[2021-01-20 09:25:37,418] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-01-20 09:25:37,419] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-01-20 09:25:37,419] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-01-20 09:25:37,419] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-01-20 09:25:37,420] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-01-20 09:25:37,420] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HM5GVAFX2/merged [2021-01-20 09:25:39,064] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-01-20 09:25:39,064] multiqc [INFO ] This is MultiQC v1.9 [2021-01-20 09:25:39,064] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HM5GVAFX2/merged [2021-01-20 09:25:39,064] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HM5GVAFX2/merged [2021-01-20 09:25:39,064] multiqc [INFO ] Template : default [2021-01-20 09:25:39,064] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-01-20 09:25:39,064] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HM5GVAFX2/merged [2021-01-20 09:25:39,065] 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 [2021-01-20 09:25:39,065] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-1337459/tmpm_azt5uq [2021-01-20 09:25:39,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-16_fastqc.html [2021-01-20 09:25:39,171] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-16_fastqc.html [2021-01-20 09:25:39,213] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded 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HM5GVAFX2_n01_ncm12-5_fastqc.html [2021-01-20 09:25:40,783] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM5GVAFX2_n02_ncm12-5_fastqc.html [2021-01-20 09:25:40,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM5GVAFX2_n02_ncm12-5_fastqc.html [2021-01-20 09:25:40,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-13_fastqc.html [2021-01-20 09:25:40,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-13_fastqc.html [2021-01-20 09:25:40,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-7_fastqc.html [2021-01-20 09:25:40,867] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-7_fastqc.html [2021-01-20 09:25:40,906] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM5GVAFX2_n02_ncm12-20_fastqc.html [2021-01-20 09:25:40,907] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM5GVAFX2_n02_ncm12-20_fastqc.html [2021-01-20 09:25:40,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-14_fastqc.html [2021-01-20 09:25:40,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM5GVAFX2_n01_ncm12-14_fastqc.html [2021-01-20 09:25:41,249] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-20 09:25:41,250] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-20 09:25:41,266] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2021-01-20 09:25:41,275] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-01-20 09:25:41,277] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-01-20 09:25:41,281] multiqc [DEBUG ] No samples found: conpair [2021-01-20 09:25:41,285] multiqc [DEBUG ] No samples found: peddy [2021-01-20 09:25:41,289] multiqc [DEBUG ] No samples found: somalier [2021-01-20 09:25:41,293] multiqc [DEBUG ] No samples found: methylQA [2021-01-20 09:25:41,300] multiqc [DEBUG ] No samples found: mosdepth [2021-01-20 09:25:41,304] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-01-20 09:25:41,307] multiqc [DEBUG ] No samples found: qualimap [2021-01-20 09:25:41,311] multiqc [DEBUG ] No samples found: preseq [2021-01-20 09:25:41,315] multiqc [DEBUG ] No samples found: quast [2021-01-20 09:25:41,319] multiqc [DEBUG ] No samples found: qorts [2021-01-20 09:25:41,323] multiqc [DEBUG ] No samples found: rna_seqc [2021-01-20 09:25:41,327] multiqc [DEBUG ] No samples found: rockhopper [2021-01-20 09:25:41,331] multiqc [DEBUG ] No samples found: rsem [2021-01-20 09:25:41,340] multiqc [DEBUG ] No samples found: rseqc [2021-01-20 09:25:41,344] multiqc [DEBUG ] No samples found: busco [2021-01-20 09:25:41,348] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-01-20 09:25:41,352] multiqc [DEBUG ] No samples found: disambiguate [2021-01-20 09:25:41,356] multiqc [DEBUG ] No samples found: supernova [2021-01-20 09:25:41,366] multiqc [DEBUG ] No samples found: deeptools [2021-01-20 09:25:41,370] multiqc [DEBUG ] No samples found: sargasso [2021-01-20 09:25:41,374] multiqc [DEBUG ] No samples found: verifybamid [2021-01-20 09:25:41,378] multiqc [DEBUG ] No samples found: mirtrace [2021-01-20 09:25:41,383] multiqc [DEBUG ] No samples found: happy [2021-01-20 09:25:41,387] multiqc [DEBUG ] No samples found: mirtop [2021-01-20 09:25:41,392] multiqc [DEBUG ] No samples found: homer [2021-01-20 09:25:41,396] multiqc [DEBUG ] No samples found: macs2 [2021-01-20 09:25:41,400] multiqc [DEBUG ] No samples found: theta2 [2021-01-20 09:25:41,405] multiqc [DEBUG ] No samples found: snpeff [2021-01-20 09:25:41,410] multiqc [DEBUG ] No samples found: gatk [2021-01-20 09:25:41,414] multiqc [DEBUG ] No samples found: htseq [2021-01-20 09:25:41,419] multiqc [DEBUG ] No samples found: bcftools [2021-01-20 09:25:41,422] multiqc [DEBUG ] No samples found: featureCounts [2021-01-20 09:25:41,428] multiqc [DEBUG ] No samples found: fgbio [2021-01-20 09:25:41,437] multiqc [DEBUG ] No samples found: dragen [2021-01-20 09:25:41,442] multiqc [DEBUG ] No samples found: dedup [2021-01-20 09:25:41,446] multiqc [DEBUG ] No samples found: damageprofiler [2021-01-20 09:25:41,463] multiqc [DEBUG ] No samples found: biobambam2 [2021-01-20 09:25:41,467] multiqc [DEBUG ] No samples found: mtnucratio [2021-01-20 09:25:41,469] multiqc [DEBUG ] No samples found: picard [2021-01-20 09:25:41,473] multiqc [DEBUG ] No samples found: prokka [2021-01-20 09:25:41,477] multiqc [DEBUG ] No samples found: samblaster [2021-01-20 09:25:41,483] multiqc [DEBUG ] No samples found: samtools [2021-01-20 09:25:41,487] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-01-20 09:25:41,492] multiqc [DEBUG ] No samples found: bamtools [2021-01-20 09:25:41,496] multiqc [DEBUG ] No samples found: jellyfish [2021-01-20 09:25:41,502] multiqc [DEBUG ] No samples found: vcftools [2021-01-20 09:25:41,506] multiqc [DEBUG ] No samples found: longranger [2021-01-20 09:25:41,510] multiqc [DEBUG ] No samples found: stacks [2021-01-20 09:25:41,514] multiqc [DEBUG ] No samples found: varscan2 [2021-01-20 09:25:41,526] multiqc [DEBUG ] No samples found: bbmap [2021-01-20 09:25:41,530] multiqc [DEBUG ] No samples found: bismark [2021-01-20 09:25:41,534] multiqc [DEBUG ] No samples found: biscuit [2021-01-20 09:25:41,538] multiqc [DEBUG ] No samples found: hicexplorer [2021-01-20 09:25:41,542] multiqc [DEBUG ] No samples found: hicup [2021-01-20 09:25:41,546] multiqc [DEBUG ] No samples found: hicpro [2021-01-20 09:25:41,550] multiqc [DEBUG ] No samples found: salmon [2021-01-20 09:25:41,554] multiqc [DEBUG ] No samples found: kallisto [2021-01-20 09:25:41,558] multiqc [DEBUG ] No samples found: slamdunk [2021-01-20 09:25:41,562] multiqc [DEBUG ] No samples found: star [2021-01-20 09:25:41,566] multiqc [DEBUG ] No samples found: hisat2 [2021-01-20 09:25:41,570] multiqc [DEBUG ] No samples found: tophat [2021-01-20 09:25:41,574] multiqc [DEBUG ] No samples found: bowtie2 [2021-01-20 09:25:41,578] multiqc [DEBUG ] No samples found: bowtie1 [2021-01-20 09:25:41,582] multiqc [DEBUG ] No samples found: snpsplit [2021-01-20 09:25:41,586] multiqc [DEBUG ] No samples found: kat [2021-01-20 09:25:41,590] multiqc [DEBUG ] No samples found: leehom [2021-01-20 09:25:41,594] multiqc [DEBUG ] No samples found: adapterRemoval [2021-01-20 09:25:41,598] multiqc [DEBUG ] No samples found: clipandmerge [2021-01-20 09:25:41,602] multiqc [DEBUG ] No samples found: cutadapt [2021-01-20 09:25:41,606] multiqc [DEBUG ] No samples found: flexbar [2021-01-20 09:25:41,610] multiqc [DEBUG ] No samples found: kaiju [2021-01-20 09:25:41,614] multiqc [DEBUG ] No samples found: kraken [2021-01-20 09:25:41,618] multiqc [DEBUG ] No samples found: malt [2021-01-20 09:25:41,622] multiqc [DEBUG ] No samples found: trimmomatic [2021-01-20 09:25:41,626] multiqc [DEBUG ] No samples found: sickle [2021-01-20 09:25:41,630] multiqc [DEBUG ] No samples found: skewer [2021-01-20 09:25:41,634] multiqc [DEBUG ] No samples found: sortmerna [2021-01-20 09:25:41,638] multiqc [DEBUG ] No samples found: biobloomtools [2021-01-20 09:25:41,642] multiqc [DEBUG ] No samples found: fastq_screen [2021-01-20 09:25:41,646] multiqc [DEBUG ] No samples found: afterqc [2021-01-20 09:25:41,650] multiqc [DEBUG ] No samples found: fastp [2021-01-20 09:25:42,655] multiqc.modules.fastqc.fastqc [INFO ] Found 42 reports [2021-01-20 09:25:43,484] multiqc [DEBUG ] No samples found: pycoqc [2021-01-20 09:25:43,488] multiqc [DEBUG ] No samples found: minionqc [2021-01-20 09:25:43,492] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-01-20 09:25:43,496] multiqc [DEBUG ] No samples found: clusterflow [2021-01-20 09:25:43,501] multiqc [DEBUG ] No samples found: bcl2fastq [2021-01-20 09:25:43,505] multiqc [DEBUG ] No samples found: interop [2021-01-20 09:25:43,509] multiqc [DEBUG ] No samples found: ivar [2021-01-20 09:25:43,513] multiqc [DEBUG ] No samples found: flash [2021-01-20 09:25:43,517] multiqc [DEBUG ] No samples found: seqyclean [2021-01-20 09:25:43,517] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-01-20 09:25:43,517] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-01-20 09:25:43,517] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-01-20 09:25:43,517] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-01-20 09:25:43,568] multiqc [INFO ] Compressing plot data [2021-01-20 09:25:44,295] multiqc [INFO ] Report : multiqc_report.html [2021-01-20 09:25:44,295] multiqc [INFO ] Data : multiqc_data [2021-01-20 09:25:44,296] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1337459/tmpm_azt5uq/multiqc_data' to '/scratch/gencore/logs/html/HM5GVAFX2/merged/multiqc_data' [2021-01-20 09:25:44,407] multiqc [INFO ] MultiQC complete