[2021-12-09 20:26:46,400] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-09 20:26:46,401] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-09 20:26:46,401] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-09 20:26:46,402] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-09 20:26:46,402] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-09 20:26:46,402] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMCFHBGXK/merged [2021-12-09 20:26:48,008] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-09 20:26:48,008] multiqc [INFO ] This is MultiQC v1.9 [2021-12-09 20:26:48,008] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMCFHBGXK/merged [2021-12-09 20:26:48,008] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMCFHBGXK/merged [2021-12-09 20:26:48,008] multiqc [INFO ] Template : default [2021-12-09 20:26:48,009] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-09 20:26:48,009] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMCFHBGXK/merged [2021-12-09 20:26:48,009] 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 [2021-12-09 20:26:48,009] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12929488/tmpck0r8m_j [2021-12-09 20:26:48,115] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM289_fastqc.html [2021-12-09 20:26:48,118] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM289_fastqc.html [2021-12-09 20:26:48,163] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_undetermined_fastqc.html [2021-12-09 20:26:48,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_undetermined_fastqc.html [2021-12-09 20:26:48,203] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM294_fastqc.html [2021-12-09 20:26:48,205] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM294_fastqc.html [2021-12-09 20:26:48,243] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM301_fastqc.html [2021-12-09 20:26:48,245] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM301_fastqc.html [2021-12-09 20:26:48,282] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-09 20:26:48,284] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-09 20:26:48,414] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM302_fastqc.html [2021-12-09 20:26:48,416] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM302_fastqc.html [2021-12-09 20:26:48,456] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM298_fastqc.html [2021-12-09 20:26:48,458] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM298_fastqc.html [2021-12-09 20:26:48,500] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM297_fastqc.html [2021-12-09 20:26:48,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM297_fastqc.html [2021-12-09 20:26:48,546] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM292_fastqc.html [2021-12-09 20:26:48,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM292_fastqc.html [2021-12-09 20:26:48,590] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM290_fastqc.html [2021-12-09 20:26:48,592] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM290_fastqc.html [2021-12-09 20:26:48,634] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM300_fastqc.html [2021-12-09 20:26:48,636] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM300_fastqc.html [2021-12-09 20:26:48,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM281_fastqc.html [2021-12-09 20:26:48,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM281_fastqc.html [2021-12-09 20:26:48,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM291_fastqc.html [2021-12-09 20:26:48,724] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM291_fastqc.html [2021-12-09 20:26:48,766] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM286_fastqc.html [2021-12-09 20:26:48,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM286_fastqc.html [2021-12-09 20:26:48,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM287_fastqc.html [2021-12-09 20:26:48,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM287_fastqc.html [2021-12-09 20:26:48,854] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM284_fastqc.html [2021-12-09 20:26:48,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM284_fastqc.html [2021-12-09 20:26:48,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM296_fastqc.html [2021-12-09 20:26:48,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM296_fastqc.html [2021-12-09 20:26:48,942] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM295_fastqc.html [2021-12-09 20:26:48,944] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM295_fastqc.html [2021-12-09 20:26:48,986] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM299_fastqc.html [2021-12-09 20:26:48,988] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM299_fastqc.html [2021-12-09 20:26:49,033] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM293_fastqc.html [2021-12-09 20:26:49,035] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM293_fastqc.html [2021-12-09 20:26:49,077] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM282_fastqc.html [2021-12-09 20:26:49,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM282_fastqc.html [2021-12-09 20:26:49,121] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM285_fastqc.html [2021-12-09 20:26:49,123] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM285_fastqc.html [2021-12-09 20:26:49,164] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM288_fastqc.html [2021-12-09 20:26:49,166] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM288_fastqc.html [2021-12-09 20:26:49,208] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM283_fastqc.html [2021-12-09 20:26:49,210] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCFHBGXK_n01_AKM283_fastqc.html [2021-12-09 20:26:49,758] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-09 20:26:49,760] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-09 20:26:49,769] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-09 20:26:49,781] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2021-12-09 20:26:49,791] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-09 20:26:49,796] multiqc [DEBUG ] No samples found: conpair [2021-12-09 20:26:49,803] multiqc [DEBUG ] No samples found: peddy [2021-12-09 20:26:49,807] multiqc [DEBUG ] No samples found: somalier [2021-12-09 20:26:49,812] multiqc [DEBUG ] No samples found: methylQA [2021-12-09 20:26:49,821] multiqc [DEBUG ] No samples found: mosdepth [2021-12-09 20:26:49,825] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-09 20:26:49,828] multiqc [DEBUG ] No samples found: qualimap [2021-12-09 20:26:49,832] multiqc [DEBUG ] No samples found: preseq [2021-12-09 20:26:49,837] multiqc [DEBUG ] No samples found: quast [2021-12-09 20:26:49,841] multiqc [DEBUG ] No samples found: qorts [2021-12-09 20:26:49,846] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-09 20:26:49,850] multiqc [DEBUG ] No samples found: rockhopper [2021-12-09 20:26:49,855] multiqc [DEBUG ] No samples found: rsem [2021-12-09 20:26:49,865] multiqc [DEBUG ] No samples found: rseqc [2021-12-09 20:26:49,869] multiqc [DEBUG ] No samples found: busco [2021-12-09 20:26:49,873] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-09 20:26:49,878] multiqc [DEBUG ] No samples found: disambiguate [2021-12-09 20:26:49,882] multiqc [DEBUG ] No samples found: supernova [2021-12-09 20:26:49,894] multiqc [DEBUG ] No samples found: deeptools [2021-12-09 20:26:49,898] multiqc [DEBUG ] No samples found: sargasso [2021-12-09 20:26:49,903] multiqc [DEBUG ] No samples found: verifybamid [2021-12-09 20:26:49,907] multiqc [DEBUG ] No samples found: mirtrace [2021-12-09 20:26:49,912] multiqc [DEBUG ] No samples found: happy [2021-12-09 20:26:49,916] multiqc [DEBUG ] No samples found: mirtop [2021-12-09 20:26:49,922] multiqc [DEBUG ] No samples found: homer [2021-12-09 20:26:49,927] multiqc [DEBUG ] No samples found: macs2 [2021-12-09 20:26:49,931] multiqc [DEBUG ] No samples found: theta2 [2021-12-09 20:26:49,936] multiqc [DEBUG ] No samples found: snpeff [2021-12-09 20:26:49,942] multiqc [DEBUG ] No samples found: gatk [2021-12-09 20:26:49,946] multiqc [DEBUG ] No samples found: htseq [2021-12-09 20:26:49,951] multiqc [DEBUG ] No samples found: bcftools [2021-12-09 20:26:49,956] multiqc [DEBUG ] No samples found: featureCounts [2021-12-09 20:26:49,962] multiqc [DEBUG ] No samples found: fgbio [2021-12-09 20:26:49,974] multiqc [DEBUG ] No samples found: dragen [2021-12-09 20:26:49,978] multiqc [DEBUG ] No samples found: dedup [2021-12-09 20:26:49,982] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-09 20:26:50,005] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-09 20:26:50,010] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-09 20:26:50,012] multiqc [DEBUG ] No samples found: picard [2021-12-09 20:26:50,017] multiqc [DEBUG ] No samples found: prokka [2021-12-09 20:26:50,021] multiqc [DEBUG ] No samples found: samblaster [2021-12-09 20:26:50,028] multiqc [DEBUG ] No samples found: samtools [2021-12-09 20:26:50,033] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-09 20:26:50,038] multiqc [DEBUG ] No samples found: bamtools [2021-12-09 20:26:50,042] multiqc [DEBUG ] No samples found: jellyfish [2021-12-09 20:26:50,049] multiqc [DEBUG ] No samples found: vcftools [2021-12-09 20:26:50,054] multiqc [DEBUG ] No samples found: longranger [2021-12-09 20:26:50,059] multiqc [DEBUG ] No samples found: stacks [2021-12-09 20:26:50,063] multiqc [DEBUG ] No samples found: varscan2 [2021-12-09 20:26:50,076] multiqc [DEBUG ] No samples found: bbmap [2021-12-09 20:26:50,081] multiqc [DEBUG ] No samples found: bismark [2021-12-09 20:26:50,087] multiqc [DEBUG ] No samples found: biscuit [2021-12-09 20:26:50,092] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-09 20:26:50,096] multiqc [DEBUG ] No samples found: hicup [2021-12-09 20:26:50,101] multiqc [DEBUG ] No samples found: hicpro [2021-12-09 20:26:50,105] multiqc [DEBUG ] No samples found: salmon [2021-12-09 20:26:50,109] multiqc [DEBUG ] No samples found: kallisto [2021-12-09 20:26:50,114] multiqc [DEBUG ] No samples found: slamdunk [2021-12-09 20:26:50,118] multiqc [DEBUG ] No samples found: star [2021-12-09 20:26:50,123] multiqc [DEBUG ] No samples found: hisat2 [2021-12-09 20:26:50,127] multiqc [DEBUG ] No samples found: tophat [2021-12-09 20:26:50,132] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-09 20:26:50,136] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-09 20:26:50,140] multiqc [DEBUG ] No samples found: snpsplit [2021-12-09 20:26:50,145] multiqc [DEBUG ] No samples found: kat [2021-12-09 20:26:50,149] multiqc [DEBUG ] No samples found: leehom [2021-12-09 20:26:50,153] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-09 20:26:50,157] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-09 20:26:50,161] multiqc [DEBUG ] No samples found: cutadapt [2021-12-09 20:26:50,166] multiqc [DEBUG ] No samples found: flexbar [2021-12-09 20:26:50,171] multiqc [DEBUG ] No samples found: kaiju [2021-12-09 20:26:50,175] multiqc [DEBUG ] No samples found: kraken [2021-12-09 20:26:50,180] multiqc [DEBUG ] No samples found: malt [2021-12-09 20:26:50,184] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-09 20:26:50,188] multiqc [DEBUG ] No samples found: sickle [2021-12-09 20:26:50,192] multiqc [DEBUG ] No samples found: skewer [2021-12-09 20:26:50,196] multiqc [DEBUG ] No samples found: sortmerna [2021-12-09 20:26:50,200] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-09 20:26:50,205] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-09 20:26:50,209] multiqc [DEBUG ] No samples found: afterqc [2021-12-09 20:26:50,213] multiqc [DEBUG ] No samples found: fastp [2021-12-09 20:26:51,963] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2021-12-09 20:26:52,486] multiqc [DEBUG ] No samples found: pycoqc [2021-12-09 20:26:52,492] multiqc [DEBUG ] No samples found: minionqc [2021-12-09 20:26:52,497] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-09 20:26:52,501] multiqc [DEBUG ] No samples found: clusterflow [2021-12-09 20:26:52,506] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-09 20:26:52,510] multiqc [DEBUG ] No samples found: interop [2021-12-09 20:26:52,515] multiqc [DEBUG ] No samples found: ivar [2021-12-09 20:26:52,519] multiqc [DEBUG ] No samples found: flash [2021-12-09 20:26:52,524] multiqc [DEBUG ] No samples found: seqyclean [2021-12-09 20:26:52,524] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-09 20:26:52,524] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-09 20:26:52,524] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-09 20:26:52,524] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-09 20:26:52,553] multiqc [INFO ] Compressing plot data [2021-12-09 20:26:52,988] multiqc [INFO ] Report : multiqc_report.html [2021-12-09 20:26:52,988] multiqc [INFO ] Data : multiqc_data [2021-12-09 20:26:52,988] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12929488/tmpck0r8m_j/multiqc_data' to '/scratch/gencore/logs/html/HMCFHBGXK/merged/multiqc_data' [2021-12-09 20:26:53,109] multiqc [INFO ] MultiQC complete