[2021-11-12 09:00:59,835] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-12 09:00:59,835] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-12 09:00:59,835] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-12 09:00:59,836] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-12 09:00:59,836] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-12 09:00:59,837] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF2T7BGXK/merged [2021-11-12 09:01:01,219] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-12 09:01:01,219] multiqc [INFO ] This is MultiQC v1.9 [2021-11-12 09:01:01,219] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF2T7BGXK/merged [2021-11-12 09:01:01,219] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HF2T7BGXK/merged [2021-11-12 09:01:01,219] multiqc [INFO ] Template : default [2021-11-12 09:01:01,219] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-12 09:01:01,219] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HF2T7BGXK/merged [2021-11-12 09:01:01,220] 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 [2021-11-12 09:01:01,220] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11931058/tmp8de8fgo3 [2021-11-12 09:01:01,353] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n02_2853_d12_rep2_fastqc.html [2021-11-12 09:01:01,356] multiqc [DEBUG ] File ignored by longranger/invocation because it 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09:01:05,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n02_2882_d10_rep2_fastqc.html [2021-11-12 09:01:05,708] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n02_2882_d10_rep2_fastqc.html [2021-11-12 09:01:05,756] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2566_d06_rep2_fastqc.html [2021-11-12 09:01:05,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2566_d06_rep2_fastqc.html [2021-11-12 09:01:05,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_3010_d02_rep2_fastqc.html [2021-11-12 09:01:05,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_3010_d02_rep2_fastqc.html 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pattern filesize limit: HF2T7BGXK_n01_3019_d04_rep2_fastqc.html [2021-11-12 09:01:21,470] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_3019_d04_rep2_fastqc.html [2021-11-12 09:01:21,526] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2858_d02_rep2_fastqc.html [2021-11-12 09:01:21,527] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2858_d02_rep2_fastqc.html [2021-11-12 09:01:21,592] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2999_d04_rep2_fastqc.html [2021-11-12 09:01:21,594] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2999_d04_rep2_fastqc.html [2021-11-12 09:01:21,640] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded 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exceeded search pattern filesize limit: HF2T7BGXK_n01_2877_d10_rep2_fastqc.html [2021-11-12 09:01:21,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2877_d10_rep2_fastqc.html [2021-11-12 09:01:21,854] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n02_3018_d08_rep2_fastqc.html [2021-11-12 09:01:21,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n02_3018_d08_rep2_fastqc.html [2021-11-12 09:01:21,913] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2857_d06_rep2_fastqc.html [2021-11-12 09:01:21,915] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2857_d06_rep2_fastqc.html [2021-11-12 09:01:21,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n02_3007_d10_rep2_fastqc.html [2021-11-12 09:01:21,977] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n02_3007_d10_rep2_fastqc.html [2021-11-12 09:01:22,019] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n02_3007_d08_rep2_fastqc.html [2021-11-12 09:01:22,021] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n02_3007_d08_rep2_fastqc.html [2021-11-12 09:01:22,070] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2855_d04_rep2_fastqc.html [2021-11-12 09:01:22,072] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2855_d04_rep2_fastqc.html [2021-11-12 09:01:22,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2853_d04_rep2_fastqc.html [2021-11-12 09:01:22,135] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2853_d04_rep2_fastqc.html [2021-11-12 09:01:22,212] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2874_d02_rep2_fastqc.html [2021-11-12 09:01:22,214] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF2T7BGXK_n01_2874_d02_rep2_fastqc.html [2021-11-12 09:01:22,617] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-12 09:01:22,620] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-12 09:01:22,712] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 181 samples (table) [2021-11-12 09:01:22,714] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-12 09:01:22,723] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-12 09:01:22,730] multiqc [DEBUG ] No samples found: conpair [2021-11-12 09:01:22,737] multiqc [DEBUG ] No samples found: peddy [2021-11-12 09:01:22,743] multiqc [DEBUG ] No samples found: somalier [2021-11-12 09:01:22,747] multiqc [DEBUG ] No samples found: methylQA [2021-11-12 09:01:22,759] multiqc [DEBUG ] No samples found: mosdepth [2021-11-12 09:01:22,765] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-12 09:01:22,771] multiqc [DEBUG ] No samples found: qualimap [2021-11-12 09:01:22,776] multiqc [DEBUG ] No samples found: preseq [2021-11-12 09:01:22,784] multiqc [DEBUG ] No samples found: quast [2021-11-12 09:01:22,791] multiqc [DEBUG ] No samples found: qorts [2021-11-12 09:01:22,799] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-12 09:01:22,805] multiqc [DEBUG ] No samples found: rockhopper [2021-11-12 09:01:22,811] multiqc [DEBUG ] No samples found: rsem [2021-11-12 09:01:22,830] multiqc [DEBUG ] No samples found: rseqc [2021-11-12 09:01:22,835] multiqc [DEBUG ] No samples found: busco [2021-11-12 09:01:22,843] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-12 09:01:22,850] multiqc [DEBUG ] No samples found: disambiguate [2021-11-12 09:01:22,856] multiqc [DEBUG ] No samples found: supernova [2021-11-12 09:01:22,880] multiqc [DEBUG ] No samples found: deeptools [2021-11-12 09:01:22,888] multiqc [DEBUG ] No samples found: sargasso [2021-11-12 09:01:22,894] multiqc [DEBUG ] No samples found: verifybamid [2021-11-12 09:01:22,900] multiqc [DEBUG ] No samples found: mirtrace [2021-11-12 09:01:22,904] multiqc [DEBUG ] No samples found: happy [2021-11-12 09:01:22,911] multiqc [DEBUG ] No samples found: mirtop [2021-11-12 09:01:22,922] multiqc [DEBUG ] No samples found: homer [2021-11-12 09:01:22,929] multiqc [DEBUG ] No samples found: macs2 [2021-11-12 09:01:22,934] multiqc [DEBUG ] No samples found: theta2 [2021-11-12 09:01:22,941] multiqc [DEBUG ] No samples found: snpeff [2021-11-12 09:01:22,950] multiqc [DEBUG ] No samples found: gatk [2021-11-12 09:01:22,956] multiqc [DEBUG ] No samples found: htseq [2021-11-12 09:01:22,963] multiqc [DEBUG ] No samples found: bcftools [2021-11-12 09:01:22,971] multiqc [DEBUG ] No samples found: featureCounts [2021-11-12 09:01:22,981] multiqc [DEBUG ] No samples found: fgbio [2021-11-12 09:01:23,006] multiqc [DEBUG ] No samples found: dragen [2021-11-12 09:01:23,011] multiqc [DEBUG ] No samples found: dedup [2021-11-12 09:01:23,016] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-12 09:01:23,063] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-12 09:01:23,069] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-12 09:01:23,072] multiqc [DEBUG ] No samples found: picard [2021-11-12 09:01:23,079] multiqc [DEBUG ] No samples found: prokka [2021-11-12 09:01:23,083] multiqc [DEBUG ] No samples found: samblaster [2021-11-12 09:01:23,101] multiqc [DEBUG ] No samples found: samtools [2021-11-12 09:01:23,107] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-12 09:01:23,114] multiqc [DEBUG ] No samples found: bamtools [2021-11-12 09:01:23,121] multiqc [DEBUG ] No samples found: jellyfish [2021-11-12 09:01:23,136] multiqc [DEBUG ] No samples found: vcftools [2021-11-12 09:01:23,144] multiqc [DEBUG ] No samples found: longranger [2021-11-12 09:01:23,150] multiqc [DEBUG ] No samples found: stacks [2021-11-12 09:01:23,157] multiqc [DEBUG ] No samples found: varscan2 [2021-11-12 09:01:23,186] multiqc [DEBUG ] No samples found: bbmap [2021-11-12 09:01:23,193] multiqc [DEBUG ] No samples found: bismark [2021-11-12 09:01:23,200] multiqc [DEBUG ] No samples found: biscuit [2021-11-12 09:01:23,207] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-12 09:01:23,214] multiqc [DEBUG ] No samples found: hicup [2021-11-12 09:01:23,220] multiqc [DEBUG ] No samples found: hicpro [2021-11-12 09:01:23,224] multiqc [DEBUG ] No samples found: salmon [2021-11-12 09:01:23,231] multiqc [DEBUG ] No samples found: kallisto [2021-11-12 09:01:23,237] multiqc [DEBUG ] No samples found: slamdunk [2021-11-12 09:01:23,244] multiqc [DEBUG ] No samples found: star [2021-11-12 09:01:23,251] multiqc [DEBUG ] No samples found: hisat2 [2021-11-12 09:01:23,258] multiqc [DEBUG ] No samples found: tophat [2021-11-12 09:01:23,264] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-12 09:01:23,272] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-12 09:01:23,278] multiqc [DEBUG ] No samples found: snpsplit [2021-11-12 09:01:23,282] multiqc [DEBUG ] No samples found: kat [2021-11-12 09:01:23,287] multiqc [DEBUG ] No samples found: leehom [2021-11-12 09:01:23,293] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-12 09:01:23,299] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-12 09:01:23,306] multiqc [DEBUG ] No samples found: cutadapt [2021-11-12 09:01:23,313] multiqc [DEBUG ] No samples found: flexbar [2021-11-12 09:01:23,321] multiqc [DEBUG ] No samples found: kaiju [2021-11-12 09:01:23,327] multiqc [DEBUG ] No samples found: kraken [2021-11-12 09:01:23,332] multiqc [DEBUG ] No samples found: malt [2021-11-12 09:01:23,339] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-12 09:01:23,346] multiqc [DEBUG ] No samples found: sickle [2021-11-12 09:01:23,353] multiqc [DEBUG ] No samples found: skewer [2021-11-12 09:01:23,359] multiqc [DEBUG ] No samples found: sortmerna [2021-11-12 09:01:23,366] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-12 09:01:23,372] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-12 09:01:23,379] multiqc [DEBUG ] No samples found: afterqc [2021-11-12 09:01:23,386] multiqc [DEBUG ] No samples found: fastp [2021-11-12 09:01:55,900] multiqc.modules.fastqc.fastqc [INFO ] Found 362 reports [2021-11-12 09:02:26,798] multiqc [DEBUG ] No samples found: pycoqc [2021-11-12 09:02:26,806] multiqc [DEBUG ] No samples found: minionqc [2021-11-12 09:02:26,813] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-12 09:02:26,820] multiqc [DEBUG ] No samples found: clusterflow [2021-11-12 09:02:26,825] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-12 09:02:26,831] multiqc [DEBUG ] No samples found: interop [2021-11-12 09:02:26,838] multiqc [DEBUG ] No samples found: ivar [2021-11-12 09:02:26,845] multiqc [DEBUG ] No samples found: flash [2021-11-12 09:02:26,852] multiqc [DEBUG ] No samples found: seqyclean [2021-11-12 09:02:26,852] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-12 09:02:26,852] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-12 09:02:26,852] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-12 09:02:26,852] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-12 09:02:27,261] multiqc [INFO ] Compressing plot data [2021-11-12 09:02:27,387] multiqc [INFO ] Report : multiqc_report.html [2021-11-12 09:02:27,387] multiqc [INFO ] Data : multiqc_data [2021-11-12 09:02:27,387] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11931058/tmp8de8fgo3/multiqc_data' to '/scratch/gencore/logs/html/HF2T7BGXK/merged/multiqc_data' [2021-11-12 09:02:28,258] multiqc [INFO ] MultiQC complete