[2022-11-09 15:23:54,600] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-09 15:23:54,600] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-09 15:23:54,600] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-09 15:23:54,601] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-09 15:23:54,601] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-09 15:23:54,601] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2CMYAFX5/merged [2022-11-09 15:23:55,085] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-09 15:23:55,085] multiqc [INFO ] This is MultiQC v1.9 [2022-11-09 15:23:55,085] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2CMYAFX5/merged [2022-11-09 15:23:55,085] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H2CMYAFX5/merged [2022-11-09 15:23:55,085] multiqc [INFO ] Template : default [2022-11-09 15:23:55,085] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-09 15:23:55,085] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H2CMYAFX5/merged [2022-11-09 15:23:55,085] 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 [2022-11-09 15:23:55,086] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26865040/tmpxesmixrb [2022-11-09 15:23:55,203] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_5_fastqc.html [2022-11-09 15:23:55,206] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_5_fastqc.html [2022-11-09 15:23:55,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:23:55,253] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-09 15:24:02,289] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_3_fastqc.html [2022-11-09 15:24:02,291] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_3_fastqc.html [2022-11-09 15:24:02,336] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_1_fastqc.html [2022-11-09 15:24:02,338] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_1_fastqc.html [2022-11-09 15:24:02,382] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_3_fastqc.html [2022-11-09 15:24:02,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_3_fastqc.html [2022-11-09 15:24:02,429] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_12_fastqc.html [2022-11-09 15:24:02,431] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_12_fastqc.html [2022-11-09 15:24:02,476] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_12_fastqc.html [2022-11-09 15:24:02,477] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_12_fastqc.html [2022-11-09 15:24:02,521] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_10_fastqc.html [2022-11-09 15:24:02,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_10_fastqc.html [2022-11-09 15:24:02,565] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_6_fastqc.html [2022-11-09 15:24:02,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_6_fastqc.html [2022-11-09 15:24:02,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_4_fastqc.html [2022-11-09 15:24:02,610] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_4_fastqc.html [2022-11-09 15:24:02,651] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_11_fastqc.html [2022-11-09 15:24:02,653] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_11_fastqc.html [2022-11-09 15:24:02,695] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_11_fastqc.html [2022-11-09 15:24:02,696] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_11_fastqc.html [2022-11-09 15:24:02,737] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_6_fastqc.html [2022-11-09 15:24:02,739] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_6_fastqc.html [2022-11-09 15:24:02,780] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_7_fastqc.html [2022-11-09 15:24:02,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_7_fastqc.html [2022-11-09 15:24:02,823] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_2_fastqc.html [2022-11-09 15:24:02,824] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_2_fastqc.html [2022-11-09 15:24:02,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_5_fastqc.html [2022-11-09 15:24:02,867] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_5_fastqc.html [2022-11-09 15:24:02,909] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_2_fastqc.html [2022-11-09 15:24:02,910] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_2_fastqc.html [2022-11-09 15:24:02,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_4_fastqc.html [2022-11-09 15:24:02,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_4_fastqc.html [2022-11-09 15:24:02,994] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_10_fastqc.html [2022-11-09 15:24:02,996] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_10_fastqc.html [2022-11-09 15:24:03,039] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_1_fastqc.html [2022-11-09 15:24:03,040] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_dad553_hrq1_1_fastqc.html [2022-11-09 15:24:03,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_undetermined_fastqc.html [2022-11-09 15:24:03,083] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_undetermined_fastqc.html [2022-11-09 15:24:03,125] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n01_undetermined_fastqc.html [2022-11-09 15:24:03,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n01_undetermined_fastqc.html [2022-11-09 15:24:03,168] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_7_fastqc.html [2022-11-09 15:24:03,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMYAFX5_n02_dad553_hrq1_7_fastqc.html [2022-11-09 15:24:03,507] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-09 15:24:03,508] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-09 15:24:03,517] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-09 15:24:03,522] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2022-11-09 15:24:03,532] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-09 15:24:03,538] multiqc [DEBUG ] No samples found: conpair [2022-11-09 15:24:03,543] multiqc [DEBUG ] No samples found: peddy [2022-11-09 15:24:03,548] multiqc [DEBUG ] No samples found: somalier [2022-11-09 15:24:03,555] multiqc [DEBUG ] No samples found: methylQA [2022-11-09 15:24:03,565] multiqc [DEBUG ] No samples found: mosdepth [2022-11-09 15:24:03,570] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-09 15:24:03,574] multiqc [DEBUG ] No samples found: qualimap [2022-11-09 15:24:03,579] multiqc [DEBUG ] No samples found: preseq [2022-11-09 15:24:03,586] multiqc [DEBUG ] No samples found: quast [2022-11-09 15:24:03,592] multiqc [DEBUG ] No samples found: qorts [2022-11-09 15:24:03,597] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-09 15:24:03,602] multiqc [DEBUG ] No samples found: rockhopper [2022-11-09 15:24:03,608] multiqc [DEBUG ] No samples found: rsem [2022-11-09 15:24:03,621] multiqc [DEBUG ] No samples found: rseqc [2022-11-09 15:24:03,626] multiqc [DEBUG ] No samples found: busco [2022-11-09 15:24:03,631] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-09 15:24:03,636] multiqc [DEBUG ] No samples found: disambiguate [2022-11-09 15:24:03,642] multiqc [DEBUG ] No samples found: supernova [2022-11-09 15:24:03,657] multiqc [DEBUG ] No samples found: deeptools [2022-11-09 15:24:03,663] multiqc [DEBUG ] No samples found: sargasso [2022-11-09 15:24:03,668] multiqc [DEBUG ] No samples found: verifybamid [2022-11-09 15:24:03,674] multiqc [DEBUG ] No samples found: mirtrace [2022-11-09 15:24:03,680] multiqc [DEBUG ] No samples found: happy [2022-11-09 15:24:03,685] multiqc [DEBUG ] No samples found: mirtop [2022-11-09 15:24:03,693] multiqc [DEBUG ] No samples found: homer [2022-11-09 15:24:03,699] multiqc [DEBUG ] No samples found: macs2 [2022-11-09 15:24:03,704] multiqc [DEBUG ] No samples found: theta2 [2022-11-09 15:24:03,710] multiqc [DEBUG ] No samples found: snpeff [2022-11-09 15:24:03,718] multiqc [DEBUG ] No samples found: gatk [2022-11-09 15:24:03,724] multiqc [DEBUG ] No samples found: htseq [2022-11-09 15:24:03,730] multiqc [DEBUG ] No samples found: bcftools [2022-11-09 15:24:03,736] multiqc [DEBUG ] No samples found: featureCounts [2022-11-09 15:24:03,744] multiqc [DEBUG ] No samples found: fgbio [2022-11-09 15:24:03,758] multiqc [DEBUG ] No samples found: dragen [2022-11-09 15:24:03,764] multiqc [DEBUG ] No samples found: dedup [2022-11-09 15:24:03,768] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-09 15:24:03,796] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-09 15:24:03,802] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-09 15:24:03,804] multiqc [DEBUG ] No samples found: picard [2022-11-09 15:24:03,818] multiqc [DEBUG ] No samples found: prokka [2022-11-09 15:24:03,822] multiqc [DEBUG ] No samples found: samblaster [2022-11-09 15:24:03,833] multiqc [DEBUG ] No samples found: samtools [2022-11-09 15:24:03,840] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-09 15:24:03,846] multiqc [DEBUG ] No samples found: bamtools [2022-11-09 15:24:03,852] multiqc [DEBUG ] No samples found: jellyfish [2022-11-09 15:24:03,860] multiqc [DEBUG ] No samples found: vcftools [2022-11-09 15:24:03,866] multiqc [DEBUG ] No samples found: longranger [2022-11-09 15:24:03,871] multiqc [DEBUG ] No samples found: stacks [2022-11-09 15:24:03,876] multiqc [DEBUG ] No samples found: varscan2 [2022-11-09 15:24:03,893] multiqc [DEBUG ] No samples found: bbmap [2022-11-09 15:24:03,898] multiqc [DEBUG ] No samples found: bismark [2022-11-09 15:24:03,904] multiqc [DEBUG ] No samples found: biscuit [2022-11-09 15:24:03,910] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-09 15:24:03,916] multiqc [DEBUG ] No samples found: hicup [2022-11-09 15:24:03,922] multiqc [DEBUG ] No samples found: hicpro [2022-11-09 15:24:03,928] multiqc [DEBUG ] No samples found: salmon [2022-11-09 15:24:03,937] multiqc [DEBUG ] No samples found: kallisto [2022-11-09 15:24:03,942] multiqc [DEBUG ] No samples found: slamdunk [2022-11-09 15:24:03,948] multiqc [DEBUG ] No samples found: star [2022-11-09 15:24:03,954] multiqc [DEBUG ] No samples found: hisat2 [2022-11-09 15:24:03,960] multiqc [DEBUG ] No samples found: tophat [2022-11-09 15:24:03,968] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-09 15:24:03,973] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-09 15:24:03,979] multiqc [DEBUG ] No samples found: snpsplit [2022-11-09 15:24:03,984] multiqc [DEBUG ] No samples found: kat [2022-11-09 15:24:03,990] multiqc [DEBUG ] No samples found: leehom [2022-11-09 15:24:03,995] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-09 15:24:04,001] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-09 15:24:04,006] multiqc [DEBUG ] No samples found: cutadapt [2022-11-09 15:24:04,011] multiqc [DEBUG ] No samples found: flexbar [2022-11-09 15:24:04,016] multiqc [DEBUG ] No samples found: kaiju [2022-11-09 15:24:04,021] multiqc [DEBUG ] No samples found: kraken [2022-11-09 15:24:04,028] multiqc [DEBUG ] No samples found: malt [2022-11-09 15:24:04,033] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-09 15:24:04,040] multiqc [DEBUG ] No samples found: sickle [2022-11-09 15:24:04,046] multiqc [DEBUG ] No samples found: skewer [2022-11-09 15:24:04,051] multiqc [DEBUG ] No samples found: sortmerna [2022-11-09 15:24:04,057] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-09 15:24:04,063] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-09 15:24:04,069] multiqc [DEBUG ] No samples found: afterqc [2022-11-09 15:24:04,075] multiqc [DEBUG ] No samples found: fastp [2022-11-09 15:24:04,655] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2022-11-09 15:24:05,154] multiqc [DEBUG ] No samples found: pycoqc [2022-11-09 15:24:05,160] multiqc [DEBUG ] No samples found: minionqc [2022-11-09 15:24:05,164] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-09 15:24:05,170] multiqc [DEBUG ] No samples found: clusterflow [2022-11-09 15:24:05,176] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-09 15:24:05,181] multiqc [DEBUG ] No samples found: interop [2022-11-09 15:24:05,187] multiqc [DEBUG ] No samples found: ivar [2022-11-09 15:24:05,192] multiqc [DEBUG ] No samples found: flash [2022-11-09 15:24:05,197] multiqc [DEBUG ] No samples found: seqyclean [2022-11-09 15:24:05,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-09 15:24:05,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-09 15:24:05,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-09 15:24:05,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-09 15:24:05,226] multiqc [INFO ] Compressing plot data [2022-11-09 15:24:05,628] multiqc [INFO ] Report : multiqc_report.html [2022-11-09 15:24:05,628] multiqc [INFO ] Data : multiqc_data [2022-11-09 15:24:05,628] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26865040/tmpxesmixrb/multiqc_data' to '/scratch/gencore/logs/html/H2CMYAFX5/merged/multiqc_data' [2022-11-09 15:24:05,765] multiqc [INFO ] MultiQC complete