[2021-03-18 15:16:31,149] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-18 15:16:31,149] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-18 15:16:31,149] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-18 15:16:31,150] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-18 15:16:31,150] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-18 15:16:31,150] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNYGNAFX2/merged [2021-03-18 15:16:32,610] multiqc [WARNING] MultiQC Version v1.10 now available! [2021-03-18 15:16:32,610] multiqc [INFO ] This is MultiQC v1.9 [2021-03-18 15:16:32,610] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNYGNAFX2/merged [2021-03-18 15:16:32,611] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNYGNAFX2/merged [2021-03-18 15:16:32,611] multiqc [INFO ] Template : default [2021-03-18 15:16:32,611] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-18 15:16:32,611] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNYGNAFX2/merged [2021-03-18 15:16:32,611] 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 [2021-03-18 15:16:32,611] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-3923334/tmpuafufqzw [2021-03-18 15:16:32,731] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n02_undetermined_fastqc.html [2021-03-18 15:16:32,734] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n02_undetermined_fastqc.html [2021-03-18 15:16:32,778] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH9643-3hr-spikein_fastqc.html [2021-03-18 15:16:32,779] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH9643-3hr-spikein_fastqc.html [2021-03-18 15:16:32,822] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-18 15:16:32,823] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-18 15:16:32,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH8967-3hr-spikein_fastqc.html [2021-03-18 15:16:32,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH8967-3hr-spikein_fastqc.html [2021-03-18 15:16:32,941] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH6179-0hr-spikein_fastqc.html [2021-03-18 15:16:32,943] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH6179-0hr-spikein_fastqc.html [2021-03-18 15:16:32,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH9643-0hr-spikein_fastqc.html [2021-03-18 15:16:32,989] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH9643-0hr-spikein_fastqc.html [2021-03-18 15:16:33,032] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH9643-3hr-spikein_fastqc.html [2021-03-18 15:16:33,034] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH9643-3hr-spikein_fastqc.html [2021-03-18 15:16:33,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH8967-3hr-spikein_fastqc.html [2021-03-18 15:16:33,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH8967-3hr-spikein_fastqc.html [2021-03-18 15:16:33,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH9643-0hr-spikein_fastqc.html [2021-03-18 15:16:33,124] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH9643-0hr-spikein_fastqc.html [2021-03-18 15:16:33,167] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n01_undetermined_fastqc.html [2021-03-18 15:16:33,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n01_undetermined_fastqc.html [2021-03-18 15:16:33,213] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH8967-0hr-spikein_fastqc.html [2021-03-18 15:16:33,215] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH8967-0hr-spikein_fastqc.html [2021-03-18 15:16:33,257] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH6179-3hr-spikein_fastqc.html [2021-03-18 15:16:33,258] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH6179-3hr-spikein_fastqc.html [2021-03-18 15:16:33,301] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH6179-0hr-spikein_fastqc.html [2021-03-18 15:16:33,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n02_AH6179-0hr-spikein_fastqc.html [2021-03-18 15:16:33,344] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH6179-3hr-spikein_fastqc.html [2021-03-18 15:16:33,346] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH6179-3hr-spikein_fastqc.html [2021-03-18 15:16:33,390] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH8967-0hr-spikein_fastqc.html [2021-03-18 15:16:33,392] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYGNAFX2_n01_AH8967-0hr-spikein_fastqc.html [2021-03-18 15:16:33,897] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-18 15:16:33,898] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-18 15:16:33,908] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2021-03-18 15:16:33,909] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-18 15:16:33,919] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-18 15:16:33,924] multiqc [DEBUG ] No samples found: conpair [2021-03-18 15:16:33,930] multiqc [DEBUG ] No samples found: peddy [2021-03-18 15:16:33,935] multiqc [DEBUG ] No samples found: somalier [2021-03-18 15:16:33,940] multiqc [DEBUG ] No samples found: methylQA [2021-03-18 15:16:33,948] multiqc [DEBUG ] No samples found: mosdepth [2021-03-18 15:16:33,953] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-18 15:16:33,956] multiqc [DEBUG ] No samples found: qualimap [2021-03-18 15:16:33,961] multiqc [DEBUG ] No samples found: preseq [2021-03-18 15:16:33,966] multiqc [DEBUG ] No samples found: quast [2021-03-18 15:16:33,973] multiqc [DEBUG ] No samples found: qorts [2021-03-18 15:16:33,978] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-18 15:16:33,982] multiqc [DEBUG ] No samples found: rockhopper [2021-03-18 15:16:33,987] multiqc [DEBUG ] No samples found: rsem [2021-03-18 15:16:33,997] multiqc [DEBUG ] No samples found: rseqc [2021-03-18 15:16:34,001] multiqc [DEBUG ] No samples found: busco [2021-03-18 15:16:34,006] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-18 15:16:34,011] multiqc [DEBUG ] No samples found: disambiguate [2021-03-18 15:16:34,016] multiqc [DEBUG ] No samples found: supernova [2021-03-18 15:16:34,028] multiqc [DEBUG ] No samples found: deeptools [2021-03-18 15:16:34,033] multiqc [DEBUG ] No samples found: sargasso [2021-03-18 15:16:34,038] multiqc [DEBUG ] No samples found: verifybamid [2021-03-18 15:16:34,043] multiqc [DEBUG ] No samples found: mirtrace [2021-03-18 15:16:34,048] multiqc [DEBUG ] No samples found: happy [2021-03-18 15:16:34,053] multiqc [DEBUG ] No samples found: mirtop [2021-03-18 15:16:34,059] multiqc [DEBUG ] No samples found: homer [2021-03-18 15:16:34,064] multiqc [DEBUG ] No samples found: macs2 [2021-03-18 15:16:34,068] multiqc [DEBUG ] No samples found: theta2 [2021-03-18 15:16:34,073] multiqc [DEBUG ] No samples found: snpeff [2021-03-18 15:16:34,080] multiqc [DEBUG ] No samples found: gatk [2021-03-18 15:16:34,085] multiqc [DEBUG ] No samples found: htseq [2021-03-18 15:16:34,091] multiqc [DEBUG ] No samples found: bcftools [2021-03-18 15:16:34,097] multiqc [DEBUG ] No samples found: featureCounts [2021-03-18 15:16:34,103] multiqc [DEBUG ] No samples found: fgbio [2021-03-18 15:16:34,115] multiqc [DEBUG ] No samples found: dragen [2021-03-18 15:16:34,120] multiqc [DEBUG ] No samples found: dedup [2021-03-18 15:16:34,125] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-18 15:16:34,147] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-18 15:16:34,152] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-18 15:16:34,154] multiqc [DEBUG ] No samples found: picard [2021-03-18 15:16:34,159] multiqc [DEBUG ] No samples found: prokka [2021-03-18 15:16:34,163] multiqc [DEBUG ] No samples found: samblaster [2021-03-18 15:16:34,172] multiqc [DEBUG ] No samples found: samtools [2021-03-18 15:16:34,177] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-18 15:16:34,182] multiqc [DEBUG ] No samples found: bamtools [2021-03-18 15:16:34,187] multiqc [DEBUG ] No samples found: jellyfish [2021-03-18 15:16:34,193] multiqc [DEBUG ] No samples found: vcftools [2021-03-18 15:16:34,198] multiqc [DEBUG ] No samples found: longranger [2021-03-18 15:16:34,203] multiqc [DEBUG ] No samples found: stacks [2021-03-18 15:16:34,208] multiqc [DEBUG ] No samples found: varscan2 [2021-03-18 15:16:34,220] multiqc [DEBUG ] No samples found: bbmap [2021-03-18 15:16:34,225] multiqc [DEBUG ] No samples found: bismark [2021-03-18 15:16:34,230] multiqc [DEBUG ] No samples found: biscuit [2021-03-18 15:16:34,235] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-18 15:16:34,240] multiqc [DEBUG ] No samples found: hicup [2021-03-18 15:16:34,245] multiqc [DEBUG ] No samples found: hicpro [2021-03-18 15:16:34,249] multiqc [DEBUG ] No samples found: salmon [2021-03-18 15:16:34,254] multiqc [DEBUG ] No samples found: kallisto [2021-03-18 15:16:34,259] multiqc [DEBUG ] No samples found: slamdunk [2021-03-18 15:16:34,263] multiqc [DEBUG ] No samples found: star [2021-03-18 15:16:34,268] multiqc [DEBUG ] No samples found: hisat2 [2021-03-18 15:16:34,272] multiqc [DEBUG ] No samples found: tophat [2021-03-18 15:16:34,277] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-18 15:16:34,282] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-18 15:16:34,286] multiqc [DEBUG ] No samples found: snpsplit [2021-03-18 15:16:34,291] multiqc [DEBUG ] No samples found: kat [2021-03-18 15:16:34,295] multiqc [DEBUG ] No samples found: leehom [2021-03-18 15:16:34,300] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-18 15:16:34,304] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-18 15:16:34,309] multiqc [DEBUG ] No samples found: cutadapt [2021-03-18 15:16:34,313] multiqc [DEBUG ] No samples found: flexbar [2021-03-18 15:16:34,318] multiqc [DEBUG ] No samples found: kaiju [2021-03-18 15:16:34,323] multiqc [DEBUG ] No samples found: kraken [2021-03-18 15:16:34,329] multiqc [DEBUG ] No samples found: malt [2021-03-18 15:16:34,333] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-18 15:16:34,338] multiqc [DEBUG ] No samples found: sickle [2021-03-18 15:16:34,342] multiqc [DEBUG ] No samples found: skewer [2021-03-18 15:16:34,346] multiqc [DEBUG ] No samples found: sortmerna [2021-03-18 15:16:34,351] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-18 15:16:34,356] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-18 15:16:34,360] multiqc [DEBUG ] No samples found: afterqc [2021-03-18 15:16:34,365] multiqc [DEBUG ] No samples found: fastp [2021-03-18 15:16:34,702] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2021-03-18 15:16:34,853] multiqc [DEBUG ] No samples found: pycoqc [2021-03-18 15:16:34,857] multiqc [DEBUG ] No samples found: minionqc [2021-03-18 15:16:34,862] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-18 15:16:34,867] multiqc [DEBUG ] No samples found: clusterflow [2021-03-18 15:16:34,872] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-18 15:16:34,877] multiqc [DEBUG ] No samples found: interop [2021-03-18 15:16:34,881] multiqc [DEBUG ] No samples found: ivar [2021-03-18 15:16:34,886] multiqc [DEBUG ] No samples found: flash [2021-03-18 15:16:34,890] multiqc [DEBUG ] No samples found: seqyclean [2021-03-18 15:16:34,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-03-18 15:16:34,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-03-18 15:16:34,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-18 15:16:34,890] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-18 15:16:34,908] multiqc [INFO ] Compressing plot data [2021-03-18 15:16:35,154] multiqc [INFO ] Report : multiqc_report.html [2021-03-18 15:16:35,154] multiqc [INFO ] Data : multiqc_data [2021-03-18 15:16:35,154] multiqc [DEBUG ] Moving data file from '/state/partition1/job-3923334/tmpuafufqzw/multiqc_data' to '/scratch/gencore/logs/html/HNYGNAFX2/merged/multiqc_data' [2021-03-18 15:16:35,276] multiqc [INFO ] MultiQC complete