[2025-01-28 12:37:46,925] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-28 12:37:46,925] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-28 12:37:46,925] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-28 12:37:46,927] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-28 12:37:46,927] 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}} [2025-01-28 12:37:46,928] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-28 12:37:46,957] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-28 12:37:46,958] multiqc [INFO ] This is MultiQC v1.9 [2025-01-28 12:37:46,958] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-28 12:37:46,958] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/61/be057248c896a2bb86a464875230df/merged [2025-01-28 12:37:46,958] multiqc [INFO ] Template : default [2025-01-28 12:37:46,958] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-28 12:37:46,958] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/61/be057248c896a2bb86a464875230df/merged [2025-01-28 12:37:46,958] 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 [2025-01-28 12:37:46,958] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-56545683/tmpytd8erqa [2025-01-28 12:37:47,070] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_undetermined_fastqc.html [2025-01-28 12:37:47,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_undetermined_fastqc.html [2025-01-28 12:37:47,135] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D30CD8_fastqc.html [2025-01-28 12:37:47,137] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D30CD8_fastqc.html [2025-01-28 12:37:47,193] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-28 12:37:47,194] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-28 12:37:47,233] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D20CD4_fastqc.html [2025-01-28 12:37:47,235] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D20CD4_fastqc.html [2025-01-28 12:37:47,292] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D17CD8_fastqc.html [2025-01-28 12:37:47,294] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D17CD8_fastqc.html [2025-01-28 12:37:47,353] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D17CD4_fastqc.html [2025-01-28 12:37:47,355] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D17CD4_fastqc.html [2025-01-28 12:37:47,413] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D14CD4_fastqc.html [2025-01-28 12:37:47,415] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D14CD4_fastqc.html [2025-01-28 12:37:47,473] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D20CD8_fastqc.html [2025-01-28 12:37:47,475] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D20CD8_fastqc.html [2025-01-28 12:37:47,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D14CD8_fastqc.html [2025-01-28 12:37:47,535] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D14CD8_fastqc.html [2025-01-28 12:37:47,593] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D30CD4_fastqc.html [2025-01-28 12:37:47,595] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHGT2BGYW_n01_D30CD4_fastqc.html [2025-01-28 12:37:48,107] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-28 12:37:48,109] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-28 12:37:48,120] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2025-01-28 12:37:48,130] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-28 12:37:48,132] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-28 12:37:48,136] multiqc [DEBUG ] No samples found: conpair [2025-01-28 12:37:48,141] multiqc [DEBUG ] No samples found: peddy [2025-01-28 12:37:48,147] multiqc [DEBUG ] No samples found: somalier [2025-01-28 12:37:48,152] multiqc [DEBUG ] No samples found: methylQA [2025-01-28 12:37:48,161] multiqc [DEBUG ] No samples found: mosdepth [2025-01-28 12:37:48,166] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-28 12:37:48,169] multiqc [DEBUG ] No samples found: qualimap [2025-01-28 12:37:48,174] multiqc [DEBUG ] No samples found: preseq [2025-01-28 12:37:48,179] multiqc [DEBUG ] No samples found: quast [2025-01-28 12:37:48,184] multiqc [DEBUG ] No samples found: qorts [2025-01-28 12:37:48,190] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-28 12:37:48,195] multiqc [DEBUG ] No samples found: rockhopper [2025-01-28 12:37:48,199] multiqc [DEBUG ] No samples found: rsem [2025-01-28 12:37:48,212] multiqc [DEBUG ] No samples found: rseqc [2025-01-28 12:37:48,216] multiqc [DEBUG ] No samples found: busco [2025-01-28 12:37:48,222] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-28 12:37:48,227] multiqc [DEBUG ] No samples found: disambiguate [2025-01-28 12:37:48,232] multiqc [DEBUG ] No samples found: supernova [2025-01-28 12:37:48,246] multiqc [DEBUG ] No samples found: deeptools [2025-01-28 12:37:48,251] multiqc [DEBUG ] No samples found: sargasso [2025-01-28 12:37:48,256] multiqc [DEBUG ] No samples found: verifybamid [2025-01-28 12:37:48,262] multiqc [DEBUG ] No samples found: mirtrace [2025-01-28 12:37:48,268] multiqc [DEBUG ] No samples found: happy [2025-01-28 12:37:48,272] multiqc [DEBUG ] No samples found: mirtop [2025-01-28 12:37:48,279] multiqc [DEBUG ] No samples found: homer [2025-01-28 12:37:48,283] multiqc [DEBUG ] No samples found: macs2 [2025-01-28 12:37:48,287] multiqc [DEBUG ] No samples found: theta2 [2025-01-28 12:37:48,292] multiqc [DEBUG ] No samples found: snpeff [2025-01-28 12:37:48,300] multiqc [DEBUG ] No samples found: gatk [2025-01-28 12:37:48,304] multiqc [DEBUG ] No samples found: htseq [2025-01-28 12:37:48,310] multiqc [DEBUG ] No samples found: bcftools [2025-01-28 12:37:48,315] multiqc [DEBUG ] No samples found: featureCounts [2025-01-28 12:37:48,323] multiqc [DEBUG ] No samples found: fgbio [2025-01-28 12:37:48,336] multiqc [DEBUG ] No samples found: dragen [2025-01-28 12:37:48,340] multiqc [DEBUG ] No samples found: dedup [2025-01-28 12:37:48,345] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-28 12:37:48,367] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-28 12:37:48,373] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-28 12:37:48,375] multiqc [DEBUG ] No samples found: picard [2025-01-28 12:37:48,379] multiqc [DEBUG ] No samples found: prokka [2025-01-28 12:37:48,384] multiqc [DEBUG ] No samples found: samblaster [2025-01-28 12:37:48,393] multiqc [DEBUG ] No samples found: samtools [2025-01-28 12:37:48,398] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-28 12:37:48,403] multiqc [DEBUG ] No samples found: bamtools [2025-01-28 12:37:48,407] multiqc [DEBUG ] No samples found: jellyfish [2025-01-28 12:37:48,415] multiqc [DEBUG ] No samples found: vcftools [2025-01-28 12:37:48,420] multiqc [DEBUG ] No samples found: longranger [2025-01-28 12:37:48,425] multiqc [DEBUG ] No samples found: stacks [2025-01-28 12:37:48,430] multiqc [DEBUG ] No samples found: varscan2 [2025-01-28 12:37:48,444] multiqc [DEBUG ] No samples found: bbmap [2025-01-28 12:37:48,449] multiqc [DEBUG ] No samples found: bismark [2025-01-28 12:37:48,455] multiqc [DEBUG ] No samples found: biscuit [2025-01-28 12:37:48,461] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-28 12:37:48,465] multiqc [DEBUG ] No samples found: hicup [2025-01-28 12:37:48,470] multiqc [DEBUG ] No samples found: hicpro [2025-01-28 12:37:48,474] multiqc [DEBUG ] No samples found: salmon [2025-01-28 12:37:48,479] multiqc [DEBUG ] No samples found: kallisto [2025-01-28 12:37:48,483] multiqc [DEBUG ] No samples found: slamdunk [2025-01-28 12:37:48,488] multiqc [DEBUG ] No samples found: star [2025-01-28 12:37:48,493] multiqc [DEBUG ] No samples found: hisat2 [2025-01-28 12:37:48,498] multiqc [DEBUG ] No samples found: tophat [2025-01-28 12:37:48,503] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-28 12:37:48,507] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-28 12:37:48,512] multiqc [DEBUG ] No samples found: snpsplit [2025-01-28 12:37:48,517] multiqc [DEBUG ] No samples found: kat [2025-01-28 12:37:48,521] multiqc [DEBUG ] No samples found: leehom [2025-01-28 12:37:48,526] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-28 12:37:48,531] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-28 12:37:48,536] multiqc [DEBUG ] No samples found: cutadapt [2025-01-28 12:37:48,542] multiqc [DEBUG ] No samples found: flexbar [2025-01-28 12:37:48,547] multiqc [DEBUG ] No samples found: kaiju [2025-01-28 12:37:48,552] multiqc [DEBUG ] No samples found: kraken [2025-01-28 12:37:48,557] multiqc [DEBUG ] No samples found: malt [2025-01-28 12:37:48,562] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-28 12:37:48,567] multiqc [DEBUG ] No samples found: sickle [2025-01-28 12:37:48,571] multiqc [DEBUG ] No samples found: skewer [2025-01-28 12:37:48,575] multiqc [DEBUG ] No samples found: sortmerna [2025-01-28 12:37:48,581] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-28 12:37:48,586] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-28 12:37:48,591] multiqc [DEBUG ] No samples found: afterqc [2025-01-28 12:37:48,596] multiqc [DEBUG ] No samples found: fastp [2025-01-28 12:37:48,677] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports [2025-01-28 12:37:48,933] multiqc [DEBUG ] No samples found: pycoqc [2025-01-28 12:37:48,938] multiqc [DEBUG ] No samples found: minionqc [2025-01-28 12:37:48,943] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-28 12:37:48,948] multiqc [DEBUG ] No samples found: clusterflow [2025-01-28 12:37:48,953] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-28 12:37:48,957] multiqc [DEBUG ] No samples found: interop [2025-01-28 12:37:48,962] multiqc [DEBUG ] No samples found: ivar [2025-01-28 12:37:48,967] multiqc [DEBUG ] No samples found: flash [2025-01-28 12:37:48,971] multiqc [DEBUG ] No samples found: seqyclean [2025-01-28 12:37:48,971] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-28 12:37:48,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-28 12:37:48,984] multiqc [INFO ] Compressing plot data [2025-01-28 12:37:49,109] multiqc [INFO ] Report : multiqc_report.html [2025-01-28 12:37:49,109] multiqc [INFO ] Data : multiqc_data [2025-01-28 12:37:49,109] multiqc [DEBUG ] Moving data file from '/state/partition1/job-56545683/tmpytd8erqa/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/61/be057248c896a2bb86a464875230df/merged/multiqc_data' [2025-01-28 12:37:49,244] multiqc [INFO ] MultiQC complete