[2022-11-22 23:14:01,401] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-22 23:14:01,402] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-22 23:14:01,402] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-22 23:14:01,403] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-22 23:14:01,403] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-22 23:14:01,403] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-22 23:14:01,934] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-22 23:14:01,935] multiqc [INFO ] This is MultiQC v1.9 [2022-11-22 23:14:01,935] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-22 23:14:01,935] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-22 23:14:01,935] multiqc [INFO ] Template : default [2022-11-22 23:14:01,935] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-22 23:14:01,935] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-22 23:14:01,935] 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 [2022-11-22 23:14:01,935] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27236745/tmpyhp455a9 [2022-11-22 23:14:02,074] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n01_DO11_2_fastqc.html [2022-11-22 23:14:02,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-11-22 23:14:04,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO35_fastqc.html [2022-11-22 23:14:04,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO11_2_fastqc.html [2022-11-22 23:14:04,827] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO11_2_fastqc.html [2022-11-22 23:14:04,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n01_DO49_fastqc.html [2022-11-22 23:14:04,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n01_DO49_fastqc.html [2022-11-22 23:14:04,957] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n01_undetermined_fastqc.html [2022-11-22 23:14:04,959] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n01_undetermined_fastqc.html [2022-11-22 23:14:05,015] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO40_fastqc.html [2022-11-22 23:14:05,017] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO40_fastqc.html [2022-11-22 23:14:05,381] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-22 23:14:05,385] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-22 23:14:05,403] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2022-11-22 23:14:05,413] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-22 23:14:05,414] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-22 23:14:05,421] multiqc [DEBUG ] No samples found: conpair [2022-11-22 23:14:05,428] multiqc [DEBUG ] No samples found: peddy [2022-11-22 23:14:05,436] multiqc [DEBUG ] No samples found: somalier [2022-11-22 23:14:05,441] multiqc [DEBUG ] No samples found: methylQA [2022-11-22 23:14:05,454] multiqc [DEBUG ] No samples found: mosdepth [2022-11-22 23:14:05,458] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-22 23:14:05,463] multiqc [DEBUG ] No samples found: qualimap [2022-11-22 23:14:05,469] multiqc [DEBUG ] No samples found: preseq [2022-11-22 23:14:05,475] multiqc [DEBUG ] No samples found: quast [2022-11-22 23:14:05,481] multiqc [DEBUG ] No samples found: qorts [2022-11-22 23:14:05,486] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-22 23:14:05,491] multiqc [DEBUG ] No samples found: rockhopper [2022-11-22 23:14:05,496] multiqc [DEBUG ] No samples found: rsem [2022-11-22 23:14:05,512] multiqc [DEBUG ] No samples found: rseqc [2022-11-22 23:14:05,516] multiqc [DEBUG ] No samples found: busco [2022-11-22 23:14:05,523] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-22 23:14:05,528] multiqc [DEBUG ] No samples found: disambiguate [2022-11-22 23:14:05,534] multiqc [DEBUG ] No samples found: supernova [2022-11-22 23:14:05,553] multiqc [DEBUG ] No samples found: deeptools [2022-11-22 23:14:05,558] multiqc [DEBUG ] No samples found: sargasso [2022-11-22 23:14:05,565] multiqc [DEBUG ] No samples found: verifybamid [2022-11-22 23:14:05,571] multiqc [DEBUG ] No samples found: mirtrace [2022-11-22 23:14:05,576] multiqc [DEBUG ] No samples found: happy [2022-11-22 23:14:05,581] multiqc [DEBUG ] No samples found: mirtop [2022-11-22 23:14:05,590] multiqc [DEBUG ] No samples found: homer [2022-11-22 23:14:05,596] multiqc [DEBUG ] No samples found: macs2 [2022-11-22 23:14:05,601] multiqc [DEBUG ] No samples found: theta2 [2022-11-22 23:14:05,609] multiqc [DEBUG ] No samples found: snpeff [2022-11-22 23:14:05,618] multiqc [DEBUG ] No samples found: gatk [2022-11-22 23:14:05,623] multiqc [DEBUG ] No samples found: htseq [2022-11-22 23:14:05,630] multiqc [DEBUG ] No samples found: bcftools [2022-11-22 23:14:05,635] multiqc [DEBUG ] No samples found: featureCounts [2022-11-22 23:14:05,646] multiqc [DEBUG ] No samples found: fgbio [2022-11-22 23:14:05,662] multiqc [DEBUG ] No samples found: dragen [2022-11-22 23:14:05,668] multiqc [DEBUG ] No samples found: dedup [2022-11-22 23:14:05,675] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-22 23:14:05,710] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-22 23:14:05,715] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-22 23:14:05,717] multiqc [DEBUG ] No samples found: picard [2022-11-22 23:14:05,722] multiqc [DEBUG ] No samples found: prokka [2022-11-22 23:14:05,727] multiqc [DEBUG ] No samples found: samblaster [2022-11-22 23:14:05,740] multiqc [DEBUG ] No samples found: samtools [2022-11-22 23:14:05,745] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-22 23:14:05,751] multiqc [DEBUG ] No samples found: bamtools [2022-11-22 23:14:05,756] multiqc [DEBUG ] No samples found: jellyfish [2022-11-22 23:14:05,770] multiqc [DEBUG ] No samples found: vcftools [2022-11-22 23:14:05,775] multiqc [DEBUG ] No samples found: longranger [2022-11-22 23:14:05,781] multiqc [DEBUG ] No samples found: stacks [2022-11-22 23:14:05,787] multiqc [DEBUG ] No samples found: varscan2 [2022-11-22 23:14:05,808] multiqc [DEBUG ] No samples found: bbmap [2022-11-22 23:14:05,815] multiqc [DEBUG ] No samples found: bismark [2022-11-22 23:14:05,822] multiqc [DEBUG ] No samples found: biscuit [2022-11-22 23:14:05,829] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-22 23:14:05,834] multiqc [DEBUG ] No samples found: hicup [2022-11-22 23:14:05,840] multiqc [DEBUG ] No samples found: hicpro [2022-11-22 23:14:05,844] multiqc [DEBUG ] No samples found: salmon [2022-11-22 23:14:05,849] multiqc [DEBUG ] No samples found: kallisto [2022-11-22 23:14:05,854] multiqc [DEBUG ] No samples found: slamdunk [2022-11-22 23:14:05,861] multiqc [DEBUG ] No samples found: star [2022-11-22 23:14:05,865] multiqc [DEBUG ] No samples found: hisat2 [2022-11-22 23:14:05,870] multiqc [DEBUG ] No samples found: tophat [2022-11-22 23:14:05,875] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-22 23:14:05,880] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-22 23:14:05,886] multiqc [DEBUG ] No samples found: snpsplit [2022-11-22 23:14:05,892] multiqc [DEBUG ] No samples found: kat [2022-11-22 23:14:05,896] multiqc [DEBUG ] No samples found: leehom [2022-11-22 23:14:05,902] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-22 23:14:05,907] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-22 23:14:05,911] multiqc [DEBUG ] No samples found: cutadapt [2022-11-22 23:14:05,916] multiqc [DEBUG ] No samples found: flexbar [2022-11-22 23:14:05,921] multiqc [DEBUG ] No samples found: kaiju [2022-11-22 23:14:05,926] multiqc [DEBUG ] No samples found: kraken [2022-11-22 23:14:05,932] multiqc [DEBUG ] No samples found: malt [2022-11-22 23:14:05,936] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-22 23:14:05,941] multiqc [DEBUG ] No samples found: sickle [2022-11-22 23:14:05,945] multiqc [DEBUG ] No samples found: skewer [2022-11-22 23:14:05,949] multiqc [DEBUG ] No samples found: sortmerna [2022-11-22 23:14:05,954] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-22 23:14:05,958] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-22 23:14:05,964] multiqc [DEBUG ] No samples found: afterqc [2022-11-22 23:14:05,969] multiqc [DEBUG ] No samples found: fastp [2022-11-22 23:14:09,329] multiqc.modules.fastqc.fastqc [INFO ] Found 42 reports [2022-11-22 23:14:09,713] multiqc [DEBUG ] No samples found: pycoqc [2022-11-22 23:14:09,719] multiqc [DEBUG ] No samples found: minionqc [2022-11-22 23:14:09,725] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-22 23:14:09,730] multiqc [DEBUG ] No samples found: clusterflow [2022-11-22 23:14:09,736] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-22 23:14:09,743] multiqc [DEBUG ] No samples found: interop [2022-11-22 23:14:09,749] multiqc [DEBUG ] No samples found: ivar [2022-11-22 23:14:09,756] multiqc [DEBUG ] No samples found: flash [2022-11-22 23:14:09,763] multiqc [DEBUG ] No samples found: seqyclean [2022-11-22 23:14:09,763] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-22 23:14:09,763] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-22 23:14:09,763] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-22 23:14:09,763] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-22 23:14:09,813] multiqc [INFO ] Compressing plot data [2022-11-22 23:14:10,525] multiqc [INFO ] Report : multiqc_report.html [2022-11-22 23:14:10,526] multiqc [INFO ] Data : multiqc_data [2022-11-22 23:14:10,526] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27236745/tmpyhp455a9/multiqc_data' to '/scratch/gencore/logs/html/HLJKYDRX2/merged/multiqc_data' [2022-11-22 23:18:55,761] multiqc [INFO ] MultiQC complete