[2024-11-27 00:53:21,564] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-11-27 00:53:21,564] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-11-27 00:53:21,564] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-11-27 00:53:21,566] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-11-27 00:53:21,566] 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}} [2024-11-27 00:53:21,566] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-27 00:53:21,597] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-11-27 00:53:21,597] multiqc [INFO ] This is MultiQC v1.9 [2024-11-27 00:53:21,597] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-27 00:53:21,597] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/f4/6ef8e9f8c124b3cc748cb3d5fe320f/merged [2024-11-27 00:53:21,597] multiqc [INFO ] Template : default [2024-11-27 00:53:21,597] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-11-27 00:53:21,598] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/f4/6ef8e9f8c124b3cc748cb3d5fe320f/merged [2024-11-27 00:53:21,598] 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 [2024-11-27 00:53:21,598] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-54053970/tmpueryihb6 [2024-11-27 00:53:21,708] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFCYCBGYW_1_fastqc.html [2024-11-27 00:53:21,710] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFCYCBGYW_1_fastqc.html [2024-11-27 00:53:22,272] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-27 00:53:22,274] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-27 00:53:22,279] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-11-27 00:53:22,284] multiqc [DEBUG ] No samples found: conpair [2024-11-27 00:53:22,290] multiqc [DEBUG ] No samples found: peddy [2024-11-27 00:53:22,296] multiqc [DEBUG ] No samples found: somalier [2024-11-27 00:53:22,302] multiqc [DEBUG ] No samples found: methylQA [2024-11-27 00:53:22,312] multiqc [DEBUG ] No samples found: mosdepth [2024-11-27 00:53:22,317] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-11-27 00:53:22,321] multiqc [DEBUG ] No samples found: qualimap [2024-11-27 00:53:22,326] multiqc [DEBUG ] No samples found: preseq [2024-11-27 00:53:22,332] multiqc [DEBUG ] No samples found: quast [2024-11-27 00:53:22,338] multiqc [DEBUG ] No samples found: qorts [2024-11-27 00:53:22,343] multiqc [DEBUG ] No samples found: rna_seqc [2024-11-27 00:53:22,349] multiqc [DEBUG ] No samples found: rockhopper [2024-11-27 00:53:22,354] multiqc [DEBUG ] No samples found: rsem [2024-11-27 00:53:22,368] multiqc [DEBUG ] No samples found: rseqc [2024-11-27 00:53:22,374] multiqc [DEBUG ] No samples found: busco [2024-11-27 00:53:22,380] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-11-27 00:53:22,385] multiqc [DEBUG ] No samples found: disambiguate [2024-11-27 00:53:22,391] multiqc [DEBUG ] No samples found: supernova [2024-11-27 00:53:22,407] multiqc [DEBUG ] No samples found: deeptools [2024-11-27 00:53:22,414] multiqc [DEBUG ] No samples found: sargasso [2024-11-27 00:53:22,420] multiqc [DEBUG ] No samples found: verifybamid [2024-11-27 00:53:22,425] multiqc [DEBUG ] No samples found: mirtrace [2024-11-27 00:53:22,431] multiqc [DEBUG ] No samples found: happy [2024-11-27 00:53:22,436] multiqc [DEBUG ] No samples found: mirtop [2024-11-27 00:53:22,444] multiqc [DEBUG ] No samples found: homer [2024-11-27 00:53:22,449] multiqc [DEBUG ] No samples found: macs2 [2024-11-27 00:53:22,455] multiqc [DEBUG ] No samples found: theta2 [2024-11-27 00:53:22,461] multiqc [DEBUG ] No samples found: snpeff [2024-11-27 00:53:22,469] multiqc [DEBUG ] No samples found: gatk [2024-11-27 00:53:22,474] multiqc [DEBUG ] No samples found: htseq [2024-11-27 00:53:22,480] multiqc [DEBUG ] No samples found: bcftools [2024-11-27 00:53:22,486] multiqc [DEBUG ] No samples found: featureCounts [2024-11-27 00:53:22,494] multiqc [DEBUG ] No samples found: fgbio [2024-11-27 00:53:22,509] multiqc [DEBUG ] No samples found: dragen [2024-11-27 00:53:22,515] multiqc [DEBUG ] No samples found: dedup [2024-11-27 00:53:22,520] multiqc [DEBUG ] No samples found: damageprofiler [2024-11-27 00:53:22,545] multiqc [DEBUG ] No samples found: biobambam2 [2024-11-27 00:53:22,551] multiqc [DEBUG ] No samples found: mtnucratio [2024-11-27 00:53:22,553] multiqc [DEBUG ] No samples found: picard [2024-11-27 00:53:22,559] multiqc [DEBUG ] No samples found: prokka [2024-11-27 00:53:22,564] multiqc [DEBUG ] No samples found: samblaster [2024-11-27 00:53:22,576] multiqc [DEBUG ] No samples found: samtools [2024-11-27 00:53:22,582] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-11-27 00:53:22,589] multiqc [DEBUG ] No samples found: bamtools [2024-11-27 00:53:22,594] multiqc [DEBUG ] No samples found: jellyfish [2024-11-27 00:53:22,605] multiqc [DEBUG ] No samples found: vcftools [2024-11-27 00:53:22,611] multiqc [DEBUG ] No samples found: longranger [2024-11-27 00:53:22,620] multiqc [DEBUG ] No samples found: stacks [2024-11-27 00:53:22,626] multiqc [DEBUG ] No samples found: varscan2 [2024-11-27 00:53:22,643] multiqc [DEBUG ] No samples found: bbmap [2024-11-27 00:53:22,649] multiqc [DEBUG ] No samples found: bismark [2024-11-27 00:53:22,655] multiqc [DEBUG ] No samples found: biscuit [2024-11-27 00:53:22,660] multiqc [DEBUG ] No samples found: hicexplorer [2024-11-27 00:53:22,666] multiqc [DEBUG ] No samples found: hicup [2024-11-27 00:53:22,671] multiqc [DEBUG ] No samples found: hicpro [2024-11-27 00:53:22,676] multiqc [DEBUG ] No samples found: salmon [2024-11-27 00:53:22,682] multiqc [DEBUG ] No samples found: kallisto [2024-11-27 00:53:22,687] multiqc [DEBUG ] No samples found: slamdunk [2024-11-27 00:53:22,692] multiqc [DEBUG ] No samples found: star [2024-11-27 00:53:22,698] multiqc [DEBUG ] No samples found: hisat2 [2024-11-27 00:53:22,703] multiqc [DEBUG ] No samples found: tophat [2024-11-27 00:53:22,708] multiqc [DEBUG ] No samples found: bowtie2 [2024-11-27 00:53:22,713] multiqc [DEBUG ] No samples found: bowtie1 [2024-11-27 00:53:22,718] multiqc [DEBUG ] No samples found: snpsplit [2024-11-27 00:53:22,724] multiqc [DEBUG ] No samples found: kat [2024-11-27 00:53:22,728] multiqc [DEBUG ] No samples found: leehom [2024-11-27 00:53:22,734] multiqc [DEBUG ] No samples found: adapterRemoval [2024-11-27 00:53:22,739] multiqc [DEBUG ] No samples found: clipandmerge [2024-11-27 00:53:22,744] multiqc [DEBUG ] No samples found: cutadapt [2024-11-27 00:53:22,749] multiqc [DEBUG ] No samples found: flexbar [2024-11-27 00:53:22,754] multiqc [DEBUG ] No samples found: kaiju [2024-11-27 00:53:22,759] multiqc [DEBUG ] No samples found: kraken [2024-11-27 00:53:22,764] multiqc [DEBUG ] No samples found: malt [2024-11-27 00:53:22,769] multiqc [DEBUG ] No samples found: trimmomatic [2024-11-27 00:53:22,775] multiqc [DEBUG ] No samples found: sickle [2024-11-27 00:53:22,780] multiqc [DEBUG ] No samples found: skewer [2024-11-27 00:53:22,785] multiqc [DEBUG ] No samples found: sortmerna [2024-11-27 00:53:22,789] multiqc [DEBUG ] No samples found: biobloomtools [2024-11-27 00:53:22,795] multiqc [DEBUG ] No samples found: fastq_screen [2024-11-27 00:53:22,800] multiqc [DEBUG ] No samples found: afterqc [2024-11-27 00:53:22,805] multiqc [DEBUG ] No samples found: fastp [2024-11-27 00:53:22,882] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports [2024-11-27 00:53:22,934] multiqc [DEBUG ] No samples found: pycoqc [2024-11-27 00:53:22,940] multiqc [DEBUG ] No samples found: minionqc [2024-11-27 00:53:22,945] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-11-27 00:53:22,951] multiqc [DEBUG ] No samples found: clusterflow [2024-11-27 00:53:22,956] multiqc [DEBUG ] No samples found: bcl2fastq [2024-11-27 00:53:22,962] multiqc [DEBUG ] No samples found: interop [2024-11-27 00:53:22,967] multiqc [DEBUG ] No samples found: ivar [2024-11-27 00:53:22,972] multiqc [DEBUG ] No samples found: flash [2024-11-27 00:53:22,978] multiqc [DEBUG ] No samples found: seqyclean [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-11-27 00:53:22,978] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-11-27 00:53:22,980] multiqc [INFO ] Compressing plot data [2024-11-27 00:53:23,007] multiqc [INFO ] Report : multiqc_report.html [2024-11-27 00:53:23,007] multiqc [INFO ] Data : multiqc_data [2024-11-27 00:53:23,007] multiqc [DEBUG ] Moving data file from '/state/partition1/job-54053970/tmpueryihb6/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/f4/6ef8e9f8c124b3cc748cb3d5fe320f/merged/multiqc_data' [2024-11-27 00:53:23,144] multiqc [INFO ] MultiQC complete