[2024-08-15 02:49:20,735] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-15 02:49:20,735] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-15 02:49:20,735] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-15 02:49:20,737] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-15 02:49:20,737] 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}} [2024-08-15 02:49:20,737] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-15 02:49:20,773] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-15 02:49:20,773] multiqc [INFO ] This is MultiQC v1.9 [2024-08-15 02:49:20,773] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-15 02:49:20,773] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/a7/d9f4bab0f5061bebaa79b35b1dfe66/merged [2024-08-15 02:49:20,773] multiqc [INFO ] Template : default [2024-08-15 02:49:20,773] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-15 02:49:20,773] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/a7/d9f4bab0f5061bebaa79b35b1dfe66/merged [2024-08-15 02:49:20,773] 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 [2024-08-15 02:49:20,773] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49934290/tmpcu1xzj88 [2024-08-15 02:49:20,883] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTYWDRX5_1_fastqc.html [2024-08-15 02:49:20,886] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTYWDRX5_1_fastqc.html [2024-08-15 02:49:20,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTYWDRX5_2_fastqc.html [2024-08-15 02:49:20,960] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTYWDRX5_2_fastqc.html [2024-08-15 02:49:21,008] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTYWDRX5_3_fastqc.html [2024-08-15 02:49:21,010] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTYWDRX5_3_fastqc.html [2024-08-15 02:49:21,519] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-15 02:49:21,521] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-15 02:49:21,527] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-15 02:49:21,531] multiqc [DEBUG ] No samples found: conpair [2024-08-15 02:49:21,536] multiqc [DEBUG ] No samples found: peddy [2024-08-15 02:49:21,542] multiqc [DEBUG ] No samples found: somalier [2024-08-15 02:49:21,546] multiqc [DEBUG ] No samples found: methylQA [2024-08-15 02:49:21,554] multiqc [DEBUG ] No samples found: mosdepth [2024-08-15 02:49:21,559] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-15 02:49:21,562] multiqc [DEBUG ] No samples found: qualimap [2024-08-15 02:49:21,567] multiqc [DEBUG ] No samples found: preseq [2024-08-15 02:49:21,572] multiqc [DEBUG ] No samples found: quast [2024-08-15 02:49:21,577] multiqc [DEBUG ] No samples found: qorts [2024-08-15 02:49:21,582] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-15 02:49:21,587] multiqc [DEBUG ] No samples found: rockhopper [2024-08-15 02:49:21,592] multiqc [DEBUG ] No samples found: rsem [2024-08-15 02:49:21,603] multiqc [DEBUG ] No samples found: rseqc [2024-08-15 02:49:21,607] multiqc [DEBUG ] No samples found: busco [2024-08-15 02:49:21,612] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-15 02:49:21,616] multiqc [DEBUG ] No samples found: disambiguate [2024-08-15 02:49:21,621] multiqc [DEBUG ] No samples found: supernova [2024-08-15 02:49:21,634] multiqc [DEBUG ] No samples found: deeptools [2024-08-15 02:49:21,639] multiqc [DEBUG ] No samples found: sargasso [2024-08-15 02:49:21,643] multiqc [DEBUG ] No samples found: verifybamid [2024-08-15 02:49:21,648] multiqc [DEBUG ] No samples found: mirtrace [2024-08-15 02:49:21,653] multiqc [DEBUG ] No samples found: happy [2024-08-15 02:49:21,658] multiqc [DEBUG ] No samples found: mirtop [2024-08-15 02:49:21,664] multiqc [DEBUG ] No samples found: homer [2024-08-15 02:49:21,669] multiqc [DEBUG ] No samples found: macs2 [2024-08-15 02:49:21,673] multiqc [DEBUG ] No samples found: theta2 [2024-08-15 02:49:21,678] multiqc [DEBUG ] No samples found: snpeff [2024-08-15 02:49:21,685] multiqc [DEBUG ] No samples found: gatk [2024-08-15 02:49:21,689] multiqc [DEBUG ] No samples found: htseq [2024-08-15 02:49:21,695] multiqc [DEBUG ] No samples found: bcftools [2024-08-15 02:49:21,699] multiqc [DEBUG ] No samples found: featureCounts [2024-08-15 02:49:21,705] multiqc [DEBUG ] No samples found: fgbio [2024-08-15 02:49:21,719] multiqc [DEBUG ] No samples found: dragen [2024-08-15 02:49:21,724] multiqc [DEBUG ] No samples found: dedup [2024-08-15 02:49:21,729] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-15 02:49:21,752] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-15 02:49:21,757] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-15 02:49:21,759] multiqc [DEBUG ] No samples found: picard [2024-08-15 02:49:21,764] multiqc [DEBUG ] No samples found: prokka [2024-08-15 02:49:21,769] multiqc [DEBUG ] No samples found: samblaster [2024-08-15 02:49:21,777] multiqc [DEBUG ] No samples found: samtools [2024-08-15 02:49:21,782] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-15 02:49:21,787] multiqc [DEBUG ] No samples found: bamtools [2024-08-15 02:49:21,792] multiqc [DEBUG ] No samples found: jellyfish [2024-08-15 02:49:21,799] multiqc [DEBUG ] No samples found: vcftools [2024-08-15 02:49:21,804] multiqc [DEBUG ] No samples found: longranger [2024-08-15 02:49:21,809] multiqc [DEBUG ] No samples found: stacks [2024-08-15 02:49:21,814] multiqc [DEBUG ] No samples found: varscan2 [2024-08-15 02:49:21,828] multiqc [DEBUG ] No samples found: bbmap [2024-08-15 02:49:21,832] multiqc [DEBUG ] No samples found: bismark [2024-08-15 02:49:21,837] multiqc [DEBUG ] No samples found: biscuit [2024-08-15 02:49:21,842] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-15 02:49:21,847] multiqc [DEBUG ] No samples found: hicup [2024-08-15 02:49:21,852] multiqc [DEBUG ] No samples found: hicpro [2024-08-15 02:49:21,856] multiqc [DEBUG ] No samples found: salmon [2024-08-15 02:49:21,861] multiqc [DEBUG ] No samples found: kallisto [2024-08-15 02:49:21,866] multiqc [DEBUG ] No samples found: slamdunk [2024-08-15 02:49:21,870] multiqc [DEBUG ] No samples found: star [2024-08-15 02:49:21,875] multiqc [DEBUG ] No samples found: hisat2 [2024-08-15 02:49:21,879] multiqc [DEBUG ] No samples found: tophat [2024-08-15 02:49:21,884] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-15 02:49:21,889] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-15 02:49:21,893] multiqc [DEBUG ] No samples found: snpsplit [2024-08-15 02:49:21,898] multiqc [DEBUG ] No samples found: kat [2024-08-15 02:49:21,902] multiqc [DEBUG ] No samples found: leehom [2024-08-15 02:49:21,907] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-15 02:49:21,911] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-15 02:49:21,916] multiqc [DEBUG ] No samples found: cutadapt [2024-08-15 02:49:21,920] multiqc [DEBUG ] No samples found: flexbar [2024-08-15 02:49:21,924] multiqc [DEBUG ] No samples found: kaiju [2024-08-15 02:49:21,929] multiqc [DEBUG ] No samples found: kraken [2024-08-15 02:49:21,934] multiqc [DEBUG ] No samples found: malt [2024-08-15 02:49:21,938] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-15 02:49:21,943] multiqc [DEBUG ] No samples found: sickle [2024-08-15 02:49:21,947] multiqc [DEBUG ] No samples found: skewer [2024-08-15 02:49:21,952] multiqc [DEBUG ] No samples found: sortmerna [2024-08-15 02:49:21,956] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-15 02:49:21,960] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-15 02:49:21,965] multiqc [DEBUG ] No samples found: afterqc [2024-08-15 02:49:21,970] multiqc [DEBUG ] No samples found: fastp [2024-08-15 02:49:22,033] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-08-15 02:49:22,088] multiqc [DEBUG ] No samples found: pycoqc [2024-08-15 02:49:22,093] multiqc [DEBUG ] No samples found: minionqc [2024-08-15 02:49:22,098] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-15 02:49:22,104] multiqc [DEBUG ] No samples found: clusterflow [2024-08-15 02:49:22,109] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-15 02:49:22,115] multiqc [DEBUG ] No samples found: interop [2024-08-15 02:49:22,120] multiqc [DEBUG ] No samples found: ivar [2024-08-15 02:49:22,126] multiqc [DEBUG ] No samples found: flash [2024-08-15 02:49:22,130] multiqc [DEBUG ] No samples found: seqyclean [2024-08-15 02:49:22,130] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-15 02:49:22,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-08-15 02:49:22,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-15 02:49:22,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-15 02:49:22,131] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-15 02:49:22,136] multiqc [INFO ] Compressing plot data [2024-08-15 02:49:22,200] multiqc [INFO ] Report : multiqc_report.html [2024-08-15 02:49:22,200] multiqc [INFO ] Data : multiqc_data [2024-08-15 02:49:22,200] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49934290/tmpcu1xzj88/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/a7/d9f4bab0f5061bebaa79b35b1dfe66/merged/multiqc_data' [2024-08-15 02:49:22,329] multiqc [INFO ] MultiQC complete