[2022-04-13 19:42:42,900] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-13 19:42:42,900] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-13 19:42:42,900] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-13 19:42:42,901] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-13 19:42:42,901] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-13 19:42:42,901] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3T7GDRX2/merged [2022-04-13 19:42:43,761] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-13 19:42:43,761] multiqc [INFO ] This is MultiQC v1.9 [2022-04-13 19:42:43,761] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3T7GDRX2/merged [2022-04-13 19:42:43,761] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3T7GDRX2/merged [2022-04-13 19:42:43,761] multiqc [INFO ] Template : default [2022-04-13 19:42:43,761] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-13 19:42:43,761] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3T7GDRX2/merged [2022-04-13 19:42:43,762] 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 [2022-04-13 19:42:43,762] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-17916794/tmpsdxxbfka [2022-04-13 19:42:43,881] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK93_hic_fastqc.html [2022-04-13 19:42:43,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK93_hic_fastqc.html [2022-04-13 19:42:43,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:43,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:43,926] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:43,926] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:43,926] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:43,926] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:43,926] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:43,995] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-13 19:42:47,092] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK92_hic_fastqc.html [2022-04-13 19:42:47,094] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK92_hic_fastqc.html [2022-04-13 19:42:47,172] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK102_fastqc.html [2022-04-13 19:42:47,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK102_fastqc.html [2022-04-13 19:42:47,211] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK93_hic_fastqc.html [2022-04-13 19:42:47,213] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK93_hic_fastqc.html [2022-04-13 19:42:47,280] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n02_undetermined_fastqc.html [2022-04-13 19:42:47,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n02_undetermined_fastqc.html [2022-04-13 19:42:47,335] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK103_fastqc.html [2022-04-13 19:42:47,337] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK103_fastqc.html [2022-04-13 19:42:47,403] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK102_fastqc.html [2022-04-13 19:42:47,405] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n02_JK102_fastqc.html [2022-04-13 19:42:47,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n01_undetermined_fastqc.html [2022-04-13 19:42:47,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n01_undetermined_fastqc.html [2022-04-13 19:42:47,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK92_hic_fastqc.html [2022-04-13 19:42:47,535] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK92_hic_fastqc.html [2022-04-13 19:42:47,588] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK103_fastqc.html [2022-04-13 19:42:47,589] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3T7GDRX2_n01_JK103_fastqc.html [2022-04-13 19:42:47,978] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-13 19:42:47,980] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-13 19:42:47,990] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2022-04-13 19:42:48,000] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-13 19:42:48,001] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-13 19:42:48,006] multiqc [DEBUG ] No samples found: conpair [2022-04-13 19:42:48,011] multiqc [DEBUG ] No samples found: peddy [2022-04-13 19:42:48,018] multiqc [DEBUG ] No samples found: somalier [2022-04-13 19:42:48,024] multiqc [DEBUG ] No samples found: methylQA [2022-04-13 19:42:48,034] multiqc [DEBUG ] No samples found: mosdepth [2022-04-13 19:42:48,040] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-13 19:42:48,043] multiqc [DEBUG ] No samples found: qualimap [2022-04-13 19:42:48,049] multiqc [DEBUG ] No samples found: preseq [2022-04-13 19:42:48,056] multiqc [DEBUG ] No samples found: quast [2022-04-13 19:42:48,062] multiqc [DEBUG ] No samples found: qorts [2022-04-13 19:42:48,067] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-13 19:42:48,071] multiqc [DEBUG ] No samples found: rockhopper [2022-04-13 19:42:48,078] multiqc [DEBUG ] No samples found: rsem [2022-04-13 19:42:48,102] multiqc [DEBUG ] No samples found: rseqc [2022-04-13 19:42:48,109] multiqc [DEBUG ] No samples found: busco [2022-04-13 19:42:48,115] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-13 19:42:48,121] multiqc [DEBUG ] No samples found: disambiguate [2022-04-13 19:42:48,128] multiqc [DEBUG ] No samples found: supernova [2022-04-13 19:42:48,148] multiqc [DEBUG ] No samples found: deeptools [2022-04-13 19:42:48,156] multiqc [DEBUG ] No samples found: sargasso [2022-04-13 19:42:48,162] multiqc [DEBUG ] No samples found: verifybamid [2022-04-13 19:42:48,169] multiqc [DEBUG ] No samples found: mirtrace [2022-04-13 19:42:48,175] multiqc [DEBUG ] No samples found: happy [2022-04-13 19:42:48,182] multiqc [DEBUG ] No samples found: mirtop [2022-04-13 19:42:48,188] multiqc [DEBUG ] No samples found: homer [2022-04-13 19:42:48,193] multiqc [DEBUG ] No samples found: macs2 [2022-04-13 19:42:48,198] multiqc [DEBUG ] No samples found: theta2 [2022-04-13 19:42:48,203] multiqc [DEBUG ] No samples found: snpeff [2022-04-13 19:42:48,212] multiqc [DEBUG ] No samples found: gatk [2022-04-13 19:42:48,217] multiqc [DEBUG ] No samples found: htseq [2022-04-13 19:42:48,223] multiqc [DEBUG ] No samples found: bcftools [2022-04-13 19:42:48,229] multiqc [DEBUG ] No samples found: featureCounts [2022-04-13 19:42:48,243] multiqc [DEBUG ] No samples found: fgbio [2022-04-13 19:42:48,265] multiqc [DEBUG ] No samples found: dragen [2022-04-13 19:42:48,271] multiqc [DEBUG ] No samples found: dedup [2022-04-13 19:42:48,277] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-13 19:42:48,313] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-13 19:42:48,321] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-13 19:42:48,323] multiqc [DEBUG ] No samples found: picard [2022-04-13 19:42:48,332] multiqc [DEBUG ] No samples found: prokka [2022-04-13 19:42:48,336] multiqc [DEBUG ] No samples found: samblaster [2022-04-13 19:42:48,345] multiqc [DEBUG ] No samples found: samtools [2022-04-13 19:42:48,350] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-13 19:42:48,355] multiqc [DEBUG ] No samples found: bamtools [2022-04-13 19:42:48,360] multiqc [DEBUG ] No samples found: jellyfish [2022-04-13 19:42:48,369] multiqc [DEBUG ] No samples found: vcftools [2022-04-13 19:42:48,374] multiqc [DEBUG ] No samples found: longranger [2022-04-13 19:42:48,378] multiqc [DEBUG ] No samples found: stacks [2022-04-13 19:42:48,383] multiqc [DEBUG ] No samples found: varscan2 [2022-04-13 19:42:48,399] multiqc [DEBUG ] No samples found: bbmap [2022-04-13 19:42:48,404] multiqc [DEBUG ] No samples found: bismark [2022-04-13 19:42:48,409] multiqc [DEBUG ] No samples found: biscuit [2022-04-13 19:42:48,414] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-13 19:42:48,418] multiqc [DEBUG ] No samples found: hicup [2022-04-13 19:42:48,423] multiqc [DEBUG ] No samples found: hicpro [2022-04-13 19:42:48,427] multiqc [DEBUG ] No samples found: salmon [2022-04-13 19:42:48,432] multiqc [DEBUG ] No samples found: kallisto [2022-04-13 19:42:48,438] multiqc [DEBUG ] No samples found: slamdunk [2022-04-13 19:42:48,446] multiqc [DEBUG ] No samples found: star [2022-04-13 19:42:48,453] multiqc [DEBUG ] No samples found: hisat2 [2022-04-13 19:42:48,458] multiqc [DEBUG ] No samples found: tophat [2022-04-13 19:42:48,465] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-13 19:42:48,473] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-13 19:42:48,480] multiqc [DEBUG ] No samples found: snpsplit [2022-04-13 19:42:48,488] multiqc [DEBUG ] No samples found: kat [2022-04-13 19:42:48,493] multiqc [DEBUG ] No samples found: leehom [2022-04-13 19:42:48,498] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-13 19:42:48,502] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-13 19:42:48,507] multiqc [DEBUG ] No samples found: cutadapt [2022-04-13 19:42:48,512] multiqc [DEBUG ] No samples found: flexbar [2022-04-13 19:42:48,516] multiqc [DEBUG ] No samples found: kaiju [2022-04-13 19:42:48,522] multiqc [DEBUG ] No samples found: kraken [2022-04-13 19:42:48,526] multiqc [DEBUG ] No samples found: malt [2022-04-13 19:42:48,531] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-13 19:42:48,536] multiqc [DEBUG ] No samples found: sickle [2022-04-13 19:42:48,540] multiqc [DEBUG ] No samples found: skewer [2022-04-13 19:42:48,546] multiqc [DEBUG ] No samples found: sortmerna [2022-04-13 19:42:48,550] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-13 19:42:48,555] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-13 19:42:48,561] multiqc [DEBUG ] No samples found: afterqc [2022-04-13 19:42:48,565] multiqc [DEBUG ] No samples found: fastp [2022-04-13 19:42:49,195] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2022-04-13 19:42:49,341] multiqc [DEBUG ] No samples found: pycoqc [2022-04-13 19:42:49,346] multiqc [DEBUG ] No samples found: minionqc [2022-04-13 19:42:49,381] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-13 19:42:49,385] multiqc [DEBUG ] No samples found: clusterflow [2022-04-13 19:42:49,391] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-13 19:42:49,396] multiqc [DEBUG ] No samples found: interop [2022-04-13 19:42:49,402] multiqc [DEBUG ] No samples found: ivar [2022-04-13 19:42:49,406] multiqc [DEBUG ] No samples found: flash [2022-04-13 19:42:49,411] multiqc [DEBUG ] No samples found: seqyclean [2022-04-13 19:42:49,411] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-13 19:42:49,411] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-13 19:42:49,411] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-13 19:42:49,411] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-13 19:42:49,424] multiqc [INFO ] Compressing plot data [2022-04-13 19:42:49,596] multiqc [INFO ] Report : multiqc_report.html [2022-04-13 19:42:49,596] multiqc [INFO ] Data : multiqc_data [2022-04-13 19:42:49,596] multiqc [DEBUG ] Moving data file from '/state/partition1/job-17916794/tmpsdxxbfka/multiqc_data' to '/scratch/gencore/logs/html/H3T7GDRX2/merged/multiqc_data' [2022-04-13 19:42:49,723] multiqc [INFO ] MultiQC complete