[2022-12-06 13:46:32,688] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-12-06 13:46:32,688] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-12-06 13:46:32,688] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-12-06 13:46:32,689] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-12-06 13:46:32,689] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-12-06 13:46:32,689] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMTJCDRX2/merged [2022-12-06 13:46:33,126] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-12-06 13:46:33,127] multiqc [INFO ] This is MultiQC v1.9 [2022-12-06 13:46:33,127] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMTJCDRX2/merged [2022-12-06 13:46:33,127] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMTJCDRX2/merged [2022-12-06 13:46:33,127] multiqc [INFO ] Template : default [2022-12-06 13:46:33,127] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-12-06 13:46:33,127] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMTJCDRX2/merged [2022-12-06 13:46:33,128] 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 [2022-12-06 13:46:33,128] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27702025/tmpkkeicb5v [2022-12-06 13:46:33,248] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN017_fastqc.html [2022-12-06 13:46:33,251] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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13:46:34,304] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN003_fastqc.html [2022-12-06 13:46:34,355] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN026_fastqc.html [2022-12-06 13:46:34,357] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN026_fastqc.html [2022-12-06 13:46:34,408] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN005_fastqc.html [2022-12-06 13:46:34,410] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN005_fastqc.html [2022-12-06 13:46:34,459] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN011_fastqc.html [2022-12-06 13:46:34,461] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN011_fastqc.html [2022-12-06 13:46:34,516] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN018_fastqc.html [2022-12-06 13:46:34,518] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN018_fastqc.html [2022-12-06 13:46:34,562] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN028_fastqc.html [2022-12-06 13:46:34,564] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN028_fastqc.html [2022-12-06 13:46:34,625] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN015_fastqc.html [2022-12-06 13:46:34,627] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN015_fastqc.html [2022-12-06 13:46:34,669] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN007_fastqc.html [2022-12-06 13:46:34,671] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN007_fastqc.html [2022-12-06 13:46:34,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN020_fastqc.html [2022-12-06 13:46:34,723] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN020_fastqc.html [2022-12-06 13:46:34,776] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN016_fastqc.html [2022-12-06 13:46:34,777] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN016_fastqc.html [2022-12-06 13:46:34,819] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN022_fastqc.html [2022-12-06 13:46:34,821] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTJCDRX2_n01_EN022_fastqc.html [2022-12-06 13:46:35,486] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-06 13:46:35,488] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-06 13:46:35,510] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 30 samples (table) [2022-12-06 13:46:35,511] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-12-06 13:46:35,521] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-12-06 13:46:35,526] multiqc [DEBUG ] No samples found: conpair [2022-12-06 13:46:35,531] multiqc [DEBUG ] No samples found: peddy [2022-12-06 13:46:35,537] multiqc [DEBUG ] No samples found: somalier [2022-12-06 13:46:35,542] multiqc [DEBUG ] No samples found: methylQA [2022-12-06 13:46:35,552] multiqc [DEBUG ] No samples found: mosdepth [2022-12-06 13:46:35,556] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-12-06 13:46:35,561] multiqc [DEBUG ] No samples found: qualimap [2022-12-06 13:46:35,567] multiqc [DEBUG ] No samples found: preseq [2022-12-06 13:46:35,574] multiqc [DEBUG ] No samples found: quast [2022-12-06 13:46:35,581] multiqc [DEBUG ] No samples found: qorts [2022-12-06 13:46:35,586] multiqc [DEBUG ] No samples found: rna_seqc [2022-12-06 13:46:35,594] multiqc [DEBUG ] No samples found: rockhopper [2022-12-06 13:46:35,600] multiqc [DEBUG ] No samples found: rsem [2022-12-06 13:46:35,614] multiqc [DEBUG ] No samples found: rseqc [2022-12-06 13:46:35,619] multiqc [DEBUG ] No samples found: busco [2022-12-06 13:46:35,624] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-12-06 13:46:35,629] multiqc [DEBUG ] No samples found: disambiguate [2022-12-06 13:46:35,637] multiqc [DEBUG ] No samples found: supernova [2022-12-06 13:46:35,656] multiqc [DEBUG ] No samples found: deeptools [2022-12-06 13:46:35,662] multiqc [DEBUG ] No samples found: sargasso [2022-12-06 13:46:35,669] multiqc [DEBUG ] No samples found: verifybamid [2022-12-06 13:46:35,675] multiqc [DEBUG ] No samples found: mirtrace [2022-12-06 13:46:35,682] multiqc [DEBUG ] No samples found: happy [2022-12-06 13:46:35,689] multiqc [DEBUG ] No samples found: mirtop [2022-12-06 13:46:35,697] multiqc [DEBUG ] No samples found: homer [2022-12-06 13:46:35,706] multiqc [DEBUG ] No samples found: macs2 [2022-12-06 13:46:35,710] multiqc [DEBUG ] No samples found: theta2 [2022-12-06 13:46:35,718] multiqc [DEBUG ] No samples found: snpeff [2022-12-06 13:46:35,727] multiqc [DEBUG ] No samples found: gatk [2022-12-06 13:46:35,733] multiqc [DEBUG ] No samples found: htseq [2022-12-06 13:46:35,741] multiqc [DEBUG ] No samples found: bcftools [2022-12-06 13:46:35,747] multiqc [DEBUG ] No samples found: featureCounts [2022-12-06 13:46:35,754] multiqc [DEBUG ] No samples found: fgbio [2022-12-06 13:46:35,776] multiqc [DEBUG ] No samples found: dragen [2022-12-06 13:46:35,781] multiqc [DEBUG ] No samples found: dedup [2022-12-06 13:46:35,787] multiqc [DEBUG ] No samples found: damageprofiler [2022-12-06 13:46:35,822] multiqc [DEBUG ] No samples found: biobambam2 [2022-12-06 13:46:35,827] multiqc [DEBUG ] No samples found: mtnucratio [2022-12-06 13:46:35,829] multiqc [DEBUG ] No samples found: picard [2022-12-06 13:46:35,836] multiqc [DEBUG ] No samples found: prokka [2022-12-06 13:46:35,841] multiqc [DEBUG ] No samples found: samblaster [2022-12-06 13:46:35,852] multiqc [DEBUG ] No samples found: samtools [2022-12-06 13:46:35,858] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-12-06 13:46:35,867] multiqc [DEBUG ] No samples found: bamtools [2022-12-06 13:46:35,872] multiqc [DEBUG ] No samples found: jellyfish [2022-12-06 13:46:35,886] multiqc [DEBUG ] No samples found: vcftools [2022-12-06 13:46:35,892] multiqc [DEBUG ] No samples found: longranger [2022-12-06 13:46:35,897] multiqc [DEBUG ] No samples found: stacks [2022-12-06 13:46:35,904] multiqc [DEBUG ] No samples found: varscan2 [2022-12-06 13:46:35,923] multiqc [DEBUG ] No samples found: bbmap [2022-12-06 13:46:35,930] multiqc [DEBUG ] No samples found: bismark [2022-12-06 13:46:35,936] multiqc [DEBUG ] No samples found: biscuit [2022-12-06 13:46:35,941] multiqc [DEBUG ] No samples found: hicexplorer [2022-12-06 13:46:35,946] multiqc [DEBUG ] No samples found: hicup [2022-12-06 13:46:35,952] multiqc [DEBUG ] No samples found: hicpro [2022-12-06 13:46:35,958] multiqc [DEBUG ] No samples found: salmon [2022-12-06 13:46:35,966] multiqc [DEBUG ] No samples found: kallisto [2022-12-06 13:46:35,973] multiqc [DEBUG ] No samples found: slamdunk [2022-12-06 13:46:35,979] multiqc [DEBUG ] No samples found: star [2022-12-06 13:46:35,986] multiqc [DEBUG ] No samples found: hisat2 [2022-12-06 13:46:35,991] multiqc [DEBUG ] No samples found: tophat [2022-12-06 13:46:35,996] multiqc [DEBUG ] No samples found: bowtie2 [2022-12-06 13:46:36,001] multiqc [DEBUG ] No samples found: bowtie1 [2022-12-06 13:46:36,008] multiqc [DEBUG ] No samples found: snpsplit [2022-12-06 13:46:36,013] multiqc [DEBUG ] No samples found: kat [2022-12-06 13:46:36,019] multiqc [DEBUG ] No samples found: leehom [2022-12-06 13:46:36,025] multiqc [DEBUG ] No samples found: adapterRemoval [2022-12-06 13:46:36,030] multiqc [DEBUG ] No samples found: clipandmerge [2022-12-06 13:46:36,035] multiqc [DEBUG ] No samples found: cutadapt [2022-12-06 13:46:36,039] multiqc [DEBUG ] No samples found: flexbar [2022-12-06 13:46:36,045] multiqc [DEBUG ] No samples found: kaiju [2022-12-06 13:46:36,052] multiqc [DEBUG ] No samples found: kraken [2022-12-06 13:46:36,059] multiqc [DEBUG ] No samples found: malt [2022-12-06 13:46:36,064] multiqc [DEBUG ] No samples found: trimmomatic [2022-12-06 13:46:36,069] multiqc [DEBUG ] No samples found: sickle [2022-12-06 13:46:36,076] multiqc [DEBUG ] No samples found: skewer [2022-12-06 13:46:36,081] multiqc [DEBUG ] No samples found: sortmerna [2022-12-06 13:46:36,086] multiqc [DEBUG ] No samples found: biobloomtools [2022-12-06 13:46:36,091] multiqc [DEBUG ] No samples found: fastq_screen [2022-12-06 13:46:36,099] multiqc [DEBUG ] No samples found: afterqc [2022-12-06 13:46:36,106] multiqc [DEBUG ] No samples found: fastp [2022-12-06 13:46:37,107] multiqc.modules.fastqc.fastqc [INFO ] Found 30 reports [2022-12-06 13:46:37,538] multiqc [DEBUG ] No samples found: pycoqc [2022-12-06 13:46:37,545] multiqc [DEBUG ] No samples found: minionqc [2022-12-06 13:46:37,550] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-12-06 13:46:37,557] multiqc [DEBUG ] No samples found: clusterflow [2022-12-06 13:46:37,565] multiqc [DEBUG ] No samples found: bcl2fastq [2022-12-06 13:46:37,572] multiqc [DEBUG ] No samples found: interop [2022-12-06 13:46:37,578] multiqc [DEBUG ] No samples found: ivar [2022-12-06 13:46:37,585] multiqc [DEBUG ] No samples found: flash [2022-12-06 13:46:37,590] multiqc [DEBUG ] No samples found: seqyclean [2022-12-06 13:46:37,590] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-12-06 13:46:37,590] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-12-06 13:46:37,590] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-12-06 13:46:37,590] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-12-06 13:46:37,626] multiqc [INFO ] Compressing plot data [2022-12-06 13:46:38,168] multiqc [INFO ] Report : multiqc_report.html [2022-12-06 13:46:38,168] multiqc [INFO ] Data : multiqc_data [2022-12-06 13:46:38,168] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27702025/tmpkkeicb5v/multiqc_data' to '/scratch/gencore/logs/html/HMTJCDRX2/merged/multiqc_data' [2022-12-06 13:46:38,328] multiqc [INFO ] MultiQC complete