[2021-02-17 18:44:19,662] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-02-17 18:44:19,662] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-02-17 18:44:19,662] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-17 18:44:19,663] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-02-17 18:44:19,663] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-02-17 18:44:19,663] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMM32AFX2/merged [2021-02-17 18:44:21,210] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-17 18:44:21,210] multiqc [INFO ] This is MultiQC v1.9 [2021-02-17 18:44:21,211] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMM32AFX2/merged [2021-02-17 18:44:21,211] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMM32AFX2/merged [2021-02-17 18:44:21,211] multiqc [INFO ] Template : default [2021-02-17 18:44:21,211] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-02-17 18:44:21,211] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMM32AFX2/merged [2021-02-17 18:44:21,211] 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 [2021-02-17 18:44:21,211] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-2905212/tmpul0httdr [2021-02-17 18:44:21,311] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-263_fastqc.html [2021-02-17 18:44:21,313] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-263_fastqc.html [2021-02-17 18:44:21,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded 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[2021-02-17 18:44:21,708] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-156_fastqc.html [2021-02-17 18:44:21,747] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-274_fastqc.html [2021-02-17 18:44:21,749] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-274_fastqc.html [2021-02-17 18:44:21,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-107_fastqc.html [2021-02-17 18:44:21,803] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-107_fastqc.html [2021-02-17 18:44:21,841] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-083_fastqc.html [2021-02-17 18:44:21,842] multiqc 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longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-138_fastqc.html [2021-02-17 18:44:22,036] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-253_fastqc.html [2021-02-17 18:44:22,038] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-253_fastqc.html [2021-02-17 18:44:22,095] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-164_fastqc.html [2021-02-17 18:44:22,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-164_fastqc.html [2021-02-17 18:44:22,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_undetermined_fastqc.html [2021-02-17 18:44:22,153] multiqc [DEBUG ] File ignored by longranger/invocation because 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filesize limit: HMM32AFX2_n01_JU75_fastqc.html [2021-02-17 18:44:22,340] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-119_fastqc.html [2021-02-17 18:44:22,342] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-119_fastqc.html [2021-02-17 18:44:22,382] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_JU75_fastqc.html [2021-02-17 18:44:22,383] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_JU75_fastqc.html [2021-02-17 18:44:22,422] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-061_fastqc.html [2021-02-17 18:44:22,423] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-061_fastqc.html [2021-02-17 18:44:22,463] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-144_fastqc.html [2021-02-17 18:44:22,464] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-144_fastqc.html [2021-02-17 18:44:22,503] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-077_fastqc.html [2021-02-17 18:44:22,504] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-077_fastqc.html [2021-02-17 18:44:22,544] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-224_fastqc.html [2021-02-17 18:44:22,546] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-224_fastqc.html [2021-02-17 18:44:22,607] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-164_fastqc.html [2021-02-17 18:44:22,608] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-164_fastqc.html [2021-02-17 18:44:22,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-263_fastqc.html [2021-02-17 18:44:22,648] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-263_fastqc.html [2021-02-17 18:44:22,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-274_fastqc.html [2021-02-17 18:44:22,688] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-274_fastqc.html [2021-02-17 18:44:22,727] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-010_fastqc.html [2021-02-17 18:44:22,728] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-010_fastqc.html [2021-02-17 18:44:22,766] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-138_fastqc.html [2021-02-17 18:44:22,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-138_fastqc.html [2021-02-17 18:44:22,820] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-010_fastqc.html [2021-02-17 18:44:22,822] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n01_CEZ-010_fastqc.html [2021-02-17 18:44:22,880] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-047_fastqc.html [2021-02-17 18:44:22,881] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-047_fastqc.html [2021-02-17 18:44:22,934] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-119_fastqc.html [2021-02-17 18:44:22,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-119_fastqc.html [2021-02-17 18:44:22,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-253_fastqc.html [2021-02-17 18:44:22,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMM32AFX2_n02_CEZ-253_fastqc.html [2021-02-17 18:44:23,474] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-17 18:44:23,475] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-17 18:44:23,490] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-02-17 18:44:23,491] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-02-17 18:44:23,500] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2021-02-17 18:44:23,504] multiqc [DEBUG ] No samples found: conpair [2021-02-17 18:44:23,508] multiqc [DEBUG ] No samples found: peddy [2021-02-17 18:44:23,512] multiqc [DEBUG ] No samples found: somalier [2021-02-17 18:44:23,516] multiqc [DEBUG ] No samples found: methylQA [2021-02-17 18:44:23,522] multiqc [DEBUG ] No samples found: mosdepth [2021-02-17 18:44:23,527] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-17 18:44:23,530] multiqc [DEBUG ] No samples found: qualimap [2021-02-17 18:44:23,535] multiqc [DEBUG ] No samples found: preseq [2021-02-17 18:44:23,539] multiqc [DEBUG ] No samples found: quast [2021-02-17 18:44:23,544] multiqc [DEBUG ] No samples found: qorts [2021-02-17 18:44:23,547] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-17 18:44:23,551] multiqc [DEBUG ] No samples found: rockhopper [2021-02-17 18:44:23,555] multiqc [DEBUG ] No samples found: rsem [2021-02-17 18:44:23,564] multiqc [DEBUG ] No samples found: rseqc [2021-02-17 18:44:23,568] multiqc [DEBUG ] No samples found: busco [2021-02-17 18:44:23,572] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-17 18:44:23,575] multiqc [DEBUG ] No samples found: disambiguate [2021-02-17 18:44:23,579] multiqc [DEBUG ] No samples found: supernova [2021-02-17 18:44:23,589] multiqc [DEBUG ] No samples found: deeptools [2021-02-17 18:44:23,593] multiqc [DEBUG ] No samples found: sargasso [2021-02-17 18:44:23,597] multiqc [DEBUG ] No samples found: verifybamid [2021-02-17 18:44:23,601] multiqc [DEBUG ] No samples found: mirtrace [2021-02-17 18:44:23,605] multiqc [DEBUG ] No samples found: happy [2021-02-17 18:44:23,608] multiqc [DEBUG ] No samples found: mirtop [2021-02-17 18:44:23,613] multiqc [DEBUG ] No samples found: homer [2021-02-17 18:44:23,617] multiqc [DEBUG ] No samples found: macs2 [2021-02-17 18:44:23,621] multiqc [DEBUG ] No samples found: theta2 [2021-02-17 18:44:23,625] multiqc [DEBUG ] No samples found: snpeff [2021-02-17 18:44:23,630] multiqc [DEBUG ] No samples found: gatk [2021-02-17 18:44:23,634] multiqc [DEBUG ] No samples found: htseq [2021-02-17 18:44:23,639] multiqc [DEBUG ] No samples found: bcftools [2021-02-17 18:44:23,643] multiqc [DEBUG ] No samples found: featureCounts [2021-02-17 18:44:23,648] multiqc [DEBUG ] No samples found: fgbio [2021-02-17 18:44:23,657] multiqc [DEBUG ] No samples found: dragen [2021-02-17 18:44:23,661] multiqc [DEBUG ] No samples found: dedup [2021-02-17 18:44:23,665] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-17 18:44:23,681] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-17 18:44:23,685] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-17 18:44:23,687] multiqc [DEBUG ] No samples found: picard [2021-02-17 18:44:23,691] multiqc [DEBUG ] No samples found: prokka [2021-02-17 18:44:23,695] multiqc [DEBUG ] No samples found: samblaster [2021-02-17 18:44:23,701] multiqc [DEBUG ] No samples found: samtools [2021-02-17 18:44:23,705] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-17 18:44:23,709] multiqc [DEBUG ] No samples found: bamtools [2021-02-17 18:44:23,713] multiqc [DEBUG ] No samples found: jellyfish [2021-02-17 18:44:23,718] multiqc [DEBUG ] No samples found: vcftools [2021-02-17 18:44:23,722] multiqc [DEBUG ] No samples found: longranger [2021-02-17 18:44:23,726] multiqc [DEBUG ] No samples found: stacks [2021-02-17 18:44:23,730] multiqc [DEBUG ] No samples found: varscan2 [2021-02-17 18:44:23,740] multiqc [DEBUG ] No samples found: bbmap [2021-02-17 18:44:23,743] multiqc [DEBUG ] No samples found: bismark [2021-02-17 18:44:23,747] multiqc [DEBUG ] No samples found: biscuit [2021-02-17 18:44:23,751] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-17 18:44:23,755] multiqc [DEBUG ] No samples found: hicup [2021-02-17 18:44:23,759] multiqc [DEBUG ] No samples found: hicpro [2021-02-17 18:44:23,763] multiqc [DEBUG ] No samples found: salmon [2021-02-17 18:44:23,767] multiqc [DEBUG ] No samples found: kallisto [2021-02-17 18:44:23,771] multiqc [DEBUG ] No samples found: slamdunk [2021-02-17 18:44:23,775] multiqc [DEBUG ] No samples found: star [2021-02-17 18:44:23,779] multiqc [DEBUG ] No samples found: hisat2 [2021-02-17 18:44:23,782] multiqc [DEBUG ] No samples found: tophat [2021-02-17 18:44:23,786] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-17 18:44:23,790] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-17 18:44:23,794] multiqc [DEBUG ] No samples found: snpsplit [2021-02-17 18:44:23,797] multiqc [DEBUG ] No samples found: kat [2021-02-17 18:44:23,801] multiqc [DEBUG ] No samples found: leehom [2021-02-17 18:44:23,805] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-17 18:44:23,808] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-17 18:44:23,812] multiqc [DEBUG ] No samples found: cutadapt [2021-02-17 18:44:23,815] multiqc [DEBUG ] No samples found: flexbar [2021-02-17 18:44:23,819] multiqc [DEBUG ] No samples found: kaiju [2021-02-17 18:44:23,823] multiqc [DEBUG ] No samples found: kraken [2021-02-17 18:44:23,827] multiqc [DEBUG ] No samples found: malt [2021-02-17 18:44:23,830] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-17 18:44:23,834] multiqc [DEBUG ] No samples found: sickle [2021-02-17 18:44:23,838] multiqc [DEBUG ] No samples found: skewer [2021-02-17 18:44:23,841] multiqc [DEBUG ] No samples found: sortmerna [2021-02-17 18:44:23,846] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-17 18:44:23,850] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-17 18:44:23,853] multiqc [DEBUG ] No samples found: afterqc [2021-02-17 18:44:23,858] multiqc [DEBUG ] No samples found: fastp [2021-02-17 18:44:24,917] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2021-02-17 18:44:25,198] multiqc [DEBUG ] No samples found: pycoqc [2021-02-17 18:44:25,202] multiqc [DEBUG ] No samples found: minionqc [2021-02-17 18:44:25,205] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-17 18:44:25,209] multiqc [DEBUG ] No samples found: clusterflow [2021-02-17 18:44:25,213] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-17 18:44:25,217] multiqc [DEBUG ] No samples found: interop [2021-02-17 18:44:25,220] multiqc [DEBUG ] No samples found: ivar [2021-02-17 18:44:25,225] multiqc [DEBUG ] No samples found: flash [2021-02-17 18:44:25,229] multiqc [DEBUG ] No samples found: seqyclean [2021-02-17 18:44:25,229] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-02-17 18:44:25,229] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-02-17 18:44:25,229] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-02-17 18:44:25,229] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-02-17 18:44:25,270] multiqc [INFO ] Compressing plot data [2021-02-17 18:44:25,816] multiqc [INFO ] Report : multiqc_report.html [2021-02-17 18:44:25,816] multiqc [INFO ] Data : multiqc_data [2021-02-17 18:44:25,816] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2905212/tmpul0httdr/multiqc_data' to '/scratch/gencore/logs/html/HMM32AFX2/merged/multiqc_data' [2021-02-17 18:44:25,923] multiqc [INFO ] MultiQC complete