[2021-03-11 01:55:01,278] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-11 01:55:01,278] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-11 01:55:01,278] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-11 01:55:01,279] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-11 01:55:01,279] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-11 01:55:01,279] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFHKTBGXG/merged [2021-03-11 01:55:02,974] multiqc [WARNING] MultiQC Version v1.10 now available! [2021-03-11 01:55:02,974] multiqc [INFO ] This is MultiQC v1.9 [2021-03-11 01:55:02,974] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFHKTBGXG/merged [2021-03-11 01:55:02,974] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFHKTBGXG/merged [2021-03-11 01:55:02,974] multiqc [INFO ] Template : default [2021-03-11 01:55:02,974] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-11 01:55:02,974] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFHKTBGXG/merged [2021-03-11 01:55:02,975] 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 [2021-03-11 01:55:02,975] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-3613571/tmp298c8m03 [2021-03-11 01:55:03,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM187_fastqc.html [2021-03-11 01:55:03,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM187_fastqc.html [2021-03-11 01:55:03,163] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-11 01:55:03,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-11 01:55:03,265] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM195_fastqc.html [2021-03-11 01:55:03,267] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM195_fastqc.html [2021-03-11 01:55:03,308] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ80_fastqc.html [2021-03-11 01:55:03,310] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ80_fastqc.html [2021-03-11 01:55:03,377] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM192_fastqc.html [2021-03-11 01:55:03,379] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM192_fastqc.html [2021-03-11 01:55:03,420] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM197_fastqc.html [2021-03-11 01:55:03,422] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM197_fastqc.html [2021-03-11 01:55:03,463] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ82_fastqc.html [2021-03-11 01:55:03,465] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ82_fastqc.html [2021-03-11 01:55:03,505] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ83_fastqc.html [2021-03-11 01:55:03,507] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ83_fastqc.html [2021-03-11 01:55:03,559] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM191_fastqc.html [2021-03-11 01:55:03,561] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM191_fastqc.html [2021-03-11 01:55:03,601] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM189_fastqc.html [2021-03-11 01:55:03,603] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM189_fastqc.html [2021-03-11 01:55:03,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM185_fastqc.html [2021-03-11 01:55:03,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM185_fastqc.html [2021-03-11 01:55:03,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM196_fastqc.html [2021-03-11 01:55:03,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM196_fastqc.html [2021-03-11 01:55:03,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ84_fastqc.html [2021-03-11 01:55:03,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ84_fastqc.html [2021-03-11 01:55:03,788] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM193_fastqc.html [2021-03-11 01:55:03,789] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM193_fastqc.html [2021-03-11 01:55:03,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_undetermined_fastqc.html [2021-03-11 01:55:03,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_undetermined_fastqc.html [2021-03-11 01:55:03,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM186_fastqc.html [2021-03-11 01:55:03,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM186_fastqc.html [2021-03-11 01:55:03,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ79_fastqc.html [2021-03-11 01:55:03,926] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ79_fastqc.html [2021-03-11 01:55:03,965] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ81_fastqc.html [2021-03-11 01:55:03,967] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ81_fastqc.html [2021-03-11 01:55:04,006] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM184_fastqc.html [2021-03-11 01:55:04,007] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM184_fastqc.html [2021-03-11 01:55:04,049] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM188_fastqc.html [2021-03-11 01:55:04,051] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM188_fastqc.html [2021-03-11 01:55:04,097] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ86_fastqc.html [2021-03-11 01:55:04,098] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ86_fastqc.html [2021-03-11 01:55:04,144] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ85_fastqc.html [2021-03-11 01:55:04,146] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_DJ85_fastqc.html [2021-03-11 01:55:04,196] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM194_fastqc.html [2021-03-11 01:55:04,198] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM194_fastqc.html [2021-03-11 01:55:04,246] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM190_fastqc.html [2021-03-11 01:55:04,248] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHKTBGXG_n01_AKM190_fastqc.html [2021-03-11 01:55:04,833] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-11 01:55:04,835] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-11 01:55:04,843] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-11 01:55:04,853] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-11 01:55:04,865] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2021-03-11 01:55:04,870] multiqc [DEBUG ] No samples found: conpair [2021-03-11 01:55:04,875] multiqc [DEBUG ] No samples found: peddy [2021-03-11 01:55:04,880] multiqc [DEBUG ] No samples found: somalier [2021-03-11 01:55:04,885] multiqc [DEBUG ] No samples found: methylQA [2021-03-11 01:55:04,894] multiqc [DEBUG ] No samples found: mosdepth [2021-03-11 01:55:04,899] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-11 01:55:04,902] multiqc [DEBUG ] No samples found: qualimap [2021-03-11 01:55:04,907] multiqc [DEBUG ] No samples found: preseq [2021-03-11 01:55:04,912] multiqc [DEBUG ] No samples found: quast [2021-03-11 01:55:04,917] multiqc [DEBUG ] No samples found: qorts [2021-03-11 01:55:04,922] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-11 01:55:04,927] multiqc [DEBUG ] No samples found: rockhopper [2021-03-11 01:55:04,932] multiqc [DEBUG ] No samples found: rsem [2021-03-11 01:55:04,942] multiqc [DEBUG ] No samples found: rseqc [2021-03-11 01:55:04,947] multiqc [DEBUG ] No samples found: busco [2021-03-11 01:55:04,952] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-11 01:55:04,957] multiqc [DEBUG ] No samples found: disambiguate [2021-03-11 01:55:04,962] multiqc [DEBUG ] No samples found: supernova [2021-03-11 01:55:04,974] multiqc [DEBUG ] No samples found: deeptools [2021-03-11 01:55:04,980] multiqc [DEBUG ] No samples found: sargasso [2021-03-11 01:55:04,985] multiqc [DEBUG ] No samples found: verifybamid [2021-03-11 01:55:04,991] multiqc [DEBUG ] No samples found: mirtrace [2021-03-11 01:55:04,996] multiqc [DEBUG ] No samples found: happy [2021-03-11 01:55:05,001] multiqc [DEBUG ] No samples found: mirtop [2021-03-11 01:55:05,007] multiqc [DEBUG ] No samples found: homer [2021-03-11 01:55:05,011] multiqc [DEBUG ] No samples found: macs2 [2021-03-11 01:55:05,017] multiqc [DEBUG ] No samples found: theta2 [2021-03-11 01:55:05,022] multiqc [DEBUG ] No samples found: snpeff [2021-03-11 01:55:05,028] multiqc [DEBUG ] No samples found: gatk [2021-03-11 01:55:05,033] multiqc [DEBUG ] No samples found: htseq [2021-03-11 01:55:05,038] multiqc [DEBUG ] No samples found: bcftools [2021-03-11 01:55:05,043] multiqc [DEBUG ] No samples found: featureCounts [2021-03-11 01:55:05,049] multiqc [DEBUG ] No samples found: fgbio [2021-03-11 01:55:05,062] multiqc [DEBUG ] No samples found: dragen [2021-03-11 01:55:05,067] multiqc [DEBUG ] No samples found: dedup [2021-03-11 01:55:05,072] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-11 01:55:05,094] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-11 01:55:05,099] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-11 01:55:05,101] multiqc [DEBUG ] No samples found: picard [2021-03-11 01:55:05,106] multiqc [DEBUG ] No samples found: prokka [2021-03-11 01:55:05,110] multiqc [DEBUG ] No samples found: samblaster [2021-03-11 01:55:05,119] multiqc [DEBUG ] No samples found: samtools [2021-03-11 01:55:05,125] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-11 01:55:05,130] multiqc [DEBUG ] No samples found: bamtools [2021-03-11 01:55:05,135] multiqc [DEBUG ] No samples found: jellyfish [2021-03-11 01:55:05,141] multiqc [DEBUG ] No samples found: vcftools [2021-03-11 01:55:05,146] multiqc [DEBUG ] No samples found: longranger [2021-03-11 01:55:05,152] multiqc [DEBUG ] No samples found: stacks [2021-03-11 01:55:05,156] multiqc [DEBUG ] No samples found: varscan2 [2021-03-11 01:55:05,169] multiqc [DEBUG ] No samples found: bbmap [2021-03-11 01:55:05,174] multiqc [DEBUG ] No samples found: bismark [2021-03-11 01:55:05,180] multiqc [DEBUG ] No samples found: biscuit [2021-03-11 01:55:05,185] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-11 01:55:05,190] multiqc [DEBUG ] No samples found: hicup [2021-03-11 01:55:05,195] multiqc [DEBUG ] No samples found: hicpro [2021-03-11 01:55:05,200] multiqc [DEBUG ] No samples found: salmon [2021-03-11 01:55:05,204] multiqc [DEBUG ] No samples found: kallisto [2021-03-11 01:55:05,210] multiqc [DEBUG ] No samples found: slamdunk [2021-03-11 01:55:05,215] multiqc [DEBUG ] No samples found: star [2021-03-11 01:55:05,219] multiqc [DEBUG ] No samples found: hisat2 [2021-03-11 01:55:05,224] multiqc [DEBUG ] No samples found: tophat [2021-03-11 01:55:05,229] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-11 01:55:05,233] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-11 01:55:05,239] multiqc [DEBUG ] No samples found: snpsplit [2021-03-11 01:55:05,244] multiqc [DEBUG ] No samples found: kat [2021-03-11 01:55:05,248] multiqc [DEBUG ] No samples found: leehom [2021-03-11 01:55:05,253] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-11 01:55:05,258] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-11 01:55:05,263] multiqc [DEBUG ] No samples found: cutadapt [2021-03-11 01:55:05,268] multiqc [DEBUG ] No samples found: flexbar [2021-03-11 01:55:05,272] multiqc [DEBUG ] No samples found: kaiju [2021-03-11 01:55:05,277] multiqc [DEBUG ] No samples found: kraken [2021-03-11 01:55:05,282] multiqc [DEBUG ] No samples found: malt [2021-03-11 01:55:05,286] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-11 01:55:05,291] multiqc [DEBUG ] No samples found: sickle [2021-03-11 01:55:05,295] multiqc [DEBUG ] No samples found: skewer [2021-03-11 01:55:05,300] multiqc [DEBUG ] No samples found: sortmerna [2021-03-11 01:55:05,304] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-11 01:55:05,309] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-11 01:55:05,314] multiqc [DEBUG ] No samples found: afterqc [2021-03-11 01:55:05,318] multiqc [DEBUG ] No samples found: fastp [2021-03-11 01:55:07,145] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2021-03-11 01:55:07,657] multiqc [DEBUG ] No samples found: pycoqc [2021-03-11 01:55:07,663] multiqc [DEBUG ] No samples found: minionqc [2021-03-11 01:55:07,668] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-11 01:55:07,674] multiqc [DEBUG ] No samples found: clusterflow [2021-03-11 01:55:07,679] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-11 01:55:07,684] multiqc [DEBUG ] No samples found: interop [2021-03-11 01:55:07,689] multiqc [DEBUG ] No samples found: ivar [2021-03-11 01:55:07,694] multiqc [DEBUG ] No samples found: flash [2021-03-11 01:55:07,699] multiqc [DEBUG ] No samples found: seqyclean [2021-03-11 01:55:07,699] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-03-11 01:55:07,699] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-03-11 01:55:07,700] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-11 01:55:07,700] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-11 01:55:07,729] multiqc [INFO ] Compressing plot data [2021-03-11 01:55:08,166] multiqc [INFO ] Report : multiqc_report.html [2021-03-11 01:55:08,166] multiqc [INFO ] Data : multiqc_data [2021-03-11 01:55:08,166] multiqc [DEBUG ] Moving data file from '/state/partition1/job-3613571/tmp298c8m03/multiqc_data' to '/scratch/gencore/logs/html/HFHKTBGXG/merged/multiqc_data' [2021-03-11 01:57:37,690] multiqc [INFO ] MultiQC complete