[2024-08-08 20:29:32,681] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-08 20:29:32,681] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-08 20:29:32,681] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-08 20:29:32,684] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-08 20:29:32,684] 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}} [2024-08-08 20:29:32,684] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-08 20:29:32,721] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-08 20:29:32,721] multiqc [INFO ] This is MultiQC v1.9 [2024-08-08 20:29:32,721] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-08 20:29:32,722] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/7e/22b999738ecb545e874d3cf52d8221/merged [2024-08-08 20:29:32,722] multiqc [INFO ] Template : default [2024-08-08 20:29:32,722] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-08 20:29:32,722] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/7e/22b999738ecb545e874d3cf52d8221/merged [2024-08-08 20:29:32,722] 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 [2024-08-08 20:29:32,722] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49555728/tmplg9vfqrr [2024-08-08 20:29:32,859] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFTWNDRX5_3_fastqc.html [2024-08-08 20:29:32,864] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFTWNDRX5_3_fastqc.html [2024-08-08 20:29:32,915] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFTWNDRX5_2_fastqc.html [2024-08-08 20:29:32,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFTWNDRX5_2_fastqc.html [2024-08-08 20:29:32,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFTWNDRX5_1_fastqc.html [2024-08-08 20:29:32,969] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFTWNDRX5_1_fastqc.html [2024-08-08 20:29:33,571] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-08 20:29:33,574] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-08 20:29:33,581] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-08 20:29:33,589] multiqc [DEBUG ] No samples found: conpair [2024-08-08 20:29:33,597] multiqc [DEBUG ] No samples found: peddy [2024-08-08 20:29:33,605] multiqc [DEBUG ] No samples found: somalier [2024-08-08 20:29:33,613] multiqc [DEBUG ] No samples found: methylQA [2024-08-08 20:29:33,627] multiqc [DEBUG ] No samples found: mosdepth [2024-08-08 20:29:33,635] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-08 20:29:33,639] multiqc [DEBUG ] No samples found: qualimap [2024-08-08 20:29:33,646] multiqc [DEBUG ] No samples found: preseq [2024-08-08 20:29:33,653] multiqc [DEBUG ] No samples found: quast [2024-08-08 20:29:33,661] multiqc [DEBUG ] No samples found: qorts [2024-08-08 20:29:33,669] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-08 20:29:33,676] multiqc [DEBUG ] No samples found: rockhopper [2024-08-08 20:29:33,685] multiqc [DEBUG ] No samples found: rsem [2024-08-08 20:29:33,705] multiqc [DEBUG ] No samples found: rseqc [2024-08-08 20:29:33,712] multiqc [DEBUG ] No samples found: busco [2024-08-08 20:29:33,719] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-08 20:29:33,726] multiqc [DEBUG ] No samples found: disambiguate [2024-08-08 20:29:33,733] multiqc [DEBUG ] No samples found: supernova [2024-08-08 20:29:33,753] multiqc [DEBUG ] No samples found: deeptools [2024-08-08 20:29:33,760] multiqc [DEBUG ] No samples found: sargasso [2024-08-08 20:29:33,767] multiqc [DEBUG ] No samples found: verifybamid [2024-08-08 20:29:33,774] multiqc [DEBUG ] No samples found: mirtrace [2024-08-08 20:29:33,781] multiqc [DEBUG ] No samples found: happy [2024-08-08 20:29:33,788] multiqc [DEBUG ] No samples found: mirtop [2024-08-08 20:29:33,797] multiqc [DEBUG ] No samples found: homer [2024-08-08 20:29:33,804] multiqc [DEBUG ] No samples found: macs2 [2024-08-08 20:29:33,811] multiqc [DEBUG ] No samples found: theta2 [2024-08-08 20:29:33,818] multiqc [DEBUG ] No samples found: snpeff [2024-08-08 20:29:33,828] multiqc [DEBUG ] No samples found: gatk [2024-08-08 20:29:33,835] multiqc [DEBUG ] No samples found: htseq [2024-08-08 20:29:33,842] multiqc [DEBUG ] No samples found: bcftools [2024-08-08 20:29:33,849] multiqc [DEBUG ] No samples found: featureCounts [2024-08-08 20:29:33,859] multiqc [DEBUG ] No samples found: fgbio [2024-08-08 20:29:33,879] multiqc [DEBUG ] No samples found: dragen [2024-08-08 20:29:33,886] multiqc [DEBUG ] No samples found: dedup [2024-08-08 20:29:33,893] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-08 20:29:33,933] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-08 20:29:33,941] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-08 20:29:33,943] multiqc [DEBUG ] No samples found: picard [2024-08-08 20:29:33,950] multiqc [DEBUG ] No samples found: prokka [2024-08-08 20:29:33,958] multiqc [DEBUG ] No samples found: samblaster [2024-08-08 20:29:33,975] multiqc [DEBUG ] No samples found: samtools [2024-08-08 20:29:33,983] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-08 20:29:33,992] multiqc [DEBUG ] No samples found: bamtools [2024-08-08 20:29:33,999] multiqc [DEBUG ] No samples found: jellyfish [2024-08-08 20:29:34,011] multiqc [DEBUG ] No samples found: vcftools [2024-08-08 20:29:34,019] multiqc [DEBUG ] No samples found: longranger [2024-08-08 20:29:34,026] multiqc [DEBUG ] No samples found: stacks [2024-08-08 20:29:34,033] multiqc [DEBUG ] No samples found: varscan2 [2024-08-08 20:29:34,055] multiqc [DEBUG ] No samples found: bbmap [2024-08-08 20:29:34,061] multiqc [DEBUG ] No samples found: bismark [2024-08-08 20:29:34,069] multiqc [DEBUG ] No samples found: biscuit [2024-08-08 20:29:34,076] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-08 20:29:34,084] multiqc [DEBUG ] No samples found: hicup [2024-08-08 20:29:34,090] multiqc [DEBUG ] No samples found: hicpro [2024-08-08 20:29:34,097] multiqc [DEBUG ] No samples found: salmon [2024-08-08 20:29:34,104] multiqc [DEBUG ] No samples found: kallisto [2024-08-08 20:29:34,111] multiqc [DEBUG ] No samples found: slamdunk [2024-08-08 20:29:34,117] multiqc [DEBUG ] No samples found: star [2024-08-08 20:29:34,124] multiqc [DEBUG ] No samples found: hisat2 [2024-08-08 20:29:34,130] multiqc [DEBUG ] No samples found: tophat [2024-08-08 20:29:34,136] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-08 20:29:34,143] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-08 20:29:34,149] multiqc [DEBUG ] No samples found: snpsplit [2024-08-08 20:29:34,156] multiqc [DEBUG ] No samples found: kat [2024-08-08 20:29:34,162] multiqc [DEBUG ] No samples found: leehom [2024-08-08 20:29:34,169] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-08 20:29:34,175] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-08 20:29:34,181] multiqc [DEBUG ] No samples found: cutadapt [2024-08-08 20:29:34,188] multiqc [DEBUG ] No samples found: flexbar [2024-08-08 20:29:34,194] multiqc [DEBUG ] No samples found: kaiju [2024-08-08 20:29:34,200] multiqc [DEBUG ] No samples found: kraken [2024-08-08 20:29:34,206] multiqc [DEBUG ] No samples found: malt [2024-08-08 20:29:34,212] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-08 20:29:34,218] multiqc [DEBUG ] No samples found: sickle [2024-08-08 20:29:34,224] multiqc [DEBUG ] No samples found: skewer [2024-08-08 20:29:34,229] multiqc [DEBUG ] No samples found: sortmerna [2024-08-08 20:29:34,235] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-08 20:29:34,241] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-08 20:29:34,247] multiqc [DEBUG ] No samples found: afterqc [2024-08-08 20:29:34,253] multiqc [DEBUG ] No samples found: fastp [2024-08-08 20:29:34,318] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-08-08 20:29:34,382] multiqc [DEBUG ] No samples found: pycoqc [2024-08-08 20:29:34,389] multiqc [DEBUG ] No samples found: minionqc [2024-08-08 20:29:34,400] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-08 20:29:34,412] multiqc [DEBUG ] No samples found: clusterflow [2024-08-08 20:29:34,418] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-08 20:29:34,425] multiqc [DEBUG ] No samples found: interop [2024-08-08 20:29:34,431] multiqc [DEBUG ] No samples found: ivar [2024-08-08 20:29:34,437] multiqc [DEBUG ] No samples found: flash [2024-08-08 20:29:34,443] multiqc [DEBUG ] No samples found: seqyclean [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-08 20:29:34,443] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-08 20:29:34,448] multiqc [INFO ] Compressing plot data [2024-08-08 20:29:34,509] multiqc [INFO ] Report : multiqc_report.html [2024-08-08 20:29:34,509] multiqc [INFO ] Data : multiqc_data [2024-08-08 20:29:34,509] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49555728/tmplg9vfqrr/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/7e/22b999738ecb545e874d3cf52d8221/merged/multiqc_data' [2024-08-08 20:29:34,691] multiqc [INFO ] MultiQC complete