[2021-04-23 01:16:30,575] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-04-23 01:16:30,575] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-04-23 01:16:30,575] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-04-23 01:16:30,576] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-04-23 01:16:30,576] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-04-23 01:16:30,576] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK377BGXH/merged [2021-04-23 01:16:31,959] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-04-23 01:16:31,959] multiqc [INFO ] This is MultiQC v1.9 [2021-04-23 01:16:31,959] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK377BGXH/merged [2021-04-23 01:16:31,959] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HK377BGXH/merged [2021-04-23 01:16:31,959] multiqc [INFO ] Template : default [2021-04-23 01:16:31,960] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-04-23 01:16:31,960] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HK377BGXH/merged [2021-04-23 01:16:31,960] 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 [2021-04-23 01:16:31,960] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-5853479/tmpgysw1u66 [2021-04-23 01:16:32,061] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-shoot.plusN-45min.rep2_fastqc.html [2021-04-23 01:16:32,064] multiqc [DEBUG ] File ignored by longranger/invocation 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pattern filesize limit: HK377BGXH_n01_042021EV2_fastqc.html [2021-04-23 01:16:34,914] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_042021EV2_fastqc.html [2021-04-23 01:16:34,982] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-root.plusN-45min.rep3_fastqc.html [2021-04-23 01:16:34,983] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-root.plusN-45min.rep3_fastqc.html [2021-04-23 01:16:35,043] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr03048-root.plusN-45min.rep2_fastqc.html [2021-04-23 01:16:35,045] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr03048-root.plusN-45min.rep2_fastqc.html [2021-04-23 01:16:35,089] multiqc 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HK377BGXH_n01_bbr03048-shoot.minusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,260] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_g200214-shoot.plusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,262] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_g200214-shoot.plusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,325] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_042021LR2-2_fastqc.html [2021-04-23 01:16:35,326] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_042021LR2-2_fastqc.html [2021-04-23 01:16:35,391] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_g200214-root.minusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,393] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_g200214-root.minusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,446] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr03048-root.minusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,448] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr03048-root.minusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_g200214-root.plusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,494] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_g200214-root.plusN-45min.rep1_fastqc.html [2021-04-23 01:16:35,557] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R28-1_fastqc.html [2021-04-23 01:16:35,559] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R28-1_fastqc.html [2021-04-23 01:16:35,620] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr03048-root.minusN-45min.rep2_fastqc.html [2021-04-23 01:16:35,622] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr03048-root.minusN-45min.rep2_fastqc.html [2021-04-23 01:16:35,667] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R27-3_fastqc.html [2021-04-23 01:16:35,668] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R27-3_fastqc.html [2021-04-23 01:16:35,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R29-1_fastqc.html [2021-04-23 01:16:35,714] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R29-1_fastqc.html [2021-04-23 01:16:35,769] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-shoot.plusN-45min.rep3_fastqc.html [2021-04-23 01:16:35,770] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-shoot.plusN-45min.rep3_fastqc.html [2021-04-23 01:16:35,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-root.minusN-45min.rep4_fastqc.html [2021-04-23 01:16:35,827] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-root.minusN-45min.rep4_fastqc.html [2021-04-23 01:16:35,887] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_W22-shoot.plusN-45min.rep2_fastqc.html [2021-04-23 01:16:35,888] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_W22-shoot.plusN-45min.rep2_fastqc.html [2021-04-23 01:16:35,940] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_042021LR2-1_fastqc.html [2021-04-23 01:16:35,942] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_042021LR2-1_fastqc.html [2021-04-23 01:16:36,009] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-root.plusN-45min.rep2_fastqc.html [2021-04-23 01:16:36,011] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_bbr01166-root.plusN-45min.rep2_fastqc.html [2021-04-23 01:16:36,073] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R10-3_fastqc.html [2021-04-23 01:16:36,075] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK377BGXH_n01_042021R10-3_fastqc.html [2021-04-23 01:16:36,422] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-23 01:16:36,424] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-23 01:16:36,432] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-04-23 01:16:36,464] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 69 samples (table) [2021-04-23 01:16:36,473] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-04-23 01:16:36,477] multiqc [DEBUG ] No samples found: conpair [2021-04-23 01:16:36,482] multiqc [DEBUG ] No samples found: peddy [2021-04-23 01:16:36,487] multiqc [DEBUG ] No samples found: somalier [2021-04-23 01:16:36,491] multiqc [DEBUG ] No samples found: methylQA [2021-04-23 01:16:36,499] multiqc [DEBUG ] No samples found: mosdepth [2021-04-23 01:16:36,503] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-04-23 01:16:36,506] multiqc [DEBUG ] No samples found: qualimap [2021-04-23 01:16:36,511] multiqc [DEBUG ] No samples found: preseq [2021-04-23 01:16:36,515] multiqc [DEBUG ] No samples found: quast [2021-04-23 01:16:36,520] multiqc [DEBUG ] No samples found: qorts [2021-04-23 01:16:36,524] multiqc [DEBUG ] No samples found: rna_seqc [2021-04-23 01:16:36,529] multiqc [DEBUG ] No samples found: rockhopper [2021-04-23 01:16:36,533] multiqc [DEBUG ] No samples found: rsem [2021-04-23 01:16:36,543] multiqc [DEBUG ] No samples found: rseqc [2021-04-23 01:16:36,547] multiqc [DEBUG ] No samples found: busco [2021-04-23 01:16:36,551] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-04-23 01:16:36,555] multiqc [DEBUG ] No samples found: disambiguate [2021-04-23 01:16:36,560] multiqc [DEBUG ] No samples found: supernova [2021-04-23 01:16:36,571] multiqc [DEBUG ] No samples found: deeptools [2021-04-23 01:16:36,576] multiqc [DEBUG ] No samples found: sargasso [2021-04-23 01:16:36,580] multiqc [DEBUG ] No samples found: verifybamid [2021-04-23 01:16:36,585] multiqc [DEBUG ] No samples found: mirtrace [2021-04-23 01:16:36,589] multiqc [DEBUG ] No samples found: happy [2021-04-23 01:16:36,594] multiqc [DEBUG ] No samples found: mirtop [2021-04-23 01:16:36,600] multiqc [DEBUG ] No samples found: homer [2021-04-23 01:16:36,604] multiqc [DEBUG ] No samples found: macs2 [2021-04-23 01:16:36,608] multiqc [DEBUG ] No samples found: theta2 [2021-04-23 01:16:36,612] multiqc [DEBUG ] No samples found: snpeff [2021-04-23 01:16:36,619] multiqc [DEBUG ] No samples found: gatk [2021-04-23 01:16:36,623] multiqc [DEBUG ] No samples found: htseq [2021-04-23 01:16:36,628] multiqc [DEBUG ] No samples found: bcftools [2021-04-23 01:16:36,632] multiqc [DEBUG ] No samples found: featureCounts [2021-04-23 01:16:36,638] multiqc [DEBUG ] No samples found: fgbio [2021-04-23 01:16:36,650] multiqc [DEBUG ] No samples found: dragen [2021-04-23 01:16:36,654] multiqc [DEBUG ] No samples found: dedup [2021-04-23 01:16:36,659] multiqc [DEBUG ] No samples found: damageprofiler [2021-04-23 01:16:36,683] multiqc [DEBUG ] No samples found: biobambam2 [2021-04-23 01:16:36,687] multiqc [DEBUG ] No samples found: mtnucratio [2021-04-23 01:16:36,689] multiqc [DEBUG ] No samples found: picard [2021-04-23 01:16:36,694] multiqc [DEBUG ] No samples found: prokka [2021-04-23 01:16:36,698] multiqc [DEBUG ] No samples found: samblaster [2021-04-23 01:16:36,707] multiqc [DEBUG ] No samples found: samtools [2021-04-23 01:16:36,713] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-04-23 01:16:36,719] multiqc [DEBUG ] No samples found: bamtools [2021-04-23 01:16:36,724] multiqc [DEBUG ] No samples found: jellyfish [2021-04-23 01:16:36,731] multiqc [DEBUG ] No samples found: vcftools [2021-04-23 01:16:36,736] multiqc [DEBUG ] No samples found: longranger [2021-04-23 01:16:36,740] multiqc [DEBUG ] No samples found: stacks [2021-04-23 01:16:36,745] multiqc [DEBUG ] No samples found: varscan2 [2021-04-23 01:16:36,757] multiqc [DEBUG ] No samples found: bbmap [2021-04-23 01:16:36,761] multiqc [DEBUG ] No samples found: bismark [2021-04-23 01:16:36,766] multiqc [DEBUG ] No samples found: biscuit [2021-04-23 01:16:36,771] multiqc [DEBUG ] No samples found: hicexplorer [2021-04-23 01:16:36,775] multiqc [DEBUG ] No samples found: hicup [2021-04-23 01:16:36,780] multiqc [DEBUG ] No samples found: hicpro [2021-04-23 01:16:36,783] multiqc [DEBUG ] No samples found: salmon [2021-04-23 01:16:36,788] multiqc [DEBUG ] No samples found: kallisto [2021-04-23 01:16:36,792] multiqc [DEBUG ] No samples found: slamdunk [2021-04-23 01:16:36,797] multiqc [DEBUG ] No samples found: star [2021-04-23 01:16:36,801] multiqc [DEBUG ] No samples found: hisat2 [2021-04-23 01:16:36,805] multiqc [DEBUG ] No samples found: tophat [2021-04-23 01:16:36,809] multiqc [DEBUG ] No samples found: bowtie2 [2021-04-23 01:16:36,813] multiqc [DEBUG ] No samples found: bowtie1 [2021-04-23 01:16:36,818] multiqc [DEBUG ] No samples found: snpsplit [2021-04-23 01:16:36,822] multiqc [DEBUG ] No samples found: kat [2021-04-23 01:16:36,825] multiqc [DEBUG ] No samples found: leehom [2021-04-23 01:16:36,830] multiqc [DEBUG ] No samples found: adapterRemoval [2021-04-23 01:16:36,834] multiqc [DEBUG ] No samples found: clipandmerge [2021-04-23 01:16:36,838] multiqc [DEBUG ] No samples found: cutadapt [2021-04-23 01:16:36,842] multiqc [DEBUG ] No samples found: flexbar [2021-04-23 01:16:36,846] multiqc [DEBUG ] No samples found: kaiju [2021-04-23 01:16:36,850] multiqc [DEBUG ] No samples found: kraken [2021-04-23 01:16:36,855] multiqc [DEBUG ] No samples found: malt [2021-04-23 01:16:36,859] multiqc [DEBUG ] No samples found: trimmomatic [2021-04-23 01:16:36,863] multiqc [DEBUG ] No samples found: sickle [2021-04-23 01:16:36,867] multiqc [DEBUG ] No samples found: skewer [2021-04-23 01:16:36,871] multiqc [DEBUG ] No samples found: sortmerna [2021-04-23 01:16:36,875] multiqc [DEBUG ] No samples found: biobloomtools [2021-04-23 01:16:36,879] multiqc [DEBUG ] No samples found: fastq_screen [2021-04-23 01:16:36,883] multiqc [DEBUG ] No samples found: afterqc [2021-04-23 01:16:36,887] multiqc [DEBUG ] No samples found: fastp [2021-04-23 01:16:43,091] multiqc.modules.fastqc.fastqc [INFO ] Found 69 reports [2021-04-23 01:16:44,451] multiqc [DEBUG ] No samples found: pycoqc [2021-04-23 01:16:44,455] multiqc [DEBUG ] No samples found: minionqc [2021-04-23 01:16:44,459] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-04-23 01:16:44,464] multiqc [DEBUG ] No samples found: clusterflow [2021-04-23 01:16:44,468] multiqc [DEBUG ] No samples found: bcl2fastq [2021-04-23 01:16:44,473] multiqc [DEBUG ] No samples found: interop [2021-04-23 01:16:44,477] multiqc [DEBUG ] No samples found: ivar [2021-04-23 01:16:44,481] multiqc [DEBUG ] No samples found: flash [2021-04-23 01:16:44,486] multiqc [DEBUG ] No samples found: seqyclean [2021-04-23 01:16:44,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-04-23 01:16:44,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-04-23 01:16:44,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-04-23 01:16:44,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-04-23 01:16:44,566] multiqc [INFO ] Compressing plot data [2021-04-23 01:16:45,766] multiqc [INFO ] Report : multiqc_report.html [2021-04-23 01:16:45,766] multiqc [INFO ] Data : multiqc_data [2021-04-23 01:16:45,766] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5853479/tmpgysw1u66/multiqc_data' to '/scratch/gencore/logs/html/HK377BGXH/merged/multiqc_data' [2021-04-23 01:16:50,698] multiqc [INFO ] MultiQC complete