[2021-03-01 15:48:40,518] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-01 15:48:40,518] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-01 15:48:40,518] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-01 15:48:40,519] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-01 15:48:40,519] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-01 15:48:40,519] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTJTLBGXH/merged [2021-03-01 15:48:41,893] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-03-01 15:48:41,893] multiqc [INFO ] This is MultiQC v1.9 [2021-03-01 15:48:41,893] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTJTLBGXH/merged [2021-03-01 15:48:41,893] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTJTLBGXH/merged [2021-03-01 15:48:41,893] multiqc [INFO ] Template : default [2021-03-01 15:48:41,893] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-01 15:48:41,893] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTJTLBGXH/merged [2021-03-01 15:48:41,894] 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 [2021-03-01 15:48:41,894] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-3255973/tmpmm8ojc7l [2021-03-01 15:48:42,001] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n02_dpr290_fastqc.html [2021-03-01 15:48:42,004] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n02_dpr290_fastqc.html [2021-03-01 15:48:42,050] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search 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HTJTLBGXH_n01_dpr202_fastqc.html [2021-03-01 15:48:50,641] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr189_fastqc.html [2021-03-01 15:48:50,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr189_fastqc.html [2021-03-01 15:48:50,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n02_dpr193_fastqc.html [2021-03-01 15:48:50,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n02_dpr193_fastqc.html [2021-03-01 15:48:50,732] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr198_fastqc.html [2021-03-01 15:48:50,734] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr198_fastqc.html [2021-03-01 15:48:50,777] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n01_undetermined_fastqc.html [2021-03-01 15:48:50,779] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n01_undetermined_fastqc.html [2021-03-01 15:48:50,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr201_fastqc.html [2021-03-01 15:48:50,827] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr201_fastqc.html [2021-03-01 15:48:50,869] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr192_fastqc.html [2021-03-01 15:48:50,871] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr192_fastqc.html [2021-03-01 15:48:50,915] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr285_fastqc.html [2021-03-01 15:48:50,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTJTLBGXH_n01_dpr285_fastqc.html [2021-03-01 15:48:51,454] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-01 15:48:51,456] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-01 15:48:51,477] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 30 samples (table) [2021-03-01 15:48:51,486] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-01 15:48:51,488] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-01 15:48:51,492] multiqc [DEBUG ] No samples found: conpair [2021-03-01 15:48:51,497] multiqc [DEBUG ] No samples found: peddy [2021-03-01 15:48:51,503] multiqc [DEBUG ] No samples found: somalier [2021-03-01 15:48:51,508] multiqc [DEBUG ] No samples found: methylQA [2021-03-01 15:48:51,515] multiqc [DEBUG ] No samples found: mosdepth [2021-03-01 15:48:51,519] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-01 15:48:51,523] multiqc [DEBUG ] No samples found: qualimap [2021-03-01 15:48:51,527] multiqc [DEBUG ] No samples found: preseq [2021-03-01 15:48:51,532] multiqc [DEBUG ] No samples found: quast [2021-03-01 15:48:51,538] multiqc [DEBUG ] No samples found: qorts [2021-03-01 15:48:51,543] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-01 15:48:51,547] multiqc [DEBUG ] No samples found: rockhopper [2021-03-01 15:48:51,551] multiqc [DEBUG ] No samples found: rsem [2021-03-01 15:48:51,561] multiqc [DEBUG ] No samples found: rseqc [2021-03-01 15:48:51,565] multiqc [DEBUG ] No samples found: busco [2021-03-01 15:48:51,569] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-01 15:48:51,573] multiqc [DEBUG ] No samples found: disambiguate [2021-03-01 15:48:51,578] multiqc [DEBUG ] No samples found: supernova [2021-03-01 15:48:51,600] multiqc [DEBUG ] No samples found: deeptools [2021-03-01 15:48:51,605] multiqc [DEBUG ] No samples found: sargasso [2021-03-01 15:48:51,610] multiqc [DEBUG ] No samples found: verifybamid [2021-03-01 15:48:51,616] multiqc [DEBUG ] No samples found: mirtrace [2021-03-01 15:48:51,620] multiqc [DEBUG ] No samples found: happy [2021-03-01 15:48:51,627] multiqc [DEBUG ] No samples found: mirtop [2021-03-01 15:48:51,633] multiqc [DEBUG ] No samples found: homer [2021-03-01 15:48:51,638] multiqc [DEBUG ] No samples found: macs2 [2021-03-01 15:48:51,644] multiqc [DEBUG ] No samples found: theta2 [2021-03-01 15:48:51,648] multiqc [DEBUG ] No samples found: snpeff [2021-03-01 15:48:51,655] multiqc [DEBUG ] No samples found: gatk [2021-03-01 15:48:51,659] multiqc [DEBUG ] No samples found: htseq [2021-03-01 15:48:51,665] multiqc [DEBUG ] No samples found: bcftools [2021-03-01 15:48:51,669] multiqc [DEBUG ] No samples found: featureCounts [2021-03-01 15:48:51,674] multiqc [DEBUG ] No samples found: fgbio [2021-03-01 15:48:51,687] multiqc [DEBUG ] No samples found: dragen [2021-03-01 15:48:51,693] multiqc [DEBUG ] No samples found: dedup [2021-03-01 15:48:51,698] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-01 15:48:51,720] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-01 15:48:51,724] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-01 15:48:51,726] multiqc [DEBUG ] No samples found: picard [2021-03-01 15:48:51,731] multiqc [DEBUG ] No samples found: prokka [2021-03-01 15:48:51,736] multiqc [DEBUG ] No samples found: samblaster [2021-03-01 15:48:51,744] multiqc [DEBUG ] No samples found: samtools [2021-03-01 15:48:51,749] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-01 15:48:51,754] multiqc [DEBUG ] No samples found: bamtools [2021-03-01 15:48:51,758] multiqc [DEBUG ] No samples found: jellyfish [2021-03-01 15:48:51,765] multiqc [DEBUG ] No samples found: vcftools [2021-03-01 15:48:51,770] multiqc [DEBUG ] No samples found: longranger [2021-03-01 15:48:51,775] multiqc [DEBUG ] No samples found: stacks [2021-03-01 15:48:51,779] multiqc [DEBUG ] No samples found: varscan2 [2021-03-01 15:48:51,795] multiqc [DEBUG ] No samples found: bbmap [2021-03-01 15:48:51,799] multiqc [DEBUG ] No samples found: bismark [2021-03-01 15:48:51,803] multiqc [DEBUG ] No samples found: biscuit [2021-03-01 15:48:51,808] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-01 15:48:51,812] multiqc [DEBUG ] No samples found: hicup [2021-03-01 15:48:51,816] multiqc [DEBUG ] No samples found: hicpro [2021-03-01 15:48:51,820] multiqc [DEBUG ] No samples found: salmon [2021-03-01 15:48:51,824] multiqc [DEBUG ] No samples found: kallisto [2021-03-01 15:48:51,831] multiqc [DEBUG ] No samples found: slamdunk [2021-03-01 15:48:51,836] multiqc [DEBUG ] No samples found: star [2021-03-01 15:48:51,840] multiqc [DEBUG ] No samples found: hisat2 [2021-03-01 15:48:51,846] multiqc [DEBUG ] No samples found: tophat [2021-03-01 15:48:51,850] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-01 15:48:51,854] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-01 15:48:51,858] multiqc [DEBUG ] No samples found: snpsplit [2021-03-01 15:48:51,862] multiqc [DEBUG ] No samples found: kat [2021-03-01 15:48:51,866] multiqc [DEBUG ] No samples found: leehom [2021-03-01 15:48:51,870] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-01 15:48:51,874] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-01 15:48:51,878] multiqc [DEBUG ] No samples found: cutadapt [2021-03-01 15:48:51,882] multiqc [DEBUG ] No samples found: flexbar [2021-03-01 15:48:51,888] multiqc [DEBUG ] No samples found: kaiju [2021-03-01 15:48:51,893] multiqc [DEBUG ] No samples found: kraken [2021-03-01 15:48:51,897] multiqc [DEBUG ] No samples found: malt [2021-03-01 15:48:51,901] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-01 15:48:51,905] multiqc [DEBUG ] No samples found: sickle [2021-03-01 15:48:51,910] multiqc [DEBUG ] No samples found: skewer [2021-03-01 15:48:51,913] multiqc [DEBUG ] No samples found: sortmerna [2021-03-01 15:48:51,917] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-01 15:48:51,922] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-01 15:48:51,926] multiqc [DEBUG ] No samples found: afterqc [2021-03-01 15:48:51,930] multiqc [DEBUG ] No samples found: fastp [2021-03-01 15:48:56,587] multiqc.modules.fastqc.fastqc [INFO ] Found 60 reports [2021-03-01 15:48:57,759] multiqc [DEBUG ] No samples found: pycoqc [2021-03-01 15:48:57,767] multiqc [DEBUG ] No samples found: minionqc [2021-03-01 15:48:57,774] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-01 15:48:57,780] multiqc [DEBUG ] No samples found: clusterflow [2021-03-01 15:48:57,846] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-01 15:48:57,851] multiqc [DEBUG ] No samples found: interop [2021-03-01 15:48:57,855] multiqc [DEBUG ] No samples found: ivar [2021-03-01 15:48:57,860] multiqc [DEBUG ] No samples found: flash [2021-03-01 15:48:57,865] multiqc [DEBUG ] No samples found: seqyclean [2021-03-01 15:48:57,865] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-01 15:48:57,865] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-03-01 15:48:57,865] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-03-01 15:48:57,865] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-01 15:48:57,935] multiqc [INFO ] Compressing plot data [2021-03-01 15:48:58,990] multiqc [INFO ] Report : multiqc_report.html [2021-03-01 15:48:58,991] multiqc [INFO ] Data : multiqc_data [2021-03-01 15:48:58,991] multiqc [DEBUG ] Moving data file from '/state/partition1/job-3255973/tmpmm8ojc7l/multiqc_data' to '/scratch/gencore/logs/html/HTJTLBGXH/merged/multiqc_data' [2021-03-01 15:49:16,800] multiqc [INFO ] MultiQC complete