[2022-07-07 06:32:38,452] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-07 06:32:38,452] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-07 06:32:38,452] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-07 06:32:38,453] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-07 06:32:38,453] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-07 06:32:38,453] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HG7LNBGXM/merged [2022-07-07 06:32:39,016] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-07 06:32:39,017] multiqc [INFO ] This is MultiQC v1.9 [2022-07-07 06:32:39,017] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HG7LNBGXM/merged [2022-07-07 06:32:39,017] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HG7LNBGXM/merged [2022-07-07 06:32:39,017] multiqc [INFO ] Template : default [2022-07-07 06:32:39,017] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-07 06:32:39,017] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HG7LNBGXM/merged [2022-07-07 06:32:39,017] 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 [2022-07-07 06:32:39,017] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-21923517/tmp1x384nl1 [2022-07-07 06:32:39,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_wt_2_fastqc.html [2022-07-07 06:32:39,136] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_wt_2_fastqc.html [2022-07-07 06:32:39,179] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-07 06:32:39,181] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-07 06:32:39,294] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE1_1_fastqc.html [2022-07-07 06:32:39,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE1_1_fastqc.html [2022-07-07 06:32:39,336] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE2_2_fastqc.html [2022-07-07 06:32:39,338] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE2_2_fastqc.html [2022-07-07 06:32:39,379] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_wt_1_fastqc.html [2022-07-07 06:32:39,381] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_wt_1_fastqc.html [2022-07-07 06:32:39,423] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE4_2_fastqc.html [2022-07-07 06:32:39,425] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE4_2_fastqc.html [2022-07-07 06:32:39,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_new1_1_fastqc.html [2022-07-07 06:32:39,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_new1_1_fastqc.html [2022-07-07 06:32:39,509] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE1_2_fastqc.html [2022-07-07 06:32:39,511] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE1_2_fastqc.html [2022-07-07 06:32:39,551] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_new1_2_fastqc.html [2022-07-07 06:32:39,553] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_new1_2_fastqc.html [2022-07-07 06:32:39,594] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_wt_1_fastqc.html [2022-07-07 06:32:39,596] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_wt_1_fastqc.html [2022-07-07 06:32:39,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_new1_2_fastqc.html [2022-07-07 06:32:39,639] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_new1_2_fastqc.html [2022-07-07 06:32:39,681] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE4_1_fastqc.html [2022-07-07 06:32:39,682] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE4_1_fastqc.html [2022-07-07 06:32:39,724] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_undetermined_fastqc.html [2022-07-07 06:32:39,726] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_undetermined_fastqc.html [2022-07-07 06:32:39,768] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_new1_1_fastqc.html [2022-07-07 06:32:39,770] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_new1_1_fastqc.html [2022-07-07 06:32:39,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE2_1_fastqc.html [2022-07-07 06:32:39,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE2_1_fastqc.html [2022-07-07 06:32:39,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_undetermined_fastqc.html [2022-07-07 06:32:39,855] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_undetermined_fastqc.html [2022-07-07 06:32:39,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE4_2_fastqc.html [2022-07-07 06:32:39,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE4_2_fastqc.html [2022-07-07 06:32:39,940] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_wt_2_fastqc.html [2022-07-07 06:32:39,942] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_wt_2_fastqc.html [2022-07-07 06:32:39,985] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE1_1_fastqc.html [2022-07-07 06:32:39,987] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE1_1_fastqc.html [2022-07-07 06:32:40,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE4_1_fastqc.html [2022-07-07 06:32:40,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE4_1_fastqc.html [2022-07-07 06:32:40,071] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE2_2_fastqc.html [2022-07-07 06:32:40,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n01_OE2_2_fastqc.html [2022-07-07 06:32:40,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE1_2_fastqc.html [2022-07-07 06:32:40,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE1_2_fastqc.html [2022-07-07 06:32:40,158] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE2_1_fastqc.html [2022-07-07 06:32:40,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LNBGXM_n02_OE2_1_fastqc.html [2022-07-07 06:32:40,560] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-07 06:32:40,562] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-07 06:32:40,573] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2022-07-07 06:32:40,583] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-07 06:32:40,584] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-07 06:32:40,590] multiqc [DEBUG ] No samples found: conpair [2022-07-07 06:32:40,595] multiqc [DEBUG ] No samples found: peddy [2022-07-07 06:32:40,602] multiqc [DEBUG ] No samples found: somalier [2022-07-07 06:32:40,606] multiqc [DEBUG ] No samples found: methylQA [2022-07-07 06:32:40,615] multiqc [DEBUG ] No samples found: mosdepth [2022-07-07 06:32:40,618] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-07 06:32:40,622] multiqc [DEBUG ] No samples found: qualimap [2022-07-07 06:32:40,626] multiqc [DEBUG ] No samples found: preseq [2022-07-07 06:32:40,631] multiqc [DEBUG ] No samples found: quast [2022-07-07 06:32:40,635] multiqc [DEBUG ] No samples found: qorts [2022-07-07 06:32:40,639] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-07 06:32:40,644] multiqc [DEBUG ] No samples found: rockhopper [2022-07-07 06:32:40,650] multiqc [DEBUG ] No samples found: rsem [2022-07-07 06:32:40,665] multiqc [DEBUG ] No samples found: rseqc [2022-07-07 06:32:40,669] multiqc [DEBUG ] No samples found: busco [2022-07-07 06:32:40,675] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-07 06:32:40,679] multiqc [DEBUG ] No samples found: disambiguate [2022-07-07 06:32:40,686] multiqc [DEBUG ] No samples found: supernova [2022-07-07 06:32:40,700] multiqc [DEBUG ] No samples found: deeptools [2022-07-07 06:32:40,708] multiqc [DEBUG ] No samples found: sargasso [2022-07-07 06:32:40,713] multiqc [DEBUG ] No samples found: verifybamid [2022-07-07 06:32:40,718] multiqc [DEBUG ] No samples found: mirtrace [2022-07-07 06:32:40,724] multiqc [DEBUG ] No samples found: happy [2022-07-07 06:32:40,728] multiqc [DEBUG ] No samples found: mirtop [2022-07-07 06:32:40,735] multiqc [DEBUG ] No samples found: homer [2022-07-07 06:32:40,739] multiqc [DEBUG ] No samples found: macs2 [2022-07-07 06:32:40,744] multiqc [DEBUG ] No samples found: theta2 [2022-07-07 06:32:40,750] multiqc [DEBUG ] No samples found: snpeff [2022-07-07 06:32:40,757] multiqc [DEBUG ] No samples found: gatk [2022-07-07 06:32:40,761] multiqc [DEBUG ] No samples found: htseq [2022-07-07 06:32:40,768] multiqc [DEBUG ] No samples found: bcftools [2022-07-07 06:32:40,774] multiqc [DEBUG ] No samples found: featureCounts [2022-07-07 06:32:40,780] multiqc [DEBUG ] No samples found: fgbio [2022-07-07 06:32:40,793] multiqc [DEBUG ] No samples found: dragen [2022-07-07 06:32:40,797] multiqc [DEBUG ] No samples found: dedup [2022-07-07 06:32:40,804] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-07 06:32:40,825] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-07 06:32:40,829] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-07 06:32:40,832] multiqc [DEBUG ] No samples found: picard [2022-07-07 06:32:40,838] multiqc [DEBUG ] No samples found: prokka [2022-07-07 06:32:40,843] multiqc [DEBUG ] No samples found: samblaster [2022-07-07 06:32:40,852] multiqc [DEBUG ] No samples found: samtools [2022-07-07 06:32:40,858] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-07 06:32:40,862] multiqc [DEBUG ] No samples found: bamtools [2022-07-07 06:32:40,866] multiqc [DEBUG ] No samples found: jellyfish [2022-07-07 06:32:40,880] multiqc [DEBUG ] No samples found: vcftools [2022-07-07 06:32:40,887] multiqc [DEBUG ] No samples found: longranger [2022-07-07 06:32:40,891] multiqc [DEBUG ] No samples found: stacks [2022-07-07 06:32:40,895] multiqc [DEBUG ] No samples found: varscan2 [2022-07-07 06:32:40,910] multiqc [DEBUG ] No samples found: bbmap [2022-07-07 06:32:40,917] multiqc [DEBUG ] No samples found: bismark [2022-07-07 06:32:40,921] multiqc [DEBUG ] No samples found: biscuit [2022-07-07 06:32:40,928] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-07 06:32:40,932] multiqc [DEBUG ] No samples found: hicup [2022-07-07 06:32:40,936] multiqc [DEBUG ] No samples found: hicpro [2022-07-07 06:32:40,940] multiqc [DEBUG ] No samples found: salmon [2022-07-07 06:32:40,945] multiqc [DEBUG ] No samples found: kallisto [2022-07-07 06:32:40,951] multiqc [DEBUG ] No samples found: slamdunk [2022-07-07 06:32:40,957] multiqc [DEBUG ] No samples found: star [2022-07-07 06:32:40,961] multiqc [DEBUG ] No samples found: hisat2 [2022-07-07 06:32:40,965] multiqc [DEBUG ] No samples found: tophat [2022-07-07 06:32:40,971] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-07 06:32:40,976] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-07 06:32:40,983] multiqc [DEBUG ] No samples found: snpsplit [2022-07-07 06:32:40,987] multiqc [DEBUG ] No samples found: kat [2022-07-07 06:32:40,992] multiqc [DEBUG ] No samples found: leehom [2022-07-07 06:32:40,996] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-07 06:32:41,002] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-07 06:32:41,006] multiqc [DEBUG ] No samples found: cutadapt [2022-07-07 06:32:41,010] multiqc [DEBUG ] No samples found: flexbar [2022-07-07 06:32:41,014] multiqc [DEBUG ] No samples found: kaiju [2022-07-07 06:32:41,018] multiqc [DEBUG ] No samples found: kraken [2022-07-07 06:32:41,025] multiqc [DEBUG ] No samples found: malt [2022-07-07 06:32:41,029] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-07 06:32:41,033] multiqc [DEBUG ] No samples found: sickle [2022-07-07 06:32:41,039] multiqc [DEBUG ] No samples found: skewer [2022-07-07 06:32:41,043] multiqc [DEBUG ] No samples found: sortmerna [2022-07-07 06:32:41,048] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-07 06:32:41,055] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-07 06:32:41,061] multiqc [DEBUG ] No samples found: afterqc [2022-07-07 06:32:41,068] multiqc [DEBUG ] No samples found: fastp [2022-07-07 06:32:42,543] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2022-07-07 06:32:43,011] multiqc [DEBUG ] No samples found: pycoqc [2022-07-07 06:32:43,016] multiqc [DEBUG ] No samples found: minionqc [2022-07-07 06:32:43,022] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-07 06:32:43,029] multiqc [DEBUG ] No samples found: clusterflow [2022-07-07 06:32:43,033] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-07 06:32:43,039] multiqc [DEBUG ] No samples found: interop [2022-07-07 06:32:43,045] multiqc [DEBUG ] No samples found: ivar [2022-07-07 06:32:43,050] multiqc [DEBUG ] No samples found: flash [2022-07-07 06:32:43,056] multiqc [DEBUG ] No samples found: seqyclean [2022-07-07 06:32:43,056] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-07 06:32:43,056] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-07 06:32:43,056] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-07 06:32:43,057] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-07 06:32:43,083] multiqc [INFO ] Compressing plot data [2022-07-07 06:32:43,488] multiqc [INFO ] Report : multiqc_report.html [2022-07-07 06:32:43,489] multiqc [INFO ] Data : multiqc_data [2022-07-07 06:32:43,489] multiqc [DEBUG ] Moving data file from '/state/partition1/job-21923517/tmp1x384nl1/multiqc_data' to '/scratch/gencore/logs/html/HG7LNBGXM/merged/multiqc_data' [2022-07-07 06:32:44,198] multiqc [INFO ] MultiQC complete