[2021-07-15 15:45:48,505] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-07-15 15:45:48,505] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-07-15 15:45:48,505] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-07-15 15:45:48,506] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-07-15 15:45:48,506] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-07-15 15:45:48,506] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTGNWAFX2/merged [2021-07-15 15:45:50,117] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-07-15 15:45:50,117] multiqc [INFO ] This is MultiQC v1.9 [2021-07-15 15:45:50,117] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTGNWAFX2/merged [2021-07-15 15:45:50,117] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTGNWAFX2/merged [2021-07-15 15:45:50,117] multiqc [INFO ] Template : default [2021-07-15 15:45:50,117] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-07-15 15:45:50,117] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTGNWAFX2/merged [2021-07-15 15:45:50,117] 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 [2021-07-15 15:45:50,118] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8695560/tmpmrozh4tm [2021-07-15 15:45:50,223] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_04_fastqc.html [2021-07-15 15:45:50,225] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_04_fastqc.html [2021-07-15 15:45:50,267] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-15 15:45:50,269] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-15 15:45:50,328] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_01_fastqc.html [2021-07-15 15:45:50,330] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_01_fastqc.html [2021-07-15 15:45:50,370] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n01_undetermined_fastqc.html [2021-07-15 15:45:50,371] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n01_undetermined_fastqc.html [2021-07-15 15:45:50,410] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_04_fastqc.html [2021-07-15 15:45:50,412] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_04_fastqc.html [2021-07-15 15:45:50,452] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n02_undetermined_fastqc.html [2021-07-15 15:45:50,454] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n02_undetermined_fastqc.html [2021-07-15 15:45:50,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_03_fastqc.html [2021-07-15 15:45:50,495] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_03_fastqc.html [2021-07-15 15:45:50,537] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_02_fastqc.html [2021-07-15 15:45:50,538] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_02_fastqc.html [2021-07-15 15:45:50,579] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_01_fastqc.html [2021-07-15 15:45:50,580] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_01_fastqc.html [2021-07-15 15:45:50,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_03_fastqc.html [2021-07-15 15:45:50,623] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n02_BS_doli_lib_03_fastqc.html [2021-07-15 15:45:50,663] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_02_fastqc.html [2021-07-15 15:45:50,664] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTGNWAFX2_n01_BS_doli_lib_02_fastqc.html [2021-07-15 15:45:51,172] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-15 15:45:51,174] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-15 15:45:51,182] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2021-07-15 15:45:51,192] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-07-15 15:45:51,193] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-07-15 15:45:51,199] multiqc [DEBUG ] No samples found: conpair [2021-07-15 15:45:51,204] multiqc [DEBUG ] No samples found: peddy [2021-07-15 15:45:51,209] multiqc [DEBUG ] No samples found: somalier [2021-07-15 15:45:51,214] multiqc [DEBUG ] No samples found: methylQA [2021-07-15 15:45:51,224] multiqc [DEBUG ] No samples found: mosdepth [2021-07-15 15:45:51,228] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-07-15 15:45:51,232] multiqc [DEBUG ] No samples found: qualimap [2021-07-15 15:45:51,237] multiqc [DEBUG ] No samples found: preseq [2021-07-15 15:45:51,243] multiqc [DEBUG ] No samples found: quast [2021-07-15 15:45:51,248] multiqc [DEBUG ] No samples found: qorts [2021-07-15 15:45:51,253] multiqc [DEBUG ] No samples found: rna_seqc [2021-07-15 15:45:51,258] multiqc [DEBUG ] No samples found: rockhopper [2021-07-15 15:45:51,264] multiqc [DEBUG ] No samples found: rsem [2021-07-15 15:45:51,275] multiqc [DEBUG ] No samples found: rseqc [2021-07-15 15:45:51,279] multiqc [DEBUG ] No samples found: busco [2021-07-15 15:45:51,284] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-07-15 15:45:51,289] multiqc [DEBUG ] No samples found: disambiguate [2021-07-15 15:45:51,295] multiqc [DEBUG ] No samples found: supernova [2021-07-15 15:45:51,310] multiqc [DEBUG ] No samples found: deeptools [2021-07-15 15:45:51,316] multiqc [DEBUG ] No samples found: sargasso [2021-07-15 15:45:51,320] multiqc [DEBUG ] No samples found: verifybamid [2021-07-15 15:45:51,326] multiqc [DEBUG ] No samples found: mirtrace [2021-07-15 15:45:51,331] multiqc [DEBUG ] No samples found: happy [2021-07-15 15:45:51,336] multiqc [DEBUG ] No samples found: mirtop [2021-07-15 15:45:51,347] multiqc [DEBUG ] No samples found: homer [2021-07-15 15:45:51,352] multiqc [DEBUG ] No samples found: macs2 [2021-07-15 15:45:51,358] multiqc [DEBUG ] No samples found: theta2 [2021-07-15 15:45:51,363] multiqc [DEBUG ] No samples found: snpeff [2021-07-15 15:45:51,371] multiqc [DEBUG ] No samples found: gatk [2021-07-15 15:45:51,376] multiqc [DEBUG ] No samples found: htseq [2021-07-15 15:45:51,381] multiqc [DEBUG ] No samples found: bcftools [2021-07-15 15:45:51,386] multiqc [DEBUG ] No samples found: featureCounts [2021-07-15 15:45:51,394] multiqc [DEBUG ] No samples found: fgbio [2021-07-15 15:45:51,408] multiqc [DEBUG ] No samples found: dragen [2021-07-15 15:45:51,413] multiqc [DEBUG ] No samples found: dedup [2021-07-15 15:45:51,418] multiqc [DEBUG ] No samples found: damageprofiler [2021-07-15 15:45:51,440] multiqc [DEBUG ] No samples found: biobambam2 [2021-07-15 15:45:51,445] multiqc [DEBUG ] No samples found: mtnucratio [2021-07-15 15:45:51,447] multiqc [DEBUG ] No samples found: picard [2021-07-15 15:45:51,452] multiqc [DEBUG ] No samples found: prokka [2021-07-15 15:45:51,457] multiqc [DEBUG ] No samples found: samblaster [2021-07-15 15:45:51,465] multiqc [DEBUG ] No samples found: samtools [2021-07-15 15:45:51,470] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-07-15 15:45:51,475] multiqc [DEBUG ] No samples found: bamtools [2021-07-15 15:45:51,481] multiqc [DEBUG ] No samples found: jellyfish [2021-07-15 15:45:51,488] multiqc [DEBUG ] No samples found: vcftools [2021-07-15 15:45:51,493] multiqc [DEBUG ] No samples found: longranger [2021-07-15 15:45:51,497] multiqc [DEBUG ] No samples found: stacks [2021-07-15 15:45:51,502] multiqc [DEBUG ] No samples found: varscan2 [2021-07-15 15:45:51,516] multiqc [DEBUG ] No samples found: bbmap [2021-07-15 15:45:51,521] multiqc [DEBUG ] No samples found: bismark [2021-07-15 15:45:51,527] multiqc [DEBUG ] No samples found: biscuit [2021-07-15 15:45:51,533] multiqc [DEBUG ] No samples found: hicexplorer [2021-07-15 15:45:51,538] multiqc [DEBUG ] No samples found: hicup [2021-07-15 15:45:51,543] multiqc [DEBUG ] No samples found: hicpro [2021-07-15 15:45:51,547] multiqc [DEBUG ] No samples found: salmon [2021-07-15 15:45:51,552] multiqc [DEBUG ] No samples found: kallisto [2021-07-15 15:45:51,557] multiqc [DEBUG ] No samples found: slamdunk [2021-07-15 15:45:51,563] multiqc [DEBUG ] No samples found: star [2021-07-15 15:45:51,567] multiqc [DEBUG ] No samples found: hisat2 [2021-07-15 15:45:51,572] multiqc [DEBUG ] No samples found: tophat [2021-07-15 15:45:51,577] multiqc [DEBUG ] No samples found: bowtie2 [2021-07-15 15:45:51,581] multiqc [DEBUG ] No samples found: bowtie1 [2021-07-15 15:45:51,587] multiqc [DEBUG ] No samples found: snpsplit [2021-07-15 15:45:51,591] multiqc [DEBUG ] No samples found: kat [2021-07-15 15:45:51,595] multiqc [DEBUG ] No samples found: leehom [2021-07-15 15:45:51,601] multiqc [DEBUG ] No samples found: adapterRemoval [2021-07-15 15:45:51,606] multiqc [DEBUG ] No samples found: clipandmerge [2021-07-15 15:45:51,610] multiqc [DEBUG ] No samples found: cutadapt [2021-07-15 15:45:51,615] multiqc [DEBUG ] No samples found: flexbar [2021-07-15 15:45:51,621] multiqc [DEBUG ] No samples found: kaiju [2021-07-15 15:45:51,626] multiqc [DEBUG ] No samples found: kraken [2021-07-15 15:45:51,631] multiqc [DEBUG ] No samples found: malt [2021-07-15 15:45:51,635] multiqc [DEBUG ] No samples found: trimmomatic [2021-07-15 15:45:51,640] multiqc [DEBUG ] No samples found: sickle [2021-07-15 15:45:51,644] multiqc [DEBUG ] No samples found: skewer [2021-07-15 15:45:51,649] multiqc [DEBUG ] No samples found: sortmerna [2021-07-15 15:45:51,654] multiqc [DEBUG ] No samples found: biobloomtools [2021-07-15 15:45:51,659] multiqc [DEBUG ] No samples found: fastq_screen [2021-07-15 15:45:51,663] multiqc [DEBUG ] No samples found: afterqc [2021-07-15 15:45:51,668] multiqc [DEBUG ] No samples found: fastp [2021-07-15 15:45:51,887] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-07-15 15:45:52,007] multiqc [DEBUG ] No samples found: pycoqc [2021-07-15 15:45:52,012] multiqc [DEBUG ] No samples found: minionqc [2021-07-15 15:45:52,016] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-07-15 15:45:52,021] multiqc [DEBUG ] No samples found: clusterflow [2021-07-15 15:45:52,026] multiqc [DEBUG ] No samples found: bcl2fastq [2021-07-15 15:45:52,031] multiqc [DEBUG ] No samples found: interop [2021-07-15 15:45:52,036] multiqc [DEBUG ] No samples found: ivar [2021-07-15 15:45:52,041] multiqc [DEBUG ] No samples found: flash [2021-07-15 15:45:52,045] multiqc [DEBUG ] No samples found: seqyclean [2021-07-15 15:45:52,045] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-07-15 15:45:52,045] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-07-15 15:45:52,045] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-07-15 15:45:52,045] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-07-15 15:45:52,058] multiqc [INFO ] Compressing plot data [2021-07-15 15:45:52,237] multiqc [INFO ] Report : multiqc_report.html [2021-07-15 15:45:52,237] multiqc [INFO ] Data : multiqc_data [2021-07-15 15:45:52,237] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8695560/tmpmrozh4tm/multiqc_data' to '/scratch/gencore/logs/html/HTGNWAFX2/merged/multiqc_data' [2021-07-15 15:45:52,378] multiqc [INFO ] MultiQC complete