[2022-11-30 18:12:45,589] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-30 18:12:45,589] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-30 18:12:45,589] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-30 18:12:45,590] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-30 18:12:45,590] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-30 18:12:45,590] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7J5KBGXN/merged [2022-11-30 18:12:46,114] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-30 18:12:46,114] multiqc [INFO ] This is MultiQC v1.9 [2022-11-30 18:12:46,115] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7J5KBGXN/merged [2022-11-30 18:12:46,115] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7J5KBGXN/merged [2022-11-30 18:12:46,115] multiqc [INFO ] Template : default [2022-11-30 18:12:46,115] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-30 18:12:46,115] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7J5KBGXN/merged [2022-11-30 18:12:46,115] 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 [2022-11-30 18:12:46,116] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27528278/tmpxuqokpp3 [2022-11-30 18:12:46,230] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-30 18:12:46,233] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-30 18:12:46,319] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7J5KBGXN_n01_undetermined_fastqc.html [2022-11-30 18:12:46,321] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7J5KBGXN_n01_undetermined_fastqc.html [2022-11-30 18:12:46,363] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S4-2022-2_fastqc.html [2022-11-30 18:12:46,365] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S4-2022-2_fastqc.html [2022-11-30 18:12:46,409] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S1-2022-2_fastqc.html [2022-11-30 18:12:46,411] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S1-2022-2_fastqc.html [2022-11-30 18:12:46,455] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S5-2022-2_fastqc.html [2022-11-30 18:12:46,457] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S5-2022-2_fastqc.html [2022-11-30 18:12:46,502] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S2-2022-2_fastqc.html [2022-11-30 18:12:46,504] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7J5KBGXN_n01_S2-2022-2_fastqc.html [2022-11-30 18:12:46,866] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-30 18:12:46,868] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-30 18:12:46,878] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2022-11-30 18:12:46,888] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-30 18:12:46,889] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-30 18:12:46,895] multiqc [DEBUG ] No samples found: conpair [2022-11-30 18:12:46,901] multiqc [DEBUG ] No samples found: peddy [2022-11-30 18:12:46,906] multiqc [DEBUG ] No samples found: somalier [2022-11-30 18:12:46,911] multiqc [DEBUG ] No samples found: methylQA [2022-11-30 18:12:46,920] multiqc [DEBUG ] No samples found: mosdepth [2022-11-30 18:12:46,926] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-30 18:12:46,929] multiqc [DEBUG ] No samples found: qualimap [2022-11-30 18:12:46,935] multiqc [DEBUG ] No samples found: preseq [2022-11-30 18:12:46,940] multiqc [DEBUG ] No samples found: quast [2022-11-30 18:12:46,945] multiqc [DEBUG ] No samples found: qorts [2022-11-30 18:12:46,950] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-30 18:12:46,955] multiqc [DEBUG ] No samples found: rockhopper [2022-11-30 18:12:46,962] multiqc [DEBUG ] No samples found: rsem [2022-11-30 18:12:46,976] multiqc [DEBUG ] No samples found: rseqc [2022-11-30 18:12:46,981] multiqc [DEBUG ] No samples found: busco [2022-11-30 18:12:46,986] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-30 18:12:46,992] multiqc [DEBUG ] No samples found: disambiguate [2022-11-30 18:12:46,997] multiqc [DEBUG ] No samples found: supernova [2022-11-30 18:12:47,012] multiqc [DEBUG ] No samples found: deeptools [2022-11-30 18:12:47,017] multiqc [DEBUG ] No samples found: sargasso [2022-11-30 18:12:47,022] multiqc [DEBUG ] No samples found: verifybamid [2022-11-30 18:12:47,028] multiqc [DEBUG ] No samples found: mirtrace [2022-11-30 18:12:47,033] multiqc [DEBUG ] No samples found: happy [2022-11-30 18:12:47,039] multiqc [DEBUG ] No samples found: mirtop [2022-11-30 18:12:47,046] multiqc [DEBUG ] No samples found: homer [2022-11-30 18:12:47,051] multiqc [DEBUG ] No samples found: macs2 [2022-11-30 18:12:47,056] multiqc [DEBUG ] No samples found: theta2 [2022-11-30 18:12:47,061] multiqc [DEBUG ] No samples found: snpeff [2022-11-30 18:12:47,069] multiqc [DEBUG ] No samples found: gatk [2022-11-30 18:12:47,074] multiqc [DEBUG ] No samples found: htseq [2022-11-30 18:12:47,080] multiqc [DEBUG ] No samples found: bcftools [2022-11-30 18:12:47,085] multiqc [DEBUG ] No samples found: featureCounts [2022-11-30 18:12:47,093] multiqc [DEBUG ] No samples found: fgbio [2022-11-30 18:12:47,107] multiqc [DEBUG ] No samples found: dragen [2022-11-30 18:12:47,112] multiqc [DEBUG ] No samples found: dedup [2022-11-30 18:12:47,117] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-30 18:12:47,144] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-30 18:12:47,149] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-30 18:12:47,151] multiqc [DEBUG ] No samples found: picard [2022-11-30 18:12:47,156] multiqc [DEBUG ] No samples found: prokka [2022-11-30 18:12:47,160] multiqc [DEBUG ] No samples found: samblaster [2022-11-30 18:12:47,169] multiqc [DEBUG ] No samples found: samtools [2022-11-30 18:12:47,174] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-30 18:12:47,180] multiqc [DEBUG ] No samples found: bamtools [2022-11-30 18:12:47,184] multiqc [DEBUG ] No samples found: jellyfish [2022-11-30 18:12:47,191] multiqc [DEBUG ] No samples found: vcftools [2022-11-30 18:12:47,196] multiqc [DEBUG ] No samples found: longranger [2022-11-30 18:12:47,201] multiqc [DEBUG ] No samples found: stacks [2022-11-30 18:12:47,207] multiqc [DEBUG ] No samples found: varscan2 [2022-11-30 18:12:47,222] multiqc [DEBUG ] No samples found: bbmap [2022-11-30 18:12:47,227] multiqc [DEBUG ] No samples found: bismark [2022-11-30 18:12:47,232] multiqc [DEBUG ] No samples found: biscuit [2022-11-30 18:12:47,237] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-30 18:12:47,242] multiqc [DEBUG ] No samples found: hicup [2022-11-30 18:12:47,247] multiqc [DEBUG ] No samples found: hicpro [2022-11-30 18:12:47,252] multiqc [DEBUG ] No samples found: salmon [2022-11-30 18:12:47,257] multiqc [DEBUG ] No samples found: kallisto [2022-11-30 18:12:47,261] multiqc [DEBUG ] No samples found: slamdunk [2022-11-30 18:12:47,267] multiqc [DEBUG ] No samples found: star [2022-11-30 18:12:47,272] multiqc [DEBUG ] No samples found: hisat2 [2022-11-30 18:12:47,277] multiqc [DEBUG ] No samples found: tophat [2022-11-30 18:12:47,281] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-30 18:12:47,287] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-30 18:12:47,291] multiqc [DEBUG ] No samples found: snpsplit [2022-11-30 18:12:47,296] multiqc [DEBUG ] No samples found: kat [2022-11-30 18:12:47,300] multiqc [DEBUG ] No samples found: leehom [2022-11-30 18:12:47,305] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-30 18:12:47,309] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-30 18:12:47,315] multiqc [DEBUG ] No samples found: cutadapt [2022-11-30 18:12:47,320] multiqc [DEBUG ] No samples found: flexbar [2022-11-30 18:12:47,325] multiqc [DEBUG ] No samples found: kaiju [2022-11-30 18:12:47,331] multiqc [DEBUG ] No samples found: kraken [2022-11-30 18:12:47,335] multiqc [DEBUG ] No samples found: malt [2022-11-30 18:12:47,340] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-30 18:12:47,345] multiqc [DEBUG ] No samples found: sickle [2022-11-30 18:12:47,350] multiqc [DEBUG ] No samples found: skewer [2022-11-30 18:12:47,355] multiqc [DEBUG ] No samples found: sortmerna [2022-11-30 18:12:47,359] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-30 18:12:47,365] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-30 18:12:47,370] multiqc [DEBUG ] No samples found: afterqc [2022-11-30 18:12:47,375] multiqc [DEBUG ] No samples found: fastp [2022-11-30 18:12:47,939] multiqc.modules.fastqc.fastqc [INFO ] Found 5 reports [2022-11-30 18:12:48,075] multiqc [DEBUG ] No samples found: pycoqc [2022-11-30 18:12:48,079] multiqc [DEBUG ] No samples found: minionqc [2022-11-30 18:12:48,085] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-30 18:12:48,092] multiqc [DEBUG ] No samples found: clusterflow [2022-11-30 18:12:48,098] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-30 18:12:48,104] multiqc [DEBUG ] No samples found: interop [2022-11-30 18:12:48,110] multiqc [DEBUG ] No samples found: ivar [2022-11-30 18:12:48,117] multiqc [DEBUG ] No samples found: flash [2022-11-30 18:12:48,122] multiqc [DEBUG ] No samples found: seqyclean [2022-11-30 18:12:48,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-30 18:12:48,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-30 18:12:48,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-30 18:12:48,122] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-30 18:12:48,129] multiqc [INFO ] Compressing plot data [2022-11-30 18:12:48,249] multiqc [INFO ] Report : multiqc_report.html [2022-11-30 18:12:48,249] multiqc [INFO ] Data : multiqc_data [2022-11-30 18:12:48,249] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27528278/tmpxuqokpp3/multiqc_data' to '/scratch/gencore/logs/html/H7J5KBGXN/merged/multiqc_data' [2022-11-30 18:12:48,583] multiqc [INFO ] MultiQC complete