[2022-03-12 01:42:55,125] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-12 01:42:55,125] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-12 01:42:55,125] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-12 01:42:55,126] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-12 01:42:55,126] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-12 01:42:55,127] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJLH2AFX3/merged [2022-03-12 01:42:55,873] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-12 01:42:55,874] multiqc [INFO ] This is MultiQC v1.9 [2022-03-12 01:42:55,874] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJLH2AFX3/merged [2022-03-12 01:42:55,874] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJLH2AFX3/merged [2022-03-12 01:42:55,874] multiqc [INFO ] Template : default [2022-03-12 01:42:55,874] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-12 01:42:55,874] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJLH2AFX3/merged [2022-03-12 01:42:55,874] 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 [2022-03-12 01:42:55,874] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15963366/tmp5wm3j62p [2022-03-12 01:42:55,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_2_fastqc.html [2022-03-12 01:42:55,993] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_2_fastqc.html [2022-03-12 01:42:56,038] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-12 01:42:56,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-12 01:42:56,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_4_fastqc.html [2022-03-12 01:42:56,264] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_4_fastqc.html [2022-03-12 01:42:56,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_5_fastqc.html [2022-03-12 01:42:56,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_5_fastqc.html [2022-03-12 01:42:56,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_7_fastqc.html [2022-03-12 01:42:56,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_7_fastqc.html [2022-03-12 01:42:56,400] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_8_fastqc.html [2022-03-12 01:42:56,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_8_fastqc.html [2022-03-12 01:42:56,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_3_fastqc.html [2022-03-12 01:42:56,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_3_fastqc.html [2022-03-12 01:42:56,492] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_5_fastqc.html [2022-03-12 01:42:56,494] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_5_fastqc.html [2022-03-12 01:42:56,536] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_1_fastqc.html [2022-03-12 01:42:56,538] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_1_fastqc.html [2022-03-12 01:42:56,580] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_1_fastqc.html [2022-03-12 01:42:56,582] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_1_fastqc.html [2022-03-12 01:42:56,625] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_6_fastqc.html [2022-03-12 01:42:56,627] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_6_fastqc.html [2022-03-12 01:42:56,672] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_4_fastqc.html [2022-03-12 01:42:56,674] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_4_fastqc.html [2022-03-12 01:42:56,715] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_2_fastqc.html [2022-03-12 01:42:56,717] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_2_fastqc.html [2022-03-12 01:42:56,757] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_3_fastqc.html [2022-03-12 01:42:56,759] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_3_fastqc.html [2022-03-12 01:42:56,798] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_undetermined_fastqc.html [2022-03-12 01:42:56,800] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_undetermined_fastqc.html [2022-03-12 01:42:56,841] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_6_fastqc.html [2022-03-12 01:42:56,843] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_dad2_6_fastqc.html [2022-03-12 01:42:56,885] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_7_fastqc.html [2022-03-12 01:42:56,887] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_7_fastqc.html [2022-03-12 01:42:56,931] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n01_undetermined_fastqc.html [2022-03-12 01:42:56,933] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n01_undetermined_fastqc.html [2022-03-12 01:42:56,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_8_fastqc.html [2022-03-12 01:42:56,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLH2AFX3_n02_dad2_8_fastqc.html [2022-03-12 01:42:57,335] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-12 01:42:57,337] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-12 01:42:57,347] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2022-03-12 01:42:57,349] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-12 01:42:57,358] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-12 01:42:57,363] multiqc [DEBUG ] No samples found: conpair [2022-03-12 01:42:57,368] multiqc [DEBUG ] No samples found: peddy [2022-03-12 01:42:57,376] multiqc [DEBUG ] No samples found: somalier [2022-03-12 01:42:57,381] multiqc [DEBUG ] No samples found: methylQA [2022-03-12 01:42:57,389] multiqc [DEBUG ] No samples found: mosdepth [2022-03-12 01:42:57,393] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-12 01:42:57,397] multiqc [DEBUG ] No samples found: qualimap [2022-03-12 01:42:57,401] multiqc [DEBUG ] No samples found: preseq [2022-03-12 01:42:57,406] multiqc [DEBUG ] No samples found: quast [2022-03-12 01:42:57,411] multiqc [DEBUG ] No samples found: qorts [2022-03-12 01:42:57,416] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-12 01:42:57,420] multiqc [DEBUG ] No samples found: rockhopper [2022-03-12 01:42:57,425] multiqc [DEBUG ] No samples found: rsem [2022-03-12 01:42:57,438] multiqc [DEBUG ] No samples found: rseqc [2022-03-12 01:42:57,442] multiqc [DEBUG ] No samples found: busco [2022-03-12 01:42:57,446] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-12 01:42:57,451] multiqc [DEBUG ] No samples found: disambiguate [2022-03-12 01:42:57,456] multiqc [DEBUG ] No samples found: supernova [2022-03-12 01:42:57,469] multiqc [DEBUG ] No samples found: deeptools [2022-03-12 01:42:57,474] multiqc [DEBUG ] No samples found: sargasso [2022-03-12 01:42:57,479] multiqc [DEBUG ] No samples found: verifybamid [2022-03-12 01:42:57,484] multiqc [DEBUG ] No samples found: mirtrace [2022-03-12 01:42:57,488] multiqc [DEBUG ] No samples found: happy [2022-03-12 01:42:57,493] multiqc [DEBUG ] No samples found: mirtop [2022-03-12 01:42:57,499] multiqc [DEBUG ] No samples found: homer [2022-03-12 01:42:57,504] multiqc [DEBUG ] No samples found: macs2 [2022-03-12 01:42:57,508] multiqc [DEBUG ] No samples found: theta2 [2022-03-12 01:42:57,513] multiqc [DEBUG ] No samples found: snpeff [2022-03-12 01:42:57,520] multiqc [DEBUG ] No samples found: gatk [2022-03-12 01:42:57,524] multiqc [DEBUG ] No samples found: htseq [2022-03-12 01:42:57,530] multiqc [DEBUG ] No samples found: bcftools [2022-03-12 01:42:57,534] multiqc [DEBUG ] No samples found: featureCounts [2022-03-12 01:42:57,541] multiqc [DEBUG ] No samples found: fgbio [2022-03-12 01:42:57,555] multiqc [DEBUG ] No samples found: dragen [2022-03-12 01:42:57,560] multiqc [DEBUG ] No samples found: dedup [2022-03-12 01:42:57,564] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-12 01:42:57,587] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-12 01:42:57,592] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-12 01:42:57,594] multiqc [DEBUG ] No samples found: picard [2022-03-12 01:42:57,599] multiqc [DEBUG ] No samples found: prokka [2022-03-12 01:42:57,603] multiqc [DEBUG ] No samples found: samblaster [2022-03-12 01:42:57,614] multiqc [DEBUG ] No samples found: samtools [2022-03-12 01:42:57,619] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-12 01:42:57,624] multiqc [DEBUG ] No samples found: bamtools [2022-03-12 01:42:57,628] multiqc [DEBUG ] No samples found: jellyfish [2022-03-12 01:42:57,637] multiqc [DEBUG ] No samples found: vcftools [2022-03-12 01:42:57,642] multiqc [DEBUG ] No samples found: longranger [2022-03-12 01:42:57,647] multiqc [DEBUG ] No samples found: stacks [2022-03-12 01:42:57,652] multiqc [DEBUG ] No samples found: varscan2 [2022-03-12 01:42:57,667] multiqc [DEBUG ] No samples found: bbmap [2022-03-12 01:42:57,671] multiqc [DEBUG ] No samples found: bismark [2022-03-12 01:42:57,676] multiqc [DEBUG ] No samples found: biscuit [2022-03-12 01:42:57,682] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-12 01:42:57,687] multiqc [DEBUG ] No samples found: hicup [2022-03-12 01:42:57,692] multiqc [DEBUG ] No samples found: hicpro [2022-03-12 01:42:57,696] multiqc [DEBUG ] No samples found: salmon [2022-03-12 01:42:57,701] multiqc [DEBUG ] No samples found: kallisto [2022-03-12 01:42:57,706] multiqc [DEBUG ] No samples found: slamdunk [2022-03-12 01:42:57,711] multiqc [DEBUG ] No samples found: star [2022-03-12 01:42:57,716] multiqc [DEBUG ] No samples found: hisat2 [2022-03-12 01:42:57,721] multiqc [DEBUG ] No samples found: tophat [2022-03-12 01:42:57,725] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-12 01:42:57,730] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-12 01:42:57,735] multiqc [DEBUG ] No samples found: snpsplit [2022-03-12 01:42:57,739] multiqc [DEBUG ] No samples found: kat [2022-03-12 01:42:57,743] multiqc [DEBUG ] No samples found: leehom [2022-03-12 01:42:57,748] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-12 01:42:57,752] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-12 01:42:57,757] multiqc [DEBUG ] No samples found: cutadapt [2022-03-12 01:42:57,761] multiqc [DEBUG ] No samples found: flexbar [2022-03-12 01:42:57,766] multiqc [DEBUG ] No samples found: kaiju [2022-03-12 01:42:57,771] multiqc [DEBUG ] No samples found: kraken [2022-03-12 01:42:57,775] multiqc [DEBUG ] No samples found: malt [2022-03-12 01:42:57,780] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-12 01:42:57,785] multiqc [DEBUG ] No samples found: sickle [2022-03-12 01:42:57,789] multiqc [DEBUG ] No samples found: skewer [2022-03-12 01:42:57,794] multiqc [DEBUG ] No samples found: sortmerna [2022-03-12 01:42:57,798] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-12 01:42:57,803] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-12 01:42:57,808] multiqc [DEBUG ] No samples found: afterqc [2022-03-12 01:42:57,812] multiqc [DEBUG ] No samples found: fastp [2022-03-12 01:42:58,286] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2022-03-12 01:42:58,657] multiqc [DEBUG ] No samples found: pycoqc [2022-03-12 01:42:58,662] multiqc [DEBUG ] No samples found: minionqc [2022-03-12 01:42:58,667] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-12 01:42:58,672] multiqc [DEBUG ] No samples found: clusterflow [2022-03-12 01:42:58,678] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-12 01:42:58,683] multiqc [DEBUG ] No samples found: interop [2022-03-12 01:42:58,687] multiqc [DEBUG ] No samples found: ivar [2022-03-12 01:42:58,692] multiqc [DEBUG ] No samples found: flash [2022-03-12 01:42:58,697] multiqc [DEBUG ] No samples found: seqyclean [2022-03-12 01:42:58,697] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-12 01:42:58,697] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-12 01:42:58,697] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-12 01:42:58,698] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-12 01:42:58,721] multiqc [INFO ] Compressing plot data [2022-03-12 01:42:59,060] multiqc [INFO ] Report : multiqc_report.html [2022-03-12 01:42:59,060] multiqc [INFO ] Data : multiqc_data [2022-03-12 01:42:59,060] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15963366/tmp5wm3j62p/multiqc_data' to '/scratch/gencore/logs/html/HJLH2AFX3/merged/multiqc_data' [2022-03-12 01:42:59,237] multiqc [INFO ] MultiQC complete