[2024-08-30 04:12:46,250] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-30 04:12:46,250] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-30 04:12:46,250] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-30 04:12:46,253] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-30 04:12:46,253] 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}} [2024-08-30 04:12:46,253] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-30 04:12:46,291] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-30 04:12:46,291] multiqc [INFO ] This is MultiQC v1.9 [2024-08-30 04:12:46,291] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-30 04:12:46,291] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/b6/35f9b8d87a42ec849fbb862d2bd5d2/merged [2024-08-30 04:12:46,291] multiqc [INFO ] Template : default [2024-08-30 04:12:46,291] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-30 04:12:46,291] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/b6/35f9b8d87a42ec849fbb862d2bd5d2/merged [2024-08-30 04:12:46,292] 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 [2024-08-30 04:12:46,292] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-50472548/tmpt862h3dp [2024-08-30 04:12:46,403] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK15_fastqc.html [2024-08-30 04:12:46,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK15_fastqc.html [2024-08-30 04:12:46,457] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-08-30 04:12:46,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK04_fastqc.html [2024-08-30 04:12:46,660] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK13_fastqc.html [2024-08-30 04:12:46,662] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK13_fastqc.html [2024-08-30 04:12:46,711] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK04_fastqc.html [2024-08-30 04:12:46,713] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK04_fastqc.html [2024-08-30 04:12:46,761] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK10_fastqc.html [2024-08-30 04:12:46,763] multiqc [DEBUG ] 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[2024-08-30 04:12:47,848] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK16_fastqc.html [2024-08-30 04:12:47,896] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK12_fastqc.html [2024-08-30 04:12:47,898] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK12_fastqc.html [2024-08-30 04:12:47,945] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK21_fastqc.html [2024-08-30 04:12:47,947] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK21_fastqc.html [2024-08-30 04:12:47,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK09_fastqc.html [2024-08-30 04:12:47,995] multiqc [DEBUG ] 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04:12:48,484] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK18_fastqc.html [2024-08-30 04:12:48,486] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK18_fastqc.html [2024-08-30 04:12:48,534] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK22_fastqc.html [2024-08-30 04:12:48,536] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK22_fastqc.html [2024-08-30 04:12:48,582] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK11_fastqc.html [2024-08-30 04:12:48,584] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK11_fastqc.html [2024-08-30 04:12:48,633] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK19_fastqc.html [2024-08-30 04:12:48,635] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n01_HEK19_fastqc.html [2024-08-30 04:12:48,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK23_fastqc.html [2024-08-30 04:12:48,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK23_fastqc.html [2024-08-30 04:12:48,735] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK09_fastqc.html [2024-08-30 04:12:48,737] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK09_fastqc.html [2024-08-30 04:12:48,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK06_fastqc.html [2024-08-30 04:12:48,786] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK06_fastqc.html [2024-08-30 04:12:48,834] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK17_fastqc.html [2024-08-30 04:12:48,836] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMKBGXW_n02_HEK17_fastqc.html [2024-08-30 04:12:49,352] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-30 04:12:49,354] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-30 04:12:49,372] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-08-30 04:12:49,382] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-30 04:12:49,384] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-30 04:12:49,389] multiqc [DEBUG ] No samples found: conpair [2024-08-30 04:12:49,394] multiqc [DEBUG ] No samples found: peddy [2024-08-30 04:12:49,400] multiqc [DEBUG ] No samples found: somalier [2024-08-30 04:12:49,405] multiqc [DEBUG ] No samples found: methylQA [2024-08-30 04:12:49,414] multiqc [DEBUG ] No samples found: mosdepth [2024-08-30 04:12:49,419] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-30 04:12:49,422] multiqc [DEBUG ] No samples found: qualimap [2024-08-30 04:12:49,428] multiqc [DEBUG ] No samples found: preseq [2024-08-30 04:12:49,433] multiqc [DEBUG ] No samples found: quast [2024-08-30 04:12:49,439] multiqc [DEBUG ] No samples found: qorts [2024-08-30 04:12:49,443] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-30 04:12:49,448] multiqc [DEBUG ] No samples found: rockhopper [2024-08-30 04:12:49,453] multiqc [DEBUG ] No samples found: rsem [2024-08-30 04:12:49,465] multiqc [DEBUG ] No samples found: rseqc [2024-08-30 04:12:49,469] multiqc [DEBUG ] No samples found: busco [2024-08-30 04:12:49,474] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-30 04:12:49,480] multiqc [DEBUG ] No samples found: disambiguate [2024-08-30 04:12:49,485] multiqc [DEBUG ] No samples found: supernova [2024-08-30 04:12:49,499] multiqc [DEBUG ] No samples found: deeptools [2024-08-30 04:12:49,504] multiqc [DEBUG ] No samples found: sargasso [2024-08-30 04:12:49,509] multiqc [DEBUG ] No samples found: verifybamid [2024-08-30 04:12:49,515] multiqc [DEBUG ] No samples found: mirtrace [2024-08-30 04:12:49,520] multiqc [DEBUG ] No samples found: happy [2024-08-30 04:12:49,525] multiqc [DEBUG ] No samples found: mirtop [2024-08-30 04:12:49,532] multiqc [DEBUG ] No samples found: homer [2024-08-30 04:12:49,536] multiqc [DEBUG ] No samples found: macs2 [2024-08-30 04:12:49,541] multiqc [DEBUG ] No samples found: theta2 [2024-08-30 04:12:49,546] multiqc [DEBUG ] No samples found: snpeff [2024-08-30 04:12:49,553] multiqc [DEBUG ] No samples found: gatk [2024-08-30 04:12:49,558] multiqc [DEBUG ] No samples found: htseq [2024-08-30 04:12:49,564] multiqc [DEBUG ] No samples found: bcftools [2024-08-30 04:12:49,569] multiqc [DEBUG ] No samples found: featureCounts [2024-08-30 04:12:49,575] multiqc [DEBUG ] No samples found: fgbio [2024-08-30 04:12:49,588] multiqc [DEBUG ] No samples found: dragen [2024-08-30 04:12:49,593] multiqc [DEBUG ] No samples found: dedup [2024-08-30 04:12:49,598] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-30 04:12:49,623] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-30 04:12:49,628] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-30 04:12:49,631] multiqc [DEBUG ] No samples found: picard [2024-08-30 04:12:49,636] multiqc [DEBUG ] No samples found: prokka [2024-08-30 04:12:49,641] multiqc [DEBUG ] No samples found: samblaster [2024-08-30 04:12:49,649] multiqc [DEBUG ] No samples found: samtools [2024-08-30 04:12:49,654] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-30 04:12:49,660] multiqc [DEBUG ] No samples found: bamtools [2024-08-30 04:12:49,664] multiqc [DEBUG ] No samples found: jellyfish [2024-08-30 04:12:49,675] multiqc [DEBUG ] No samples found: vcftools [2024-08-30 04:12:49,681] multiqc [DEBUG ] No samples found: longranger [2024-08-30 04:12:49,686] multiqc [DEBUG ] No samples found: stacks [2024-08-30 04:12:49,692] multiqc [DEBUG ] No samples found: varscan2 [2024-08-30 04:12:49,707] multiqc [DEBUG ] No samples found: bbmap [2024-08-30 04:12:49,713] multiqc [DEBUG ] No samples found: bismark [2024-08-30 04:12:49,719] multiqc [DEBUG ] No samples found: biscuit [2024-08-30 04:12:49,724] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-30 04:12:49,729] multiqc [DEBUG ] No samples found: hicup [2024-08-30 04:12:49,734] multiqc [DEBUG ] No samples found: hicpro [2024-08-30 04:12:49,739] multiqc [DEBUG ] No samples found: salmon [2024-08-30 04:12:49,743] multiqc [DEBUG ] No samples found: kallisto [2024-08-30 04:12:49,749] multiqc [DEBUG ] No samples found: slamdunk [2024-08-30 04:12:49,754] multiqc [DEBUG ] No samples found: star [2024-08-30 04:12:49,759] multiqc [DEBUG ] No samples found: hisat2 [2024-08-30 04:12:49,764] multiqc [DEBUG ] No samples found: tophat [2024-08-30 04:12:49,769] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-30 04:12:49,773] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-30 04:12:49,778] multiqc [DEBUG ] No samples found: snpsplit [2024-08-30 04:12:49,783] multiqc [DEBUG ] No samples found: kat [2024-08-30 04:12:49,787] multiqc [DEBUG ] No samples found: leehom [2024-08-30 04:12:49,792] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-30 04:12:49,796] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-30 04:12:49,801] multiqc [DEBUG ] No samples found: cutadapt [2024-08-30 04:12:49,806] multiqc [DEBUG ] No samples found: flexbar [2024-08-30 04:12:49,811] multiqc [DEBUG ] No samples found: kaiju [2024-08-30 04:12:49,816] multiqc [DEBUG ] No samples found: kraken [2024-08-30 04:12:49,820] multiqc [DEBUG ] No samples found: malt [2024-08-30 04:12:49,825] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-30 04:12:49,830] multiqc [DEBUG ] No samples found: sickle [2024-08-30 04:12:49,835] multiqc [DEBUG ] No samples found: skewer [2024-08-30 04:12:49,840] multiqc [DEBUG ] No samples found: sortmerna [2024-08-30 04:12:49,844] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-30 04:12:49,849] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-30 04:12:49,854] multiqc [DEBUG ] No samples found: afterqc [2024-08-30 04:12:49,859] multiqc [DEBUG ] No samples found: fastp [2024-08-30 04:12:52,401] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2024-08-30 04:12:52,664] multiqc [DEBUG ] No samples found: pycoqc [2024-08-30 04:12:52,669] multiqc [DEBUG ] No samples found: minionqc [2024-08-30 04:12:52,674] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-30 04:12:52,679] multiqc [DEBUG ] No samples found: clusterflow [2024-08-30 04:12:52,684] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-30 04:12:52,690] multiqc [DEBUG ] No samples found: interop [2024-08-30 04:12:52,694] multiqc [DEBUG ] No samples found: ivar [2024-08-30 04:12:52,699] multiqc [DEBUG ] No samples found: flash [2024-08-30 04:12:52,704] multiqc [DEBUG ] No samples found: seqyclean [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-30 04:12:52,704] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-30 04:12:52,705] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-30 04:12:52,705] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-30 04:12:52,705] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-30 04:12:52,705] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-30 04:12:52,705] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-30 04:12:52,705] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-30 04:12:52,705] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-30 04:12:52,764] multiqc [INFO ] Compressing plot data [2024-08-30 04:12:53,563] multiqc [INFO ] Report : multiqc_report.html [2024-08-30 04:12:53,564] multiqc [INFO ] Data : multiqc_data [2024-08-30 04:12:53,564] multiqc [DEBUG ] Moving data file from '/state/partition1/job-50472548/tmpt862h3dp/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/b6/35f9b8d87a42ec849fbb862d2bd5d2/merged/multiqc_data' [2024-08-30 04:12:53,709] multiqc [INFO ] MultiQC complete