[2024-11-13 11:27:28,755] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-11-13 11:27:28,755] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-11-13 11:27:28,755] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-11-13 11:27:28,757] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-11-13 11:27:28,757] 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}} [2024-11-13 11:27:28,758] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-13 11:27:28,788] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-11-13 11:27:28,789] multiqc [INFO ] This is MultiQC v1.9 [2024-11-13 11:27:28,789] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-13 11:27:28,789] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/e7/d090d521e43c2ddc0260d39d8b4402/1 [2024-11-13 11:27:28,789] multiqc [INFO ] Template : default [2024-11-13 11:27:28,789] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-11-13 11:27:28,789] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/e7/d090d521e43c2ddc0260d39d8b4402/1 [2024-11-13 11:27:28,789] 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 [2024-11-13 11:27:28,789] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-53403887/tmps6fm1fuu [2024-11-13 11:27:28,881] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNBP7_l01.3_fastqc.html [2024-11-13 11:27:28,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNBP7_l01.3_fastqc.html [2024-11-13 11:27:28,935] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNBP7_l01.2_fastqc.html [2024-11-13 11:27:28,937] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNBP7_l01.2_fastqc.html [2024-11-13 11:27:28,984] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNBP7_l01.1_fastqc.html [2024-11-13 11:27:28,986] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNBP7_l01.1_fastqc.html [2024-11-13 11:27:29,327] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-13 11:27:29,327] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-13 11:27:29,331] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-11-13 11:27:29,334] multiqc [DEBUG ] No samples found: conpair [2024-11-13 11:27:29,337] multiqc [DEBUG ] No samples found: peddy [2024-11-13 11:27:29,340] multiqc [DEBUG ] No samples found: somalier [2024-11-13 11:27:29,343] multiqc [DEBUG ] No samples found: methylQA [2024-11-13 11:27:29,346] multiqc [DEBUG ] No samples found: mosdepth [2024-11-13 11:27:29,349] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-11-13 11:27:29,352] multiqc [DEBUG ] No samples found: qualimap [2024-11-13 11:27:29,354] multiqc [DEBUG ] No samples found: preseq [2024-11-13 11:27:29,357] multiqc [DEBUG ] No samples found: quast [2024-11-13 11:27:29,360] multiqc [DEBUG ] No samples found: qorts [2024-11-13 11:27:29,363] multiqc [DEBUG ] No samples found: rna_seqc [2024-11-13 11:27:29,366] multiqc [DEBUG ] No samples found: rockhopper [2024-11-13 11:27:29,369] multiqc [DEBUG ] No samples found: rsem [2024-11-13 11:27:29,373] multiqc [DEBUG ] No samples found: rseqc [2024-11-13 11:27:29,376] multiqc [DEBUG ] No samples found: busco [2024-11-13 11:27:29,379] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-11-13 11:27:29,382] multiqc [DEBUG ] No samples found: disambiguate [2024-11-13 11:27:29,384] multiqc [DEBUG ] No samples found: supernova [2024-11-13 11:27:29,389] multiqc [DEBUG ] No samples found: deeptools [2024-11-13 11:27:29,392] multiqc [DEBUG ] No samples found: sargasso [2024-11-13 11:27:29,395] multiqc [DEBUG ] No samples found: verifybamid [2024-11-13 11:27:29,398] multiqc [DEBUG ] No samples found: mirtrace [2024-11-13 11:27:29,401] multiqc [DEBUG ] No samples found: happy [2024-11-13 11:27:29,403] multiqc [DEBUG ] No samples found: mirtop [2024-11-13 11:27:29,407] multiqc [DEBUG ] No samples found: homer [2024-11-13 11:27:29,409] multiqc [DEBUG ] No samples found: macs2 [2024-11-13 11:27:29,412] multiqc [DEBUG ] No samples found: theta2 [2024-11-13 11:27:29,415] multiqc [DEBUG ] No samples found: snpeff [2024-11-13 11:27:29,418] multiqc [DEBUG ] No samples found: gatk [2024-11-13 11:27:29,421] multiqc [DEBUG ] No samples found: htseq [2024-11-13 11:27:29,424] multiqc [DEBUG ] No samples found: bcftools [2024-11-13 11:27:29,427] multiqc [DEBUG ] No samples found: featureCounts [2024-11-13 11:27:29,431] multiqc [DEBUG ] No samples found: fgbio [2024-11-13 11:27:29,436] multiqc [DEBUG ] No samples found: dragen [2024-11-13 11:27:29,439] multiqc [DEBUG ] No samples found: dedup [2024-11-13 11:27:29,442] multiqc [DEBUG ] No samples found: damageprofiler [2024-11-13 11:27:29,449] multiqc [DEBUG ] No samples found: biobambam2 [2024-11-13 11:27:29,453] multiqc [DEBUG ] No samples found: mtnucratio [2024-11-13 11:27:29,455] multiqc [DEBUG ] No samples found: picard [2024-11-13 11:27:29,458] multiqc [DEBUG ] No samples found: prokka [2024-11-13 11:27:29,460] multiqc [DEBUG ] No samples found: samblaster [2024-11-13 11:27:29,464] multiqc [DEBUG ] No samples found: samtools [2024-11-13 11:27:29,467] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-11-13 11:27:29,470] multiqc [DEBUG ] No samples found: bamtools [2024-11-13 11:27:29,473] multiqc [DEBUG ] No samples found: jellyfish [2024-11-13 11:27:29,476] multiqc [DEBUG ] No samples found: vcftools [2024-11-13 11:27:29,479] multiqc [DEBUG ] No samples found: longranger [2024-11-13 11:27:29,482] multiqc [DEBUG ] No samples found: stacks [2024-11-13 11:27:29,484] multiqc [DEBUG ] No samples found: varscan2 [2024-11-13 11:27:29,490] multiqc [DEBUG ] No samples found: bbmap [2024-11-13 11:27:29,493] multiqc [DEBUG ] No samples found: bismark [2024-11-13 11:27:29,496] multiqc [DEBUG ] No samples found: biscuit [2024-11-13 11:27:29,498] multiqc [DEBUG ] No samples found: hicexplorer [2024-11-13 11:27:29,501] multiqc [DEBUG ] No samples found: hicup [2024-11-13 11:27:29,504] multiqc [DEBUG ] No samples found: hicpro [2024-11-13 11:27:29,507] multiqc [DEBUG ] No samples found: salmon [2024-11-13 11:27:29,510] multiqc [DEBUG ] No samples found: kallisto [2024-11-13 11:27:29,512] multiqc [DEBUG ] No samples found: slamdunk [2024-11-13 11:27:29,515] multiqc [DEBUG ] No samples found: star [2024-11-13 11:27:29,518] multiqc [DEBUG ] No samples found: hisat2 [2024-11-13 11:27:29,521] multiqc [DEBUG ] No samples found: tophat [2024-11-13 11:27:29,523] multiqc [DEBUG ] No samples found: bowtie2 [2024-11-13 11:27:29,526] multiqc [DEBUG ] No samples found: bowtie1 [2024-11-13 11:27:29,529] multiqc [DEBUG ] No samples found: snpsplit [2024-11-13 11:27:29,532] multiqc [DEBUG ] No samples found: kat [2024-11-13 11:27:29,534] multiqc [DEBUG ] No samples found: leehom [2024-11-13 11:27:29,537] multiqc [DEBUG ] No samples found: adapterRemoval [2024-11-13 11:27:29,540] multiqc [DEBUG ] No samples found: clipandmerge [2024-11-13 11:27:29,543] multiqc [DEBUG ] No samples found: cutadapt [2024-11-13 11:27:29,546] multiqc [DEBUG ] No samples found: flexbar [2024-11-13 11:27:29,548] multiqc [DEBUG ] No samples found: kaiju [2024-11-13 11:27:29,551] multiqc [DEBUG ] No samples found: kraken [2024-11-13 11:27:29,555] multiqc [DEBUG ] No samples found: malt [2024-11-13 11:27:29,557] multiqc [DEBUG ] No samples found: trimmomatic [2024-11-13 11:27:29,560] multiqc [DEBUG ] No samples found: sickle [2024-11-13 11:27:29,563] multiqc [DEBUG ] No samples found: skewer [2024-11-13 11:27:29,565] multiqc [DEBUG ] No samples found: sortmerna [2024-11-13 11:27:29,568] multiqc [DEBUG ] No samples found: biobloomtools [2024-11-13 11:27:29,571] multiqc [DEBUG ] No samples found: fastq_screen [2024-11-13 11:27:29,574] multiqc [DEBUG ] No samples found: afterqc [2024-11-13 11:27:29,577] multiqc [DEBUG ] No samples found: fastp [2024-11-13 11:27:29,591] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-11-13 11:27:29,644] multiqc [DEBUG ] No samples found: pycoqc [2024-11-13 11:27:29,647] multiqc [DEBUG ] No samples found: minionqc [2024-11-13 11:27:29,650] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-11-13 11:27:29,653] multiqc [DEBUG ] No samples found: clusterflow [2024-11-13 11:27:29,655] multiqc [DEBUG ] No samples found: bcl2fastq [2024-11-13 11:27:29,658] multiqc [DEBUG ] No samples found: interop [2024-11-13 11:27:29,661] multiqc [DEBUG ] No samples found: ivar [2024-11-13 11:27:29,664] multiqc [DEBUG ] No samples found: flash [2024-11-13 11:27:29,667] multiqc [DEBUG ] No samples found: seqyclean [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-11-13 11:27:29,667] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-11-13 11:27:29,672] multiqc [INFO ] Compressing plot data [2024-11-13 11:27:29,730] multiqc [INFO ] Report : multiqc_report.html [2024-11-13 11:27:29,730] multiqc [INFO ] Data : multiqc_data [2024-11-13 11:27:29,730] multiqc [DEBUG ] Moving data file from '/state/partition1/job-53403887/tmps6fm1fuu/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/e7/d090d521e43c2ddc0260d39d8b4402/1/multiqc_data' [2024-11-13 11:27:29,824] multiqc [INFO ] MultiQC complete