[2021-05-14 04:29:51,380] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-05-14 04:29:51,380] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-05-14 04:29:51,381] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-05-14 04:29:51,381] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-05-14 04:29:51,381] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-05-14 04:29:51,382] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWMWVAFX2/merged [2021-05-14 04:29:52,731] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-05-14 04:29:52,731] multiqc [INFO ] This is MultiQC v1.9 [2021-05-14 04:29:52,731] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWMWVAFX2/merged [2021-05-14 04:29:52,731] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWMWVAFX2/merged [2021-05-14 04:29:52,731] multiqc [INFO ] Template : default [2021-05-14 04:29:52,731] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-05-14 04:29:52,731] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWMWVAFX2/merged [2021-05-14 04:29:52,731] 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 [2021-05-14 04:29:52,732] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-6810457/tmplk601e48 [2021-05-14 04:29:52,836] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2447.dk_fastqc.html [2021-05-14 04:29:52,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2021-05-14 04:29:53,952] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2438.dk_fastqc.html [2021-05-14 04:29:53,991] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2434.dk_fastqc.html [2021-05-14 04:29:53,993] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2434.dk_fastqc.html [2021-05-14 04:29:54,034] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2449.dk_fastqc.html [2021-05-14 04:29:54,036] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2449.dk_fastqc.html [2021-05-14 04:29:54,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2455.dk_fastqc.html [2021-05-14 04:29:54,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2455.dk_fastqc.html [2021-05-14 04:29:54,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2445.dk_fastqc.html [2021-05-14 04:29:54,118] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2445.dk_fastqc.html [2021-05-14 04:29:54,159] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2435.dk_fastqc.html [2021-05-14 04:29:54,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2435.dk_fastqc.html [2021-05-14 04:29:54,200] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2454.dk_fastqc.html [2021-05-14 04:29:54,202] multiqc [DEBUG ] File ignored by 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because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2440.dk_fastqc.html [2021-05-14 04:29:54,366] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2446.dk_fastqc.html [2021-05-14 04:29:54,368] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2446.dk_fastqc.html [2021-05-14 04:29:54,408] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2449.dk_fastqc.html [2021-05-14 04:29:54,409] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2449.dk_fastqc.html [2021-05-14 04:29:54,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2450.dk_fastqc.html [2021-05-14 04:29:54,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n01_2450.dk_fastqc.html [2021-05-14 04:29:54,490] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2444.dk_fastqc.html [2021-05-14 04:29:54,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2444.dk_fastqc.html [2021-05-14 04:29:54,531] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2437.dk_fastqc.html [2021-05-14 04:29:54,533] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2437.dk_fastqc.html [2021-05-14 04:29:54,572] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2447.dk_fastqc.html [2021-05-14 04:29:54,574] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2447.dk_fastqc.html [2021-05-14 04:29:54,614] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2440.dk_fastqc.html [2021-05-14 04:29:54,616] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2440.dk_fastqc.html [2021-05-14 04:29:54,656] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2445.dk_fastqc.html [2021-05-14 04:29:54,657] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMWVAFX2_n02_2445.dk_fastqc.html [2021-05-14 04:29:55,143] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-14 04:29:55,144] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-14 04:29:55,159] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-05-14 04:29:55,161] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-05-14 04:29:55,171] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2021-05-14 04:29:55,176] multiqc [DEBUG ] No samples found: conpair [2021-05-14 04:29:55,180] multiqc [DEBUG ] No samples found: peddy [2021-05-14 04:29:55,184] multiqc [DEBUG ] No samples found: somalier [2021-05-14 04:29:55,189] multiqc [DEBUG ] No samples found: methylQA [2021-05-14 04:29:55,195] multiqc [DEBUG ] No samples found: mosdepth [2021-05-14 04:29:55,199] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-05-14 04:29:55,203] multiqc [DEBUG ] No samples found: qualimap [2021-05-14 04:29:55,207] multiqc [DEBUG ] No samples found: preseq [2021-05-14 04:29:55,211] multiqc [DEBUG ] No samples found: quast [2021-05-14 04:29:55,216] multiqc [DEBUG ] No samples found: qorts [2021-05-14 04:29:55,220] multiqc [DEBUG ] No samples found: rna_seqc [2021-05-14 04:29:55,224] multiqc [DEBUG ] No samples found: rockhopper [2021-05-14 04:29:55,228] multiqc [DEBUG ] No samples found: rsem [2021-05-14 04:29:55,237] multiqc [DEBUG ] No samples found: rseqc [2021-05-14 04:29:55,241] multiqc [DEBUG ] No samples found: busco [2021-05-14 04:29:55,245] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-05-14 04:29:55,249] multiqc [DEBUG ] No samples found: disambiguate [2021-05-14 04:29:55,253] multiqc [DEBUG ] No samples found: supernova [2021-05-14 04:29:55,263] multiqc [DEBUG ] No samples found: deeptools [2021-05-14 04:29:55,267] multiqc [DEBUG ] No samples found: sargasso [2021-05-14 04:29:55,271] multiqc [DEBUG ] No samples found: verifybamid [2021-05-14 04:29:55,275] multiqc [DEBUG ] No samples found: mirtrace [2021-05-14 04:29:55,279] multiqc [DEBUG ] No samples found: happy [2021-05-14 04:29:55,284] multiqc [DEBUG ] No samples found: mirtop [2021-05-14 04:29:55,289] multiqc [DEBUG ] No samples found: homer [2021-05-14 04:29:55,293] multiqc [DEBUG ] No samples found: macs2 [2021-05-14 04:29:55,298] multiqc [DEBUG ] No samples found: theta2 [2021-05-14 04:29:55,302] multiqc [DEBUG ] No samples found: snpeff [2021-05-14 04:29:55,308] multiqc [DEBUG ] No samples found: gatk [2021-05-14 04:29:55,312] multiqc [DEBUG ] No samples found: htseq [2021-05-14 04:29:55,317] multiqc [DEBUG ] No samples found: bcftools [2021-05-14 04:29:55,321] multiqc [DEBUG ] No samples found: featureCounts [2021-05-14 04:29:55,326] multiqc [DEBUG ] No samples found: fgbio [2021-05-14 04:29:55,336] multiqc [DEBUG ] No samples found: dragen [2021-05-14 04:29:55,341] multiqc [DEBUG ] No samples found: dedup [2021-05-14 04:29:55,345] multiqc [DEBUG ] No samples found: damageprofiler [2021-05-14 04:29:55,362] multiqc [DEBUG ] No samples found: biobambam2 [2021-05-14 04:29:55,366] multiqc [DEBUG ] No samples found: mtnucratio [2021-05-14 04:29:55,369] multiqc [DEBUG ] No samples found: picard [2021-05-14 04:29:55,373] multiqc [DEBUG ] No samples found: prokka [2021-05-14 04:29:55,377] multiqc [DEBUG ] No samples found: samblaster [2021-05-14 04:29:55,384] multiqc [DEBUG ] No samples found: samtools [2021-05-14 04:29:55,388] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-05-14 04:29:55,392] multiqc [DEBUG ] No samples found: bamtools [2021-05-14 04:29:55,396] multiqc [DEBUG ] No samples found: jellyfish [2021-05-14 04:29:55,402] multiqc [DEBUG ] No samples found: vcftools [2021-05-14 04:29:55,406] multiqc [DEBUG ] No samples found: longranger [2021-05-14 04:29:55,410] multiqc [DEBUG ] No samples found: stacks [2021-05-14 04:29:55,414] multiqc [DEBUG ] No samples found: varscan2 [2021-05-14 04:29:55,425] multiqc [DEBUG ] No samples found: bbmap [2021-05-14 04:29:55,430] multiqc [DEBUG ] No samples found: bismark [2021-05-14 04:29:55,434] multiqc [DEBUG ] No samples found: biscuit [2021-05-14 04:29:55,438] multiqc [DEBUG ] No samples found: hicexplorer [2021-05-14 04:29:55,443] multiqc [DEBUG ] No samples found: hicup [2021-05-14 04:29:55,447] multiqc [DEBUG ] No samples found: hicpro [2021-05-14 04:29:55,450] multiqc [DEBUG ] No samples found: salmon [2021-05-14 04:29:55,454] multiqc [DEBUG ] No samples found: kallisto [2021-05-14 04:29:55,459] multiqc [DEBUG ] No samples found: slamdunk [2021-05-14 04:29:55,463] multiqc [DEBUG ] No samples found: star [2021-05-14 04:29:55,467] multiqc [DEBUG ] No samples found: hisat2 [2021-05-14 04:29:55,471] multiqc [DEBUG ] No samples found: tophat [2021-05-14 04:29:55,475] multiqc [DEBUG ] No samples found: bowtie2 [2021-05-14 04:29:55,479] multiqc [DEBUG ] No samples found: bowtie1 [2021-05-14 04:29:55,483] multiqc [DEBUG ] No samples found: snpsplit [2021-05-14 04:29:55,487] multiqc [DEBUG ] No samples found: kat [2021-05-14 04:29:55,490] multiqc [DEBUG ] No samples found: leehom [2021-05-14 04:29:55,495] multiqc [DEBUG ] No samples found: adapterRemoval [2021-05-14 04:29:55,499] multiqc [DEBUG ] No samples found: clipandmerge [2021-05-14 04:29:55,503] multiqc [DEBUG ] No samples found: cutadapt [2021-05-14 04:29:55,507] multiqc [DEBUG ] No samples found: flexbar [2021-05-14 04:29:55,511] multiqc [DEBUG ] No samples found: kaiju [2021-05-14 04:29:55,515] multiqc [DEBUG ] No samples found: kraken [2021-05-14 04:29:55,519] multiqc [DEBUG ] No samples found: malt [2021-05-14 04:29:55,523] multiqc [DEBUG ] No samples found: trimmomatic [2021-05-14 04:29:55,528] multiqc [DEBUG ] No samples found: sickle [2021-05-14 04:29:55,532] multiqc [DEBUG ] No samples found: skewer [2021-05-14 04:29:55,536] multiqc [DEBUG ] No samples found: sortmerna [2021-05-14 04:29:55,540] multiqc [DEBUG ] No samples found: biobloomtools [2021-05-14 04:29:55,544] multiqc [DEBUG ] No samples found: fastq_screen [2021-05-14 04:29:55,548] multiqc [DEBUG ] No samples found: afterqc [2021-05-14 04:29:55,552] multiqc [DEBUG ] No samples found: fastp [2021-05-14 04:29:56,576] multiqc.modules.fastqc.fastqc [INFO ] Found 42 reports [2021-05-14 04:29:57,420] multiqc [DEBUG ] No samples found: pycoqc [2021-05-14 04:29:57,425] multiqc [DEBUG ] No samples found: minionqc [2021-05-14 04:29:57,429] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-05-14 04:29:57,433] multiqc [DEBUG ] No samples found: clusterflow [2021-05-14 04:29:57,438] multiqc [DEBUG ] No samples found: bcl2fastq [2021-05-14 04:29:57,442] multiqc [DEBUG ] No samples found: interop [2021-05-14 04:29:57,446] multiqc [DEBUG ] No samples found: ivar [2021-05-14 04:29:57,457] multiqc [DEBUG ] No samples found: flash [2021-05-14 04:29:57,461] multiqc [DEBUG ] No samples found: seqyclean [2021-05-14 04:29:57,461] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-05-14 04:29:57,461] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-05-14 04:29:57,461] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-05-14 04:29:57,461] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-05-14 04:29:57,510] multiqc [INFO ] Compressing plot data [2021-05-14 04:29:58,265] multiqc [INFO ] Report : multiqc_report.html [2021-05-14 04:29:58,266] multiqc [INFO ] Data : multiqc_data [2021-05-14 04:29:58,266] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6810457/tmplk601e48/multiqc_data' to '/scratch/gencore/logs/html/HWMWVAFX2/merged/multiqc_data' [2021-05-14 04:29:58,394] multiqc [INFO ] MultiQC complete