[2022-01-26 17:06:12,356] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-26 17:06:12,356] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-26 17:06:12,356] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-26 17:06:12,357] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-26 17:06:12,357] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-26 17:06:12,357] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFL7VAFX3/merged [2022-01-26 17:06:13,985] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-26 17:06:13,985] multiqc [INFO ] This is MultiQC v1.9 [2022-01-26 17:06:13,985] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFL7VAFX3/merged [2022-01-26 17:06:13,985] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFL7VAFX3/merged [2022-01-26 17:06:13,985] multiqc [INFO ] Template : default [2022-01-26 17:06:13,986] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-26 17:06:13,986] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFL7VAFX3/merged [2022-01-26 17:06:13,986] 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 [2022-01-26 17:06:13,987] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14375019/tmprlco09cp [2022-01-26 17:06:14,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFL7VAFX3_n02_10956-in_fastqc.html [2022-01-26 17:06:14,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HFL7VAFX3_n02_11757-Hop1NH_fastqc.html [2022-01-26 17:06:15,705] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFL7VAFX3_n01_7797-in_fastqc.html [2022-01-26 17:06:15,707] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFL7VAFX3_n01_7797-in_fastqc.html [2022-01-26 17:06:15,747] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFL7VAFX3_n01_10956-Myc_fastqc.html [2022-01-26 17:06:15,749] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFL7VAFX3_n01_10956-Myc_fastqc.html [2022-01-26 17:06:15,789] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFL7VAFX3_n01_10962-Red1_fastqc.html [2022-01-26 17:06:15,791] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFL7VAFX3_n01_10962-Red1_fastqc.html [2022-01-26 17:06:15,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFL7VAFX3_n01_11644-in_fastqc.html [2022-01-26 17:06:15,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFL7VAFX3_n01_11644-in_fastqc.html [2022-01-26 17:06:15,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFL7VAFX3_n02_5184-in_fastqc.html [2022-01-26 17:06:15,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFL7VAFX3_n02_5184-in_fastqc.html [2022-01-26 17:06:15,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFL7VAFX3_n02_11689-in_fastqc.html [2022-01-26 17:06:15,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFL7VAFX3_n02_11689-in_fastqc.html [2022-01-26 17:06:16,282] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-26 17:06:16,284] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-26 17:06:16,292] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-26 17:06:16,302] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-26 17:06:16,313] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2022-01-26 17:06:16,319] multiqc [DEBUG ] No samples found: conpair [2022-01-26 17:06:16,325] multiqc [DEBUG ] No samples found: peddy [2022-01-26 17:06:16,330] multiqc [DEBUG ] No samples found: somalier [2022-01-26 17:06:16,336] multiqc [DEBUG ] No samples found: methylQA [2022-01-26 17:06:16,346] multiqc [DEBUG ] No samples found: mosdepth [2022-01-26 17:06:16,352] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-26 17:06:16,356] multiqc [DEBUG ] No samples found: qualimap [2022-01-26 17:06:16,362] multiqc [DEBUG ] No samples found: preseq [2022-01-26 17:06:16,368] multiqc [DEBUG ] No samples found: quast [2022-01-26 17:06:16,374] multiqc [DEBUG ] No samples found: qorts [2022-01-26 17:06:16,379] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-26 17:06:16,384] multiqc [DEBUG ] No samples found: rockhopper [2022-01-26 17:06:16,389] multiqc [DEBUG ] No samples found: rsem [2022-01-26 17:06:16,403] multiqc [DEBUG ] No samples found: rseqc [2022-01-26 17:06:16,408] multiqc [DEBUG ] No samples found: busco [2022-01-26 17:06:16,414] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-26 17:06:16,419] multiqc [DEBUG ] No samples found: disambiguate [2022-01-26 17:06:16,425] multiqc [DEBUG ] No samples found: supernova [2022-01-26 17:06:16,440] multiqc [DEBUG ] No samples found: deeptools [2022-01-26 17:06:16,446] multiqc [DEBUG ] No samples found: sargasso [2022-01-26 17:06:16,452] multiqc [DEBUG ] No samples found: verifybamid [2022-01-26 17:06:16,458] multiqc [DEBUG ] No samples found: mirtrace [2022-01-26 17:06:16,463] multiqc [DEBUG ] No samples found: happy [2022-01-26 17:06:16,468] multiqc [DEBUG ] No samples found: mirtop [2022-01-26 17:06:16,475] multiqc [DEBUG ] No samples found: homer [2022-01-26 17:06:16,480] multiqc [DEBUG ] No samples found: macs2 [2022-01-26 17:06:16,486] multiqc [DEBUG ] No samples found: theta2 [2022-01-26 17:06:16,491] multiqc [DEBUG ] No samples found: snpeff [2022-01-26 17:06:16,498] multiqc [DEBUG ] No samples found: gatk [2022-01-26 17:06:16,504] multiqc [DEBUG ] No samples found: htseq [2022-01-26 17:06:16,510] multiqc [DEBUG ] No samples found: bcftools [2022-01-26 17:06:16,515] multiqc [DEBUG ] No samples found: featureCounts [2022-01-26 17:06:16,523] multiqc [DEBUG ] No samples found: fgbio [2022-01-26 17:06:16,536] multiqc [DEBUG ] No samples found: dragen [2022-01-26 17:06:16,542] multiqc [DEBUG ] No samples found: dedup [2022-01-26 17:06:16,547] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-26 17:06:16,573] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-26 17:06:16,579] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-26 17:06:16,581] multiqc [DEBUG ] No samples found: picard [2022-01-26 17:06:16,587] multiqc [DEBUG ] No samples found: prokka [2022-01-26 17:06:16,592] multiqc [DEBUG ] No samples found: samblaster [2022-01-26 17:06:16,601] multiqc [DEBUG ] No samples found: samtools [2022-01-26 17:06:16,607] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-26 17:06:16,613] multiqc [DEBUG ] No samples found: bamtools [2022-01-26 17:06:16,618] multiqc [DEBUG ] No samples found: jellyfish [2022-01-26 17:06:16,627] multiqc [DEBUG ] No samples found: vcftools [2022-01-26 17:06:16,633] multiqc [DEBUG ] No samples found: longranger [2022-01-26 17:06:16,638] multiqc [DEBUG ] No samples found: stacks [2022-01-26 17:06:16,644] multiqc [DEBUG ] No samples found: varscan2 [2022-01-26 17:06:16,661] multiqc [DEBUG ] No samples found: bbmap [2022-01-26 17:06:16,667] multiqc [DEBUG ] No samples found: bismark [2022-01-26 17:06:16,673] multiqc [DEBUG ] No samples found: biscuit [2022-01-26 17:06:16,678] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-26 17:06:16,684] multiqc [DEBUG ] No samples found: hicup [2022-01-26 17:06:16,689] multiqc [DEBUG ] No samples found: hicpro [2022-01-26 17:06:16,695] multiqc [DEBUG ] No samples found: salmon [2022-01-26 17:06:16,700] multiqc [DEBUG ] No samples found: kallisto [2022-01-26 17:06:16,705] multiqc [DEBUG ] No samples found: slamdunk [2022-01-26 17:06:16,711] multiqc [DEBUG ] No samples found: star [2022-01-26 17:06:16,716] multiqc [DEBUG ] No samples found: hisat2 [2022-01-26 17:06:16,721] multiqc [DEBUG ] No samples found: tophat [2022-01-26 17:06:16,727] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-26 17:06:16,732] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-26 17:06:16,737] multiqc [DEBUG ] No samples found: snpsplit [2022-01-26 17:06:16,742] multiqc [DEBUG ] No samples found: kat [2022-01-26 17:06:16,747] multiqc [DEBUG ] No samples found: leehom [2022-01-26 17:06:16,752] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-26 17:06:16,758] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-26 17:06:16,763] multiqc [DEBUG ] No samples found: cutadapt [2022-01-26 17:06:16,769] multiqc [DEBUG ] No samples found: flexbar [2022-01-26 17:06:16,774] multiqc [DEBUG ] No samples found: kaiju [2022-01-26 17:06:16,779] multiqc [DEBUG ] No samples found: kraken [2022-01-26 17:06:16,784] multiqc [DEBUG ] No samples found: malt [2022-01-26 17:06:16,789] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-26 17:06:16,795] multiqc [DEBUG ] No samples found: sickle [2022-01-26 17:06:16,800] multiqc [DEBUG ] No samples found: skewer [2022-01-26 17:06:16,805] multiqc [DEBUG ] No samples found: sortmerna [2022-01-26 17:06:16,810] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-26 17:06:16,815] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-26 17:06:16,820] multiqc [DEBUG ] No samples found: afterqc [2022-01-26 17:06:16,825] multiqc [DEBUG ] No samples found: fastp [2022-01-26 17:06:17,751] multiqc.modules.fastqc.fastqc [INFO ] Found 42 reports [2022-01-26 17:06:18,141] multiqc [DEBUG ] No samples found: pycoqc [2022-01-26 17:06:18,146] multiqc [DEBUG ] No samples found: minionqc [2022-01-26 17:06:18,151] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-26 17:06:18,157] multiqc [DEBUG ] No samples found: clusterflow [2022-01-26 17:06:18,163] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-26 17:06:18,169] multiqc [DEBUG ] No samples found: interop [2022-01-26 17:06:18,173] multiqc [DEBUG ] No samples found: ivar [2022-01-26 17:06:18,178] multiqc [DEBUG ] No samples found: flash [2022-01-26 17:06:18,183] multiqc [DEBUG ] No samples found: seqyclean [2022-01-26 17:06:18,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-26 17:06:18,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-26 17:06:18,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-26 17:06:18,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-26 17:06:18,234] multiqc [INFO ] Compressing plot data [2022-01-26 17:06:18,941] multiqc [INFO ] Report : multiqc_report.html [2022-01-26 17:06:18,942] multiqc [INFO ] Data : multiqc_data [2022-01-26 17:06:18,942] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14375019/tmprlco09cp/multiqc_data' to '/scratch/gencore/logs/html/HFL7VAFX3/merged/multiqc_data' [2022-01-26 17:06:19,075] multiqc [INFO ] MultiQC complete