[2022-01-07 14:33:53,270] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-07 14:33:53,270] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-07 14:33:53,270] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-07 14:33:53,271] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-07 14:33:53,271] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-07 14:33:53,271] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF55KAFX3/merged [2022-01-07 14:33:54,569] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-07 14:33:54,569] multiqc [INFO ] This is MultiQC v1.9 [2022-01-07 14:33:54,569] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF55KAFX3/merged [2022-01-07 14:33:54,569] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HF55KAFX3/merged [2022-01-07 14:33:54,570] multiqc [INFO ] Template : default [2022-01-07 14:33:54,570] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-07 14:33:54,570] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HF55KAFX3/merged [2022-01-07 14:33:54,571] 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 [2022-01-07 14:33:54,571] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13623213/tmpb_m0prbd [2022-01-07 14:33:54,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRBB7LB_fastqc.html [2022-01-07 14:33:54,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0149_fastqc.html [2022-01-07 14:33:58,819] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0225_fastqc.html [2022-01-07 14:33:58,820] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0225_fastqc.html [2022-01-07 14:33:58,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n02_undetermined_fastqc.html [2022-01-07 14:33:58,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n02_undetermined_fastqc.html [2022-01-07 14:33:58,896] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0236_fastqc.html [2022-01-07 14:33:58,898] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0236_fastqc.html [2022-01-07 14:33:58,935] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRBB5LB_fastqc.html [2022-01-07 14:33:58,937] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRBB5LB_fastqc.html [2022-01-07 14:33:58,979] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0073_fastqc.html [2022-01-07 14:33:58,980] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0073_fastqc.html [2022-01-07 14:33:59,021] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0082_fastqc.html [2022-01-07 14:33:59,022] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0082_fastqc.html [2022-01-07 14:33:59,059] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0083_fastqc.html [2022-01-07 14:33:59,061] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0083_fastqc.html [2022-01-07 14:33:59,098] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRBB5EB_fastqc.html [2022-01-07 14:33:59,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRBB5EB_fastqc.html [2022-01-07 14:33:59,140] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRBB7EB_fastqc.html [2022-01-07 14:33:59,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRBB7EB_fastqc.html [2022-01-07 14:33:59,182] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0221_fastqc.html [2022-01-07 14:33:59,183] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0221_fastqc.html [2022-01-07 14:33:59,222] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0238_fastqc.html [2022-01-07 14:33:59,224] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n02_HRB0238_fastqc.html [2022-01-07 14:33:59,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0168_fastqc.html [2022-01-07 14:33:59,264] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0168_fastqc.html [2022-01-07 14:33:59,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRBB6EB_fastqc.html [2022-01-07 14:33:59,303] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRBB6EB_fastqc.html [2022-01-07 14:33:59,342] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0226_fastqc.html [2022-01-07 14:33:59,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0226_fastqc.html [2022-01-07 14:33:59,383] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0234_fastqc.html [2022-01-07 14:33:59,385] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF55KAFX3_n01_HRB0234_fastqc.html [2022-01-07 14:33:59,828] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-07 14:33:59,830] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-07 14:33:59,838] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-07 14:33:59,848] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-07 14:33:59,864] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 37 samples (table) [2022-01-07 14:33:59,870] multiqc [DEBUG ] No samples found: conpair [2022-01-07 14:33:59,876] multiqc [DEBUG ] No samples found: peddy [2022-01-07 14:33:59,881] multiqc [DEBUG ] No samples found: somalier [2022-01-07 14:33:59,886] multiqc [DEBUG ] No samples found: methylQA [2022-01-07 14:33:59,896] multiqc [DEBUG ] No samples found: mosdepth [2022-01-07 14:33:59,901] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-07 14:33:59,904] multiqc [DEBUG ] No samples found: qualimap [2022-01-07 14:33:59,910] multiqc [DEBUG ] No samples found: preseq [2022-01-07 14:33:59,915] multiqc [DEBUG ] No samples found: quast [2022-01-07 14:33:59,920] multiqc [DEBUG ] No samples found: qorts [2022-01-07 14:33:59,926] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-07 14:33:59,930] multiqc [DEBUG ] No samples found: rockhopper [2022-01-07 14:33:59,934] multiqc [DEBUG ] No samples found: rsem [2022-01-07 14:33:59,948] multiqc [DEBUG ] No samples found: rseqc [2022-01-07 14:33:59,953] multiqc [DEBUG ] No samples found: busco [2022-01-07 14:33:59,960] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-07 14:33:59,965] multiqc [DEBUG ] No samples found: disambiguate [2022-01-07 14:33:59,971] multiqc [DEBUG ] No samples found: supernova [2022-01-07 14:33:59,989] multiqc [DEBUG ] No samples found: deeptools [2022-01-07 14:33:59,998] multiqc [DEBUG ] No samples found: sargasso [2022-01-07 14:34:00,005] multiqc [DEBUG ] No samples found: verifybamid [2022-01-07 14:34:00,011] multiqc [DEBUG ] No samples found: mirtrace [2022-01-07 14:34:00,015] multiqc [DEBUG ] No samples found: happy [2022-01-07 14:34:00,021] multiqc [DEBUG ] No samples found: mirtop [2022-01-07 14:34:00,032] multiqc [DEBUG ] No samples found: homer [2022-01-07 14:34:00,038] multiqc [DEBUG ] No samples found: macs2 [2022-01-07 14:34:00,042] multiqc [DEBUG ] No samples found: theta2 [2022-01-07 14:34:00,047] multiqc [DEBUG ] No samples found: snpeff [2022-01-07 14:34:00,054] multiqc [DEBUG ] No samples found: gatk [2022-01-07 14:34:00,058] multiqc [DEBUG ] No samples found: htseq [2022-01-07 14:34:00,064] multiqc [DEBUG ] No samples found: bcftools [2022-01-07 14:34:00,070] multiqc [DEBUG ] No samples found: featureCounts [2022-01-07 14:34:00,080] multiqc [DEBUG ] No samples found: fgbio [2022-01-07 14:34:00,096] multiqc [DEBUG ] No samples found: dragen [2022-01-07 14:34:00,102] multiqc [DEBUG ] No samples found: dedup [2022-01-07 14:34:00,106] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-07 14:34:00,136] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-07 14:34:00,144] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-07 14:34:00,148] multiqc [DEBUG ] No samples found: picard [2022-01-07 14:34:00,155] multiqc [DEBUG ] No samples found: prokka [2022-01-07 14:34:00,159] multiqc [DEBUG ] No samples found: samblaster [2022-01-07 14:34:00,169] multiqc [DEBUG ] No samples found: samtools [2022-01-07 14:34:00,174] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-07 14:34:00,180] multiqc [DEBUG ] No samples found: bamtools [2022-01-07 14:34:00,184] multiqc [DEBUG ] No samples found: jellyfish [2022-01-07 14:34:00,193] multiqc [DEBUG ] No samples found: vcftools [2022-01-07 14:34:00,198] multiqc [DEBUG ] No samples found: longranger [2022-01-07 14:34:00,202] multiqc [DEBUG ] No samples found: stacks [2022-01-07 14:34:00,207] multiqc [DEBUG ] No samples found: varscan2 [2022-01-07 14:34:00,226] multiqc [DEBUG ] No samples found: bbmap [2022-01-07 14:34:00,236] multiqc [DEBUG ] No samples found: bismark [2022-01-07 14:34:00,244] multiqc [DEBUG ] No samples found: biscuit [2022-01-07 14:34:00,248] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-07 14:34:00,254] multiqc [DEBUG ] No samples found: hicup [2022-01-07 14:34:00,261] multiqc [DEBUG ] No samples found: hicpro [2022-01-07 14:34:00,267] multiqc [DEBUG ] No samples found: salmon [2022-01-07 14:34:00,272] multiqc [DEBUG ] No samples found: kallisto [2022-01-07 14:34:00,278] multiqc [DEBUG ] No samples found: slamdunk [2022-01-07 14:34:00,283] multiqc [DEBUG ] No samples found: star [2022-01-07 14:34:00,290] multiqc [DEBUG ] No samples found: hisat2 [2022-01-07 14:34:00,296] multiqc [DEBUG ] No samples found: tophat [2022-01-07 14:34:00,302] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-07 14:34:00,307] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-07 14:34:00,312] multiqc [DEBUG ] No samples found: snpsplit [2022-01-07 14:34:00,317] multiqc [DEBUG ] No samples found: kat [2022-01-07 14:34:00,322] multiqc [DEBUG ] No samples found: leehom [2022-01-07 14:34:00,327] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-07 14:34:00,332] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-07 14:34:00,336] multiqc [DEBUG ] No samples found: cutadapt [2022-01-07 14:34:00,342] multiqc [DEBUG ] No samples found: flexbar [2022-01-07 14:34:00,346] multiqc [DEBUG ] No samples found: kaiju [2022-01-07 14:34:00,351] multiqc [DEBUG ] No samples found: kraken [2022-01-07 14:34:00,357] multiqc [DEBUG ] No samples found: malt [2022-01-07 14:34:00,362] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-07 14:34:00,368] multiqc [DEBUG ] No samples found: sickle [2022-01-07 14:34:00,372] multiqc [DEBUG ] No samples found: skewer [2022-01-07 14:34:00,378] multiqc [DEBUG ] No samples found: sortmerna [2022-01-07 14:34:00,384] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-07 14:34:00,389] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-07 14:34:00,394] multiqc [DEBUG ] No samples found: afterqc [2022-01-07 14:34:00,401] multiqc [DEBUG ] No samples found: fastp [2022-01-07 14:34:01,839] multiqc.modules.fastqc.fastqc [INFO ] Found 74 reports [2022-01-07 14:34:02,315] multiqc [DEBUG ] No samples found: pycoqc [2022-01-07 14:34:02,320] multiqc [DEBUG ] No samples found: minionqc [2022-01-07 14:34:02,326] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-07 14:34:02,332] multiqc [DEBUG ] No samples found: clusterflow [2022-01-07 14:34:02,338] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-07 14:34:02,342] multiqc [DEBUG ] No samples found: interop [2022-01-07 14:34:02,347] multiqc [DEBUG ] No samples found: ivar [2022-01-07 14:34:02,353] multiqc [DEBUG ] No samples found: flash [2022-01-07 14:34:02,358] multiqc [DEBUG ] No samples found: seqyclean [2022-01-07 14:34:02,358] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-07 14:34:02,358] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-07 14:34:02,358] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-07 14:34:02,358] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-07 14:34:02,436] multiqc [INFO ] Compressing plot data [2022-01-07 14:34:03,446] multiqc [INFO ] Report : multiqc_report.html [2022-01-07 14:34:03,446] multiqc [INFO ] Data : multiqc_data [2022-01-07 14:34:03,446] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13623213/tmpb_m0prbd/multiqc_data' to '/scratch/gencore/logs/html/HF55KAFX3/merged/multiqc_data' [2022-01-07 14:34:03,573] multiqc [INFO ] MultiQC complete