663] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM276_fastqc.html [2021-10-06 23:26:17,665] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM276_fastqc.html [2021-10-06 23:26:17,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM274_fastqc.html [2021-10-06 23:26:17,706] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM274_fastqc.html [2021-10-06 23:26:17,744] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM271_fastqc.html [2021-10-06 23:26:17,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM271_fastqc.html [2021-10-06 23:26:17,784] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM270_fastqc.html [2021-10-06 23:26:17,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5G5CBGXK_n01_AKM270_fastqc.html [2021-10-06 23:26:18,609] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-06 23:26:18,610] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-06 23:26:18,626] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-06 23:26:18,627] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-06 23:26:18,639] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2021-10-06 23:26:18,645] multiqc [DEBUG ] No samples found: conpair [2021-10-06 23:26:18,650] multiqc [DEBUG ] No samples found: peddy [2021-10-06 23:26:18,654] multiqc [DEBUG ] No samples found: somalier [2021-10-06 23:26:18,658] multiqc [DEBUG ] No samples found: methylQA [2021-10-06 23:26:18,665] multiqc [DEBUG ] No samples found: mosdepth [2021-10-06 23:26:18,669] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-06 23:26:18,672] multiqc [DEBUG ] No samples found: qualimap [2021-10-06 23:26:18,677] multiqc [DEBUG ] No samples found: preseq [2021-10-06 23:26:18,681] multiqc [DEBUG ] No samples found: quast [2021-10-06 23:26:18,685] multiqc [DEBUG ] No samples found: qorts [2021-10-06 23:26:18,690] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-06 23:26:18,694] multiqc [DEBUG ] No samples found: rockhopper [2021-10-06 23:26:18,700] multiqc [DEBUG ] No samples found: rsem [2021-10-06 23:26:18,712] multiqc [DEBUG ] No samples found: rseqc [2021-10-06 23:26:18,716] multiqc [DEBUG ] No samples found: busco [2021-10-06 23:26:18,720] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-06 23:26:18,724] multiqc [DEBUG ] No samples found: disambiguate [2021-10-06 23:26:18,728] multiqc [DEBUG ] No samples found: supernova [2021-10-06 23:26:18,739] multiqc [DEBUG ] No samples found: deeptools [2021-10-06 23:26:18,743] multiqc [DEBUG ] No samples found: sargasso [2021-10-06 23:26:18,747] multiqc [DEBUG ] No samples found: verifybamid [2021-10-06 23:26:18,751] multiqc [DEBUG ] No samples found: mirtrace [2021-10-06 23:26:18,755] multiqc [DEBUG ] No samples found: happy [2021-10-06 23:26:18,760] multiqc [DEBUG ] No samples found: mirtop [2021-10-06 23:26:18,767] multiqc [DEBUG ] No samples found: homer [2021-10-06 23:26:18,772] multiqc [DEBUG ] No samples found: macs2 [2021-10-06 23:26:18,777] multiqc [DEBUG ] No samples found: theta2 [2021-10-06 23:26:18,781] multiqc [DEBUG ] No samples found: snpeff [2021-10-06 23:26:18,787] multiqc [DEBUG ] No samples found: gatk [2021-10-06 23:26:18,792] multiqc [DEBUG ] No samples found: htseq [2021-10-06 23:26:18,798] multiqc [DEBUG ] No samples found: bcftools [2021-10-06 23:26:18,802] multiqc [DEBUG ] No samples found: featureCounts [2021-10-06 23:26:18,808] multiqc [DEBUG ] No samples found: fgbio [2021-10-06 23:26:18,819] multiqc [DEBUG ] No samples found: dragen [2021-10-06 23:26:18,823] multiqc [DEBUG ] No samples found: dedup [2021-10-06 23:26:18,827] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-06 23:26:18,847] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-06 23:26:18,851] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-06 23:26:18,853] multiqc [DEBUG ] No samples found: picard [2021-10-06 23:26:18,857] multiqc [DEBUG ] No samples found: prokka [2021-10-06 23:26:18,861] multiqc [DEBUG ] No samples found: samblaster [2021-10-06 23:26:18,869] multiqc [DEBUG ] No samples found: samtools [2021-10-06 23:26:18,873] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-06 23:26:18,877] multiqc [DEBUG ] No samples found: bamtools [2021-10-06 23:26:18,881] multiqc [DEBUG ] No samples found: jellyfish [2021-10-06 23:26:18,889] multiqc [DEBUG ] No samples found: vcftools [2021-10-06 23:26:18,893] multiqc [DEBUG ] No samples found: longranger [2021-10-06 23:26:18,898] multiqc [DEBUG ] No samples found: stacks [2021-10-06 23:26:18,903] multiqc [DEBUG ] No samples found: varscan2 [2021-10-06 23:26:18,916] multiqc [DEBUG ] No samples found: bbmap [2021-10-06 23:26:18,921] multiqc [DEBUG ] No samples found: bismark [2021-10-06 23:26:18,925] multiqc [DEBUG ] No samples found: biscuit [2021-10-06 23:26:18,929] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-06 23:26:18,935] multiqc [DEBUG ] No samples found: hicup [2021-10-06 23:26:18,939] multiqc [DEBUG ] No samples found: hicpro [2021-10-06 23:26:18,943] multiqc [DEBUG ] No samples found: salmon [2021-10-06 23:26:18,947] multiqc [DEBUG ] No samples found: kallisto [2021-10-06 23:26:18,951] multiqc [DEBUG ] No samples found: slamdunk [2021-10-06 23:26:18,955] multiqc [DEBUG ] No samples found: star [2021-10-06 23:26:18,960] multiqc [DEBUG ] No samples found: hisat2 [2021-10-06 23:26:18,964] multiqc [DEBUG ] No samples found: tophat [2021-10-06 23:26:18,968] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-06 23:26:18,972] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-06 23:26:18,978] multiqc [DEBUG ] No samples found: snpsplit [2021-10-06 23:26:18,982] multiqc [DEBUG ] No samples found: kat [2021-10-06 23:26:18,985] multiqc [DEBUG ] No samples found: leehom [2021-10-06 23:26:18,989] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-06 23:26:18,993] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-06 23:26:18,997] multiqc [DEBUG ] No samples found: cutadapt [2021-10-06 23:26:19,001] multiqc [DEBUG ] No samples found: flexbar [2021-10-06 23:26:19,005] multiqc [DEBUG ] No samples found: kaiju [2021-10-06 23:26:19,009] multiqc [DEBUG ] No samples found: kraken [2021-10-06 23:26:19,013] multiqc [DEBUG ] No samples found: malt [2021-10-06 23:26:19,017] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-06 23:26:19,022] multiqc [DEBUG ] No samples found: sickle [2021-10-06 23:26:19,027] multiqc [DEBUG ] No samples found: skewer [2021-10-06 23:26:19,030] multiqc [DEBUG ] No samples found: sortmerna [2021-10-06 23:26:19,034] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-06 23:26:19,038] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-06 23:26:19,043] multiqc [DEBUG ] No samples found: afterqc [2021-10-06 23:26:19,047] multiqc [DEBUG ] No samples found: fastp [2021-10-06 23:26:20,763] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2021-10-06 23:26:21,286] multiqc [DEBUG ] No samples found: pycoqc [2021-10-06 23:26:21,291] multiqc [DEBUG ] No samples found: minionqc [2021-10-06 23:26:21,295] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-06 23:26:21,299] multiqc [DEBUG ] No samples found: clusterflow [2021-10-06 23:26:21,303] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-06 23:26:21,307] multiqc [DEBUG ] No samples found: interop [2021-10-06 23:26:21,312] multiqc [DEBUG ] No samples found: ivar [2021-10-06 23:26:21,316] multiqc [DEBUG ] No samples found: flash [2021-10-06 23:26:21,320] multiqc [DEBUG ] No samples found: seqyclean [2021-10-06 23:26:21,320] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-06 23:26:21,320] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-10-06 23:26:21,320] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-06 23:26:21,320] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-06 23:26:21,349] multiqc [INFO ] Compressing plot data [2021-10-06 23:26:21,760] multiqc [INFO ] Report : multiqc_report.html [2021-10-06 23:26:21,760] multiqc [INFO ] Data : multiqc_data [2021-10-06 23:26:21,760] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10636199/tmp4eau4fjx/multiqc_data' to '/scratch/gencore/logs/html/H5G5CBGXK/merged/multiqc_data' [2021-10-06 23:26:28,118] multiqc [INFO ] MultiQC complete