[2022-02-05 15:09:16,430] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-02-05 15:09:16,430] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-02-05 15:09:16,430] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-05 15:09:16,431] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-02-05 15:09:16,431] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-02-05 15:09:16,431] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHKFVAFX3/merged [2022-02-05 15:09:17,855] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-02-05 15:09:17,855] multiqc [INFO ] This is MultiQC v1.9 [2022-02-05 15:09:17,855] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHKFVAFX3/merged [2022-02-05 15:09:17,855] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HHKFVAFX3/merged [2022-02-05 15:09:17,855] multiqc [INFO ] Template : default [2022-02-05 15:09:17,855] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-02-05 15:09:17,855] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HHKFVAFX3/merged [2022-02-05 15:09:17,855] 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 [2022-02-05 15:09:17,856] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14680989/tmpbz5e48fi [2022-02-05 15:09:17,947] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A3_fastqc.html [2022-02-05 15:09:17,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HHKFVAFX3_n02_7797-T0-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,286] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-C2_fastqc.html [2022-02-05 15:09:18,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-C2_fastqc.html [2022-02-05 15:09:18,327] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A4_fastqc.html [2022-02-05 15:09:18,329] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A4_fastqc.html [2022-02-05 15:09:18,368] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A4_fastqc.html [2022-02-05 15:09:18,370] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A4_fastqc.html [2022-02-05 15:09:18,408] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-T3-Input-Sir4_fastqc.html [2022-02-05 15:09:18,410] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-T3-Input-Sir4_fastqc.html [2022-02-05 15:09:18,449] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-C3_fastqc.html [2022-02-05 15:09:18,451] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-C3_fastqc.html [2022-02-05 15:09:18,490] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-C1_fastqc.html [2022-02-05 15:09:18,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-C1_fastqc.html [2022-02-05 15:09:18,530] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A5_fastqc.html [2022-02-05 15:09:18,532] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A5_fastqc.html [2022-02-05 15:09:18,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A3_fastqc.html [2022-02-05 15:09:18,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A3_fastqc.html [2022-02-05 15:09:18,613] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-T3-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-T3-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,653] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-log-Input-Sir4_fastqc.html [2022-02-05 15:09:18,655] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-log-Input-Sir4_fastqc.html [2022-02-05 15:09:18,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-C2_fastqc.html [2022-02-05 15:09:18,695] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-C2_fastqc.html [2022-02-05 15:09:18,735] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_undetermined_fastqc.html [2022-02-05 15:09:18,737] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_undetermined_fastqc.html [2022-02-05 15:09:18,776] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-T3-Input-Sir4_fastqc.html [2022-02-05 15:09:18,777] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-T3-Input-Sir4_fastqc.html [2022-02-05 15:09:18,816] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-log-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-log-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,857] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-log-Input-Sir4_fastqc.html [2022-02-05 15:09:18,859] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-log-Input-Sir4_fastqc.html [2022-02-05 15:09:18,899] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-log-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,901] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-log-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,941] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-T0-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,943] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_7797-T0-ChIP-Sir4_fastqc.html [2022-02-05 15:09:18,981] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A1_fastqc.html [2022-02-05 15:09:18,983] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A1_fastqc.html [2022-02-05 15:09:19,024] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A6_fastqc.html [2022-02-05 15:09:19,025] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A6_fastqc.html [2022-02-05 15:09:19,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A5_fastqc.html [2022-02-05 15:09:19,066] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A5_fastqc.html [2022-02-05 15:09:19,105] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_undetermined_fastqc.html [2022-02-05 15:09:19,106] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_undetermined_fastqc.html [2022-02-05 15:09:19,145] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-C1_fastqc.html [2022-02-05 15:09:19,147] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-C1_fastqc.html [2022-02-05 15:09:19,185] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A1_fastqc.html [2022-02-05 15:09:19,187] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A1_fastqc.html [2022-02-05 15:09:19,225] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-T0-Input-Sir4_fastqc.html [2022-02-05 15:09:19,227] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_7797-T0-Input-Sir4_fastqc.html [2022-02-05 15:09:19,266] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A2_fastqc.html [2022-02-05 15:09:19,268] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n02_p25-A2_fastqc.html [2022-02-05 15:09:19,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A2_fastqc.html [2022-02-05 15:09:19,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHKFVAFX3_n01_p25-A2_fastqc.html [2022-02-05 15:09:19,605] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-05 15:09:19,605] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-05 15:09:19,612] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-02-05 15:09:19,621] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-02-05 15:09:19,629] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 16 samples (table) [2022-02-05 15:09:19,632] multiqc [DEBUG ] No samples found: conpair [2022-02-05 15:09:19,635] multiqc [DEBUG ] No samples found: peddy [2022-02-05 15:09:19,639] multiqc [DEBUG ] No samples found: somalier [2022-02-05 15:09:19,641] multiqc [DEBUG ] No samples found: methylQA [2022-02-05 15:09:19,646] multiqc [DEBUG ] No samples found: mosdepth [2022-02-05 15:09:19,649] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-05 15:09:19,651] multiqc [DEBUG ] No samples found: qualimap [2022-02-05 15:09:19,654] multiqc [DEBUG ] No samples found: preseq [2022-02-05 15:09:19,657] multiqc [DEBUG ] No samples found: quast [2022-02-05 15:09:19,660] multiqc [DEBUG ] No samples found: qorts [2022-02-05 15:09:19,663] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-05 15:09:19,666] multiqc [DEBUG ] No samples found: rockhopper [2022-02-05 15:09:19,669] multiqc [DEBUG ] No samples found: rsem [2022-02-05 15:09:19,675] multiqc [DEBUG ] No samples found: rseqc [2022-02-05 15:09:19,678] multiqc [DEBUG ] No samples found: busco [2022-02-05 15:09:19,681] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-05 15:09:19,684] multiqc [DEBUG ] No samples found: disambiguate [2022-02-05 15:09:19,687] multiqc [DEBUG ] No samples found: supernova [2022-02-05 15:09:19,693] multiqc [DEBUG ] No samples found: deeptools [2022-02-05 15:09:19,696] multiqc [DEBUG ] No samples found: sargasso [2022-02-05 15:09:19,699] multiqc [DEBUG ] No samples found: verifybamid [2022-02-05 15:09:19,702] multiqc [DEBUG ] No samples found: mirtrace [2022-02-05 15:09:19,705] multiqc [DEBUG ] No samples found: happy [2022-02-05 15:09:19,708] multiqc [DEBUG ] No samples found: mirtop [2022-02-05 15:09:19,712] multiqc [DEBUG ] No samples found: homer [2022-02-05 15:09:19,715] multiqc [DEBUG ] No samples found: macs2 [2022-02-05 15:09:19,718] multiqc [DEBUG ] No samples found: theta2 [2022-02-05 15:09:19,720] multiqc [DEBUG ] No samples found: snpeff [2022-02-05 15:09:19,724] multiqc [DEBUG ] No samples found: gatk [2022-02-05 15:09:19,727] multiqc [DEBUG ] No samples found: htseq [2022-02-05 15:09:19,730] multiqc [DEBUG ] No samples found: bcftools [2022-02-05 15:09:19,733] multiqc [DEBUG ] No samples found: featureCounts [2022-02-05 15:09:19,737] multiqc [DEBUG ] No samples found: fgbio [2022-02-05 15:09:19,743] multiqc [DEBUG ] No samples found: dragen [2022-02-05 15:09:19,746] multiqc [DEBUG ] No samples found: dedup [2022-02-05 15:09:19,749] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-05 15:09:19,758] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-05 15:09:19,761] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-05 15:09:19,764] multiqc [DEBUG ] No samples found: picard [2022-02-05 15:09:19,766] multiqc [DEBUG ] No samples found: prokka [2022-02-05 15:09:19,769] multiqc [DEBUG ] No samples found: samblaster [2022-02-05 15:09:19,774] multiqc [DEBUG ] No samples found: samtools [2022-02-05 15:09:19,777] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-05 15:09:19,780] multiqc [DEBUG ] No samples found: bamtools [2022-02-05 15:09:19,783] multiqc [DEBUG ] No samples found: jellyfish [2022-02-05 15:09:19,787] multiqc [DEBUG ] No samples found: vcftools [2022-02-05 15:09:19,790] multiqc [DEBUG ] No samples found: longranger [2022-02-05 15:09:19,793] multiqc [DEBUG ] No samples found: stacks [2022-02-05 15:09:19,796] multiqc [DEBUG ] No samples found: varscan2 [2022-02-05 15:09:19,802] multiqc [DEBUG ] No samples found: bbmap [2022-02-05 15:09:19,805] multiqc [DEBUG ] No samples found: bismark [2022-02-05 15:09:19,808] multiqc [DEBUG ] No samples found: biscuit [2022-02-05 15:09:19,811] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-05 15:09:19,814] multiqc [DEBUG ] No samples found: hicup [2022-02-05 15:09:19,817] multiqc [DEBUG ] No samples found: hicpro [2022-02-05 15:09:19,820] multiqc [DEBUG ] No samples found: salmon [2022-02-05 15:09:19,823] multiqc [DEBUG ] No samples found: kallisto [2022-02-05 15:09:19,826] multiqc [DEBUG ] No samples found: slamdunk [2022-02-05 15:09:19,829] multiqc [DEBUG ] No samples found: star [2022-02-05 15:09:19,832] multiqc [DEBUG ] No samples found: hisat2 [2022-02-05 15:09:19,835] multiqc [DEBUG ] No samples found: tophat [2022-02-05 15:09:19,838] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-05 15:09:19,841] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-05 15:09:19,844] multiqc [DEBUG ] No samples found: snpsplit [2022-02-05 15:09:19,847] multiqc [DEBUG ] No samples found: kat [2022-02-05 15:09:19,850] multiqc [DEBUG ] No samples found: leehom [2022-02-05 15:09:19,853] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-05 15:09:19,856] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-05 15:09:19,859] multiqc [DEBUG ] No samples found: cutadapt [2022-02-05 15:09:19,862] multiqc [DEBUG ] No samples found: flexbar [2022-02-05 15:09:19,865] multiqc [DEBUG ] No samples found: kaiju [2022-02-05 15:09:19,868] multiqc [DEBUG ] No samples found: kraken [2022-02-05 15:09:19,870] multiqc [DEBUG ] No samples found: malt [2022-02-05 15:09:19,873] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-05 15:09:19,876] multiqc [DEBUG ] No samples found: sickle [2022-02-05 15:09:19,879] multiqc [DEBUG ] No samples found: skewer [2022-02-05 15:09:19,882] multiqc [DEBUG ] No samples found: sortmerna [2022-02-05 15:09:19,885] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-05 15:09:19,888] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-05 15:09:19,891] multiqc [DEBUG ] No samples found: afterqc [2022-02-05 15:09:19,894] multiqc [DEBUG ] No samples found: fastp [2022-02-05 15:09:20,576] multiqc.modules.fastqc.fastqc [INFO ] Found 32 reports [2022-02-05 15:09:20,842] multiqc [DEBUG ] No samples found: pycoqc [2022-02-05 15:09:20,845] multiqc [DEBUG ] No samples found: minionqc [2022-02-05 15:09:20,848] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-02-05 15:09:20,851] multiqc [DEBUG ] No samples found: clusterflow [2022-02-05 15:09:20,854] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-05 15:09:20,857] multiqc [DEBUG ] No samples found: interop [2022-02-05 15:09:20,860] multiqc [DEBUG ] No samples found: ivar [2022-02-05 15:09:20,863] multiqc [DEBUG ] No samples found: flash [2022-02-05 15:09:20,866] multiqc [DEBUG ] No samples found: seqyclean [2022-02-05 15:09:20,866] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-02-05 15:09:20,866] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-02-05 15:09:20,866] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-02-05 15:09:20,867] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-02-05 15:09:20,904] multiqc [INFO ] Compressing plot data [2022-02-05 15:09:21,445] multiqc [INFO ] Report : multiqc_report.html [2022-02-05 15:09:21,445] multiqc [INFO ] Data : multiqc_data [2022-02-05 15:09:21,445] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14680989/tmpbz5e48fi/multiqc_data' to '/scratch/gencore/logs/html/HHKFVAFX3/merged/multiqc_data' [2022-02-05 15:09:21,545] multiqc [INFO ] MultiQC complete