[2021-01-14 16:40:36,759] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-01-14 16:40:36,760] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-01-14 16:40:36,760] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-01-14 16:40:36,760] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-01-14 16:40:36,761] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-01-14 16:40:36,761] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNCFAFX2/merged [2021-01-14 16:40:38,129] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-01-14 16:40:38,129] multiqc [INFO ] This is MultiQC v1.9 [2021-01-14 16:40:38,130] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNCFAFX2/merged [2021-01-14 16:40:38,130] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLNCFAFX2/merged [2021-01-14 16:40:38,130] multiqc [INFO ] Template : default [2021-01-14 16:40:38,130] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-01-14 16:40:38,130] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLNCFAFX2/merged [2021-01-14 16:40:38,130] 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 [2021-01-14 16:40:38,130] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-1140148/tmpywj231j1 [2021-01-14 16:40:38,232] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A16_fastqc.html [2021-01-14 16:40:38,235] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A16_fastqc.html [2021-01-14 16:40:38,290] multiqc [DEBUG ] File ignored by 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ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_s.061.2_fastqc.html [2021-01-14 16:40:44,267] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_s.061.2_fastqc.html [2021-01-14 16:40:44,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A19_fastqc.html [2021-01-14 16:40:44,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A19_fastqc.html [2021-01-14 16:40:44,348] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A13_fastqc.html [2021-01-14 16:40:44,350] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A13_fastqc.html [2021-01-14 16:40:44,391] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A32_fastqc.html [2021-01-14 16:40:44,393] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A32_fastqc.html [2021-01-14 16:40:44,434] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A20_fastqc.html [2021-01-14 16:40:44,435] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A20_fastqc.html [2021-01-14 16:40:44,476] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A15_fastqc.html [2021-01-14 16:40:44,478] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A15_fastqc.html [2021-01-14 16:40:44,517] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_C3_fastqc.html [2021-01-14 16:40:44,519] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_C3_fastqc.html [2021-01-14 16:40:44,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A29_fastqc.html [2021-01-14 16:40:44,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A29_fastqc.html [2021-01-14 16:40:44,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_s.061.2_fastqc.html [2021-01-14 16:40:44,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_s.061.2_fastqc.html [2021-01-14 16:40:44,645] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A35_fastqc.html [2021-01-14 16:40:44,646] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A35_fastqc.html [2021-01-14 16:40:44,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_Federica.B251.ChrI.3_fastqc.html [2021-01-14 16:40:44,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_Federica.B251.ChrI.3_fastqc.html [2021-01-14 16:40:44,727] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A21_fastqc.html [2021-01-14 16:40:44,729] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A21_fastqc.html [2021-01-14 16:40:44,768] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A28_fastqc.html [2021-01-14 16:40:44,770] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A28_fastqc.html [2021-01-14 16:40:44,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A26_fastqc.html [2021-01-14 16:40:44,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A26_fastqc.html [2021-01-14 16:40:44,851] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A33_fastqc.html [2021-01-14 16:40:44,853] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A33_fastqc.html [2021-01-14 16:40:44,893] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A15_fastqc.html [2021-01-14 16:40:44,894] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A15_fastqc.html [2021-01-14 16:40:44,934] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A26_fastqc.html [2021-01-14 16:40:44,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A26_fastqc.html [2021-01-14 16:40:44,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A34_fastqc.html [2021-01-14 16:40:44,977] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A34_fastqc.html [2021-01-14 16:40:45,017] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A30_fastqc.html [2021-01-14 16:40:45,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A30_fastqc.html [2021-01-14 16:40:45,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A12_fastqc.html [2021-01-14 16:40:45,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n02_lib.v2_msh3_MA_strain_A12_fastqc.html [2021-01-14 16:40:45,098] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A13_fastqc.html [2021-01-14 16:40:45,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_msh3_MA_strain_A13_fastqc.html [2021-01-14 16:40:45,140] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_Federica.B251.ChrI.3_fastqc.html [2021-01-14 16:40:45,141] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNCFAFX2_n01_lib.v2_Federica.B251.ChrI.3_fastqc.html [2021-01-14 16:40:45,751] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-14 16:40:45,752] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-14 16:40:45,769] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-01-14 16:40:45,786] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 36 samples (table) [2021-01-14 16:40:45,787] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-01-14 16:40:45,791] multiqc [DEBUG ] No samples found: conpair [2021-01-14 16:40:45,795] multiqc [DEBUG ] No samples found: peddy [2021-01-14 16:40:45,799] multiqc [DEBUG ] No samples found: somalier [2021-01-14 16:40:45,803] multiqc [DEBUG ] No samples found: methylQA [2021-01-14 16:40:45,809] multiqc [DEBUG ] No samples found: mosdepth [2021-01-14 16:40:45,813] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-01-14 16:40:45,816] multiqc [DEBUG ] No samples found: qualimap [2021-01-14 16:40:45,820] multiqc [DEBUG ] No samples found: preseq [2021-01-14 16:40:45,824] multiqc [DEBUG ] No samples found: quast [2021-01-14 16:40:45,828] multiqc [DEBUG ] No samples found: qorts [2021-01-14 16:40:45,832] multiqc [DEBUG ] No samples found: rna_seqc [2021-01-14 16:40:45,836] multiqc [DEBUG ] No samples found: rockhopper [2021-01-14 16:40:45,840] multiqc [DEBUG ] No samples found: rsem [2021-01-14 16:40:45,849] multiqc [DEBUG ] No samples found: rseqc [2021-01-14 16:40:45,853] multiqc [DEBUG ] No samples found: busco [2021-01-14 16:40:45,857] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-01-14 16:40:45,861] multiqc [DEBUG ] No samples found: disambiguate [2021-01-14 16:40:45,865] multiqc [DEBUG ] No samples found: supernova [2021-01-14 16:40:45,875] multiqc [DEBUG ] No samples found: deeptools [2021-01-14 16:40:45,879] multiqc [DEBUG ] No samples found: sargasso [2021-01-14 16:40:45,883] multiqc [DEBUG ] No samples found: verifybamid [2021-01-14 16:40:45,887] multiqc [DEBUG ] No samples found: mirtrace [2021-01-14 16:40:45,891] multiqc [DEBUG ] No samples found: happy [2021-01-14 16:40:45,895] multiqc [DEBUG ] No samples found: mirtop [2021-01-14 16:40:45,901] multiqc [DEBUG ] No samples found: homer [2021-01-14 16:40:45,905] multiqc [DEBUG ] No samples found: macs2 [2021-01-14 16:40:45,908] multiqc [DEBUG ] No samples found: theta2 [2021-01-14 16:40:45,912] multiqc [DEBUG ] No samples found: snpeff [2021-01-14 16:40:45,918] multiqc [DEBUG ] No samples found: gatk [2021-01-14 16:40:45,922] multiqc [DEBUG ] No samples found: htseq [2021-01-14 16:40:45,927] multiqc [DEBUG ] No samples found: bcftools [2021-01-14 16:40:45,931] multiqc [DEBUG ] No samples found: featureCounts [2021-01-14 16:40:45,936] multiqc [DEBUG ] No samples found: fgbio [2021-01-14 16:40:45,946] multiqc [DEBUG ] No samples found: dragen [2021-01-14 16:40:45,950] multiqc [DEBUG ] No samples found: dedup [2021-01-14 16:40:45,954] multiqc [DEBUG ] No samples found: damageprofiler [2021-01-14 16:40:45,972] multiqc [DEBUG ] No samples found: biobambam2 [2021-01-14 16:40:45,976] multiqc [DEBUG ] No samples found: mtnucratio [2021-01-14 16:40:45,978] multiqc [DEBUG ] No samples found: picard [2021-01-14 16:40:45,982] multiqc [DEBUG ] No samples found: prokka [2021-01-14 16:40:45,986] multiqc [DEBUG ] No samples found: samblaster [2021-01-14 16:40:45,993] multiqc [DEBUG ] No samples found: samtools [2021-01-14 16:40:45,997] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-01-14 16:40:46,001] multiqc [DEBUG ] No samples found: bamtools [2021-01-14 16:40:46,005] multiqc [DEBUG ] No samples found: jellyfish [2021-01-14 16:40:46,011] multiqc [DEBUG ] No samples found: vcftools [2021-01-14 16:40:46,016] multiqc [DEBUG ] No samples found: longranger [2021-01-14 16:40:46,020] multiqc [DEBUG ] No samples found: stacks [2021-01-14 16:40:46,024] multiqc [DEBUG ] No samples found: varscan2 [2021-01-14 16:40:46,035] multiqc [DEBUG ] No samples found: bbmap [2021-01-14 16:40:46,040] multiqc [DEBUG ] No samples found: bismark [2021-01-14 16:40:46,044] multiqc [DEBUG ] No samples found: biscuit [2021-01-14 16:40:46,048] multiqc [DEBUG ] No samples found: hicexplorer [2021-01-14 16:40:46,052] multiqc [DEBUG ] No samples found: hicup [2021-01-14 16:40:46,057] multiqc [DEBUG ] No samples found: hicpro [2021-01-14 16:40:46,060] multiqc [DEBUG ] No samples found: salmon [2021-01-14 16:40:46,064] multiqc [DEBUG ] No samples found: kallisto [2021-01-14 16:40:46,069] multiqc [DEBUG ] No samples found: slamdunk [2021-01-14 16:40:46,073] multiqc [DEBUG ] No samples found: star [2021-01-14 16:40:46,077] multiqc [DEBUG ] No samples found: hisat2 [2021-01-14 16:40:46,082] multiqc [DEBUG ] No samples found: tophat [2021-01-14 16:40:46,086] multiqc [DEBUG ] No samples found: bowtie2 [2021-01-14 16:40:46,090] multiqc [DEBUG ] No samples found: bowtie1 [2021-01-14 16:40:46,094] multiqc [DEBUG ] No samples found: snpsplit [2021-01-14 16:40:46,098] multiqc [DEBUG ] No samples found: kat [2021-01-14 16:40:46,101] multiqc [DEBUG ] No samples found: leehom [2021-01-14 16:40:46,106] multiqc [DEBUG ] No samples found: adapterRemoval [2021-01-14 16:40:46,110] multiqc [DEBUG ] No samples found: clipandmerge [2021-01-14 16:40:46,114] multiqc [DEBUG ] No samples found: cutadapt [2021-01-14 16:40:46,118] multiqc [DEBUG ] No samples found: flexbar [2021-01-14 16:40:46,122] multiqc [DEBUG ] No samples found: kaiju [2021-01-14 16:40:46,126] multiqc [DEBUG ] No samples found: kraken [2021-01-14 16:40:46,130] multiqc [DEBUG ] No samples found: malt [2021-01-14 16:40:46,134] multiqc [DEBUG ] No samples found: trimmomatic [2021-01-14 16:40:46,138] multiqc [DEBUG ] No samples found: sickle [2021-01-14 16:40:46,142] multiqc [DEBUG ] No samples found: skewer [2021-01-14 16:40:46,146] multiqc [DEBUG ] No samples found: sortmerna [2021-01-14 16:40:46,150] multiqc [DEBUG ] No samples found: biobloomtools [2021-01-14 16:40:46,154] multiqc [DEBUG ] No samples found: fastq_screen [2021-01-14 16:40:46,158] multiqc [DEBUG ] No samples found: afterqc [2021-01-14 16:40:46,162] multiqc [DEBUG ] No samples found: fastp [2021-01-14 16:40:47,941] multiqc.modules.fastqc.fastqc [INFO ] Found 72 reports [2021-01-14 16:40:48,480] multiqc [DEBUG ] No samples found: pycoqc [2021-01-14 16:40:48,484] multiqc [DEBUG ] No samples found: minionqc [2021-01-14 16:40:48,488] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-01-14 16:40:48,492] multiqc [DEBUG ] No samples found: clusterflow [2021-01-14 16:40:48,496] multiqc [DEBUG ] No samples found: bcl2fastq [2021-01-14 16:40:48,500] multiqc [DEBUG ] No samples found: interop [2021-01-14 16:40:48,504] multiqc [DEBUG ] No samples found: ivar [2021-01-14 16:40:48,508] multiqc [DEBUG ] No samples found: flash [2021-01-14 16:40:48,512] multiqc [DEBUG ] No samples found: seqyclean [2021-01-14 16:40:48,512] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-01-14 16:40:48,512] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-01-14 16:40:48,512] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-01-14 16:40:48,512] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-01-14 16:40:48,596] multiqc [INFO ] Compressing plot data [2021-01-14 16:40:49,701] multiqc [INFO ] Report : multiqc_report.html [2021-01-14 16:40:49,701] multiqc [INFO ] Data : multiqc_data [2021-01-14 16:40:49,701] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1140148/tmpywj231j1/multiqc_data' to '/scratch/gencore/logs/html/HLNCFAFX2/merged/multiqc_data' [2021-01-14 16:40:49,819] multiqc [INFO ] MultiQC complete