[2021-06-16 06:30:26,739] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-16 06:30:26,739] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-16 06:30:26,739] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-16 06:30:26,740] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-16 06:30:26,740] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-16 06:30:26,740] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWGTLAFX2/merged [2021-06-16 06:30:28,091] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-16 06:30:28,091] multiqc [INFO ] This is MultiQC v1.9 [2021-06-16 06:30:28,091] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWGTLAFX2/merged [2021-06-16 06:30:28,091] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWGTLAFX2/merged [2021-06-16 06:30:28,091] multiqc [INFO ] Template : default [2021-06-16 06:30:28,091] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-16 06:30:28,091] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWGTLAFX2/merged [2021-06-16 06:30:28,092] 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 [2021-06-16 06:30:28,092] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7658376/tmpwfc1pkpl [2021-06-16 06:30:28,228] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT002_fastqc.html [2021-06-16 06:30:28,230] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT002_fastqc.html [2021-06-16 06:30:28,273] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-06-16 06:30:28,274] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-06-16 06:30:28,356] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_N1_003_fastqc.html [2021-06-16 06:30:28,357] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_N1_003_fastqc.html [2021-06-16 06:30:28,398] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT004_fastqc.html [2021-06-16 06:30:28,399] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT004_fastqc.html [2021-06-16 06:30:28,440] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_undetermined_fastqc.html [2021-06-16 06:30:28,441] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_undetermined_fastqc.html [2021-06-16 06:30:28,481] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT002_fastqc.html [2021-06-16 06:30:28,483] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT002_fastqc.html [2021-06-16 06:30:28,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT004_fastqc.html [2021-06-16 06:30:28,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT004_fastqc.html [2021-06-16 06:30:28,567] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_undetermined_fastqc.html [2021-06-16 06:30:28,569] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_undetermined_fastqc.html [2021-06-16 06:30:28,609] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_N1_001_fastqc.html [2021-06-16 06:30:28,611] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_N1_001_fastqc.html [2021-06-16 06:30:28,651] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_N1_002_fastqc.html [2021-06-16 06:30:28,653] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_N1_002_fastqc.html [2021-06-16 06:30:28,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_N1_003_fastqc.html [2021-06-16 06:30:28,695] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_N1_003_fastqc.html [2021-06-16 06:30:28,735] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_N1_001_fastqc.html [2021-06-16 06:30:28,737] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_N1_001_fastqc.html [2021-06-16 06:30:28,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT003_fastqc.html [2021-06-16 06:30:28,780] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT003_fastqc.html [2021-06-16 06:30:28,821] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT003_fastqc.html [2021-06-16 06:30:28,823] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT003_fastqc.html [2021-06-16 06:30:28,863] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT001_fastqc.html [2021-06-16 06:30:28,865] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n02_WT001_fastqc.html [2021-06-16 06:30:28,905] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_N1_002_fastqc.html [2021-06-16 06:30:28,907] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_N1_002_fastqc.html [2021-06-16 06:30:28,952] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT001_fastqc.html [2021-06-16 06:30:28,954] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWGTLAFX2_n01_WT001_fastqc.html [2021-06-16 06:30:29,395] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-16 06:30:29,396] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-16 06:30:29,403] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-16 06:30:29,408] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2021-06-16 06:30:29,417] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-06-16 06:30:29,421] multiqc [DEBUG ] No samples found: conpair [2021-06-16 06:30:29,426] multiqc [DEBUG ] No samples found: peddy [2021-06-16 06:30:29,430] multiqc [DEBUG ] No samples found: somalier [2021-06-16 06:30:29,434] multiqc [DEBUG ] No samples found: methylQA [2021-06-16 06:30:29,441] multiqc [DEBUG ] No samples found: mosdepth [2021-06-16 06:30:29,445] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-16 06:30:29,449] multiqc [DEBUG ] No samples found: qualimap [2021-06-16 06:30:29,453] multiqc [DEBUG ] No samples found: preseq [2021-06-16 06:30:29,457] multiqc [DEBUG ] No samples found: quast [2021-06-16 06:30:29,461] multiqc [DEBUG ] No samples found: qorts [2021-06-16 06:30:29,466] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-16 06:30:29,470] multiqc [DEBUG ] No samples found: rockhopper [2021-06-16 06:30:29,475] multiqc [DEBUG ] No samples found: rsem [2021-06-16 06:30:29,485] multiqc [DEBUG ] No samples found: rseqc [2021-06-16 06:30:29,489] multiqc [DEBUG ] No samples found: busco [2021-06-16 06:30:29,493] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-16 06:30:29,496] multiqc [DEBUG ] No samples found: disambiguate [2021-06-16 06:30:29,501] multiqc [DEBUG ] No samples found: supernova [2021-06-16 06:30:29,514] multiqc [DEBUG ] No samples found: deeptools [2021-06-16 06:30:29,518] multiqc [DEBUG ] No samples found: sargasso [2021-06-16 06:30:29,522] multiqc [DEBUG ] No samples found: verifybamid [2021-06-16 06:30:29,526] multiqc [DEBUG ] No samples found: mirtrace [2021-06-16 06:30:29,531] multiqc [DEBUG ] No samples found: happy [2021-06-16 06:30:29,536] multiqc [DEBUG ] No samples found: mirtop [2021-06-16 06:30:29,542] multiqc [DEBUG ] No samples found: homer [2021-06-16 06:30:29,547] multiqc [DEBUG ] No samples found: macs2 [2021-06-16 06:30:29,551] multiqc [DEBUG ] No samples found: theta2 [2021-06-16 06:30:29,555] multiqc [DEBUG ] No samples found: snpeff [2021-06-16 06:30:29,562] multiqc [DEBUG ] No samples found: gatk [2021-06-16 06:30:29,565] multiqc [DEBUG ] No samples found: htseq [2021-06-16 06:30:29,570] multiqc [DEBUG ] No samples found: bcftools [2021-06-16 06:30:29,574] multiqc [DEBUG ] No samples found: featureCounts [2021-06-16 06:30:29,580] multiqc [DEBUG ] No samples found: fgbio [2021-06-16 06:30:29,593] multiqc [DEBUG ] No samples found: dragen [2021-06-16 06:30:29,598] multiqc [DEBUG ] No samples found: dedup [2021-06-16 06:30:29,602] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-16 06:30:29,624] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-16 06:30:29,627] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-16 06:30:29,630] multiqc [DEBUG ] No samples found: picard [2021-06-16 06:30:29,634] multiqc [DEBUG ] No samples found: prokka [2021-06-16 06:30:29,638] multiqc [DEBUG ] No samples found: samblaster [2021-06-16 06:30:29,647] multiqc [DEBUG ] No samples found: samtools [2021-06-16 06:30:29,652] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-16 06:30:29,656] multiqc [DEBUG ] No samples found: bamtools [2021-06-16 06:30:29,660] multiqc [DEBUG ] No samples found: jellyfish [2021-06-16 06:30:29,668] multiqc [DEBUG ] No samples found: vcftools [2021-06-16 06:30:29,673] multiqc [DEBUG ] No samples found: longranger [2021-06-16 06:30:29,677] multiqc [DEBUG ] No samples found: stacks [2021-06-16 06:30:29,681] multiqc [DEBUG ] No samples found: varscan2 [2021-06-16 06:30:29,694] multiqc [DEBUG ] No samples found: bbmap [2021-06-16 06:30:29,699] multiqc [DEBUG ] No samples found: bismark [2021-06-16 06:30:29,704] multiqc [DEBUG ] No samples found: biscuit [2021-06-16 06:30:29,708] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-16 06:30:29,712] multiqc [DEBUG ] No samples found: hicup [2021-06-16 06:30:29,717] multiqc [DEBUG ] No samples found: hicpro [2021-06-16 06:30:29,721] multiqc [DEBUG ] No samples found: salmon [2021-06-16 06:30:29,725] multiqc [DEBUG ] No samples found: kallisto [2021-06-16 06:30:29,729] multiqc [DEBUG ] No samples found: slamdunk [2021-06-16 06:30:29,734] multiqc [DEBUG ] No samples found: star [2021-06-16 06:30:29,738] multiqc [DEBUG ] No samples found: hisat2 [2021-06-16 06:30:29,743] multiqc [DEBUG ] No samples found: tophat [2021-06-16 06:30:29,747] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-16 06:30:29,751] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-16 06:30:29,755] multiqc [DEBUG ] No samples found: snpsplit [2021-06-16 06:30:29,759] multiqc [DEBUG ] No samples found: kat [2021-06-16 06:30:29,763] multiqc [DEBUG ] No samples found: leehom [2021-06-16 06:30:29,767] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-16 06:30:29,771] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-16 06:30:29,775] multiqc [DEBUG ] No samples found: cutadapt [2021-06-16 06:30:29,779] multiqc [DEBUG ] No samples found: flexbar [2021-06-16 06:30:29,783] multiqc [DEBUG ] No samples found: kaiju [2021-06-16 06:30:29,788] multiqc [DEBUG ] No samples found: kraken [2021-06-16 06:30:29,792] multiqc [DEBUG ] No samples found: malt [2021-06-16 06:30:29,796] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-16 06:30:29,800] multiqc [DEBUG ] No samples found: sickle [2021-06-16 06:30:29,805] multiqc [DEBUG ] No samples found: skewer [2021-06-16 06:30:29,809] multiqc [DEBUG ] No samples found: sortmerna [2021-06-16 06:30:29,813] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-16 06:30:29,817] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-16 06:30:29,822] multiqc [DEBUG ] No samples found: afterqc [2021-06-16 06:30:29,826] multiqc [DEBUG ] No samples found: fastp [2021-06-16 06:30:30,216] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2021-06-16 06:30:30,580] multiqc [DEBUG ] No samples found: pycoqc [2021-06-16 06:30:30,591] multiqc [DEBUG ] No samples found: minionqc [2021-06-16 06:30:30,596] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-16 06:30:30,601] multiqc [DEBUG ] No samples found: clusterflow [2021-06-16 06:30:30,613] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-16 06:30:30,636] multiqc [DEBUG ] No samples found: interop [2021-06-16 06:30:30,641] multiqc [DEBUG ] No samples found: ivar [2021-06-16 06:30:30,648] multiqc [DEBUG ] No samples found: flash [2021-06-16 06:30:30,665] multiqc [DEBUG ] No samples found: seqyclean [2021-06-16 06:30:30,666] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-06-16 06:30:30,666] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-06-16 06:30:30,666] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-06-16 06:30:30,666] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-16 06:30:30,685] multiqc [INFO ] Compressing plot data [2021-06-16 06:30:30,981] multiqc [INFO ] Report : multiqc_report.html [2021-06-16 06:30:30,982] multiqc [INFO ] Data : multiqc_data [2021-06-16 06:30:30,982] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7658376/tmpwfc1pkpl/multiqc_data' to '/scratch/gencore/logs/html/HWGTLAFX2/merged/multiqc_data' [2021-06-16 06:30:31,115] multiqc [INFO ] MultiQC complete