[2021-09-09 23:30:28,649] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-09 23:30:28,649] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-09 23:30:28,649] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-09 23:30:28,650] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-09 23:30:28,650] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-09 23:30:28,650] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5H3VBGXK/merged [2021-09-09 23:30:30,297] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-09 23:30:30,297] multiqc [INFO ] This is MultiQC v1.9 [2021-09-09 23:30:30,297] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5H3VBGXK/merged [2021-09-09 23:30:30,297] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5H3VBGXK/merged [2021-09-09 23:30:30,297] multiqc [INFO ] Template : default [2021-09-09 23:30:30,297] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-09 23:30:30,297] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5H3VBGXK/merged [2021-09-09 23:30:30,298] 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 [2021-09-09 23:30:30,298] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9883478/tmpc1jt_zmk [2021-09-09 23:30:30,402] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br14_fastqc.html [2021-09-09 23:30:30,404] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br14_fastqc.html [2021-09-09 23:30:30,445] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-09 23:30:30,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-09 23:30:30,576] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br6_fastqc.html [2021-09-09 23:30:30,578] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br6_fastqc.html [2021-09-09 23:30:30,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br9_fastqc.html [2021-09-09 23:30:30,619] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br9_fastqc.html [2021-09-09 23:30:30,659] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br8_fastqc.html [2021-09-09 23:30:30,661] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br8_fastqc.html [2021-09-09 23:30:30,701] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br7_fastqc.html [2021-09-09 23:30:30,703] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br7_fastqc.html [2021-09-09 23:30:30,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br16_fastqc.html [2021-09-09 23:30:30,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br16_fastqc.html [2021-09-09 23:30:30,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br15_fastqc.html [2021-09-09 23:30:30,786] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br15_fastqc.html [2021-09-09 23:30:30,826] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br12_fastqc.html [2021-09-09 23:30:30,828] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br12_fastqc.html [2021-09-09 23:30:30,869] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br5_fastqc.html [2021-09-09 23:30:30,870] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br5_fastqc.html [2021-09-09 23:30:30,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br11_fastqc.html [2021-09-09 23:30:30,911] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br11_fastqc.html [2021-09-09 23:30:30,952] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br10_fastqc.html [2021-09-09 23:30:30,954] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br10_fastqc.html [2021-09-09 23:30:30,994] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_undetermined_fastqc.html [2021-09-09 23:30:30,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_undetermined_fastqc.html [2021-09-09 23:30:31,035] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br13_fastqc.html [2021-09-09 23:30:31,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5H3VBGXK_n01_br13_fastqc.html [2021-09-09 23:30:31,513] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-09 23:30:31,515] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-09 23:30:31,527] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 13 samples (table) [2021-09-09 23:30:31,529] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-09 23:30:31,539] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-09 23:30:31,544] multiqc [DEBUG ] No samples found: conpair [2021-09-09 23:30:31,549] multiqc [DEBUG ] No samples found: peddy [2021-09-09 23:30:31,553] multiqc [DEBUG ] No samples found: somalier [2021-09-09 23:30:31,558] multiqc [DEBUG ] No samples found: methylQA [2021-09-09 23:30:31,566] multiqc [DEBUG ] No samples found: mosdepth [2021-09-09 23:30:31,571] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-09 23:30:31,574] multiqc [DEBUG ] No samples found: qualimap [2021-09-09 23:30:31,579] multiqc [DEBUG ] No samples found: preseq [2021-09-09 23:30:31,584] multiqc [DEBUG ] No samples found: quast [2021-09-09 23:30:31,590] multiqc [DEBUG ] No samples found: qorts [2021-09-09 23:30:31,594] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-09 23:30:31,599] multiqc [DEBUG ] No samples found: rockhopper [2021-09-09 23:30:31,604] multiqc [DEBUG ] No samples found: rsem [2021-09-09 23:30:31,613] multiqc [DEBUG ] No samples found: rseqc [2021-09-09 23:30:31,618] multiqc [DEBUG ] No samples found: busco [2021-09-09 23:30:31,623] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-09 23:30:31,627] multiqc [DEBUG ] No samples found: disambiguate [2021-09-09 23:30:31,632] multiqc [DEBUG ] No samples found: supernova [2021-09-09 23:30:31,651] multiqc [DEBUG ] No samples found: deeptools [2021-09-09 23:30:31,656] multiqc [DEBUG ] No samples found: sargasso [2021-09-09 23:30:31,660] multiqc [DEBUG ] No samples found: verifybamid [2021-09-09 23:30:31,665] multiqc [DEBUG ] No samples found: mirtrace [2021-09-09 23:30:31,670] multiqc [DEBUG ] No samples found: happy [2021-09-09 23:30:31,674] multiqc [DEBUG ] No samples found: mirtop [2021-09-09 23:30:31,680] multiqc [DEBUG ] No samples found: homer [2021-09-09 23:30:31,685] multiqc [DEBUG ] No samples found: macs2 [2021-09-09 23:30:31,689] multiqc [DEBUG ] No samples found: theta2 [2021-09-09 23:30:31,694] multiqc [DEBUG ] No samples found: snpeff [2021-09-09 23:30:31,700] multiqc [DEBUG ] No samples found: gatk [2021-09-09 23:30:31,705] multiqc [DEBUG ] No samples found: htseq [2021-09-09 23:30:31,710] multiqc [DEBUG ] No samples found: bcftools [2021-09-09 23:30:31,715] multiqc [DEBUG ] No samples found: featureCounts [2021-09-09 23:30:31,720] multiqc [DEBUG ] No samples found: fgbio [2021-09-09 23:30:31,733] multiqc [DEBUG ] No samples found: dragen [2021-09-09 23:30:31,737] multiqc [DEBUG ] No samples found: dedup [2021-09-09 23:30:31,742] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-09 23:30:31,765] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-09 23:30:31,769] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-09 23:30:31,771] multiqc [DEBUG ] No samples found: picard [2021-09-09 23:30:31,776] multiqc [DEBUG ] No samples found: prokka [2021-09-09 23:30:31,780] multiqc [DEBUG ] No samples found: samblaster [2021-09-09 23:30:31,788] multiqc [DEBUG ] No samples found: samtools [2021-09-09 23:30:31,793] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-09 23:30:31,798] multiqc [DEBUG ] No samples found: bamtools [2021-09-09 23:30:31,802] multiqc [DEBUG ] No samples found: jellyfish [2021-09-09 23:30:31,808] multiqc [DEBUG ] No samples found: vcftools [2021-09-09 23:30:31,813] multiqc [DEBUG ] No samples found: longranger [2021-09-09 23:30:31,818] multiqc [DEBUG ] No samples found: stacks [2021-09-09 23:30:31,822] multiqc [DEBUG ] No samples found: varscan2 [2021-09-09 23:30:31,834] multiqc [DEBUG ] No samples found: bbmap [2021-09-09 23:30:31,840] multiqc [DEBUG ] No samples found: bismark [2021-09-09 23:30:31,845] multiqc [DEBUG ] No samples found: biscuit [2021-09-09 23:30:31,850] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-09 23:30:31,854] multiqc [DEBUG ] No samples found: hicup [2021-09-09 23:30:31,859] multiqc [DEBUG ] No samples found: hicpro [2021-09-09 23:30:31,863] multiqc [DEBUG ] No samples found: salmon [2021-09-09 23:30:31,868] multiqc [DEBUG ] No samples found: kallisto [2021-09-09 23:30:31,873] multiqc [DEBUG ] No samples found: slamdunk [2021-09-09 23:30:31,878] multiqc [DEBUG ] No samples found: star [2021-09-09 23:30:31,882] multiqc [DEBUG ] No samples found: hisat2 [2021-09-09 23:30:31,887] multiqc [DEBUG ] No samples found: tophat [2021-09-09 23:30:31,892] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-09 23:30:31,896] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-09 23:30:31,901] multiqc [DEBUG ] No samples found: snpsplit [2021-09-09 23:30:31,905] multiqc [DEBUG ] No samples found: kat [2021-09-09 23:30:31,909] multiqc [DEBUG ] No samples found: leehom [2021-09-09 23:30:31,914] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-09 23:30:31,918] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-09 23:30:31,922] multiqc [DEBUG ] No samples found: cutadapt [2021-09-09 23:30:31,926] multiqc [DEBUG ] No samples found: flexbar [2021-09-09 23:30:31,931] multiqc [DEBUG ] No samples found: kaiju [2021-09-09 23:30:31,936] multiqc [DEBUG ] No samples found: kraken [2021-09-09 23:30:31,941] multiqc [DEBUG ] No samples found: malt [2021-09-09 23:30:31,944] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-09 23:30:31,949] multiqc [DEBUG ] No samples found: sickle [2021-09-09 23:30:31,954] multiqc [DEBUG ] No samples found: skewer [2021-09-09 23:30:31,958] multiqc [DEBUG ] No samples found: sortmerna [2021-09-09 23:30:31,961] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-09 23:30:31,966] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-09 23:30:31,972] multiqc [DEBUG ] No samples found: afterqc [2021-09-09 23:30:31,977] multiqc [DEBUG ] No samples found: fastp [2021-09-09 23:30:32,857] multiqc.modules.fastqc.fastqc [INFO ] Found 13 reports [2021-09-09 23:30:33,128] multiqc [DEBUG ] No samples found: pycoqc [2021-09-09 23:30:33,138] multiqc [DEBUG ] No samples found: minionqc [2021-09-09 23:30:33,142] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-09 23:30:33,147] multiqc [DEBUG ] No samples found: clusterflow [2021-09-09 23:30:33,152] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-09 23:30:33,157] multiqc [DEBUG ] No samples found: interop [2021-09-09 23:30:33,162] multiqc [DEBUG ] No samples found: ivar [2021-09-09 23:30:33,166] multiqc [DEBUG ] No samples found: flash [2021-09-09 23:30:33,170] multiqc [DEBUG ] No samples found: seqyclean [2021-09-09 23:30:33,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-09-09 23:30:33,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-09-09 23:30:33,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-09 23:30:33,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-09 23:30:33,186] multiqc [INFO ] Compressing plot data [2021-09-09 23:30:33,425] multiqc [INFO ] Report : multiqc_report.html [2021-09-09 23:30:33,425] multiqc [INFO ] Data : multiqc_data [2021-09-09 23:30:33,425] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9883478/tmpc1jt_zmk/multiqc_data' to '/scratch/gencore/logs/html/H5H3VBGXK/merged/multiqc_data' [2021-09-09 23:30:33,576] multiqc [INFO ] MultiQC complete