[2025-02-19 18:33:10,256] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-02-19 18:33:10,256] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-02-19 18:33:10,256] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-02-19 18:33:10,258] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-02-19 18:33:10,258] 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}} [2025-02-19 18:33:10,258] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-19 18:33:10,292] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-02-19 18:33:10,292] multiqc [INFO ] This is MultiQC v1.9 [2025-02-19 18:33:10,292] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-19 18:33:10,292] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/a6/a99320b19f3cdb878d9d8be6141ca1/1 [2025-02-19 18:33:10,292] multiqc [INFO ] Template : default [2025-02-19 18:33:10,292] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-02-19 18:33:10,292] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/a6/a99320b19f3cdb878d9d8be6141ca1/1 [2025-02-19 18:33:10,293] 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 [2025-02-19 18:33:10,293] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-57429214/tmpgjycjjac [2025-02-19 18:33:10,401] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.1_fastqc.html [2025-02-19 18:33:10,404] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.1_fastqc.html [2025-02-19 18:33:10,476] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.2_fastqc.html [2025-02-19 18:33:10,478] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.2_fastqc.html [2025-02-19 18:33:10,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.3_fastqc.html [2025-02-19 18:33:10,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.3_fastqc.html [2025-02-19 18:33:10,574] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.4_fastqc.html [2025-02-19 18:33:10,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.4_fastqc.html [2025-02-19 18:33:10,576] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.4_fastqc.html [2025-02-19 18:33:10,576] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.4_fastqc.html [2025-02-19 18:33:10,577] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.4_fastqc.html [2025-02-19 18:33:10,577] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.4_fastqc.html [2025-02-19 18:33:10,577] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 000000000-LPC4P_l01.4_fastqc.html [2025-02-19 18:33:11,088] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-19 18:33:11,090] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-19 18:33:11,096] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-02-19 18:33:11,103] multiqc [DEBUG ] No samples found: conpair [2025-02-19 18:33:11,109] multiqc [DEBUG ] No samples found: peddy [2025-02-19 18:33:11,115] multiqc [DEBUG ] No samples found: somalier [2025-02-19 18:33:11,121] multiqc [DEBUG ] No samples found: methylQA [2025-02-19 18:33:11,132] multiqc [DEBUG ] No samples found: mosdepth [2025-02-19 18:33:11,137] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-02-19 18:33:11,141] multiqc [DEBUG ] No samples found: qualimap [2025-02-19 18:33:11,147] multiqc [DEBUG ] No samples found: preseq [2025-02-19 18:33:11,153] multiqc [DEBUG ] No samples found: quast [2025-02-19 18:33:11,159] multiqc [DEBUG ] No samples found: qorts [2025-02-19 18:33:11,165] multiqc [DEBUG ] No samples found: rna_seqc [2025-02-19 18:33:11,171] multiqc [DEBUG ] No samples found: rockhopper [2025-02-19 18:33:11,176] multiqc [DEBUG ] No samples found: rsem [2025-02-19 18:33:11,192] multiqc [DEBUG ] No samples found: rseqc [2025-02-19 18:33:11,197] multiqc [DEBUG ] No samples found: busco [2025-02-19 18:33:11,203] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-02-19 18:33:11,208] multiqc [DEBUG ] No samples found: disambiguate [2025-02-19 18:33:11,215] multiqc [DEBUG ] No samples found: supernova [2025-02-19 18:33:11,232] multiqc [DEBUG ] No samples found: deeptools [2025-02-19 18:33:11,239] multiqc [DEBUG ] No samples found: sargasso [2025-02-19 18:33:11,245] multiqc [DEBUG ] No samples found: verifybamid [2025-02-19 18:33:11,251] multiqc [DEBUG ] No samples found: mirtrace [2025-02-19 18:33:11,256] multiqc [DEBUG ] No samples found: happy [2025-02-19 18:33:11,262] multiqc [DEBUG ] No samples found: mirtop [2025-02-19 18:33:11,270] multiqc [DEBUG ] No samples found: homer [2025-02-19 18:33:11,276] multiqc [DEBUG ] No samples found: macs2 [2025-02-19 18:33:11,282] multiqc [DEBUG ] No samples found: theta2 [2025-02-19 18:33:11,288] multiqc [DEBUG ] No samples found: snpeff [2025-02-19 18:33:11,297] multiqc [DEBUG ] No samples found: gatk [2025-02-19 18:33:11,302] multiqc [DEBUG ] No samples found: htseq [2025-02-19 18:33:11,309] multiqc [DEBUG ] No samples found: bcftools [2025-02-19 18:33:11,315] multiqc [DEBUG ] No samples found: featureCounts [2025-02-19 18:33:11,323] multiqc [DEBUG ] No samples found: fgbio [2025-02-19 18:33:11,339] multiqc [DEBUG ] No samples found: dragen [2025-02-19 18:33:11,345] multiqc [DEBUG ] No samples found: dedup [2025-02-19 18:33:11,351] multiqc [DEBUG ] No samples found: damageprofiler [2025-02-19 18:33:11,379] multiqc [DEBUG ] No samples found: biobambam2 [2025-02-19 18:33:11,385] multiqc [DEBUG ] No samples found: mtnucratio [2025-02-19 18:33:11,387] multiqc [DEBUG ] No samples found: picard [2025-02-19 18:33:11,393] multiqc [DEBUG ] No samples found: prokka [2025-02-19 18:33:11,399] multiqc [DEBUG ] No samples found: samblaster [2025-02-19 18:33:11,410] multiqc [DEBUG ] No samples found: samtools [2025-02-19 18:33:11,415] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-02-19 18:33:11,423] multiqc [DEBUG ] No samples found: bamtools [2025-02-19 18:33:11,428] multiqc [DEBUG ] No samples found: jellyfish [2025-02-19 18:33:11,438] multiqc [DEBUG ] No samples found: vcftools [2025-02-19 18:33:11,444] multiqc [DEBUG ] No samples found: longranger [2025-02-19 18:33:11,449] multiqc [DEBUG ] No samples found: stacks [2025-02-19 18:33:11,455] multiqc [DEBUG ] No samples found: varscan2 [2025-02-19 18:33:11,475] multiqc [DEBUG ] No samples found: bbmap [2025-02-19 18:33:11,480] multiqc [DEBUG ] No samples found: bismark [2025-02-19 18:33:11,486] multiqc [DEBUG ] No samples found: biscuit [2025-02-19 18:33:11,492] multiqc [DEBUG ] No samples found: hicexplorer [2025-02-19 18:33:11,497] multiqc [DEBUG ] No samples found: hicup [2025-02-19 18:33:11,503] multiqc [DEBUG ] No samples found: hicpro [2025-02-19 18:33:11,508] multiqc [DEBUG ] No samples found: salmon [2025-02-19 18:33:11,514] multiqc [DEBUG ] No samples found: kallisto [2025-02-19 18:33:11,520] multiqc [DEBUG ] No samples found: slamdunk [2025-02-19 18:33:11,526] multiqc [DEBUG ] No samples found: star [2025-02-19 18:33:11,531] multiqc [DEBUG ] No samples found: hisat2 [2025-02-19 18:33:11,537] multiqc [DEBUG ] No samples found: tophat [2025-02-19 18:33:11,542] multiqc [DEBUG ] No samples found: bowtie2 [2025-02-19 18:33:11,548] multiqc [DEBUG ] No samples found: bowtie1 [2025-02-19 18:33:11,553] multiqc [DEBUG ] No samples found: snpsplit [2025-02-19 18:33:11,559] multiqc [DEBUG ] No samples found: kat [2025-02-19 18:33:11,564] multiqc [DEBUG ] No samples found: leehom [2025-02-19 18:33:11,570] multiqc [DEBUG ] No samples found: adapterRemoval [2025-02-19 18:33:11,575] multiqc [DEBUG ] No samples found: clipandmerge [2025-02-19 18:33:11,581] multiqc [DEBUG ] No samples found: cutadapt [2025-02-19 18:33:11,586] multiqc [DEBUG ] No samples found: flexbar [2025-02-19 18:33:11,592] multiqc [DEBUG ] No samples found: kaiju [2025-02-19 18:33:11,597] multiqc [DEBUG ] No samples found: kraken [2025-02-19 18:33:11,603] multiqc [DEBUG ] No samples found: malt [2025-02-19 18:33:11,608] multiqc [DEBUG ] No samples found: trimmomatic [2025-02-19 18:33:11,614] multiqc [DEBUG ] No samples found: sickle [2025-02-19 18:33:11,619] multiqc [DEBUG ] No samples found: skewer [2025-02-19 18:33:11,624] multiqc [DEBUG ] No samples found: sortmerna [2025-02-19 18:33:11,629] multiqc [DEBUG ] No samples found: biobloomtools [2025-02-19 18:33:11,635] multiqc [DEBUG ] No samples found: fastq_screen [2025-02-19 18:33:11,641] multiqc [DEBUG ] No samples found: afterqc [2025-02-19 18:33:11,646] multiqc [DEBUG ] No samples found: fastp [2025-02-19 18:33:11,667] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2025-02-19 18:33:11,742] multiqc [DEBUG ] No samples found: pycoqc [2025-02-19 18:33:11,747] multiqc [DEBUG ] No samples found: minionqc [2025-02-19 18:33:11,752] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-02-19 18:33:11,758] multiqc [DEBUG ] No samples found: clusterflow [2025-02-19 18:33:11,763] multiqc [DEBUG ] No samples found: bcl2fastq [2025-02-19 18:33:11,769] multiqc [DEBUG ] No samples found: interop [2025-02-19 18:33:11,774] multiqc [DEBUG ] No samples found: ivar [2025-02-19 18:33:11,779] multiqc [DEBUG ] No samples found: flash [2025-02-19 18:33:11,784] multiqc [DEBUG ] No samples found: seqyclean [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-02-19 18:33:11,785] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-02-19 18:33:11,791] multiqc [INFO ] Compressing plot data [2025-02-19 18:33:11,861] multiqc [INFO ] Report : multiqc_report.html [2025-02-19 18:33:11,861] multiqc [INFO ] Data : multiqc_data [2025-02-19 18:33:11,861] multiqc [DEBUG ] Moving data file from '/state/partition1/job-57429214/tmpgjycjjac/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/a6/a99320b19f3cdb878d9d8be6141ca1/1/multiqc_data' [2025-02-19 18:33:11,995] multiqc [INFO ] MultiQC complete