[2022-11-12 04:17:28,093] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-12 04:17:28,093] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-12 04:17:28,093] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-12 04:17:28,094] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-12 04:17:28,094] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-12 04:17:28,094] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H37NLDSX5/merged [2022-11-12 04:17:28,624] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-12 04:17:28,624] multiqc [INFO ] This is MultiQC v1.9 [2022-11-12 04:17:28,624] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H37NLDSX5/merged [2022-11-12 04:17:28,624] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H37NLDSX5/merged [2022-11-12 04:17:28,624] multiqc [INFO ] Template : default [2022-11-12 04:17:28,624] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-12 04:17:28,624] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H37NLDSX5/merged [2022-11-12 04:17:28,625] 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 [2022-11-12 04:17:28,625] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26916636/tmp2lx8jj7w [2022-11-12 04:17:28,781] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n02_f2HRB0313_fastqc.html [2022-11-12 04:17:28,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H37NLDSX5_n02_f2HRB0233_fastqc.html [2022-11-12 04:17:40,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0169_fastqc.html [2022-11-12 04:17:40,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0169_fastqc.html [2022-11-12 04:17:40,131] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n02_f2HRB0330_fastqc.html [2022-11-12 04:17:40,133] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n02_f2HRB0330_fastqc.html [2022-11-12 04:17:40,194] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0228_fastqc.html [2022-11-12 04:17:40,196] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0228_fastqc.html [2022-11-12 04:17:40,247] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0245_fastqc.html [2022-11-12 04:17:40,249] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0245_fastqc.html [2022-11-12 04:17:40,305] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0014_fastqc.html [2022-11-12 04:17:40,308] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0014_fastqc.html [2022-11-12 04:17:40,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0076_fastqc.html [2022-11-12 04:17:40,355] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0076_fastqc.html [2022-11-12 04:17:40,416] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0074_fastqc.html [2022-11-12 04:17:40,418] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2HRB0074_fastqc.html [2022-11-12 04:17:40,966] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-12 04:17:40,968] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-12 04:17:41,019] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 97 samples (table) [2022-11-12 04:17:41,021] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-12 04:17:41,030] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-12 04:17:41,036] multiqc [DEBUG ] No samples found: conpair [2022-11-12 04:17:41,042] multiqc [DEBUG ] No samples found: peddy [2022-11-12 04:17:41,047] multiqc [DEBUG ] No samples found: somalier [2022-11-12 04:17:41,052] multiqc [DEBUG ] No samples found: methylQA [2022-11-12 04:17:41,061] multiqc [DEBUG ] No samples found: mosdepth [2022-11-12 04:17:41,066] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-12 04:17:41,070] multiqc [DEBUG ] No samples found: qualimap [2022-11-12 04:17:41,076] multiqc [DEBUG ] No samples found: preseq [2022-11-12 04:17:41,082] multiqc [DEBUG ] No samples found: quast [2022-11-12 04:17:41,087] multiqc [DEBUG ] No samples found: qorts [2022-11-12 04:17:41,093] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-12 04:17:41,098] multiqc [DEBUG ] No samples found: rockhopper [2022-11-12 04:17:41,104] multiqc [DEBUG ] No samples found: rsem [2022-11-12 04:17:41,116] multiqc [DEBUG ] No samples found: rseqc [2022-11-12 04:17:41,121] multiqc [DEBUG ] No samples found: busco [2022-11-12 04:17:41,126] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-12 04:17:41,131] multiqc [DEBUG ] No samples found: disambiguate [2022-11-12 04:17:41,136] multiqc [DEBUG ] No samples found: supernova [2022-11-12 04:17:41,151] multiqc [DEBUG ] No samples found: deeptools [2022-11-12 04:17:41,156] multiqc [DEBUG ] No samples found: sargasso [2022-11-12 04:17:41,161] multiqc [DEBUG ] No samples found: verifybamid [2022-11-12 04:17:41,166] multiqc [DEBUG ] No samples found: mirtrace [2022-11-12 04:17:41,172] multiqc [DEBUG ] No samples found: happy [2022-11-12 04:17:41,177] multiqc [DEBUG ] No samples found: mirtop [2022-11-12 04:17:41,184] multiqc [DEBUG ] No samples found: homer [2022-11-12 04:17:41,190] multiqc [DEBUG ] No samples found: macs2 [2022-11-12 04:17:41,195] multiqc [DEBUG ] No samples found: theta2 [2022-11-12 04:17:41,200] multiqc [DEBUG ] No samples found: snpeff [2022-11-12 04:17:41,208] multiqc [DEBUG ] No samples found: gatk [2022-11-12 04:17:41,212] multiqc [DEBUG ] No samples found: htseq [2022-11-12 04:17:41,219] multiqc [DEBUG ] No samples found: bcftools [2022-11-12 04:17:41,224] multiqc [DEBUG ] No samples found: featureCounts [2022-11-12 04:17:41,230] multiqc [DEBUG ] No samples found: fgbio [2022-11-12 04:17:41,244] multiqc [DEBUG ] No samples found: dragen [2022-11-12 04:17:41,249] multiqc [DEBUG ] No samples found: dedup [2022-11-12 04:17:41,254] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-12 04:17:41,281] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-12 04:17:41,285] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-12 04:17:41,287] multiqc [DEBUG ] No samples found: picard [2022-11-12 04:17:41,293] multiqc [DEBUG ] No samples found: prokka [2022-11-12 04:17:41,297] multiqc [DEBUG ] No samples found: samblaster [2022-11-12 04:17:41,306] multiqc [DEBUG ] No samples found: samtools [2022-11-12 04:17:41,311] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-12 04:17:41,316] multiqc [DEBUG ] No samples found: bamtools [2022-11-12 04:17:41,320] multiqc [DEBUG ] No samples found: jellyfish [2022-11-12 04:17:41,328] multiqc [DEBUG ] No samples found: vcftools [2022-11-12 04:17:41,333] multiqc [DEBUG ] No samples found: longranger [2022-11-12 04:17:41,338] multiqc [DEBUG ] No samples found: stacks [2022-11-12 04:17:41,343] multiqc [DEBUG ] No samples found: varscan2 [2022-11-12 04:17:41,359] multiqc [DEBUG ] No samples found: bbmap [2022-11-12 04:17:41,364] multiqc [DEBUG ] No samples found: bismark [2022-11-12 04:17:41,369] multiqc [DEBUG ] No samples found: biscuit [2022-11-12 04:17:41,374] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-12 04:17:41,379] multiqc [DEBUG ] No samples found: hicup [2022-11-12 04:17:41,385] multiqc [DEBUG ] No samples found: hicpro [2022-11-12 04:17:41,389] multiqc [DEBUG ] No samples found: salmon [2022-11-12 04:17:41,394] multiqc [DEBUG ] No samples found: kallisto [2022-11-12 04:17:41,400] multiqc [DEBUG ] No samples found: slamdunk [2022-11-12 04:17:41,406] multiqc [DEBUG ] No samples found: star [2022-11-12 04:17:41,410] multiqc [DEBUG ] No samples found: hisat2 [2022-11-12 04:17:41,415] multiqc [DEBUG ] No samples found: tophat [2022-11-12 04:17:41,420] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-12 04:17:41,425] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-12 04:17:41,430] multiqc [DEBUG ] No samples found: snpsplit [2022-11-12 04:17:41,435] multiqc [DEBUG ] No samples found: kat [2022-11-12 04:17:41,440] multiqc [DEBUG ] No samples found: leehom [2022-11-12 04:17:41,445] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-12 04:17:41,449] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-12 04:17:41,454] multiqc [DEBUG ] No samples found: cutadapt [2022-11-12 04:17:41,458] multiqc [DEBUG ] No samples found: flexbar [2022-11-12 04:17:41,463] multiqc [DEBUG ] No samples found: kaiju [2022-11-12 04:17:41,468] multiqc [DEBUG ] No samples found: kraken [2022-11-12 04:17:41,473] multiqc [DEBUG ] No samples found: malt [2022-11-12 04:17:41,478] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-12 04:17:41,483] multiqc [DEBUG ] No samples found: sickle [2022-11-12 04:17:41,488] multiqc [DEBUG ] No samples found: skewer [2022-11-12 04:17:41,492] multiqc [DEBUG ] No samples found: sortmerna [2022-11-12 04:17:41,497] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-12 04:17:41,502] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-12 04:17:41,506] multiqc [DEBUG ] No samples found: afterqc [2022-11-12 04:17:41,511] multiqc [DEBUG ] No samples found: fastp [2022-11-12 04:18:15,088] multiqc.modules.fastqc.fastqc [INFO ] Found 194 reports [2022-11-12 04:18:39,767] multiqc [DEBUG ] No samples found: pycoqc [2022-11-12 04:18:39,772] multiqc [DEBUG ] No samples found: minionqc [2022-11-12 04:18:39,778] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-12 04:18:39,783] multiqc [DEBUG ] No samples found: clusterflow [2022-11-12 04:18:39,788] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-12 04:18:39,794] multiqc [DEBUG ] No samples found: interop [2022-11-12 04:18:39,800] multiqc [DEBUG ] No samples found: ivar [2022-11-12 04:18:39,805] multiqc [DEBUG ] No samples found: flash [2022-11-12 04:18:39,810] multiqc [DEBUG ] No samples found: seqyclean [2022-11-12 04:18:39,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-12 04:18:39,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-12 04:18:39,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-12 04:18:39,810] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-12 04:18:40,029] multiqc [INFO ] Compressing plot data [2022-11-12 04:18:40,095] multiqc [INFO ] Report : multiqc_report.html [2022-11-12 04:18:40,096] multiqc [INFO ] Data : multiqc_data [2022-11-12 04:18:40,096] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26916636/tmp2lx8jj7w/multiqc_data' to '/scratch/gencore/logs/html/H37NLDSX5/merged/multiqc_data' [2022-11-12 04:18:40,245] multiqc [INFO ] MultiQC complete