[2022-11-17 23:55:46,535] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-17 23:55:46,535] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-17 23:55:46,535] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-17 23:55:46,536] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-17 23:55:46,536] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-17 23:55:46,536] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMGL2DRX2/2 [2022-11-17 23:55:46,937] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-17 23:55:46,937] multiqc [INFO ] This is MultiQC v1.9 [2022-11-17 23:55:46,937] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMGL2DRX2/2 [2022-11-17 23:55:46,937] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMGL2DRX2/2 [2022-11-17 23:55:46,937] multiqc [INFO ] Template : default [2022-11-17 23:55:46,937] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-17 23:55:46,937] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMGL2DRX2/2 [2022-11-17 23:55:46,938] 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 [2022-11-17 23:55:46,938] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27096729/tmp415sotvs [2022-11-17 23:55:47,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 23:55:47,031] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 23:55:47,113] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_undetermined_fastqc.html [2022-11-17 23:55:47,115] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_undetermined_fastqc.html [2022-11-17 23:55:47,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_104_fastqc.html [2022-11-17 23:55:47,159] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_104_fastqc.html [2022-11-17 23:55:47,200] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_101_fastqc.html [2022-11-17 23:55:47,202] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_101_fastqc.html [2022-11-17 23:55:47,244] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL4_fastqc.html [2022-11-17 23:55:47,245] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL4_fastqc.html [2022-11-17 23:55:47,291] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_102_fastqc.html [2022-11-17 23:55:47,293] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_102_fastqc.html [2022-11-17 23:55:47,335] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL5_fastqc.html [2022-11-17 23:55:47,336] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL5_fastqc.html [2022-11-17 23:55:47,378] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_105_fastqc.html [2022-11-17 23:55:47,380] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_105_fastqc.html [2022-11-17 23:55:47,422] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL3_fastqc.html [2022-11-17 23:55:47,423] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL3_fastqc.html [2022-11-17 23:55:47,465] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL4_fastqc.html [2022-11-17 23:55:47,467] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL4_fastqc.html [2022-11-17 23:55:47,508] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL1_fastqc.html [2022-11-17 23:55:47,510] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL1_fastqc.html [2022-11-17 23:55:47,553] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_103_fastqc.html [2022-11-17 23:55:47,555] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_103_fastqc.html [2022-11-17 23:55:47,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL6_fastqc.html [2022-11-17 23:55:47,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL6_fastqc.html [2022-11-17 23:55:47,643] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL6_fastqc.html [2022-11-17 23:55:47,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL6_fastqc.html [2022-11-17 23:55:47,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL2_fastqc.html [2022-11-17 23:55:47,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL2_fastqc.html [2022-11-17 23:55:47,732] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_undetermined_fastqc.html [2022-11-17 23:55:47,734] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_undetermined_fastqc.html [2022-11-17 23:55:47,775] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL3_fastqc.html [2022-11-17 23:55:47,777] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL3_fastqc.html [2022-11-17 23:55:47,820] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_102_fastqc.html [2022-11-17 23:55:47,822] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_102_fastqc.html [2022-11-17 23:55:47,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL2_fastqc.html [2022-11-17 23:55:47,866] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_RL2_fastqc.html [2022-11-17 23:55:47,908] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_103_fastqc.html [2022-11-17 23:55:47,910] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_103_fastqc.html [2022-11-17 23:55:47,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL1_fastqc.html [2022-11-17 23:55:47,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL1_fastqc.html [2022-11-17 23:55:47,995] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL5_fastqc.html [2022-11-17 23:55:47,996] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_RL5_fastqc.html [2022-11-17 23:55:48,039] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_105_fastqc.html [2022-11-17 23:55:48,041] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n01_bulk_105_fastqc.html [2022-11-17 23:55:48,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_104_fastqc.html [2022-11-17 23:55:48,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_104_fastqc.html [2022-11-17 23:55:48,132] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_101_fastqc.html [2022-11-17 23:55:48,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMGL2DRX2_l02_n02_bulk_101_fastqc.html [2022-11-17 23:55:48,453] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 23:55:48,454] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 23:55:48,469] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 12 samples (table) [2022-11-17 23:55:48,471] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-17 23:55:48,481] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-17 23:55:48,485] multiqc [DEBUG ] No samples found: conpair [2022-11-17 23:55:48,488] multiqc [DEBUG ] No samples found: peddy [2022-11-17 23:55:48,492] multiqc [DEBUG ] No samples found: somalier [2022-11-17 23:55:48,495] multiqc [DEBUG ] No samples found: methylQA [2022-11-17 23:55:48,499] multiqc [DEBUG ] No samples found: mosdepth [2022-11-17 23:55:48,503] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-17 23:55:48,505] multiqc [DEBUG ] No samples found: qualimap [2022-11-17 23:55:48,509] multiqc [DEBUG ] No samples found: preseq [2022-11-17 23:55:48,512] multiqc [DEBUG ] No samples found: quast [2022-11-17 23:55:48,515] multiqc [DEBUG ] No samples found: qorts [2022-11-17 23:55:48,518] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-17 23:55:48,521] multiqc [DEBUG ] No samples found: rockhopper [2022-11-17 23:55:48,524] multiqc [DEBUG ] No samples found: rsem [2022-11-17 23:55:48,530] multiqc [DEBUG ] No samples found: rseqc [2022-11-17 23:55:48,533] multiqc [DEBUG ] No samples found: busco [2022-11-17 23:55:48,536] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-17 23:55:48,540] multiqc [DEBUG ] No samples found: disambiguate [2022-11-17 23:55:48,543] multiqc [DEBUG ] No samples found: supernova [2022-11-17 23:55:48,550] multiqc [DEBUG ] No samples found: deeptools [2022-11-17 23:55:48,553] multiqc [DEBUG ] No samples found: sargasso [2022-11-17 23:55:48,557] multiqc [DEBUG ] No samples found: verifybamid [2022-11-17 23:55:48,560] multiqc [DEBUG ] No samples found: mirtrace [2022-11-17 23:55:48,563] multiqc [DEBUG ] No samples found: happy [2022-11-17 23:55:48,567] multiqc [DEBUG ] No samples found: mirtop [2022-11-17 23:55:48,571] multiqc [DEBUG ] No samples found: homer [2022-11-17 23:55:48,574] multiqc [DEBUG ] No samples found: macs2 [2022-11-17 23:55:48,577] multiqc [DEBUG ] No samples found: theta2 [2022-11-17 23:55:48,580] multiqc [DEBUG ] No samples found: snpeff [2022-11-17 23:55:48,584] multiqc [DEBUG ] No samples found: gatk [2022-11-17 23:55:48,588] multiqc [DEBUG ] No samples found: htseq [2022-11-17 23:55:48,592] multiqc [DEBUG ] No samples found: bcftools [2022-11-17 23:55:48,595] multiqc [DEBUG ] No samples found: featureCounts [2022-11-17 23:55:48,599] multiqc [DEBUG ] No samples found: fgbio [2022-11-17 23:55:48,606] multiqc [DEBUG ] No samples found: dragen [2022-11-17 23:55:48,609] multiqc [DEBUG ] No samples found: dedup [2022-11-17 23:55:48,612] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-17 23:55:48,622] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-17 23:55:48,626] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-17 23:55:48,628] multiqc [DEBUG ] No samples found: picard [2022-11-17 23:55:48,631] multiqc [DEBUG ] No samples found: prokka [2022-11-17 23:55:48,634] multiqc [DEBUG ] No samples found: samblaster [2022-11-17 23:55:48,638] multiqc [DEBUG ] No samples found: samtools [2022-11-17 23:55:48,641] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-17 23:55:48,644] multiqc [DEBUG ] No samples found: bamtools [2022-11-17 23:55:48,647] multiqc [DEBUG ] No samples found: jellyfish [2022-11-17 23:55:48,651] multiqc [DEBUG ] No samples found: vcftools [2022-11-17 23:55:48,654] multiqc [DEBUG ] No samples found: longranger [2022-11-17 23:55:48,657] multiqc [DEBUG ] No samples found: stacks [2022-11-17 23:55:48,660] multiqc [DEBUG ] No samples found: varscan2 [2022-11-17 23:55:48,667] multiqc [DEBUG ] No samples found: bbmap [2022-11-17 23:55:48,670] multiqc [DEBUG ] No samples found: bismark [2022-11-17 23:55:48,673] multiqc [DEBUG ] No samples found: biscuit [2022-11-17 23:55:48,676] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-17 23:55:48,679] multiqc [DEBUG ] No samples found: hicup [2022-11-17 23:55:48,682] multiqc [DEBUG ] No samples found: hicpro [2022-11-17 23:55:48,685] multiqc [DEBUG ] No samples found: salmon [2022-11-17 23:55:48,688] multiqc [DEBUG ] No samples found: kallisto [2022-11-17 23:55:48,691] multiqc [DEBUG ] No samples found: slamdunk [2022-11-17 23:55:48,694] multiqc [DEBUG ] No samples found: star [2022-11-17 23:55:48,697] multiqc [DEBUG ] No samples found: hisat2 [2022-11-17 23:55:48,700] multiqc [DEBUG ] No samples found: tophat [2022-11-17 23:55:48,703] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-17 23:55:48,706] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-17 23:55:48,709] multiqc [DEBUG ] No samples found: snpsplit [2022-11-17 23:55:48,712] multiqc [DEBUG ] No samples found: kat [2022-11-17 23:55:48,715] multiqc [DEBUG ] No samples found: leehom [2022-11-17 23:55:48,718] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-17 23:55:48,721] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-17 23:55:48,724] multiqc [DEBUG ] No samples found: cutadapt [2022-11-17 23:55:48,727] multiqc [DEBUG ] No samples found: flexbar [2022-11-17 23:55:48,730] multiqc [DEBUG ] No samples found: kaiju [2022-11-17 23:55:48,734] multiqc [DEBUG ] No samples found: kraken [2022-11-17 23:55:48,737] multiqc [DEBUG ] No samples found: malt [2022-11-17 23:55:48,740] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-17 23:55:48,743] multiqc [DEBUG ] No samples found: sickle [2022-11-17 23:55:48,746] multiqc [DEBUG ] No samples found: skewer [2022-11-17 23:55:48,750] multiqc [DEBUG ] No samples found: sortmerna [2022-11-17 23:55:48,753] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-17 23:55:48,756] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-17 23:55:48,759] multiqc [DEBUG ] No samples found: afterqc [2022-11-17 23:55:48,762] multiqc [DEBUG ] No samples found: fastp [2022-11-17 23:55:49,568] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2022-11-17 23:55:49,956] multiqc [DEBUG ] No samples found: pycoqc [2022-11-17 23:55:49,959] multiqc [DEBUG ] No samples found: minionqc [2022-11-17 23:55:49,963] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-17 23:55:49,966] multiqc [DEBUG ] No samples found: clusterflow [2022-11-17 23:55:49,969] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-17 23:55:49,972] multiqc [DEBUG ] No samples found: interop [2022-11-17 23:55:49,975] multiqc [DEBUG ] No samples found: ivar [2022-11-17 23:55:49,978] multiqc [DEBUG ] No samples found: flash [2022-11-17 23:55:49,981] multiqc [DEBUG ] No samples found: seqyclean [2022-11-17 23:55:49,981] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-17 23:55:49,981] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2022-11-17 23:55:49,981] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-11-17 23:55:49,981] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-17 23:55:49,981] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-17 23:55:50,011] multiqc [INFO ] Compressing plot data [2022-11-17 23:55:50,477] multiqc [INFO ] Report : multiqc_report.html [2022-11-17 23:55:50,478] multiqc [INFO ] Data : multiqc_data [2022-11-17 23:55:50,478] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27096729/tmp415sotvs/multiqc_data' to '/scratch/gencore/logs/html/HMGL2DRX2/2/multiqc_data' [2022-11-17 23:57:55,401] multiqc [INFO ] MultiQC complete