[2025-01-08 23:29:47,616] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-08 23:29:47,616] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-08 23:29:47,616] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-08 23:29:47,618] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-08 23:29:47,619] 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}} [2025-01-08 23:29:47,619] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-08 23:29:47,649] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-08 23:29:47,649] multiqc [INFO ] This is MultiQC v1.9 [2025-01-08 23:29:47,649] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-08 23:29:47,649] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/34/916994ab9836f30749d0be4b0346c2/merged [2025-01-08 23:29:47,649] multiqc [INFO ] Template : default [2025-01-08 23:29:47,649] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-08 23:29:47,649] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/34/916994ab9836f30749d0be4b0346c2/merged [2025-01-08 23:29:47,650] 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 [2025-01-08 23:29:47,650] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55707482/tmpsylm6r4z [2025-01-08 23:29:47,775] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_HW40_1_fastqc.html [2025-01-08 23:29:47,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_HW40_1_fastqc.html [2025-01-08 23:29:47,840] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 23:29:47,842] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 23:29:47,969] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO151_fastqc.html [2025-01-08 23:29:47,971] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO151_fastqc.html [2025-01-08 23:29:48,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO162_fastqc.html [2025-01-08 23:29:48,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO162_fastqc.html [2025-01-08 23:29:48,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR20_fastqc.html [2025-01-08 23:29:48,077] 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pattern filesize limit: HHJ73BGYW_n01_DO157_fastqc.html [2025-01-08 23:29:48,555] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR21_fastqc.html [2025-01-08 23:29:48,557] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR21_fastqc.html [2025-01-08 23:29:48,619] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR18_fastqc.html [2025-01-08 23:29:48,621] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR18_fastqc.html [2025-01-08 23:29:48,684] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO152_fastqc.html [2025-01-08 23:29:48,686] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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[2025-01-08 23:29:48,954] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_HW38_1_fastqc.html [2025-01-08 23:29:48,956] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_HW38_1_fastqc.html [2025-01-08 23:29:49,012] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO155_fastqc.html [2025-01-08 23:29:49,014] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO155_fastqc.html [2025-01-08 23:29:49,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO156_fastqc.html [2025-01-08 23:29:49,066] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO156_fastqc.html [2025-01-08 23:29:49,125] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR17_fastqc.html [2025-01-08 23:29:49,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR17_fastqc.html [2025-01-08 23:29:49,180] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR19_fastqc.html [2025-01-08 23:29:49,182] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DR19_fastqc.html [2025-01-08 23:29:49,265] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO153_fastqc.html [2025-01-08 23:29:49,267] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJ73BGYW_n01_DO153_fastqc.html [2025-01-08 23:29:49,765] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-08 23:29:49,767] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-08 23:29:49,784] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 22 samples (table) [2025-01-08 23:29:49,786] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-08 23:29:49,796] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-08 23:29:49,801] multiqc [DEBUG ] No samples found: conpair [2025-01-08 23:29:49,806] multiqc [DEBUG ] No samples found: peddy [2025-01-08 23:29:49,814] multiqc [DEBUG ] No samples found: somalier [2025-01-08 23:29:49,818] multiqc [DEBUG ] No samples found: methylQA [2025-01-08 23:29:49,826] multiqc [DEBUG ] No samples found: mosdepth [2025-01-08 23:29:49,830] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-08 23:29:49,833] multiqc [DEBUG ] No samples found: qualimap [2025-01-08 23:29:49,838] multiqc [DEBUG ] No samples found: preseq [2025-01-08 23:29:49,842] multiqc [DEBUG ] No samples found: quast [2025-01-08 23:29:49,847] multiqc [DEBUG ] No samples found: qorts [2025-01-08 23:29:49,851] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-08 23:29:49,856] multiqc [DEBUG ] No samples found: rockhopper [2025-01-08 23:29:49,860] multiqc [DEBUG ] No samples found: rsem [2025-01-08 23:29:49,872] multiqc [DEBUG ] No samples found: rseqc [2025-01-08 23:29:49,876] multiqc [DEBUG ] No samples found: busco [2025-01-08 23:29:49,881] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-08 23:29:49,885] multiqc [DEBUG ] No samples found: disambiguate [2025-01-08 23:29:49,890] multiqc [DEBUG ] No samples found: supernova [2025-01-08 23:29:49,902] multiqc [DEBUG ] No samples found: deeptools [2025-01-08 23:29:49,907] multiqc [DEBUG ] No samples found: sargasso [2025-01-08 23:29:49,911] multiqc [DEBUG ] No samples found: verifybamid [2025-01-08 23:29:49,916] multiqc [DEBUG ] No samples found: mirtrace [2025-01-08 23:29:49,920] multiqc [DEBUG ] No samples found: happy [2025-01-08 23:29:49,925] multiqc [DEBUG ] No samples found: mirtop [2025-01-08 23:29:49,931] multiqc [DEBUG ] No samples found: homer [2025-01-08 23:29:49,935] multiqc [DEBUG ] No samples found: macs2 [2025-01-08 23:29:49,939] multiqc [DEBUG ] No samples found: theta2 [2025-01-08 23:29:49,944] multiqc [DEBUG ] No samples found: snpeff [2025-01-08 23:29:49,950] multiqc [DEBUG ] No samples found: gatk [2025-01-08 23:29:49,954] multiqc [DEBUG ] No samples found: htseq [2025-01-08 23:29:49,959] multiqc [DEBUG ] No samples found: bcftools [2025-01-08 23:29:49,963] multiqc [DEBUG ] No samples found: featureCounts [2025-01-08 23:29:49,969] multiqc [DEBUG ] No samples found: fgbio [2025-01-08 23:29:49,981] multiqc [DEBUG ] No samples found: dragen [2025-01-08 23:29:49,986] multiqc [DEBUG ] No samples found: dedup [2025-01-08 23:29:49,990] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-08 23:29:50,011] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-08 23:29:50,015] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-08 23:29:50,017] multiqc [DEBUG ] No samples found: picard [2025-01-08 23:29:50,022] multiqc [DEBUG ] No samples found: prokka [2025-01-08 23:29:50,026] multiqc [DEBUG ] No samples found: samblaster [2025-01-08 23:29:50,035] multiqc [DEBUG ] No samples found: samtools [2025-01-08 23:29:50,040] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-08 23:29:50,045] multiqc [DEBUG ] No samples found: bamtools [2025-01-08 23:29:50,049] multiqc [DEBUG ] No samples found: jellyfish [2025-01-08 23:29:50,059] multiqc [DEBUG ] No samples found: vcftools [2025-01-08 23:29:50,064] multiqc [DEBUG ] No samples found: longranger [2025-01-08 23:29:50,068] multiqc [DEBUG ] No samples found: stacks [2025-01-08 23:29:50,074] multiqc [DEBUG ] No samples found: varscan2 [2025-01-08 23:29:50,087] multiqc [DEBUG ] No samples found: bbmap [2025-01-08 23:29:50,092] multiqc [DEBUG ] No samples found: bismark [2025-01-08 23:29:50,097] multiqc [DEBUG ] No samples found: biscuit [2025-01-08 23:29:50,102] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-08 23:29:50,106] multiqc [DEBUG ] No samples found: hicup [2025-01-08 23:29:50,111] multiqc [DEBUG ] No samples found: hicpro [2025-01-08 23:29:50,115] multiqc [DEBUG ] No samples found: salmon [2025-01-08 23:29:50,119] multiqc [DEBUG ] No samples found: kallisto [2025-01-08 23:29:50,124] multiqc [DEBUG ] No samples found: slamdunk [2025-01-08 23:29:50,128] multiqc [DEBUG ] No samples found: star [2025-01-08 23:29:50,133] multiqc [DEBUG ] No samples found: hisat2 [2025-01-08 23:29:50,137] multiqc [DEBUG ] No samples found: tophat [2025-01-08 23:29:50,142] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-08 23:29:50,146] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-08 23:29:50,150] multiqc [DEBUG ] No samples found: snpsplit [2025-01-08 23:29:50,154] multiqc [DEBUG ] No samples found: kat [2025-01-08 23:29:50,159] multiqc [DEBUG ] No samples found: leehom [2025-01-08 23:29:50,163] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-08 23:29:50,168] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-08 23:29:50,172] multiqc [DEBUG ] No samples found: cutadapt [2025-01-08 23:29:50,176] multiqc [DEBUG ] No samples found: flexbar [2025-01-08 23:29:50,180] multiqc [DEBUG ] No samples found: kaiju [2025-01-08 23:29:50,185] multiqc [DEBUG ] No samples found: kraken [2025-01-08 23:29:50,189] multiqc [DEBUG ] No samples found: malt [2025-01-08 23:29:50,194] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-08 23:29:50,198] multiqc [DEBUG ] No samples found: sickle [2025-01-08 23:29:50,202] multiqc [DEBUG ] No samples found: skewer [2025-01-08 23:29:50,207] multiqc [DEBUG ] No samples found: sortmerna [2025-01-08 23:29:50,211] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-08 23:29:50,215] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-08 23:29:50,220] multiqc [DEBUG ] No samples found: afterqc [2025-01-08 23:29:50,224] multiqc [DEBUG ] No samples found: fastp [2025-01-08 23:29:52,431] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2025-01-08 23:29:52,929] multiqc [DEBUG ] No samples found: pycoqc [2025-01-08 23:29:52,934] multiqc [DEBUG ] No samples found: minionqc [2025-01-08 23:29:52,938] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-08 23:29:52,943] multiqc [DEBUG ] No samples found: clusterflow [2025-01-08 23:29:52,947] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-08 23:29:52,951] multiqc [DEBUG ] No samples found: interop [2025-01-08 23:29:52,956] multiqc [DEBUG ] No samples found: ivar [2025-01-08 23:29:52,960] multiqc [DEBUG ] No samples found: flash [2025-01-08 23:29:52,964] multiqc [DEBUG ] No samples found: seqyclean [2025-01-08 23:29:52,964] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-08 23:29:52,965] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-08 23:29:52,993] multiqc [INFO ] Compressing plot data [2025-01-08 23:29:53,427] multiqc [INFO ] Report : multiqc_report.html [2025-01-08 23:29:53,427] multiqc [INFO ] Data : multiqc_data [2025-01-08 23:29:53,427] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55707482/tmpsylm6r4z/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/34/916994ab9836f30749d0be4b0346c2/merged/multiqc_data' [2025-01-08 23:29:53,565] multiqc [INFO ] MultiQC complete