[2021-05-28 07:03:48,118] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-05-28 07:03:48,118] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-05-28 07:03:48,118] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-05-28 07:03:48,119] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-05-28 07:03:48,119] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-05-28 07:03:48,119] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2Y77BGXJ/merged [2021-05-28 07:03:49,629] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-05-28 07:03:49,629] multiqc [INFO ] This is MultiQC v1.9 [2021-05-28 07:03:49,629] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2Y77BGXJ/merged [2021-05-28 07:03:49,629] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H2Y77BGXJ/merged [2021-05-28 07:03:49,629] multiqc [INFO ] Template : default [2021-05-28 07:03:49,629] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-05-28 07:03:49,629] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H2Y77BGXJ/merged [2021-05-28 07:03:49,630] 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 [2021-05-28 07:03:49,630] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7205406/tmpbw8r8rdo [2021-05-28 07:03:49,740] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_IL12B_stim_2_fastqc.html [2021-05-28 07:03:49,743] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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filesize limit: H2Y77BGXJ_n02_LTBR_no_stim_3_fastqc.html [2021-05-28 07:03:52,462] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_LTBR_no_stim_3_fastqc.html [2021-05-28 07:03:52,503] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_DUPD1_stim_2_fastqc.html [2021-05-28 07:03:52,505] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_DUPD1_stim_2_fastqc.html [2021-05-28 07:03:52,572] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_LTBR_no_stim_2_fastqc.html [2021-05-28 07:03:52,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_LTBR_no_stim_2_fastqc.html [2021-05-28 07:03:52,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search 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search pattern filesize limit: H2Y77BGXJ_n01_NGFR_stim_1_fastqc.html [2021-05-28 07:03:52,786] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_NGFR_stim_1_fastqc.html [2021-05-28 07:03:52,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_undetermined_fastqc.html [2021-05-28 07:03:52,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_undetermined_fastqc.html [2021-05-28 07:03:52,895] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_IFNL2_stim_3_fastqc.html [2021-05-28 07:03:52,897] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_IFNL2_stim_3_fastqc.html [2021-05-28 07:03:52,941] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_NGFR_no_stim_1_fastqc.html [2021-05-28 07:03:52,942] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_NGFR_no_stim_1_fastqc.html [2021-05-28 07:03:52,986] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_AKR1C4_stim_1_fastqc.html [2021-05-28 07:03:52,988] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_AKR1C4_stim_1_fastqc.html [2021-05-28 07:03:53,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_LTBR_no_stim_2_fastqc.html [2021-05-28 07:03:53,047] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_LTBR_no_stim_2_fastqc.html [2021-05-28 07:03:53,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_LTBR_stim_1_fastqc.html [2021-05-28 07:03:53,108] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_LTBR_stim_1_fastqc.html [2021-05-28 07:03:53,150] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_AKR1C4_no_stim_2_fastqc.html [2021-05-28 07:03:53,151] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_AKR1C4_no_stim_2_fastqc.html [2021-05-28 07:03:53,207] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_DUPD1_stim_2_fastqc.html [2021-05-28 07:03:53,209] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_DUPD1_stim_2_fastqc.html [2021-05-28 07:03:53,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_LTBR_no_stim_1_fastqc.html [2021-05-28 07:03:53,273] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_LTBR_no_stim_1_fastqc.html [2021-05-28 07:03:53,314] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_IFNL2_stim_1_fastqc.html [2021-05-28 07:03:53,316] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_IFNL2_stim_1_fastqc.html [2021-05-28 07:03:53,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_AKR1C4_no_stim_1_fastqc.html [2021-05-28 07:03:53,373] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_AKR1C4_no_stim_1_fastqc.html [2021-05-28 07:03:53,415] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_LTBR_stim_1_fastqc.html [2021-05-28 07:03:53,416] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_LTBR_stim_1_fastqc.html [2021-05-28 07:03:53,461] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_DUPD1_no_stim_1_fastqc.html [2021-05-28 07:03:53,463] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n02_DUPD1_no_stim_1_fastqc.html [2021-05-28 07:03:53,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_DUPD1_no_stim_3_fastqc.html [2021-05-28 07:03:53,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2Y77BGXJ_n01_DUPD1_no_stim_3_fastqc.html [2021-05-28 07:03:54,038] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-28 07:03:54,039] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-28 07:03:54,063] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 36 samples (table) [2021-05-28 07:03:54,073] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-05-28 07:03:54,075] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-05-28 07:03:54,079] multiqc [DEBUG ] No samples found: conpair [2021-05-28 07:03:54,084] multiqc [DEBUG ] No samples found: peddy [2021-05-28 07:03:54,088] multiqc [DEBUG ] No samples found: somalier [2021-05-28 07:03:54,092] multiqc [DEBUG ] No samples found: methylQA [2021-05-28 07:03:54,100] multiqc [DEBUG ] No samples found: mosdepth [2021-05-28 07:03:54,104] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-05-28 07:03:54,107] multiqc [DEBUG ] No samples found: qualimap [2021-05-28 07:03:54,111] multiqc [DEBUG ] No samples found: preseq [2021-05-28 07:03:54,116] multiqc [DEBUG ] No samples found: quast [2021-05-28 07:03:54,120] multiqc [DEBUG ] No samples found: qorts [2021-05-28 07:03:54,124] multiqc [DEBUG ] No samples found: rna_seqc [2021-05-28 07:03:54,128] multiqc [DEBUG ] No samples found: rockhopper [2021-05-28 07:03:54,133] multiqc [DEBUG ] No samples found: rsem [2021-05-28 07:03:54,142] multiqc [DEBUG ] No samples found: rseqc [2021-05-28 07:03:54,146] multiqc [DEBUG ] No samples found: busco [2021-05-28 07:03:54,151] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-05-28 07:03:54,154] multiqc [DEBUG ] No samples found: disambiguate [2021-05-28 07:03:54,159] multiqc [DEBUG ] No samples found: supernova [2021-05-28 07:03:54,170] multiqc [DEBUG ] No samples found: deeptools [2021-05-28 07:03:54,175] multiqc [DEBUG ] No samples found: sargasso [2021-05-28 07:03:54,179] multiqc [DEBUG ] No samples found: verifybamid [2021-05-28 07:03:54,184] multiqc [DEBUG ] No samples found: mirtrace [2021-05-28 07:03:54,188] multiqc [DEBUG ] No samples found: happy [2021-05-28 07:03:54,192] multiqc [DEBUG ] No samples found: mirtop [2021-05-28 07:03:54,198] multiqc [DEBUG ] No samples found: homer [2021-05-28 07:03:54,202] multiqc [DEBUG ] No samples found: macs2 [2021-05-28 07:03:54,206] multiqc [DEBUG ] No samples found: theta2 [2021-05-28 07:03:54,211] multiqc [DEBUG ] No samples found: snpeff [2021-05-28 07:03:54,217] multiqc [DEBUG ] No samples found: gatk [2021-05-28 07:03:54,222] multiqc [DEBUG ] No samples found: htseq [2021-05-28 07:03:54,227] multiqc [DEBUG ] No samples found: bcftools [2021-05-28 07:03:54,231] multiqc [DEBUG ] No samples found: featureCounts [2021-05-28 07:03:54,237] multiqc [DEBUG ] No samples found: fgbio [2021-05-28 07:03:54,249] multiqc [DEBUG ] No samples found: dragen [2021-05-28 07:03:54,253] multiqc [DEBUG ] No samples found: dedup [2021-05-28 07:03:54,258] multiqc [DEBUG ] No samples found: damageprofiler [2021-05-28 07:03:54,280] multiqc [DEBUG ] No samples found: biobambam2 [2021-05-28 07:03:54,284] multiqc [DEBUG ] No samples found: mtnucratio [2021-05-28 07:03:54,286] multiqc [DEBUG ] No samples found: picard [2021-05-28 07:03:54,290] multiqc [DEBUG ] No samples found: prokka [2021-05-28 07:03:54,294] multiqc [DEBUG ] No samples found: samblaster [2021-05-28 07:03:54,303] multiqc [DEBUG ] No samples found: samtools [2021-05-28 07:03:54,308] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-05-28 07:03:54,312] multiqc [DEBUG ] No samples found: bamtools [2021-05-28 07:03:54,316] multiqc [DEBUG ] No samples found: jellyfish [2021-05-28 07:03:54,324] multiqc [DEBUG ] No samples found: vcftools [2021-05-28 07:03:54,329] multiqc [DEBUG ] No samples found: longranger [2021-05-28 07:03:54,333] multiqc [DEBUG ] No samples found: stacks [2021-05-28 07:03:54,338] multiqc [DEBUG ] No samples found: varscan2 [2021-05-28 07:03:54,351] multiqc [DEBUG ] No samples found: bbmap [2021-05-28 07:03:54,356] multiqc [DEBUG ] No samples found: bismark [2021-05-28 07:03:54,361] multiqc [DEBUG ] No samples found: biscuit [2021-05-28 07:03:54,365] multiqc [DEBUG ] No samples found: hicexplorer [2021-05-28 07:03:54,369] multiqc [DEBUG ] No samples found: hicup [2021-05-28 07:03:54,373] multiqc [DEBUG ] No samples found: hicpro [2021-05-28 07:03:54,377] multiqc [DEBUG ] No samples found: salmon [2021-05-28 07:03:54,381] multiqc [DEBUG ] No samples found: kallisto [2021-05-28 07:03:54,386] multiqc [DEBUG ] No samples found: slamdunk [2021-05-28 07:03:54,390] multiqc [DEBUG ] No samples found: star [2021-05-28 07:03:54,394] multiqc [DEBUG ] No samples found: hisat2 [2021-05-28 07:03:54,398] multiqc [DEBUG ] No samples found: tophat [2021-05-28 07:03:54,403] multiqc [DEBUG ] No samples found: bowtie2 [2021-05-28 07:03:54,407] multiqc [DEBUG ] No samples found: bowtie1 [2021-05-28 07:03:54,411] multiqc [DEBUG ] No samples found: snpsplit [2021-05-28 07:03:54,415] multiqc [DEBUG ] No samples found: kat [2021-05-28 07:03:54,419] multiqc [DEBUG ] No samples found: leehom [2021-05-28 07:03:54,424] multiqc [DEBUG ] No samples found: adapterRemoval [2021-05-28 07:03:54,428] multiqc [DEBUG ] No samples found: clipandmerge [2021-05-28 07:03:54,432] multiqc [DEBUG ] No samples found: cutadapt [2021-05-28 07:03:54,436] multiqc [DEBUG ] No samples found: flexbar [2021-05-28 07:03:54,440] multiqc [DEBUG ] No samples found: kaiju [2021-05-28 07:03:54,444] multiqc [DEBUG ] No samples found: kraken [2021-05-28 07:03:54,449] multiqc [DEBUG ] No samples found: malt [2021-05-28 07:03:54,453] multiqc [DEBUG ] No samples found: trimmomatic [2021-05-28 07:03:54,457] multiqc [DEBUG ] No samples found: sickle [2021-05-28 07:03:54,461] multiqc [DEBUG ] No samples found: skewer [2021-05-28 07:03:54,465] multiqc [DEBUG ] No samples found: sortmerna [2021-05-28 07:03:54,469] multiqc [DEBUG ] No samples found: biobloomtools [2021-05-28 07:03:54,474] multiqc [DEBUG ] No samples found: fastq_screen [2021-05-28 07:03:54,478] multiqc [DEBUG ] No samples found: afterqc [2021-05-28 07:03:54,482] multiqc [DEBUG ] No samples found: fastp [2021-05-28 07:03:59,465] multiqc.modules.fastqc.fastqc [INFO ] Found 72 reports [2021-05-28 07:03:59,822] multiqc [DEBUG ] No samples found: pycoqc [2021-05-28 07:03:59,827] multiqc [DEBUG ] No samples found: minionqc [2021-05-28 07:03:59,832] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-05-28 07:03:59,838] multiqc [DEBUG ] No samples found: clusterflow [2021-05-28 07:03:59,846] multiqc [DEBUG ] No samples found: bcl2fastq [2021-05-28 07:03:59,850] multiqc [DEBUG ] No samples found: interop [2021-05-28 07:03:59,854] multiqc [DEBUG ] No samples found: ivar [2021-05-28 07:03:59,859] multiqc [DEBUG ] No samples found: flash [2021-05-28 07:03:59,863] multiqc [DEBUG ] No samples found: seqyclean [2021-05-28 07:03:59,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-05-28 07:03:59,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-05-28 07:03:59,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-05-28 07:03:59,863] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-05-28 07:04:00,004] multiqc [INFO ] Compressing plot data [2021-05-28 07:04:01,136] multiqc [INFO ] Report : multiqc_report.html [2021-05-28 07:04:01,136] multiqc [INFO ] Data : multiqc_data [2021-05-28 07:04:01,136] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7205406/tmpbw8r8rdo/multiqc_data' to '/scratch/gencore/logs/html/H2Y77BGXJ/merged/multiqc_data' [2021-05-28 07:04:01,266] multiqc [INFO ] MultiQC complete