[2022-04-01 15:12:31,127] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-01 15:12:31,127] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-01 15:12:31,127] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-01 15:12:31,128] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-01 15:12:31,128] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-01 15:12:31,128] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKTVNAFX3/merged [2022-04-01 15:12:31,672] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-01 15:12:31,672] multiqc [INFO ] This is MultiQC v1.9 [2022-04-01 15:12:31,672] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKTVNAFX3/merged [2022-04-01 15:12:31,672] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKTVNAFX3/merged [2022-04-01 15:12:31,672] multiqc [INFO ] Template : default [2022-04-01 15:12:31,672] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-01 15:12:31,672] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKTVNAFX3/merged [2022-04-01 15:12:31,672] 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 [2022-04-01 15:12:31,673] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16993675/tmp_kxfyq4m [2022-04-01 15:12:31,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n02_10676-in_fastqc.html [2022-04-01 15:12:31,788] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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filesize limit: HKTVNAFX3_n01_7797hop1-phd_fastqc.html [2022-04-01 15:12:33,154] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10676spikein-in_fastqc.html [2022-04-01 15:12:33,156] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10676spikein-in_fastqc.html [2022-04-01 15:12:33,200] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_11689in_fastqc.html [2022-04-01 15:12:33,202] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_11689in_fastqc.html [2022-04-01 15:12:33,242] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_undetermined_fastqc.html [2022-04-01 15:12:33,244] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_undetermined_fastqc.html [2022-04-01 15:12:33,287] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10676-hop1_fastqc.html [2022-04-01 15:12:33,289] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10676-hop1_fastqc.html [2022-04-01 15:12:33,331] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10677-hop1_fastqc.html [2022-04-01 15:12:33,333] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10677-hop1_fastqc.html [2022-04-01 15:12:33,373] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10677spikin-hop1_fastqc.html [2022-04-01 15:12:33,375] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10677spikin-hop1_fastqc.html [2022-04-01 15:12:33,414] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_7797-hop1-sm_fastqc.html [2022-04-01 15:12:33,416] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_7797-hop1-sm_fastqc.html [2022-04-01 15:12:33,456] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10962red1_fastqc.html [2022-04-01 15:12:33,458] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10962red1_fastqc.html [2022-04-01 15:12:33,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n02_7797in-phd_fastqc.html [2022-04-01 15:12:33,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n02_7797in-phd_fastqc.html [2022-04-01 15:12:33,540] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10676spikein-hop1_fastqc.html [2022-04-01 15:12:33,542] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKTVNAFX3_n01_10676spikein-hop1_fastqc.html [2022-04-01 15:12:33,904] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-01 15:12:33,906] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-01 15:12:33,922] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 20 samples (table) [2022-04-01 15:12:33,924] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-01 15:12:33,934] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-01 15:12:33,939] multiqc [DEBUG ] No samples found: conpair [2022-04-01 15:12:33,945] multiqc [DEBUG ] No samples found: peddy [2022-04-01 15:12:33,950] multiqc [DEBUG ] No samples found: somalier [2022-04-01 15:12:33,955] multiqc [DEBUG ] No samples found: methylQA [2022-04-01 15:12:33,964] multiqc [DEBUG ] No samples found: mosdepth [2022-04-01 15:12:33,969] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-01 15:12:33,972] multiqc [DEBUG ] No samples found: qualimap [2022-04-01 15:12:33,977] multiqc [DEBUG ] No samples found: preseq [2022-04-01 15:12:33,982] multiqc [DEBUG ] No samples found: quast [2022-04-01 15:12:33,988] multiqc [DEBUG ] No samples found: qorts [2022-04-01 15:12:33,993] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-01 15:12:33,998] multiqc [DEBUG ] No samples found: rockhopper [2022-04-01 15:12:34,003] multiqc [DEBUG ] No samples found: rsem [2022-04-01 15:12:34,014] multiqc [DEBUG ] No samples found: rseqc [2022-04-01 15:12:34,019] multiqc [DEBUG ] No samples found: busco [2022-04-01 15:12:34,024] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-01 15:12:34,028] multiqc [DEBUG ] No samples found: disambiguate [2022-04-01 15:12:34,034] multiqc [DEBUG ] No samples found: supernova [2022-04-01 15:12:34,047] multiqc [DEBUG ] No samples found: deeptools [2022-04-01 15:12:34,052] multiqc [DEBUG ] No samples found: sargasso [2022-04-01 15:12:34,057] multiqc [DEBUG ] No samples found: verifybamid [2022-04-01 15:12:34,062] multiqc [DEBUG ] No samples found: mirtrace [2022-04-01 15:12:34,067] multiqc [DEBUG ] No samples found: happy [2022-04-01 15:12:34,072] multiqc [DEBUG ] No samples found: mirtop [2022-04-01 15:12:34,079] multiqc [DEBUG ] No samples found: homer [2022-04-01 15:12:34,084] multiqc [DEBUG ] No samples found: macs2 [2022-04-01 15:12:34,088] multiqc [DEBUG ] No samples found: theta2 [2022-04-01 15:12:34,094] multiqc [DEBUG ] No samples found: snpeff [2022-04-01 15:12:34,101] multiqc [DEBUG ] No samples found: gatk [2022-04-01 15:12:34,105] multiqc [DEBUG ] No samples found: htseq [2022-04-01 15:12:34,111] multiqc [DEBUG ] No samples found: bcftools [2022-04-01 15:12:34,116] multiqc [DEBUG ] No samples found: featureCounts [2022-04-01 15:12:34,122] multiqc [DEBUG ] No samples found: fgbio [2022-04-01 15:12:34,135] multiqc [DEBUG ] No samples found: dragen [2022-04-01 15:12:34,140] multiqc [DEBUG ] No samples found: dedup [2022-04-01 15:12:34,145] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-01 15:12:34,169] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-01 15:12:34,174] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-01 15:12:34,176] multiqc [DEBUG ] No samples found: picard [2022-04-01 15:12:34,181] multiqc [DEBUG ] No samples found: prokka [2022-04-01 15:12:34,186] multiqc [DEBUG ] No samples found: samblaster [2022-04-01 15:12:34,194] multiqc [DEBUG ] No samples found: samtools [2022-04-01 15:12:34,199] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-01 15:12:34,205] multiqc [DEBUG ] No samples found: bamtools [2022-04-01 15:12:34,210] multiqc [DEBUG ] No samples found: jellyfish [2022-04-01 15:12:34,217] multiqc [DEBUG ] No samples found: vcftools [2022-04-01 15:12:34,223] multiqc [DEBUG ] No samples found: longranger [2022-04-01 15:12:34,228] multiqc [DEBUG ] No samples found: stacks [2022-04-01 15:12:34,233] multiqc [DEBUG ] No samples found: varscan2 [2022-04-01 15:12:34,247] multiqc [DEBUG ] No samples found: bbmap [2022-04-01 15:12:34,252] multiqc [DEBUG ] No samples found: bismark [2022-04-01 15:12:34,258] multiqc [DEBUG ] No samples found: biscuit [2022-04-01 15:12:34,264] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-01 15:12:34,269] multiqc [DEBUG ] No samples found: hicup [2022-04-01 15:12:34,274] multiqc [DEBUG ] No samples found: hicpro [2022-04-01 15:12:34,279] multiqc [DEBUG ] No samples found: salmon [2022-04-01 15:12:34,284] multiqc [DEBUG ] No samples found: kallisto [2022-04-01 15:12:34,289] multiqc [DEBUG ] No samples found: slamdunk [2022-04-01 15:12:34,294] multiqc [DEBUG ] No samples found: star [2022-04-01 15:12:34,299] multiqc [DEBUG ] No samples found: hisat2 [2022-04-01 15:12:34,304] multiqc [DEBUG ] No samples found: tophat [2022-04-01 15:12:34,310] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-01 15:12:34,315] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-01 15:12:34,320] multiqc [DEBUG ] No samples found: snpsplit [2022-04-01 15:12:34,324] multiqc [DEBUG ] No samples found: kat [2022-04-01 15:12:34,329] multiqc [DEBUG ] No samples found: leehom [2022-04-01 15:12:34,334] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-01 15:12:34,339] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-01 15:12:34,345] multiqc [DEBUG ] No samples found: cutadapt [2022-04-01 15:12:34,349] multiqc [DEBUG ] No samples found: flexbar [2022-04-01 15:12:34,354] multiqc [DEBUG ] No samples found: kaiju [2022-04-01 15:12:34,359] multiqc [DEBUG ] No samples found: kraken [2022-04-01 15:12:34,364] multiqc [DEBUG ] No samples found: malt [2022-04-01 15:12:34,369] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-01 15:12:34,374] multiqc [DEBUG ] No samples found: sickle [2022-04-01 15:12:34,379] multiqc [DEBUG ] No samples found: skewer [2022-04-01 15:12:34,384] multiqc [DEBUG ] No samples found: sortmerna [2022-04-01 15:12:34,388] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-01 15:12:34,393] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-01 15:12:34,398] multiqc [DEBUG ] No samples found: afterqc [2022-04-01 15:12:34,403] multiqc [DEBUG ] No samples found: fastp [2022-04-01 15:12:35,284] multiqc.modules.fastqc.fastqc [INFO ] Found 40 reports [2022-04-01 15:12:35,619] multiqc [DEBUG ] No samples found: pycoqc [2022-04-01 15:12:35,624] multiqc [DEBUG ] No samples found: minionqc [2022-04-01 15:12:35,629] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-01 15:12:35,635] multiqc [DEBUG ] No samples found: clusterflow [2022-04-01 15:12:35,640] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-01 15:12:35,645] multiqc [DEBUG ] No samples found: interop [2022-04-01 15:12:35,650] multiqc [DEBUG ] No samples found: ivar [2022-04-01 15:12:35,655] multiqc [DEBUG ] No samples found: flash [2022-04-01 15:12:35,660] multiqc [DEBUG ] No samples found: seqyclean [2022-04-01 15:12:35,660] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-01 15:12:35,660] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-01 15:12:35,660] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-01 15:12:35,660] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-01 15:12:35,707] multiqc [INFO ] Compressing plot data [2022-04-01 15:12:36,387] multiqc [INFO ] Report : multiqc_report.html [2022-04-01 15:12:36,387] multiqc [INFO ] Data : multiqc_data [2022-04-01 15:12:36,387] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16993675/tmp_kxfyq4m/multiqc_data' to '/scratch/gencore/logs/html/HKTVNAFX3/merged/multiqc_data' [2022-04-01 15:12:36,517] multiqc [INFO ] MultiQC complete