[2023-04-15 08:17:18,609] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-04-15 08:17:18,610] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-04-15 08:17:18,610] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-04-15 08:17:18,612] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-04-15 08:17:18,612] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-04-15 08:17:18,612] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWCM5BGXN/merged [2023-04-15 08:17:18,858] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-04-15 08:17:18,858] multiqc [INFO ] This is MultiQC v1.9 [2023-04-15 08:17:18,858] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWCM5BGXN/merged [2023-04-15 08:17:18,858] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWCM5BGXN/merged [2023-04-15 08:17:18,858] multiqc [INFO ] Template : default [2023-04-15 08:17:18,859] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-04-15 08:17:18,859] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWCM5BGXN/merged [2023-04-15 08:17:18,859] 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 [2023-04-15 08:17:18,859] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-32351283/tmp3sv4eagv [2023-04-15 08:17:18,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWCM5BGXN_2_fastqc.html [2023-04-15 08:17:18,982] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWCM5BGXN_2_fastqc.html [2023-04-15 08:17:19,025] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWCM5BGXN_1_fastqc.html [2023-04-15 08:17:19,027] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWCM5BGXN_1_fastqc.html [2023-04-15 08:17:19,070] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWCM5BGXN_3_fastqc.html [2023-04-15 08:17:19,072] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWCM5BGXN_3_fastqc.html [2023-04-15 08:17:19,115] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWCM5BGXN_4_fastqc.html [2023-04-15 08:17:19,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWCM5BGXN_4_fastqc.html [2023-04-15 08:17:19,478] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-15 08:17:19,480] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-15 08:17:19,484] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-04-15 08:17:19,487] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-04-15 08:17:19,491] multiqc [DEBUG ] No samples found: conpair [2023-04-15 08:17:19,496] multiqc [DEBUG ] No samples found: peddy [2023-04-15 08:17:19,502] multiqc [DEBUG ] No samples found: somalier [2023-04-15 08:17:19,506] multiqc [DEBUG ] No samples found: methylQA [2023-04-15 08:17:19,516] multiqc [DEBUG ] No samples found: mosdepth [2023-04-15 08:17:19,520] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-04-15 08:17:19,524] multiqc [DEBUG ] No samples found: qualimap [2023-04-15 08:17:19,529] multiqc [DEBUG ] No samples found: preseq [2023-04-15 08:17:19,534] multiqc [DEBUG ] No samples found: quast [2023-04-15 08:17:19,539] multiqc [DEBUG ] No samples found: qorts [2023-04-15 08:17:19,544] multiqc [DEBUG ] No samples found: rna_seqc [2023-04-15 08:17:19,549] multiqc [DEBUG ] No samples found: rockhopper [2023-04-15 08:17:19,554] multiqc [DEBUG ] No samples found: rsem [2023-04-15 08:17:19,567] multiqc [DEBUG ] No samples found: rseqc [2023-04-15 08:17:19,571] multiqc [DEBUG ] No samples found: busco [2023-04-15 08:17:19,576] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-04-15 08:17:19,581] multiqc [DEBUG ] No samples found: disambiguate [2023-04-15 08:17:19,586] multiqc [DEBUG ] No samples found: supernova [2023-04-15 08:17:19,600] multiqc [DEBUG ] No samples found: deeptools [2023-04-15 08:17:19,606] multiqc [DEBUG ] No samples found: sargasso [2023-04-15 08:17:19,610] multiqc [DEBUG ] No samples found: verifybamid [2023-04-15 08:17:19,615] multiqc [DEBUG ] No samples found: mirtrace [2023-04-15 08:17:19,620] multiqc [DEBUG ] No samples found: happy [2023-04-15 08:17:19,625] multiqc [DEBUG ] No samples found: mirtop [2023-04-15 08:17:19,631] multiqc [DEBUG ] No samples found: homer [2023-04-15 08:17:19,636] multiqc [DEBUG ] No samples found: macs2 [2023-04-15 08:17:19,641] multiqc [DEBUG ] No samples found: theta2 [2023-04-15 08:17:19,646] multiqc [DEBUG ] No samples found: snpeff [2023-04-15 08:17:19,653] multiqc [DEBUG ] No samples found: gatk [2023-04-15 08:17:19,657] multiqc [DEBUG ] No samples found: htseq [2023-04-15 08:17:19,663] multiqc [DEBUG ] No samples found: bcftools [2023-04-15 08:17:19,667] multiqc [DEBUG ] No samples found: featureCounts [2023-04-15 08:17:19,673] multiqc [DEBUG ] No samples found: fgbio [2023-04-15 08:17:19,686] multiqc [DEBUG ] No samples found: dragen [2023-04-15 08:17:19,691] multiqc [DEBUG ] No samples found: dedup [2023-04-15 08:17:19,696] multiqc [DEBUG ] No samples found: damageprofiler [2023-04-15 08:17:19,716] multiqc [DEBUG ] No samples found: biobambam2 [2023-04-15 08:17:19,722] multiqc [DEBUG ] No samples found: mtnucratio [2023-04-15 08:17:19,724] multiqc [DEBUG ] No samples found: picard [2023-04-15 08:17:19,729] multiqc [DEBUG ] No samples found: prokka [2023-04-15 08:17:19,734] multiqc [DEBUG ] No samples found: samblaster [2023-04-15 08:17:19,742] multiqc [DEBUG ] No samples found: samtools [2023-04-15 08:17:19,747] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-04-15 08:17:19,752] multiqc [DEBUG ] No samples found: bamtools [2023-04-15 08:17:19,756] multiqc [DEBUG ] No samples found: jellyfish [2023-04-15 08:17:19,765] multiqc [DEBUG ] No samples found: vcftools [2023-04-15 08:17:19,770] multiqc [DEBUG ] No samples found: longranger [2023-04-15 08:17:19,775] multiqc [DEBUG ] No samples found: stacks [2023-04-15 08:17:19,780] multiqc [DEBUG ] No samples found: varscan2 [2023-04-15 08:17:19,793] multiqc [DEBUG ] No samples found: bbmap [2023-04-15 08:17:19,798] multiqc [DEBUG ] No samples found: bismark [2023-04-15 08:17:19,803] multiqc [DEBUG ] No samples found: biscuit [2023-04-15 08:17:19,808] multiqc [DEBUG ] No samples found: hicexplorer [2023-04-15 08:17:19,812] multiqc [DEBUG ] No samples found: hicup [2023-04-15 08:17:19,817] multiqc [DEBUG ] No samples found: hicpro [2023-04-15 08:17:19,822] multiqc [DEBUG ] No samples found: salmon [2023-04-15 08:17:19,826] multiqc [DEBUG ] No samples found: kallisto [2023-04-15 08:17:19,831] multiqc [DEBUG ] No samples found: slamdunk [2023-04-15 08:17:19,836] multiqc [DEBUG ] No samples found: star [2023-04-15 08:17:19,840] multiqc [DEBUG ] No samples found: hisat2 [2023-04-15 08:17:19,845] multiqc [DEBUG ] No samples found: tophat [2023-04-15 08:17:19,850] multiqc [DEBUG ] No samples found: bowtie2 [2023-04-15 08:17:19,854] multiqc [DEBUG ] No samples found: bowtie1 [2023-04-15 08:17:19,859] multiqc [DEBUG ] No samples found: snpsplit [2023-04-15 08:17:19,863] multiqc [DEBUG ] No samples found: kat [2023-04-15 08:17:19,868] multiqc [DEBUG ] No samples found: leehom [2023-04-15 08:17:19,872] multiqc [DEBUG ] No samples found: adapterRemoval [2023-04-15 08:17:19,877] multiqc [DEBUG ] No samples found: clipandmerge [2023-04-15 08:17:19,881] multiqc [DEBUG ] No samples found: cutadapt [2023-04-15 08:17:19,885] multiqc [DEBUG ] No samples found: flexbar [2023-04-15 08:17:19,890] multiqc [DEBUG ] No samples found: kaiju [2023-04-15 08:17:19,895] multiqc [DEBUG ] No samples found: kraken [2023-04-15 08:17:19,899] multiqc [DEBUG ] No samples found: malt [2023-04-15 08:17:19,904] multiqc [DEBUG ] No samples found: trimmomatic [2023-04-15 08:17:19,908] multiqc [DEBUG ] No samples found: sickle [2023-04-15 08:17:19,913] multiqc [DEBUG ] No samples found: skewer [2023-04-15 08:17:19,917] multiqc [DEBUG ] No samples found: sortmerna [2023-04-15 08:17:19,921] multiqc [DEBUG ] No samples found: biobloomtools [2023-04-15 08:17:19,926] multiqc [DEBUG ] No samples found: fastq_screen [2023-04-15 08:17:19,931] multiqc [DEBUG ] No samples found: afterqc [2023-04-15 08:17:19,935] multiqc [DEBUG ] No samples found: fastp [2023-04-15 08:17:20,157] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-04-15 08:17:20,205] multiqc [DEBUG ] No samples found: pycoqc [2023-04-15 08:17:20,210] multiqc [DEBUG ] No samples found: minionqc [2023-04-15 08:17:20,215] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-04-15 08:17:20,220] multiqc [DEBUG ] No samples found: clusterflow [2023-04-15 08:17:20,225] multiqc [DEBUG ] No samples found: bcl2fastq [2023-04-15 08:17:20,230] multiqc [DEBUG ] No samples found: interop [2023-04-15 08:17:20,235] multiqc [DEBUG ] No samples found: ivar [2023-04-15 08:17:20,240] multiqc [DEBUG ] No samples found: flash [2023-04-15 08:17:20,246] multiqc [DEBUG ] No samples found: seqyclean [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-04-15 08:17:20,246] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-04-15 08:17:20,252] multiqc [INFO ] Compressing plot data [2023-04-15 08:17:20,326] multiqc [INFO ] Report : multiqc_report.html [2023-04-15 08:17:20,327] multiqc [INFO ] Data : multiqc_data [2023-04-15 08:17:20,327] multiqc [DEBUG ] Moving data file from '/state/partition1/job-32351283/tmp3sv4eagv/multiqc_data' to '/scratch/gencore/logs/html/HWCM5BGXN/merged/multiqc_data' [2023-04-15 08:17:20,451] multiqc [INFO ] MultiQC complete