[2021-03-04 06:25:05,366] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-04 06:25:05,366] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-04 06:25:05,366] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-04 06:25:05,367] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-04 06:25:05,367] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-04 06:25:05,367] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN7VJAFX2/merged [2021-03-04 06:25:07,020] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-03-04 06:25:07,020] multiqc [INFO ] This is MultiQC v1.9 [2021-03-04 06:25:07,020] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN7VJAFX2/merged [2021-03-04 06:25:07,020] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HN7VJAFX2/merged [2021-03-04 06:25:07,020] multiqc [INFO ] Template : default [2021-03-04 06:25:07,020] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-04 06:25:07,020] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HN7VJAFX2/merged [2021-03-04 06:25:07,021] 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 [2021-03-04 06:25:07,021] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-3325071/tmpvd17fa4g [2021-03-04 06:25:07,153] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10703_input_fastqc.html [2021-03-04 06:25:07,157] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10703_input_fastqc.html [2021-03-04 06:25:07,214] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10703_flag_fastqc.html [2021-03-04 06:25:07,216] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10703_flag_fastqc.html [2021-03-04 06:25:07,256] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-04 06:25:07,258] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-04 06:25:07,348] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10705_input_fastqc.html [2021-03-04 06:25:07,350] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10705_input_fastqc.html [2021-03-04 06:25:07,416] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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HN7VJAFX2_n01_10705_input_fastqc.html [2021-03-04 06:25:07,585] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10705_input_fastqc.html [2021-03-04 06:25:07,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10705_flag_fastqc.html [2021-03-04 06:25:07,637] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10705_flag_fastqc.html [2021-03-04 06:25:07,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_XQTL_control_fastqc.html [2021-03-04 06:25:07,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_XQTL_control_fastqc.html [2021-03-04 06:25:07,757] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_undetermined_fastqc.html [2021-03-04 06:25:07,759] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_undetermined_fastqc.html [2021-03-04 06:25:07,814] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_undetermined_fastqc.html [2021-03-04 06:25:07,816] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_undetermined_fastqc.html [2021-03-04 06:25:07,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10704_flag_fastqc.html [2021-03-04 06:25:07,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_10704_flag_fastqc.html [2021-03-04 06:25:07,941] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10703_input_fastqc.html [2021-03-04 06:25:07,943] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10703_input_fastqc.html [2021-03-04 06:25:08,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_XQTL_MMS_fastqc.html [2021-03-04 06:25:08,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_XQTL_MMS_fastqc.html [2021-03-04 06:25:08,087] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10704_flag_fastqc.html [2021-03-04 06:25:08,089] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10704_flag_fastqc.html [2021-03-04 06:25:08,131] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_XQTL_HU_fastqc.html [2021-03-04 06:25:08,133] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_XQTL_HU_fastqc.html [2021-03-04 06:25:08,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_7797_flag_fastqc.html [2021-03-04 06:25:08,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_7797_flag_fastqc.html [2021-03-04 06:25:08,240] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_XQTL_control_fastqc.html [2021-03-04 06:25:08,242] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_XQTL_control_fastqc.html [2021-03-04 06:25:08,324] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10703_flag_fastqc.html [2021-03-04 06:25:08,326] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10703_flag_fastqc.html [2021-03-04 06:25:08,396] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_7797_input_fastqc.html [2021-03-04 06:25:08,398] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_7797_input_fastqc.html [2021-03-04 06:25:08,457] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_7797_input_fastqc.html [2021-03-04 06:25:08,459] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_7797_input_fastqc.html [2021-03-04 06:25:08,520] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_XQTL_MMS_fastqc.html [2021-03-04 06:25:08,522] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_XQTL_MMS_fastqc.html [2021-03-04 06:25:08,580] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n01_7797_flag_fastqc.html [2021-03-04 06:25:08,582] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n01_7797_flag_fastqc.html [2021-03-04 06:25:08,643] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10704_input_fastqc.html [2021-03-04 06:25:08,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7VJAFX2_n02_10704_input_fastqc.html [2021-03-04 06:25:09,232] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-04 06:25:09,235] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-04 06:25:09,248] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 12 samples (table) [2021-03-04 06:25:09,259] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-04 06:25:09,261] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-04 06:25:09,266] multiqc [DEBUG ] No samples found: conpair [2021-03-04 06:25:09,272] multiqc [DEBUG ] No samples found: peddy [2021-03-04 06:25:09,277] multiqc [DEBUG ] No samples found: somalier [2021-03-04 06:25:09,282] multiqc [DEBUG ] No samples found: methylQA [2021-03-04 06:25:09,291] multiqc [DEBUG ] No samples found: mosdepth [2021-03-04 06:25:09,296] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-04 06:25:09,300] multiqc [DEBUG ] No samples found: qualimap [2021-03-04 06:25:09,305] multiqc [DEBUG ] No samples found: preseq [2021-03-04 06:25:09,310] multiqc [DEBUG ] No samples found: quast [2021-03-04 06:25:09,315] multiqc [DEBUG ] No samples found: qorts [2021-03-04 06:25:09,320] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-04 06:25:09,326] multiqc [DEBUG ] No samples found: rockhopper [2021-03-04 06:25:09,331] multiqc [DEBUG ] No samples found: rsem [2021-03-04 06:25:09,343] multiqc [DEBUG ] No samples found: rseqc [2021-03-04 06:25:09,347] multiqc [DEBUG ] No samples found: busco [2021-03-04 06:25:09,353] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-04 06:25:09,358] multiqc [DEBUG ] No samples found: disambiguate [2021-03-04 06:25:09,363] multiqc [DEBUG ] No samples found: supernova [2021-03-04 06:25:09,378] multiqc [DEBUG ] No samples found: deeptools [2021-03-04 06:25:09,383] multiqc [DEBUG ] No samples found: sargasso [2021-03-04 06:25:09,389] multiqc [DEBUG ] No samples found: verifybamid [2021-03-04 06:25:09,394] multiqc [DEBUG ] No samples found: mirtrace [2021-03-04 06:25:09,399] multiqc [DEBUG ] No samples found: happy [2021-03-04 06:25:09,404] multiqc [DEBUG ] No samples found: mirtop [2021-03-04 06:25:09,412] multiqc [DEBUG ] No samples found: homer [2021-03-04 06:25:09,417] multiqc [DEBUG ] No samples found: macs2 [2021-03-04 06:25:09,422] multiqc [DEBUG ] No samples found: theta2 [2021-03-04 06:25:09,427] multiqc [DEBUG ] No samples found: snpeff [2021-03-04 06:25:09,434] multiqc [DEBUG ] No samples found: gatk [2021-03-04 06:25:09,439] multiqc [DEBUG ] No samples found: htseq [2021-03-04 06:25:09,445] multiqc [DEBUG ] No samples found: bcftools [2021-03-04 06:25:09,450] multiqc [DEBUG ] No samples found: featureCounts [2021-03-04 06:25:09,457] multiqc [DEBUG ] No samples found: fgbio [2021-03-04 06:25:09,470] multiqc [DEBUG ] No samples found: dragen [2021-03-04 06:25:09,476] multiqc [DEBUG ] No samples found: dedup [2021-03-04 06:25:09,481] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-04 06:25:09,506] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-04 06:25:09,510] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-04 06:25:09,513] multiqc [DEBUG ] No samples found: picard [2021-03-04 06:25:09,517] multiqc [DEBUG ] No samples found: prokka [2021-03-04 06:25:09,522] multiqc [DEBUG ] No samples found: samblaster [2021-03-04 06:25:09,530] multiqc [DEBUG ] No samples found: samtools [2021-03-04 06:25:09,535] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-04 06:25:09,541] multiqc [DEBUG ] No samples found: bamtools [2021-03-04 06:25:09,545] multiqc [DEBUG ] No samples found: jellyfish [2021-03-04 06:25:09,552] multiqc [DEBUG ] No samples found: vcftools [2021-03-04 06:25:09,557] multiqc [DEBUG ] No samples found: longranger [2021-03-04 06:25:09,562] multiqc [DEBUG ] No samples found: stacks [2021-03-04 06:25:09,567] multiqc [DEBUG ] No samples found: varscan2 [2021-03-04 06:25:09,581] multiqc [DEBUG ] No samples found: bbmap [2021-03-04 06:25:09,586] multiqc [DEBUG ] No samples found: bismark [2021-03-04 06:25:09,592] multiqc [DEBUG ] No samples found: biscuit [2021-03-04 06:25:09,597] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-04 06:25:09,602] multiqc [DEBUG ] No samples found: hicup [2021-03-04 06:25:09,607] multiqc [DEBUG ] No samples found: hicpro [2021-03-04 06:25:09,612] multiqc [DEBUG ] No samples found: salmon [2021-03-04 06:25:09,616] multiqc [DEBUG ] No samples found: kallisto [2021-03-04 06:25:09,622] multiqc [DEBUG ] No samples found: slamdunk [2021-03-04 06:25:09,626] multiqc [DEBUG ] No samples found: star [2021-03-04 06:25:09,631] multiqc [DEBUG ] No samples found: hisat2 [2021-03-04 06:25:09,636] multiqc [DEBUG ] No samples found: tophat [2021-03-04 06:25:09,641] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-04 06:25:09,646] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-04 06:25:09,651] multiqc [DEBUG ] No samples found: snpsplit [2021-03-04 06:25:09,656] multiqc [DEBUG ] No samples found: kat [2021-03-04 06:25:09,660] multiqc [DEBUG ] No samples found: leehom [2021-03-04 06:25:09,666] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-04 06:25:09,671] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-04 06:25:09,676] multiqc [DEBUG ] No samples found: cutadapt [2021-03-04 06:25:09,680] multiqc [DEBUG ] No samples found: flexbar [2021-03-04 06:25:09,685] multiqc [DEBUG ] No samples found: kaiju [2021-03-04 06:25:09,690] multiqc [DEBUG ] No samples found: kraken [2021-03-04 06:25:09,694] multiqc [DEBUG ] No samples found: malt [2021-03-04 06:25:09,699] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-04 06:25:09,704] multiqc [DEBUG ] No samples found: sickle [2021-03-04 06:25:09,709] multiqc [DEBUG ] No samples found: skewer [2021-03-04 06:25:09,713] multiqc [DEBUG ] No samples found: sortmerna [2021-03-04 06:25:09,718] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-04 06:25:09,723] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-04 06:25:09,728] multiqc [DEBUG ] No samples found: afterqc [2021-03-04 06:25:09,734] multiqc [DEBUG ] No samples found: fastp [2021-03-04 06:25:11,007] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2021-03-04 06:25:11,520] multiqc [DEBUG ] No samples found: pycoqc [2021-03-04 06:25:11,525] multiqc [DEBUG ] No samples found: minionqc [2021-03-04 06:25:11,529] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-04 06:25:11,534] multiqc [DEBUG ] No samples found: clusterflow [2021-03-04 06:25:11,539] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-04 06:25:11,544] multiqc [DEBUG ] No samples found: interop [2021-03-04 06:25:11,549] multiqc [DEBUG ] No samples found: ivar [2021-03-04 06:25:11,553] multiqc [DEBUG ] No samples found: flash [2021-03-04 06:25:11,557] multiqc [DEBUG ] No samples found: seqyclean [2021-03-04 06:25:11,558] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-04 06:25:11,558] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-03-04 06:25:11,558] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-03-04 06:25:11,558] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-04 06:25:11,588] multiqc [INFO ] Compressing plot data [2021-03-04 06:25:11,981] multiqc [INFO ] Report : multiqc_report.html [2021-03-04 06:25:11,981] multiqc [INFO ] Data : multiqc_data [2021-03-04 06:25:11,981] multiqc [DEBUG ] Moving data file from '/state/partition1/job-3325071/tmpvd17fa4g/multiqc_data' to '/scratch/gencore/logs/html/HN7VJAFX2/merged/multiqc_data' [2021-03-04 06:25:12,108] multiqc [INFO ] MultiQC complete