[2022-04-10 22:03:37,451] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-10 22:03:37,451] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-10 22:03:37,451] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-10 22:03:37,452] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-10 22:03:37,452] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-10 22:03:37,453] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HC33GDMXY/merged [2022-04-10 22:03:37,932] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-10 22:03:37,932] multiqc [INFO ] This is MultiQC v1.9 [2022-04-10 22:03:37,933] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HC33GDMXY/merged [2022-04-10 22:03:37,933] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HC33GDMXY/merged [2022-04-10 22:03:37,933] multiqc [INFO ] Template : default [2022-04-10 22:03:37,933] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-10 22:03:37,933] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HC33GDMXY/merged [2022-04-10 22:03:37,933] 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 [2022-04-10 22:03:37,933] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-17565477/tmp8g5bsgsa [2022-04-10 22:03:38,072] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33GDMXY_n01_T12_B09_fastqc.html [2022-04-10 22:03:38,075] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HC33GDMXY_n02_T14_E06_fastqc.html [2022-04-10 22:03:51,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33GDMXY_n02_T14_E06_fastqc.html [2022-04-10 22:03:51,664] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33GDMXY_n01_T16_F03_fastqc.html [2022-04-10 22:03:51,666] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33GDMXY_n01_T16_F03_fastqc.html [2022-04-10 22:03:52,186] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-10 22:03:52,188] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-10 22:03:52,239] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 97 samples (table) [2022-04-10 22:03:52,241] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-10 22:03:52,250] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-10 22:03:52,256] multiqc [DEBUG ] No samples found: conpair [2022-04-10 22:03:52,262] multiqc [DEBUG ] No samples found: peddy [2022-04-10 22:03:52,267] multiqc [DEBUG ] No samples found: somalier [2022-04-10 22:03:52,273] multiqc [DEBUG ] No samples found: methylQA [2022-04-10 22:03:52,282] multiqc [DEBUG ] No samples found: mosdepth [2022-04-10 22:03:52,287] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-10 22:03:52,290] multiqc [DEBUG ] No samples found: qualimap [2022-04-10 22:03:52,296] multiqc [DEBUG ] No samples found: preseq [2022-04-10 22:03:52,301] multiqc [DEBUG ] No samples found: quast [2022-04-10 22:03:52,307] multiqc [DEBUG ] No samples found: qorts [2022-04-10 22:03:52,312] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-10 22:03:52,317] multiqc [DEBUG ] No samples found: rockhopper [2022-04-10 22:03:52,323] multiqc [DEBUG ] No samples found: rsem [2022-04-10 22:03:52,335] multiqc [DEBUG ] No samples found: rseqc [2022-04-10 22:03:52,340] multiqc [DEBUG ] No samples found: busco [2022-04-10 22:03:52,345] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-10 22:03:52,350] multiqc [DEBUG ] No samples found: disambiguate [2022-04-10 22:03:52,356] multiqc [DEBUG ] No samples found: supernova [2022-04-10 22:03:52,370] multiqc [DEBUG ] No samples found: deeptools [2022-04-10 22:03:52,376] multiqc [DEBUG ] No samples found: sargasso [2022-04-10 22:03:52,381] multiqc [DEBUG ] No samples found: verifybamid [2022-04-10 22:03:52,387] multiqc [DEBUG ] No samples found: mirtrace [2022-04-10 22:03:52,392] multiqc [DEBUG ] No samples found: happy [2022-04-10 22:03:52,397] multiqc [DEBUG ] No samples found: mirtop [2022-04-10 22:03:52,405] multiqc [DEBUG ] No samples found: homer [2022-04-10 22:03:52,410] multiqc [DEBUG ] No samples found: macs2 [2022-04-10 22:03:52,415] multiqc [DEBUG ] No samples found: theta2 [2022-04-10 22:03:52,421] multiqc [DEBUG ] No samples found: snpeff [2022-04-10 22:03:52,428] multiqc [DEBUG ] No samples found: gatk [2022-04-10 22:03:52,433] multiqc [DEBUG ] No samples found: htseq [2022-04-10 22:03:52,439] multiqc [DEBUG ] No samples found: bcftools [2022-04-10 22:03:52,444] multiqc [DEBUG ] No samples found: featureCounts [2022-04-10 22:03:52,451] multiqc [DEBUG ] No samples found: fgbio [2022-04-10 22:03:52,466] multiqc [DEBUG ] No samples found: dragen [2022-04-10 22:03:52,471] multiqc [DEBUG ] No samples found: dedup [2022-04-10 22:03:52,476] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-10 22:03:52,501] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-10 22:03:52,505] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-10 22:03:52,507] multiqc [DEBUG ] No samples found: picard [2022-04-10 22:03:52,512] multiqc [DEBUG ] No samples found: prokka [2022-04-10 22:03:52,517] multiqc [DEBUG ] No samples found: samblaster [2022-04-10 22:03:52,528] multiqc [DEBUG ] No samples found: samtools [2022-04-10 22:03:52,533] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-10 22:03:52,539] multiqc [DEBUG ] No samples found: bamtools [2022-04-10 22:03:52,544] multiqc [DEBUG ] No samples found: jellyfish [2022-04-10 22:03:52,554] multiqc [DEBUG ] No samples found: vcftools [2022-04-10 22:03:52,567] multiqc [DEBUG ] No samples found: longranger [2022-04-10 22:03:52,572] multiqc [DEBUG ] No samples found: stacks [2022-04-10 22:03:52,578] multiqc [DEBUG ] No samples found: varscan2 [2022-04-10 22:03:52,594] multiqc [DEBUG ] No samples found: bbmap [2022-04-10 22:03:52,600] multiqc [DEBUG ] No samples found: bismark [2022-04-10 22:03:52,605] multiqc [DEBUG ] No samples found: biscuit [2022-04-10 22:03:52,610] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-10 22:03:52,616] multiqc [DEBUG ] No samples found: hicup [2022-04-10 22:03:52,621] multiqc [DEBUG ] No samples found: hicpro [2022-04-10 22:03:52,625] multiqc [DEBUG ] No samples found: salmon [2022-04-10 22:03:52,630] multiqc [DEBUG ] No samples found: kallisto [2022-04-10 22:03:52,636] multiqc [DEBUG ] No samples found: slamdunk [2022-04-10 22:03:52,641] multiqc [DEBUG ] No samples found: star [2022-04-10 22:03:52,645] multiqc [DEBUG ] No samples found: hisat2 [2022-04-10 22:03:52,650] multiqc [DEBUG ] No samples found: tophat [2022-04-10 22:03:52,655] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-10 22:03:52,660] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-10 22:03:52,665] multiqc [DEBUG ] No samples found: snpsplit [2022-04-10 22:03:52,670] multiqc [DEBUG ] No samples found: kat [2022-04-10 22:03:52,674] multiqc [DEBUG ] No samples found: leehom [2022-04-10 22:03:52,679] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-10 22:03:52,684] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-10 22:03:52,690] multiqc [DEBUG ] No samples found: cutadapt [2022-04-10 22:03:52,695] multiqc [DEBUG ] No samples found: flexbar [2022-04-10 22:03:52,700] multiqc [DEBUG ] No samples found: kaiju [2022-04-10 22:03:52,705] multiqc [DEBUG ] No samples found: kraken [2022-04-10 22:03:52,711] multiqc [DEBUG ] No samples found: malt [2022-04-10 22:03:52,715] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-10 22:03:52,721] multiqc [DEBUG ] No samples found: sickle [2022-04-10 22:03:52,725] multiqc [DEBUG ] No samples found: skewer [2022-04-10 22:03:52,730] multiqc [DEBUG ] No samples found: sortmerna [2022-04-10 22:03:52,735] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-10 22:03:52,740] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-10 22:03:52,745] multiqc [DEBUG ] No samples found: afterqc [2022-04-10 22:03:52,750] multiqc [DEBUG ] No samples found: fastp [2022-04-10 22:04:31,164] multiqc.modules.fastqc.fastqc [INFO ] Found 194 reports [2022-04-10 22:04:54,543] multiqc [DEBUG ] No samples found: pycoqc [2022-04-10 22:04:54,548] multiqc [DEBUG ] No samples found: minionqc [2022-04-10 22:04:54,553] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-10 22:04:54,558] multiqc [DEBUG ] No samples found: clusterflow [2022-04-10 22:04:54,564] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-10 22:04:54,569] multiqc [DEBUG ] No samples found: interop [2022-04-10 22:04:54,573] multiqc [DEBUG ] No samples found: ivar [2022-04-10 22:04:54,578] multiqc [DEBUG ] No samples found: flash [2022-04-10 22:04:54,583] multiqc [DEBUG ] No samples found: seqyclean [2022-04-10 22:04:54,583] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-10 22:04:54,583] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-10 22:04:54,583] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-10 22:04:54,583] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-10 22:04:54,803] multiqc [INFO ] Compressing plot data [2022-04-10 22:04:54,869] multiqc [INFO ] Report : multiqc_report.html [2022-04-10 22:04:54,870] multiqc [INFO ] Data : multiqc_data [2022-04-10 22:04:54,870] multiqc [DEBUG ] Moving data file from '/state/partition1/job-17565477/tmp8g5bsgsa/multiqc_data' to '/scratch/gencore/logs/html/HC33GDMXY/merged/multiqc_data' [2022-04-10 22:04:55,018] multiqc [INFO ] MultiQC complete