[2022-07-19 04:56:47,976] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-19 04:56:47,977] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-19 04:56:47,977] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-19 04:56:47,978] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-19 04:56:47,978] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-19 04:56:47,978] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCL3BGXM/merged [2022-07-19 04:56:48,572] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-19 04:56:48,572] multiqc [INFO ] This is MultiQC v1.9 [2022-07-19 04:56:48,572] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCL3BGXM/merged [2022-07-19 04:56:48,572] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGCL3BGXM/merged [2022-07-19 04:56:48,572] multiqc [INFO ] Template : default [2022-07-19 04:56:48,572] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-19 04:56:48,572] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGCL3BGXM/merged [2022-07-19 04:56:48,572] 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 [2022-07-19 04:56:48,572] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22543820/tmpv5ekv1t6 [2022-07-19 04:56:48,676] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-19 04:56:48,678] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-19 04:56:48,679] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-19 04:56:48,679] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-19 04:56:48,679] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-19 04:56:48,679] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-19 04:56:48,679] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-19 04:56:49,452] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R20_fastqc.html [2022-07-19 04:56:49,454] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R20_fastqc.html [2022-07-19 04:56:49,512] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R18_fastqc.html [2022-07-19 04:56:49,514] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R18_fastqc.html [2022-07-19 04:56:49,573] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R16_fastqc.html [2022-07-19 04:56:49,575] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R16_fastqc.html [2022-07-19 04:56:49,633] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R21_fastqc.html [2022-07-19 04:56:49,635] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R21_fastqc.html [2022-07-19 04:56:49,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R15_fastqc.html [2022-07-19 04:56:49,694] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R15_fastqc.html [2022-07-19 04:56:49,752] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R17_fastqc.html [2022-07-19 04:56:49,754] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R17_fastqc.html [2022-07-19 04:56:49,812] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R13_fastqc.html [2022-07-19 04:56:49,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R13_fastqc.html [2022-07-19 04:56:49,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_undetermined_fastqc.html [2022-07-19 04:56:49,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_undetermined_fastqc.html [2022-07-19 04:56:49,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R14_fastqc.html [2022-07-19 04:56:49,926] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R14_fastqc.html [2022-07-19 04:56:49,984] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R19_fastqc.html [2022-07-19 04:56:49,985] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCL3BGXM_n01_R19_fastqc.html [2022-07-19 04:56:50,556] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-19 04:56:50,557] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-19 04:56:50,568] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 10 samples (table) [2022-07-19 04:56:50,570] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-19 04:56:50,579] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-19 04:56:50,584] multiqc [DEBUG ] No samples found: conpair [2022-07-19 04:56:50,589] multiqc [DEBUG ] No samples found: peddy [2022-07-19 04:56:50,594] multiqc [DEBUG ] No samples found: somalier [2022-07-19 04:56:50,599] multiqc [DEBUG ] No samples found: methylQA [2022-07-19 04:56:50,607] multiqc [DEBUG ] No samples found: mosdepth [2022-07-19 04:56:50,611] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-19 04:56:50,615] multiqc [DEBUG ] No samples found: qualimap [2022-07-19 04:56:50,620] multiqc [DEBUG ] No samples found: preseq [2022-07-19 04:56:50,625] multiqc [DEBUG ] No samples found: quast [2022-07-19 04:56:50,630] multiqc [DEBUG ] No samples found: qorts [2022-07-19 04:56:50,635] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-19 04:56:50,640] multiqc [DEBUG ] No samples found: rockhopper [2022-07-19 04:56:50,644] multiqc [DEBUG ] No samples found: rsem [2022-07-19 04:56:50,655] multiqc [DEBUG ] No samples found: rseqc [2022-07-19 04:56:50,659] multiqc [DEBUG ] No samples found: busco [2022-07-19 04:56:50,664] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-19 04:56:50,669] multiqc [DEBUG ] No samples found: disambiguate [2022-07-19 04:56:50,674] multiqc [DEBUG ] No samples found: supernova [2022-07-19 04:56:50,686] multiqc [DEBUG ] No samples found: deeptools [2022-07-19 04:56:50,691] multiqc [DEBUG ] No samples found: sargasso [2022-07-19 04:56:50,696] multiqc [DEBUG ] No samples found: verifybamid [2022-07-19 04:56:50,701] multiqc [DEBUG ] No samples found: mirtrace [2022-07-19 04:56:50,706] multiqc [DEBUG ] No samples found: happy [2022-07-19 04:56:50,711] multiqc [DEBUG ] No samples found: mirtop [2022-07-19 04:56:50,717] multiqc [DEBUG ] No samples found: homer [2022-07-19 04:56:50,722] multiqc [DEBUG ] No samples found: macs2 [2022-07-19 04:56:50,726] multiqc [DEBUG ] No samples found: theta2 [2022-07-19 04:56:50,731] multiqc [DEBUG ] No samples found: snpeff [2022-07-19 04:56:50,738] multiqc [DEBUG ] No samples found: gatk [2022-07-19 04:56:50,743] multiqc [DEBUG ] No samples found: htseq [2022-07-19 04:56:50,748] multiqc [DEBUG ] No samples found: bcftools [2022-07-19 04:56:50,753] multiqc [DEBUG ] No samples found: featureCounts [2022-07-19 04:56:50,759] multiqc [DEBUG ] No samples found: fgbio [2022-07-19 04:56:50,772] multiqc [DEBUG ] No samples found: dragen [2022-07-19 04:56:50,777] multiqc [DEBUG ] No samples found: dedup [2022-07-19 04:56:50,781] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-19 04:56:50,805] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-19 04:56:50,809] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-19 04:56:50,811] multiqc [DEBUG ] No samples found: picard [2022-07-19 04:56:50,816] multiqc [DEBUG ] No samples found: prokka [2022-07-19 04:56:50,820] multiqc [DEBUG ] No samples found: samblaster [2022-07-19 04:56:50,828] multiqc [DEBUG ] No samples found: samtools [2022-07-19 04:56:50,833] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-19 04:56:50,839] multiqc [DEBUG ] No samples found: bamtools [2022-07-19 04:56:50,843] multiqc [DEBUG ] No samples found: jellyfish [2022-07-19 04:56:50,850] multiqc [DEBUG ] No samples found: vcftools [2022-07-19 04:56:50,855] multiqc [DEBUG ] No samples found: longranger [2022-07-19 04:56:50,860] multiqc [DEBUG ] No samples found: stacks [2022-07-19 04:56:50,865] multiqc [DEBUG ] No samples found: varscan2 [2022-07-19 04:56:50,878] multiqc [DEBUG ] No samples found: bbmap [2022-07-19 04:56:50,883] multiqc [DEBUG ] No samples found: bismark [2022-07-19 04:56:50,888] multiqc [DEBUG ] No samples found: biscuit [2022-07-19 04:56:50,892] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-19 04:56:50,897] multiqc [DEBUG ] No samples found: hicup [2022-07-19 04:56:50,902] multiqc [DEBUG ] No samples found: hicpro [2022-07-19 04:56:50,906] multiqc [DEBUG ] No samples found: salmon [2022-07-19 04:56:50,911] multiqc [DEBUG ] No samples found: kallisto [2022-07-19 04:56:50,916] multiqc [DEBUG ] No samples found: slamdunk [2022-07-19 04:56:50,921] multiqc [DEBUG ] No samples found: star [2022-07-19 04:56:50,925] multiqc [DEBUG ] No samples found: hisat2 [2022-07-19 04:56:50,930] multiqc [DEBUG ] No samples found: tophat [2022-07-19 04:56:50,934] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-19 04:56:50,939] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-19 04:56:50,944] multiqc [DEBUG ] No samples found: snpsplit [2022-07-19 04:56:50,948] multiqc [DEBUG ] No samples found: kat [2022-07-19 04:56:50,953] multiqc [DEBUG ] No samples found: leehom [2022-07-19 04:56:50,957] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-19 04:56:50,962] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-19 04:56:50,966] multiqc [DEBUG ] No samples found: cutadapt [2022-07-19 04:56:50,970] multiqc [DEBUG ] No samples found: flexbar [2022-07-19 04:56:50,975] multiqc [DEBUG ] No samples found: kaiju [2022-07-19 04:56:50,980] multiqc [DEBUG ] No samples found: kraken [2022-07-19 04:56:50,985] multiqc [DEBUG ] No samples found: malt [2022-07-19 04:56:50,989] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-19 04:56:50,994] multiqc [DEBUG ] No samples found: sickle [2022-07-19 04:56:50,999] multiqc [DEBUG ] No samples found: skewer [2022-07-19 04:56:51,003] multiqc [DEBUG ] No samples found: sortmerna [2022-07-19 04:56:51,007] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-19 04:56:51,012] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-19 04:56:51,018] multiqc [DEBUG ] No samples found: afterqc [2022-07-19 04:56:51,022] multiqc [DEBUG ] No samples found: fastp [2022-07-19 04:56:52,137] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2022-07-19 04:56:52,356] multiqc [DEBUG ] No samples found: pycoqc [2022-07-19 04:56:52,361] multiqc [DEBUG ] No samples found: minionqc [2022-07-19 04:56:52,397] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-19 04:56:52,402] multiqc [DEBUG ] No samples found: clusterflow [2022-07-19 04:56:52,407] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-19 04:56:52,412] multiqc [DEBUG ] No samples found: interop [2022-07-19 04:56:52,417] multiqc [DEBUG ] No samples found: ivar [2022-07-19 04:56:52,421] multiqc [DEBUG ] No samples found: flash [2022-07-19 04:56:52,426] multiqc [DEBUG ] No samples found: seqyclean [2022-07-19 04:56:52,426] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-19 04:56:52,426] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-19 04:56:52,426] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-19 04:56:52,426] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-19 04:56:52,439] multiqc [INFO ] Compressing plot data [2022-07-19 04:56:52,622] multiqc [INFO ] Report : multiqc_report.html [2022-07-19 04:56:52,622] multiqc [INFO ] Data : multiqc_data [2022-07-19 04:56:52,622] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22543820/tmpv5ekv1t6/multiqc_data' to '/scratch/gencore/logs/html/HGCL3BGXM/merged/multiqc_data' [2022-07-19 04:56:52,748] multiqc [INFO ] MultiQC complete