[2022-02-25 11:10:56,951] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-02-25 11:10:56,951] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-02-25 11:10:56,951] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-25 11:10:56,952] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-02-25 11:10:56,952] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-02-25 11:10:56,952] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVGTVDRXY/merged [2022-02-25 11:10:57,516] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-02-25 11:10:57,516] multiqc [INFO ] This is MultiQC v1.9 [2022-02-25 11:10:57,516] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVGTVDRXY/merged [2022-02-25 11:10:57,516] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVGTVDRXY/merged [2022-02-25 11:10:57,516] multiqc [INFO ] Template : default [2022-02-25 11:10:57,516] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-02-25 11:10:57,516] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVGTVDRXY/merged [2022-02-25 11:10:57,516] 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 [2022-02-25 11:10:57,516] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15288853/tmpdriu2q58 [2022-02-25 11:10:57,626] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT3_C_72_fastqc.html [2022-02-25 11:10:57,629] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-02-25 11:11:00,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT3_Y_11_fastqc.html [2022-02-25 11:11:00,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT3_Y_11_fastqc.html [2022-02-25 11:11:00,916] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT2_N_48_fastqc.html [2022-02-25 11:11:00,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT2_N_48_fastqc.html [2022-02-25 11:11:00,955] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT1_C_2_fastqc.html [2022-02-25 11:11:00,957] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT1_C_2_fastqc.html [2022-02-25 11:11:00,997] 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filesize limit: HVGTVDRXY_n02_WT3_Y_72_fastqc.html [2022-02-25 11:11:01,376] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT3_Y_72_fastqc.html [2022-02-25 11:11:01,416] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT2_N_11_fastqc.html [2022-02-25 11:11:01,418] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT2_N_11_fastqc.html [2022-02-25 11:11:01,458] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT3_N_5_fastqc.html [2022-02-25 11:11:01,460] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT3_N_5_fastqc.html [2022-02-25 11:11:01,499] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HVGTVDRXY_n02_WT2_N_2_fastqc.html [2022-02-25 11:11:01,622] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT2_N_2_fastqc.html [2022-02-25 11:11:01,661] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT2_C_2_fastqc.html [2022-02-25 11:11:01,663] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT2_C_2_fastqc.html [2022-02-25 11:11:01,703] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT2_C_8_fastqc.html [2022-02-25 11:11:01,705] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT2_C_8_fastqc.html [2022-02-25 11:11:01,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT2_Y_72_fastqc.html [2022-02-25 11:11:01,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n02_WT2_Y_72_fastqc.html [2022-02-25 11:11:01,787] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT2_N_11_fastqc.html [2022-02-25 11:11:01,789] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT2_N_11_fastqc.html [2022-02-25 11:11:01,828] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT3_C_24_fastqc.html [2022-02-25 11:11:01,830] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGTVDRXY_n01_WT3_C_24_fastqc.html [2022-02-25 11:11:02,335] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-25 11:11:02,337] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-25 11:11:02,344] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-02-25 11:11:02,354] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-02-25 11:11:02,377] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 50 samples (table) [2022-02-25 11:11:02,381] multiqc [DEBUG ] No samples found: conpair [2022-02-25 11:11:02,386] multiqc [DEBUG ] No samples found: peddy [2022-02-25 11:11:02,391] multiqc [DEBUG ] No samples found: somalier [2022-02-25 11:11:02,395] multiqc [DEBUG ] No samples found: methylQA [2022-02-25 11:11:02,403] multiqc [DEBUG ] No samples found: mosdepth [2022-02-25 11:11:02,407] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-25 11:11:02,411] multiqc [DEBUG ] No samples found: qualimap [2022-02-25 11:11:02,415] multiqc [DEBUG ] No samples found: preseq [2022-02-25 11:11:02,420] multiqc [DEBUG ] No samples found: quast [2022-02-25 11:11:02,424] multiqc [DEBUG ] No samples found: qorts [2022-02-25 11:11:02,429] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-25 11:11:02,433] multiqc [DEBUG ] No samples found: rockhopper [2022-02-25 11:11:02,437] multiqc [DEBUG ] No samples found: rsem [2022-02-25 11:11:02,449] multiqc [DEBUG ] No samples found: rseqc [2022-02-25 11:11:02,453] multiqc [DEBUG ] No samples found: busco [2022-02-25 11:11:02,457] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-25 11:11:02,461] multiqc [DEBUG ] No samples found: disambiguate [2022-02-25 11:11:02,466] multiqc [DEBUG ] No samples found: supernova [2022-02-25 11:11:02,478] multiqc [DEBUG ] No samples found: deeptools [2022-02-25 11:11:02,482] multiqc [DEBUG ] No samples found: sargasso [2022-02-25 11:11:02,486] multiqc [DEBUG ] No samples found: verifybamid [2022-02-25 11:11:02,491] multiqc [DEBUG ] No samples found: mirtrace [2022-02-25 11:11:02,495] multiqc [DEBUG ] No samples found: happy [2022-02-25 11:11:02,500] multiqc [DEBUG ] No samples found: mirtop [2022-02-25 11:11:02,505] multiqc [DEBUG ] No samples found: homer [2022-02-25 11:11:02,510] multiqc [DEBUG ] No samples found: macs2 [2022-02-25 11:11:02,514] multiqc [DEBUG ] No samples found: theta2 [2022-02-25 11:11:02,519] multiqc [DEBUG ] No samples found: snpeff [2022-02-25 11:11:02,525] multiqc [DEBUG ] No samples found: gatk [2022-02-25 11:11:02,529] multiqc [DEBUG ] No samples found: htseq [2022-02-25 11:11:02,534] multiqc [DEBUG ] No samples found: bcftools [2022-02-25 11:11:02,538] multiqc [DEBUG ] No samples found: featureCounts [2022-02-25 11:11:02,544] multiqc [DEBUG ] No samples found: fgbio [2022-02-25 11:11:02,556] multiqc [DEBUG ] No samples found: dragen [2022-02-25 11:11:02,561] multiqc [DEBUG ] No samples found: dedup [2022-02-25 11:11:02,565] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-25 11:11:02,587] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-25 11:11:02,591] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-25 11:11:02,593] multiqc [DEBUG ] No samples found: picard [2022-02-25 11:11:02,598] multiqc [DEBUG ] No samples found: prokka [2022-02-25 11:11:02,602] multiqc [DEBUG ] No samples found: samblaster [2022-02-25 11:11:02,610] multiqc [DEBUG ] No samples found: samtools [2022-02-25 11:11:02,614] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-25 11:11:02,619] multiqc [DEBUG ] No samples found: bamtools [2022-02-25 11:11:02,623] multiqc [DEBUG ] No samples found: jellyfish [2022-02-25 11:11:02,630] multiqc [DEBUG ] No samples found: vcftools [2022-02-25 11:11:02,634] multiqc [DEBUG ] No samples found: longranger [2022-02-25 11:11:02,638] multiqc [DEBUG ] No samples found: stacks [2022-02-25 11:11:02,643] multiqc [DEBUG ] No samples found: varscan2 [2022-02-25 11:11:02,655] multiqc [DEBUG ] No samples found: bbmap [2022-02-25 11:11:02,660] multiqc [DEBUG ] No samples found: bismark [2022-02-25 11:11:02,665] multiqc [DEBUG ] No samples found: biscuit [2022-02-25 11:11:02,669] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-25 11:11:02,674] multiqc [DEBUG ] No samples found: hicup [2022-02-25 11:11:02,678] multiqc [DEBUG ] No samples found: hicpro [2022-02-25 11:11:02,682] multiqc [DEBUG ] No samples found: salmon [2022-02-25 11:11:02,687] multiqc [DEBUG ] No samples found: kallisto [2022-02-25 11:11:02,691] multiqc [DEBUG ] No samples found: slamdunk [2022-02-25 11:11:02,695] multiqc [DEBUG ] No samples found: star [2022-02-25 11:11:02,700] multiqc [DEBUG ] No samples found: hisat2 [2022-02-25 11:11:02,704] multiqc [DEBUG ] No samples found: tophat [2022-02-25 11:11:02,708] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-25 11:11:02,713] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-25 11:11:02,717] multiqc [DEBUG ] No samples found: snpsplit [2022-02-25 11:11:02,721] multiqc [DEBUG ] No samples found: kat [2022-02-25 11:11:02,725] multiqc [DEBUG ] No samples found: leehom [2022-02-25 11:11:02,730] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-25 11:11:02,734] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-25 11:11:02,738] multiqc [DEBUG ] No samples found: cutadapt [2022-02-25 11:11:02,743] multiqc [DEBUG ] No samples found: flexbar [2022-02-25 11:11:02,748] multiqc [DEBUG ] No samples found: kaiju [2022-02-25 11:11:02,752] multiqc [DEBUG ] No samples found: kraken [2022-02-25 11:11:02,756] multiqc [DEBUG ] No samples found: malt [2022-02-25 11:11:02,760] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-25 11:11:02,765] multiqc [DEBUG ] No samples found: sickle [2022-02-25 11:11:02,769] multiqc [DEBUG ] No samples found: skewer [2022-02-25 11:11:02,773] multiqc [DEBUG ] No samples found: sortmerna [2022-02-25 11:11:02,777] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-25 11:11:02,781] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-25 11:11:02,785] multiqc [DEBUG ] No samples found: afterqc [2022-02-25 11:11:02,790] multiqc [DEBUG ] No samples found: fastp [2022-02-25 11:11:06,095] multiqc.modules.fastqc.fastqc [INFO ] Found 100 reports [2022-02-25 11:11:07,361] multiqc [DEBUG ] No samples found: pycoqc [2022-02-25 11:11:07,365] multiqc [DEBUG ] No samples found: minionqc [2022-02-25 11:11:07,370] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-02-25 11:11:07,374] multiqc [DEBUG ] No samples found: clusterflow [2022-02-25 11:11:07,379] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-25 11:11:07,383] multiqc [DEBUG ] No samples found: interop [2022-02-25 11:11:07,388] multiqc [DEBUG ] No samples found: ivar [2022-02-25 11:11:07,392] multiqc [DEBUG ] No samples found: flash [2022-02-25 11:11:07,397] multiqc [DEBUG ] No samples found: seqyclean [2022-02-25 11:11:07,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-02-25 11:11:07,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-02-25 11:11:07,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-02-25 11:11:07,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-02-25 11:11:07,511] multiqc [INFO ] Compressing plot data [2022-02-25 11:11:09,342] multiqc [INFO ] Report : multiqc_report.html [2022-02-25 11:11:09,342] multiqc [INFO ] Data : multiqc_data [2022-02-25 11:11:09,342] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15288853/tmpdriu2q58/multiqc_data' to '/scratch/gencore/logs/html/HVGTVDRXY/merged/multiqc_data' [2022-02-25 11:11:09,477] multiqc [INFO ] MultiQC complete