[2025-02-07 20:12:07,854] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-02-07 20:12:07,855] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-02-07 20:12:07,855] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-02-07 20:12:07,857] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-02-07 20:12:07,857] 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}} [2025-02-07 20:12:07,857] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-07 20:12:07,888] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-02-07 20:12:07,888] multiqc [INFO ] This is MultiQC v1.9 [2025-02-07 20:12:07,888] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-07 20:12:07,888] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/6e/836fc13ec3c3f70ad7660861095195/merged [2025-02-07 20:12:07,888] multiqc [INFO ] Template : default [2025-02-07 20:12:07,888] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-02-07 20:12:07,888] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/6e/836fc13ec3c3f70ad7660861095195/merged [2025-02-07 20:12:07,888] 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 [2025-02-07 20:12:07,889] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-57045087/tmp7viy2vb_ [2025-02-07 20:12:07,992] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n02_AH9643-0hr-Rep2_fastqc.html [2025-02-07 20:12:07,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n02_AH9643-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,041] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-02-07 20:12:08,042] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-02-07 20:12:08,115] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n01_AH9643-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n01_AH9643-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,162] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n02_AH6179-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,164] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n02_AH6179-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,208] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n01_AH8967-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,210] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n01_AH8967-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,258] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n01_AH9643-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n01_AH9643-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n01_undetermined_fastqc.html [2025-02-07 20:12:08,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n01_undetermined_fastqc.html [2025-02-07 20:12:08,355] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n02_AH8967-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,356] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n02_AH8967-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,401] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n02_undetermined_fastqc.html [2025-02-07 20:12:08,403] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n02_undetermined_fastqc.html [2025-02-07 20:12:08,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n01_AH6179-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n01_AH6179-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,496] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n02_AH9643-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,498] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n02_AH9643-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,543] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n01_AH8967-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n01_AH8967-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,591] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n01_AH6179-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,593] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n01_AH6179-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,641] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n02_AH8967-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n02_AH8967-0hr-Rep2_fastqc.html [2025-02-07 20:12:08,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN277AFX7_n02_AH6179-3hr-Rep2_fastqc.html [2025-02-07 20:12:08,689] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN277AFX7_n02_AH6179-3hr-Rep2_fastqc.html [2025-02-07 20:12:09,143] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-07 20:12:09,144] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-07 20:12:09,156] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2025-02-07 20:12:09,166] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-02-07 20:12:09,167] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-02-07 20:12:09,172] multiqc [DEBUG ] No samples found: conpair [2025-02-07 20:12:09,177] multiqc [DEBUG ] No samples found: peddy [2025-02-07 20:12:09,182] multiqc [DEBUG ] No samples found: somalier [2025-02-07 20:12:09,187] multiqc [DEBUG ] No samples found: methylQA [2025-02-07 20:12:09,196] multiqc [DEBUG ] No samples found: mosdepth [2025-02-07 20:12:09,201] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-02-07 20:12:09,204] multiqc [DEBUG ] No samples found: qualimap [2025-02-07 20:12:09,209] multiqc [DEBUG ] No samples found: preseq [2025-02-07 20:12:09,215] multiqc [DEBUG ] No samples found: quast [2025-02-07 20:12:09,219] multiqc [DEBUG ] No samples found: qorts [2025-02-07 20:12:09,225] multiqc [DEBUG ] No samples found: rna_seqc [2025-02-07 20:12:09,229] multiqc [DEBUG ] No samples found: rockhopper [2025-02-07 20:12:09,234] multiqc [DEBUG ] No samples found: rsem [2025-02-07 20:12:09,245] multiqc [DEBUG ] No samples found: rseqc [2025-02-07 20:12:09,249] multiqc [DEBUG ] No samples found: busco [2025-02-07 20:12:09,254] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-02-07 20:12:09,259] multiqc [DEBUG ] No samples found: disambiguate [2025-02-07 20:12:09,264] multiqc [DEBUG ] No samples found: supernova [2025-02-07 20:12:09,277] multiqc [DEBUG ] No samples found: deeptools [2025-02-07 20:12:09,282] multiqc [DEBUG ] No samples found: sargasso [2025-02-07 20:12:09,287] multiqc [DEBUG ] No samples found: verifybamid [2025-02-07 20:12:09,292] multiqc [DEBUG ] No samples found: mirtrace [2025-02-07 20:12:09,297] multiqc [DEBUG ] No samples found: happy [2025-02-07 20:12:09,302] multiqc [DEBUG ] No samples found: mirtop [2025-02-07 20:12:09,309] multiqc [DEBUG ] No samples found: homer [2025-02-07 20:12:09,314] multiqc [DEBUG ] No samples found: macs2 [2025-02-07 20:12:09,318] multiqc [DEBUG ] No samples found: theta2 [2025-02-07 20:12:09,323] multiqc [DEBUG ] No samples found: snpeff [2025-02-07 20:12:09,330] multiqc [DEBUG ] No samples found: gatk [2025-02-07 20:12:09,334] multiqc [DEBUG ] No samples found: htseq [2025-02-07 20:12:09,340] multiqc [DEBUG ] No samples found: bcftools [2025-02-07 20:12:09,344] multiqc [DEBUG ] No samples found: featureCounts [2025-02-07 20:12:09,351] multiqc [DEBUG ] No samples found: fgbio [2025-02-07 20:12:09,363] multiqc [DEBUG ] No samples found: dragen [2025-02-07 20:12:09,368] multiqc [DEBUG ] No samples found: dedup [2025-02-07 20:12:09,373] multiqc [DEBUG ] No samples found: damageprofiler [2025-02-07 20:12:09,395] multiqc [DEBUG ] No samples found: biobambam2 [2025-02-07 20:12:09,400] multiqc [DEBUG ] No samples found: mtnucratio [2025-02-07 20:12:09,403] multiqc [DEBUG ] No samples found: picard [2025-02-07 20:12:09,407] multiqc [DEBUG ] No samples found: prokka [2025-02-07 20:12:09,412] multiqc [DEBUG ] No samples found: samblaster [2025-02-07 20:12:09,420] multiqc [DEBUG ] No samples found: samtools [2025-02-07 20:12:09,425] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-02-07 20:12:09,430] multiqc [DEBUG ] No samples found: bamtools [2025-02-07 20:12:09,435] multiqc [DEBUG ] No samples found: jellyfish [2025-02-07 20:12:09,442] multiqc [DEBUG ] No samples found: vcftools [2025-02-07 20:12:09,447] multiqc [DEBUG ] No samples found: longranger [2025-02-07 20:12:09,452] multiqc [DEBUG ] No samples found: stacks [2025-02-07 20:12:09,457] multiqc [DEBUG ] No samples found: varscan2 [2025-02-07 20:12:09,470] multiqc [DEBUG ] No samples found: bbmap [2025-02-07 20:12:09,475] multiqc [DEBUG ] No samples found: bismark [2025-02-07 20:12:09,480] multiqc [DEBUG ] No samples found: biscuit [2025-02-07 20:12:09,485] multiqc [DEBUG ] No samples found: hicexplorer [2025-02-07 20:12:09,490] multiqc [DEBUG ] No samples found: hicup [2025-02-07 20:12:09,495] multiqc [DEBUG ] No samples found: hicpro [2025-02-07 20:12:09,500] multiqc [DEBUG ] No samples found: salmon [2025-02-07 20:12:09,504] multiqc [DEBUG ] No samples found: kallisto [2025-02-07 20:12:09,510] multiqc [DEBUG ] No samples found: slamdunk [2025-02-07 20:12:09,514] multiqc [DEBUG ] No samples found: star [2025-02-07 20:12:09,519] multiqc [DEBUG ] No samples found: hisat2 [2025-02-07 20:12:09,524] multiqc [DEBUG ] No samples found: tophat [2025-02-07 20:12:09,528] multiqc [DEBUG ] No samples found: bowtie2 [2025-02-07 20:12:09,533] multiqc [DEBUG ] No samples found: bowtie1 [2025-02-07 20:12:09,538] multiqc [DEBUG ] No samples found: snpsplit [2025-02-07 20:12:09,542] multiqc [DEBUG ] No samples found: kat [2025-02-07 20:12:09,546] multiqc [DEBUG ] No samples found: leehom [2025-02-07 20:12:09,551] multiqc [DEBUG ] No samples found: adapterRemoval [2025-02-07 20:12:09,556] multiqc [DEBUG ] No samples found: clipandmerge [2025-02-07 20:12:09,560] multiqc [DEBUG ] No samples found: cutadapt [2025-02-07 20:12:09,565] multiqc [DEBUG ] No samples found: flexbar [2025-02-07 20:12:09,570] multiqc [DEBUG ] No samples found: kaiju [2025-02-07 20:12:09,574] multiqc [DEBUG ] No samples found: kraken [2025-02-07 20:12:09,579] multiqc [DEBUG ] No samples found: malt [2025-02-07 20:12:09,584] multiqc [DEBUG ] No samples found: trimmomatic [2025-02-07 20:12:09,589] multiqc [DEBUG ] No samples found: sickle [2025-02-07 20:12:09,594] multiqc [DEBUG ] No samples found: skewer [2025-02-07 20:12:09,599] multiqc [DEBUG ] No samples found: sortmerna [2025-02-07 20:12:09,603] multiqc [DEBUG ] No samples found: biobloomtools [2025-02-07 20:12:09,608] multiqc [DEBUG ] No samples found: fastq_screen [2025-02-07 20:12:09,613] multiqc [DEBUG ] No samples found: afterqc [2025-02-07 20:12:09,619] multiqc [DEBUG ] No samples found: fastp [2025-02-07 20:12:09,933] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2025-02-07 20:12:10,087] multiqc [DEBUG ] No samples found: pycoqc [2025-02-07 20:12:10,092] multiqc [DEBUG ] No samples found: minionqc [2025-02-07 20:12:10,096] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-02-07 20:12:10,101] multiqc [DEBUG ] No samples found: clusterflow [2025-02-07 20:12:10,106] multiqc [DEBUG ] No samples found: bcl2fastq [2025-02-07 20:12:10,111] multiqc [DEBUG ] No samples found: interop [2025-02-07 20:12:10,116] multiqc [DEBUG ] No samples found: ivar [2025-02-07 20:12:10,121] multiqc [DEBUG ] No samples found: flash [2025-02-07 20:12:10,125] multiqc [DEBUG ] No samples found: seqyclean [2025-02-07 20:12:10,125] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-02-07 20:12:10,125] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-02-07 20:12:10,125] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-02-07 20:12:10,125] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-02-07 20:12:10,125] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-02-07 20:12:10,125] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-02-07 20:12:10,126] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-02-07 20:12:10,144] multiqc [INFO ] Compressing plot data [2025-02-07 20:12:10,396] multiqc [INFO ] Report : multiqc_report.html [2025-02-07 20:12:10,396] multiqc [INFO ] Data : multiqc_data [2025-02-07 20:12:10,396] multiqc [DEBUG ] Moving data file from '/state/partition1/job-57045087/tmp7viy2vb_/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/6e/836fc13ec3c3f70ad7660861095195/merged/multiqc_data' [2025-02-07 20:12:10,526] multiqc [INFO ] MultiQC complete