[2022-04-23 03:40:50,362] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-23 03:40:50,362] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-23 03:40:50,362] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-23 03:40:50,363] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-23 03:40:50,363] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-23 03:40:50,363] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLG55AFX3/merged [2022-04-23 03:40:50,760] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-23 03:40:50,760] multiqc [INFO ] This is MultiQC v1.9 [2022-04-23 03:40:50,760] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLG55AFX3/merged [2022-04-23 03:40:50,760] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLG55AFX3/merged [2022-04-23 03:40:50,760] multiqc [INFO ] Template : default [2022-04-23 03:40:50,760] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-23 03:40:50,760] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLG55AFX3/merged [2022-04-23 03:40:50,760] 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 [2022-04-23 03:40:50,761] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-18470386/tmpsp4zo5f1 [2022-04-23 03:40:50,877] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLG55AFX3_4_fastqc.html [2022-04-23 03:40:50,879] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLG55AFX3_4_fastqc.html [2022-04-23 03:40:50,932] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLG55AFX3_2_fastqc.html [2022-04-23 03:40:50,934] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLG55AFX3_2_fastqc.html [2022-04-23 03:40:50,981] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLG55AFX3_1_fastqc.html [2022-04-23 03:40:50,982] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLG55AFX3_1_fastqc.html [2022-04-23 03:40:51,022] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLG55AFX3_3_fastqc.html [2022-04-23 03:40:51,024] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLG55AFX3_3_fastqc.html [2022-04-23 03:40:51,637] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-23 03:40:51,639] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-23 03:40:51,643] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-04-23 03:40:51,645] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-23 03:40:51,650] multiqc [DEBUG ] No samples found: conpair [2022-04-23 03:40:51,655] multiqc [DEBUG ] No samples found: peddy [2022-04-23 03:40:51,660] multiqc [DEBUG ] No samples found: somalier [2022-04-23 03:40:51,668] multiqc [DEBUG ] No samples found: methylQA [2022-04-23 03:40:51,678] multiqc [DEBUG ] No samples found: mosdepth [2022-04-23 03:40:51,683] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-23 03:40:51,686] multiqc [DEBUG ] No samples found: qualimap [2022-04-23 03:40:51,691] multiqc [DEBUG ] No samples found: preseq [2022-04-23 03:40:51,696] multiqc [DEBUG ] No samples found: quast [2022-04-23 03:40:51,701] multiqc [DEBUG ] No samples found: qorts [2022-04-23 03:40:51,706] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-23 03:40:51,711] multiqc [DEBUG ] No samples found: rockhopper [2022-04-23 03:40:51,716] multiqc [DEBUG ] No samples found: rsem [2022-04-23 03:40:51,732] multiqc [DEBUG ] No samples found: rseqc [2022-04-23 03:40:51,738] multiqc [DEBUG ] No samples found: busco [2022-04-23 03:40:51,743] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-23 03:40:51,748] multiqc [DEBUG ] No samples found: disambiguate [2022-04-23 03:40:51,754] multiqc [DEBUG ] No samples found: supernova [2022-04-23 03:40:51,770] multiqc [DEBUG ] No samples found: deeptools [2022-04-23 03:40:51,775] multiqc [DEBUG ] No samples found: sargasso [2022-04-23 03:40:51,780] multiqc [DEBUG ] No samples found: verifybamid [2022-04-23 03:40:51,785] multiqc [DEBUG ] No samples found: mirtrace [2022-04-23 03:40:51,789] multiqc [DEBUG ] No samples found: happy [2022-04-23 03:40:51,794] multiqc [DEBUG ] No samples found: mirtop [2022-04-23 03:40:51,801] multiqc [DEBUG ] No samples found: homer [2022-04-23 03:40:51,805] multiqc [DEBUG ] No samples found: macs2 [2022-04-23 03:40:51,810] multiqc [DEBUG ] No samples found: theta2 [2022-04-23 03:40:51,815] multiqc [DEBUG ] No samples found: snpeff [2022-04-23 03:40:51,822] multiqc [DEBUG ] No samples found: gatk [2022-04-23 03:40:51,826] multiqc [DEBUG ] No samples found: htseq [2022-04-23 03:40:51,832] multiqc [DEBUG ] No samples found: bcftools [2022-04-23 03:40:51,837] multiqc [DEBUG ] No samples found: featureCounts [2022-04-23 03:40:51,845] multiqc [DEBUG ] No samples found: fgbio [2022-04-23 03:40:51,862] multiqc [DEBUG ] No samples found: dragen [2022-04-23 03:40:51,867] multiqc [DEBUG ] No samples found: dedup [2022-04-23 03:40:51,874] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-23 03:40:51,898] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-23 03:40:51,903] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-23 03:40:51,905] multiqc [DEBUG ] No samples found: picard [2022-04-23 03:40:51,911] multiqc [DEBUG ] No samples found: prokka [2022-04-23 03:40:51,915] multiqc [DEBUG ] No samples found: samblaster [2022-04-23 03:40:51,924] multiqc [DEBUG ] No samples found: samtools [2022-04-23 03:40:51,929] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-23 03:40:51,934] multiqc [DEBUG ] No samples found: bamtools [2022-04-23 03:40:51,939] multiqc [DEBUG ] No samples found: jellyfish [2022-04-23 03:40:51,947] multiqc [DEBUG ] No samples found: vcftools [2022-04-23 03:40:51,952] multiqc [DEBUG ] No samples found: longranger [2022-04-23 03:40:51,958] multiqc [DEBUG ] No samples found: stacks [2022-04-23 03:40:51,963] multiqc [DEBUG ] No samples found: varscan2 [2022-04-23 03:40:51,979] multiqc [DEBUG ] No samples found: bbmap [2022-04-23 03:40:51,984] multiqc [DEBUG ] No samples found: bismark [2022-04-23 03:40:51,989] multiqc [DEBUG ] No samples found: biscuit [2022-04-23 03:40:51,994] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-23 03:40:52,000] multiqc [DEBUG ] No samples found: hicup [2022-04-23 03:40:52,004] multiqc [DEBUG ] No samples found: hicpro [2022-04-23 03:40:52,011] multiqc [DEBUG ] No samples found: salmon [2022-04-23 03:40:52,015] multiqc [DEBUG ] No samples found: kallisto [2022-04-23 03:40:52,020] multiqc [DEBUG ] No samples found: slamdunk [2022-04-23 03:40:52,025] multiqc [DEBUG ] No samples found: star [2022-04-23 03:40:52,030] multiqc [DEBUG ] No samples found: hisat2 [2022-04-23 03:40:52,035] multiqc [DEBUG ] No samples found: tophat [2022-04-23 03:40:52,040] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-23 03:40:52,044] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-23 03:40:52,049] multiqc [DEBUG ] No samples found: snpsplit [2022-04-23 03:40:52,053] multiqc [DEBUG ] No samples found: kat [2022-04-23 03:40:52,058] multiqc [DEBUG ] No samples found: leehom [2022-04-23 03:40:52,063] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-23 03:40:52,067] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-23 03:40:52,072] multiqc [DEBUG ] No samples found: cutadapt [2022-04-23 03:40:52,077] multiqc [DEBUG ] No samples found: flexbar [2022-04-23 03:40:52,081] multiqc [DEBUG ] No samples found: kaiju [2022-04-23 03:40:52,088] multiqc [DEBUG ] No samples found: kraken [2022-04-23 03:40:52,093] multiqc [DEBUG ] No samples found: malt [2022-04-23 03:40:52,097] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-23 03:40:52,102] multiqc [DEBUG ] No samples found: sickle [2022-04-23 03:40:52,107] multiqc [DEBUG ] No samples found: skewer [2022-04-23 03:40:52,111] multiqc [DEBUG ] No samples found: sortmerna [2022-04-23 03:40:52,116] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-23 03:40:52,121] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-23 03:40:52,126] multiqc [DEBUG ] No samples found: afterqc [2022-04-23 03:40:52,130] multiqc [DEBUG ] No samples found: fastp [2022-04-23 03:40:52,189] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-04-23 03:40:52,233] multiqc [DEBUG ] No samples found: pycoqc [2022-04-23 03:40:52,238] multiqc [DEBUG ] No samples found: minionqc [2022-04-23 03:40:52,243] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-23 03:40:52,248] multiqc [DEBUG ] No samples found: clusterflow [2022-04-23 03:40:52,253] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-23 03:40:52,257] multiqc [DEBUG ] No samples found: interop [2022-04-23 03:40:52,264] multiqc [DEBUG ] No samples found: ivar [2022-04-23 03:40:52,269] multiqc [DEBUG ] No samples found: flash [2022-04-23 03:40:52,274] multiqc [DEBUG ] No samples found: seqyclean [2022-04-23 03:40:52,274] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-04-23 03:40:52,274] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-23 03:40:52,274] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-23 03:40:52,280] multiqc [INFO ] Compressing plot data [2022-04-23 03:40:52,347] multiqc [INFO ] Report : multiqc_report.html [2022-04-23 03:40:52,348] multiqc [INFO ] Data : multiqc_data [2022-04-23 03:40:52,348] multiqc [DEBUG ] Moving data file from '/state/partition1/job-18470386/tmpsp4zo5f1/multiqc_data' to '/scratch/gencore/logs/html/HLG55AFX3/merged/multiqc_data' [2022-04-23 03:40:52,475] multiqc [INFO ] MultiQC complete