[2024-12-22 15:48:14,181] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-22 15:48:14,181] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-22 15:48:14,181] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-22 15:48:14,183] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-22 15:48:14,183] 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}} [2024-12-22 15:48:14,183] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-22 15:48:14,221] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-22 15:48:14,221] multiqc [INFO ] This is MultiQC v1.9 [2024-12-22 15:48:14,221] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-22 15:48:14,221] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/d3/e95967b0c661b84efb93c881db1784/merged [2024-12-22 15:48:14,221] multiqc [INFO ] Template : default [2024-12-22 15:48:14,221] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-22 15:48:14,221] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/d3/e95967b0c661b84efb93c881db1784/merged [2024-12-22 15:48:14,221] 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 [2024-12-22 15:48:14,221] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55277614/tmp1cf08ukw [2024-12-22 15:48:14,335] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-22 15:48:14,338] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-22 15:48:14,397] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN77LDRX5_n02_SC_15_fastqc.html [2024-12-22 15:48:14,398] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN77LDRX5_n02_SC_15_fastqc.html [2024-12-22 15:48:14,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN77LDRX5_n02_SC_17_fastqc.html [2024-12-22 15:48:14,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN77LDRX5_n02_SC_17_fastqc.html [2024-12-22 15:48:14,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN77LDRX5_n01_undetermined_fastqc.html [2024-12-22 15:48:14,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN77LDRX5_n01_undetermined_fastqc.html [2024-12-22 15:48:14,546] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN77LDRX5_n01_SC_15_fastqc.html [2024-12-22 15:48:14,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN77LDRX5_n01_SC_15_fastqc.html [2024-12-22 15:48:14,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN77LDRX5_n01_SC_17_fastqc.html [2024-12-22 15:48:14,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN77LDRX5_n01_SC_17_fastqc.html [2024-12-22 15:48:14,653] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN77LDRX5_n02_undetermined_fastqc.html [2024-12-22 15:48:14,655] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN77LDRX5_n02_undetermined_fastqc.html [2024-12-22 15:48:15,211] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-22 15:48:15,213] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-22 15:48:15,222] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2024-12-22 15:48:15,232] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-22 15:48:15,233] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-22 15:48:15,239] multiqc [DEBUG ] No samples found: conpair [2024-12-22 15:48:15,245] multiqc [DEBUG ] No samples found: peddy [2024-12-22 15:48:15,250] multiqc [DEBUG ] No samples found: somalier [2024-12-22 15:48:15,256] multiqc [DEBUG ] No samples found: methylQA [2024-12-22 15:48:15,266] multiqc [DEBUG ] No samples found: mosdepth [2024-12-22 15:48:15,271] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-22 15:48:15,275] multiqc [DEBUG ] No samples found: qualimap [2024-12-22 15:48:15,281] multiqc [DEBUG ] No samples found: preseq [2024-12-22 15:48:15,287] multiqc [DEBUG ] No samples found: quast [2024-12-22 15:48:15,293] multiqc [DEBUG ] No samples found: qorts [2024-12-22 15:48:15,299] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-22 15:48:15,304] multiqc [DEBUG ] No samples found: rockhopper [2024-12-22 15:48:15,310] multiqc [DEBUG ] No samples found: rsem [2024-12-22 15:48:15,325] multiqc [DEBUG ] No samples found: rseqc [2024-12-22 15:48:15,330] multiqc [DEBUG ] No samples found: busco [2024-12-22 15:48:15,337] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-22 15:48:15,342] multiqc [DEBUG ] No samples found: disambiguate [2024-12-22 15:48:15,348] multiqc [DEBUG ] No samples found: supernova [2024-12-22 15:48:15,366] multiqc [DEBUG ] No samples found: deeptools [2024-12-22 15:48:15,371] multiqc [DEBUG ] No samples found: sargasso [2024-12-22 15:48:15,377] multiqc [DEBUG ] No samples found: verifybamid [2024-12-22 15:48:15,383] multiqc [DEBUG ] No samples found: mirtrace [2024-12-22 15:48:15,388] multiqc [DEBUG ] No samples found: happy [2024-12-22 15:48:15,394] multiqc [DEBUG ] No samples found: mirtop [2024-12-22 15:48:15,402] multiqc [DEBUG ] No samples found: homer [2024-12-22 15:48:15,408] multiqc [DEBUG ] No samples found: macs2 [2024-12-22 15:48:15,413] multiqc [DEBUG ] No samples found: theta2 [2024-12-22 15:48:15,419] multiqc [DEBUG ] No samples found: snpeff [2024-12-22 15:48:15,428] multiqc [DEBUG ] No samples found: gatk [2024-12-22 15:48:15,434] multiqc [DEBUG ] No samples found: htseq [2024-12-22 15:48:15,440] multiqc [DEBUG ] No samples found: bcftools [2024-12-22 15:48:15,446] multiqc [DEBUG ] No samples found: featureCounts [2024-12-22 15:48:15,454] multiqc [DEBUG ] No samples found: fgbio [2024-12-22 15:48:15,470] multiqc [DEBUG ] No samples found: dragen [2024-12-22 15:48:15,476] multiqc [DEBUG ] No samples found: dedup [2024-12-22 15:48:15,481] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-22 15:48:15,510] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-22 15:48:15,515] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-22 15:48:15,517] multiqc [DEBUG ] No samples found: picard [2024-12-22 15:48:15,523] multiqc [DEBUG ] No samples found: prokka [2024-12-22 15:48:15,528] multiqc [DEBUG ] No samples found: samblaster [2024-12-22 15:48:15,538] multiqc [DEBUG ] No samples found: samtools [2024-12-22 15:48:15,544] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-22 15:48:15,549] multiqc [DEBUG ] No samples found: bamtools [2024-12-22 15:48:15,554] multiqc [DEBUG ] No samples found: jellyfish [2024-12-22 15:48:15,563] multiqc [DEBUG ] No samples found: vcftools [2024-12-22 15:48:15,568] multiqc [DEBUG ] No samples found: longranger [2024-12-22 15:48:15,574] multiqc [DEBUG ] No samples found: stacks [2024-12-22 15:48:15,579] multiqc [DEBUG ] No samples found: varscan2 [2024-12-22 15:48:15,596] multiqc [DEBUG ] No samples found: bbmap [2024-12-22 15:48:15,602] multiqc [DEBUG ] No samples found: bismark [2024-12-22 15:48:15,608] multiqc [DEBUG ] No samples found: biscuit [2024-12-22 15:48:15,614] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-22 15:48:15,619] multiqc [DEBUG ] No samples found: hicup [2024-12-22 15:48:15,625] multiqc [DEBUG ] No samples found: hicpro [2024-12-22 15:48:15,630] multiqc [DEBUG ] No samples found: salmon [2024-12-22 15:48:15,636] multiqc [DEBUG ] No samples found: kallisto [2024-12-22 15:48:15,644] multiqc [DEBUG ] No samples found: slamdunk [2024-12-22 15:48:15,649] multiqc [DEBUG ] No samples found: star [2024-12-22 15:48:15,654] multiqc [DEBUG ] No samples found: hisat2 [2024-12-22 15:48:15,660] multiqc [DEBUG ] No samples found: tophat [2024-12-22 15:48:15,665] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-22 15:48:15,671] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-22 15:48:15,676] multiqc [DEBUG ] No samples found: snpsplit [2024-12-22 15:48:15,681] multiqc [DEBUG ] No samples found: kat [2024-12-22 15:48:15,686] multiqc [DEBUG ] No samples found: leehom [2024-12-22 15:48:15,692] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-22 15:48:15,697] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-22 15:48:15,702] multiqc [DEBUG ] No samples found: cutadapt [2024-12-22 15:48:15,707] multiqc [DEBUG ] No samples found: flexbar [2024-12-22 15:48:15,712] multiqc [DEBUG ] No samples found: kaiju [2024-12-22 15:48:15,718] multiqc [DEBUG ] No samples found: kraken [2024-12-22 15:48:15,723] multiqc [DEBUG ] No samples found: malt [2024-12-22 15:48:15,729] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-22 15:48:15,734] multiqc [DEBUG ] No samples found: sickle [2024-12-22 15:48:15,739] multiqc [DEBUG ] No samples found: skewer [2024-12-22 15:48:15,744] multiqc [DEBUG ] No samples found: sortmerna [2024-12-22 15:48:15,749] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-22 15:48:15,755] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-22 15:48:15,760] multiqc [DEBUG ] No samples found: afterqc [2024-12-22 15:48:15,766] multiqc [DEBUG ] No samples found: fastp [2024-12-22 15:48:16,144] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2024-12-22 15:48:16,253] multiqc [DEBUG ] No samples found: pycoqc [2024-12-22 15:48:16,258] multiqc [DEBUG ] No samples found: minionqc [2024-12-22 15:48:16,263] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-22 15:48:16,269] multiqc [DEBUG ] No samples found: clusterflow [2024-12-22 15:48:16,274] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-22 15:48:16,280] multiqc [DEBUG ] No samples found: interop [2024-12-22 15:48:16,285] multiqc [DEBUG ] No samples found: ivar [2024-12-22 15:48:16,291] multiqc [DEBUG ] No samples found: flash [2024-12-22 15:48:16,296] multiqc [DEBUG ] No samples found: seqyclean [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-22 15:48:16,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-22 15:48:16,297] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-22 15:48:16,305] multiqc [INFO ] Compressing plot data [2024-12-22 15:48:16,424] multiqc [INFO ] Report : multiqc_report.html [2024-12-22 15:48:16,425] multiqc [INFO ] Data : multiqc_data [2024-12-22 15:48:16,425] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55277614/tmp1cf08ukw/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/d3/e95967b0c661b84efb93c881db1784/merged/multiqc_data' [2024-12-22 15:48:16,560] multiqc [INFO ] MultiQC complete