[2025-01-06 18:58:35,786] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-06 18:58:35,786] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-06 18:58:35,786] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-06 18:58:35,789] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-06 18:58:35,789] 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}} [2025-01-06 18:58:35,789] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-06 18:58:35,820] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-06 18:58:35,821] multiqc [INFO ] This is MultiQC v1.9 [2025-01-06 18:58:35,821] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-06 18:58:35,821] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/5f/bcde37364857bbba559aadfb15cf9b/merged [2025-01-06 18:58:35,821] multiqc [INFO ] Template : default [2025-01-06 18:58:35,821] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-06 18:58:35,821] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/5f/bcde37364857bbba559aadfb15cf9b/merged [2025-01-06 18:58:35,821] 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 [2025-01-06 18:58:35,821] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55617279/tmp225cexuu [2025-01-06 18:58:35,937] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNC3VDRX5_2_fastqc.html [2025-01-06 18:58:35,940] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNC3VDRX5_2_fastqc.html [2025-01-06 18:58:35,989] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNC3VDRX5_3_fastqc.html [2025-01-06 18:58:35,991] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNC3VDRX5_3_fastqc.html [2025-01-06 18:58:36,055] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNC3VDRX5_1_fastqc.html [2025-01-06 18:58:36,057] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNC3VDRX5_1_fastqc.html [2025-01-06 18:58:36,582] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-06 18:58:36,586] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-06 18:58:36,592] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-06 18:58:36,598] multiqc [DEBUG ] No samples found: conpair [2025-01-06 18:58:36,605] multiqc [DEBUG ] No samples found: peddy [2025-01-06 18:58:36,611] multiqc [DEBUG ] No samples found: somalier [2025-01-06 18:58:36,618] multiqc [DEBUG ] No samples found: methylQA [2025-01-06 18:58:36,629] multiqc [DEBUG ] No samples found: mosdepth [2025-01-06 18:58:36,635] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-06 18:58:36,639] multiqc [DEBUG ] No samples found: qualimap [2025-01-06 18:58:36,646] multiqc [DEBUG ] No samples found: preseq [2025-01-06 18:58:36,652] multiqc [DEBUG ] No samples found: quast [2025-01-06 18:58:36,659] multiqc [DEBUG ] No samples found: qorts [2025-01-06 18:58:36,665] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-06 18:58:36,671] multiqc [DEBUG ] No samples found: rockhopper [2025-01-06 18:58:36,678] multiqc [DEBUG ] No samples found: rsem [2025-01-06 18:58:36,692] multiqc [DEBUG ] No samples found: rseqc [2025-01-06 18:58:36,698] multiqc [DEBUG ] No samples found: busco [2025-01-06 18:58:36,704] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-06 18:58:36,710] multiqc [DEBUG ] No samples found: disambiguate [2025-01-06 18:58:36,717] multiqc [DEBUG ] No samples found: supernova [2025-01-06 18:58:36,735] multiqc [DEBUG ] No samples found: deeptools [2025-01-06 18:58:36,741] multiqc [DEBUG ] No samples found: sargasso [2025-01-06 18:58:36,747] multiqc [DEBUG ] No samples found: verifybamid [2025-01-06 18:58:36,754] multiqc [DEBUG ] No samples found: mirtrace [2025-01-06 18:58:36,760] multiqc [DEBUG ] No samples found: happy [2025-01-06 18:58:36,766] multiqc [DEBUG ] No samples found: mirtop [2025-01-06 18:58:36,775] multiqc [DEBUG ] No samples found: homer [2025-01-06 18:58:36,781] multiqc [DEBUG ] No samples found: macs2 [2025-01-06 18:58:36,787] multiqc [DEBUG ] No samples found: theta2 [2025-01-06 18:58:36,794] multiqc [DEBUG ] No samples found: snpeff [2025-01-06 18:58:36,802] multiqc [DEBUG ] No samples found: gatk [2025-01-06 18:58:36,808] multiqc [DEBUG ] No samples found: htseq [2025-01-06 18:58:36,816] multiqc [DEBUG ] No samples found: bcftools [2025-01-06 18:58:36,822] multiqc [DEBUG ] No samples found: featureCounts [2025-01-06 18:58:36,830] multiqc [DEBUG ] No samples found: fgbio [2025-01-06 18:58:36,846] multiqc [DEBUG ] No samples found: dragen [2025-01-06 18:58:36,852] multiqc [DEBUG ] No samples found: dedup [2025-01-06 18:58:36,859] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-06 18:58:36,887] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-06 18:58:36,894] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-06 18:58:36,896] multiqc [DEBUG ] No samples found: picard [2025-01-06 18:58:36,902] multiqc [DEBUG ] No samples found: prokka [2025-01-06 18:58:36,908] multiqc [DEBUG ] No samples found: samblaster [2025-01-06 18:58:36,918] multiqc [DEBUG ] No samples found: samtools [2025-01-06 18:58:36,925] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-06 18:58:36,932] multiqc [DEBUG ] No samples found: bamtools [2025-01-06 18:58:36,937] multiqc [DEBUG ] No samples found: jellyfish [2025-01-06 18:58:36,947] multiqc [DEBUG ] No samples found: vcftools [2025-01-06 18:58:36,954] multiqc [DEBUG ] No samples found: longranger [2025-01-06 18:58:36,960] multiqc [DEBUG ] No samples found: stacks [2025-01-06 18:58:36,967] multiqc [DEBUG ] No samples found: varscan2 [2025-01-06 18:58:36,985] multiqc [DEBUG ] No samples found: bbmap [2025-01-06 18:58:36,991] multiqc [DEBUG ] No samples found: bismark [2025-01-06 18:58:36,998] multiqc [DEBUG ] No samples found: biscuit [2025-01-06 18:58:37,005] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-06 18:58:37,011] multiqc [DEBUG ] No samples found: hicup [2025-01-06 18:58:37,017] multiqc [DEBUG ] No samples found: hicpro [2025-01-06 18:58:37,023] multiqc [DEBUG ] No samples found: salmon [2025-01-06 18:58:37,029] multiqc [DEBUG ] No samples found: kallisto [2025-01-06 18:58:37,036] multiqc [DEBUG ] No samples found: slamdunk [2025-01-06 18:58:37,041] multiqc [DEBUG ] No samples found: star [2025-01-06 18:58:37,047] multiqc [DEBUG ] No samples found: hisat2 [2025-01-06 18:58:37,053] multiqc [DEBUG ] No samples found: tophat [2025-01-06 18:58:37,059] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-06 18:58:37,065] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-06 18:58:37,071] multiqc [DEBUG ] No samples found: snpsplit [2025-01-06 18:58:37,077] multiqc [DEBUG ] No samples found: kat [2025-01-06 18:58:37,082] multiqc [DEBUG ] No samples found: leehom [2025-01-06 18:58:37,089] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-06 18:58:37,095] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-06 18:58:37,100] multiqc [DEBUG ] No samples found: cutadapt [2025-01-06 18:58:37,106] multiqc [DEBUG ] No samples found: flexbar [2025-01-06 18:58:37,112] multiqc [DEBUG ] No samples found: kaiju [2025-01-06 18:58:37,118] multiqc [DEBUG ] No samples found: kraken [2025-01-06 18:58:37,124] multiqc [DEBUG ] No samples found: malt [2025-01-06 18:58:37,130] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-06 18:58:37,136] multiqc [DEBUG ] No samples found: sickle [2025-01-06 18:58:37,142] multiqc [DEBUG ] No samples found: skewer [2025-01-06 18:58:37,147] multiqc [DEBUG ] No samples found: sortmerna [2025-01-06 18:58:37,153] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-06 18:58:37,159] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-06 18:58:37,165] multiqc [DEBUG ] No samples found: afterqc [2025-01-06 18:58:37,171] multiqc [DEBUG ] No samples found: fastp [2025-01-06 18:58:37,301] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2025-01-06 18:58:37,358] multiqc [DEBUG ] No samples found: pycoqc [2025-01-06 18:58:37,364] multiqc [DEBUG ] No samples found: minionqc [2025-01-06 18:58:37,370] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-06 18:58:37,377] multiqc [DEBUG ] No samples found: clusterflow [2025-01-06 18:58:37,383] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-06 18:58:37,390] multiqc [DEBUG ] No samples found: interop [2025-01-06 18:58:37,396] multiqc [DEBUG ] No samples found: ivar [2025-01-06 18:58:37,401] multiqc [DEBUG ] No samples found: flash [2025-01-06 18:58:37,407] multiqc [DEBUG ] No samples found: seqyclean [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-06 18:58:37,407] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-06 18:58:37,408] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-06 18:58:37,412] multiqc [INFO ] Compressing plot data [2025-01-06 18:58:37,470] multiqc [INFO ] Report : multiqc_report.html [2025-01-06 18:58:37,470] multiqc [INFO ] Data : multiqc_data [2025-01-06 18:58:37,470] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55617279/tmp225cexuu/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/5f/bcde37364857bbba559aadfb15cf9b/merged/multiqc_data' [2025-01-06 18:58:37,607] multiqc [INFO ] MultiQC complete