[2025-01-30 13:07:43,958] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-30 13:07:43,959] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-30 13:07:43,959] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-30 13:07:43,961] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-30 13:07:43,961] 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}} [2025-01-30 13:07:43,961] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 13:07:43,997] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-30 13:07:43,997] multiqc [INFO ] This is MultiQC v1.9 [2025-01-30 13:07:43,997] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 13:07:43,997] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/b1/0aeabf6406c8a66d66f3584f87f356/merged [2025-01-30 13:07:43,997] multiqc [INFO ] Template : default [2025-01-30 13:07:43,997] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-30 13:07:43,997] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/b1/0aeabf6406c8a66d66f3584f87f356/merged [2025-01-30 13:07:43,997] 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 [2025-01-30 13:07:43,998] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-56654485/tmpvaiw_70t [2025-01-30 13:07:44,108] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D20CD8_fastqc.html [2025-01-30 13:07:44,111] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D20CD8_fastqc.html [2025-01-30 13:07:44,172] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D30CD4_fastqc.html [2025-01-30 13:07:44,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D30CD4_fastqc.html [2025-01-30 13:07:44,230] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-30 13:07:44,232] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-30 13:07:44,328] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D14CD4_fastqc.html [2025-01-30 13:07:44,331] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D14CD4_fastqc.html [2025-01-30 13:07:44,389] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D30CD8_fastqc.html [2025-01-30 13:07:44,391] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D30CD8_fastqc.html [2025-01-30 13:07:44,449] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D20CD4_fastqc.html [2025-01-30 13:07:44,451] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D20CD4_fastqc.html [2025-01-30 13:07:44,509] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D17CD4_fastqc.html [2025-01-30 13:07:44,511] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D17CD4_fastqc.html [2025-01-30 13:07:44,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D17CD8_fastqc.html [2025-01-30 13:07:44,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D17CD8_fastqc.html [2025-01-30 13:07:44,631] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D14CD8_fastqc.html [2025-01-30 13:07:44,633] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_D14CD8_fastqc.html [2025-01-30 13:07:44,690] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLWFBGYW_n01_undetermined_fastqc.html [2025-01-30 13:07:44,692] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLWFBGYW_n01_undetermined_fastqc.html [2025-01-30 13:07:45,217] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 13:07:45,219] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 13:07:45,227] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-30 13:07:45,237] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-30 13:07:45,242] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2025-01-30 13:07:45,247] multiqc [DEBUG ] No samples found: conpair [2025-01-30 13:07:45,252] multiqc [DEBUG ] No samples found: peddy [2025-01-30 13:07:45,260] multiqc [DEBUG ] No samples found: somalier [2025-01-30 13:07:45,268] multiqc [DEBUG ] No samples found: methylQA [2025-01-30 13:07:45,277] multiqc [DEBUG ] No samples found: mosdepth [2025-01-30 13:07:45,281] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-30 13:07:45,285] multiqc [DEBUG ] No samples found: qualimap [2025-01-30 13:07:45,290] multiqc [DEBUG ] No samples found: preseq [2025-01-30 13:07:45,295] multiqc [DEBUG ] No samples found: quast [2025-01-30 13:07:45,300] multiqc [DEBUG ] No samples found: qorts [2025-01-30 13:07:45,305] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-30 13:07:45,310] multiqc [DEBUG ] No samples found: rockhopper [2025-01-30 13:07:45,315] multiqc [DEBUG ] No samples found: rsem [2025-01-30 13:07:45,327] multiqc [DEBUG ] No samples found: rseqc [2025-01-30 13:07:45,331] multiqc [DEBUG ] No samples found: busco [2025-01-30 13:07:45,337] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-30 13:07:45,341] multiqc [DEBUG ] No samples found: disambiguate [2025-01-30 13:07:45,346] multiqc [DEBUG ] No samples found: supernova [2025-01-30 13:07:45,360] multiqc [DEBUG ] No samples found: deeptools [2025-01-30 13:07:45,365] multiqc [DEBUG ] No samples found: sargasso [2025-01-30 13:07:45,371] multiqc [DEBUG ] No samples found: verifybamid [2025-01-30 13:07:45,376] multiqc [DEBUG ] No samples found: mirtrace [2025-01-30 13:07:45,381] multiqc [DEBUG ] No samples found: happy [2025-01-30 13:07:45,387] multiqc [DEBUG ] No samples found: mirtop [2025-01-30 13:07:45,394] multiqc [DEBUG ] No samples found: homer [2025-01-30 13:07:45,399] multiqc [DEBUG ] No samples found: macs2 [2025-01-30 13:07:45,403] multiqc [DEBUG ] No samples found: theta2 [2025-01-30 13:07:45,409] multiqc [DEBUG ] No samples found: snpeff [2025-01-30 13:07:45,416] multiqc [DEBUG ] No samples found: gatk [2025-01-30 13:07:45,421] multiqc [DEBUG ] No samples found: htseq [2025-01-30 13:07:45,427] multiqc [DEBUG ] No samples found: bcftools [2025-01-30 13:07:45,433] multiqc [DEBUG ] No samples found: featureCounts [2025-01-30 13:07:45,440] multiqc [DEBUG ] No samples found: fgbio [2025-01-30 13:07:45,455] multiqc [DEBUG ] No samples found: dragen [2025-01-30 13:07:45,461] multiqc [DEBUG ] No samples found: dedup [2025-01-30 13:07:45,466] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-30 13:07:45,490] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-30 13:07:45,495] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-30 13:07:45,498] multiqc [DEBUG ] No samples found: picard [2025-01-30 13:07:45,503] multiqc [DEBUG ] No samples found: prokka [2025-01-30 13:07:45,507] multiqc [DEBUG ] No samples found: samblaster [2025-01-30 13:07:45,517] multiqc [DEBUG ] No samples found: samtools [2025-01-30 13:07:45,523] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-30 13:07:45,528] multiqc [DEBUG ] No samples found: bamtools [2025-01-30 13:07:45,533] multiqc [DEBUG ] No samples found: jellyfish [2025-01-30 13:07:45,542] multiqc [DEBUG ] No samples found: vcftools [2025-01-30 13:07:45,547] multiqc [DEBUG ] No samples found: longranger [2025-01-30 13:07:45,552] multiqc [DEBUG ] No samples found: stacks [2025-01-30 13:07:45,557] multiqc [DEBUG ] No samples found: varscan2 [2025-01-30 13:07:45,571] multiqc [DEBUG ] No samples found: bbmap [2025-01-30 13:07:45,576] multiqc [DEBUG ] No samples found: bismark [2025-01-30 13:07:45,581] multiqc [DEBUG ] No samples found: biscuit [2025-01-30 13:07:45,586] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-30 13:07:45,591] multiqc [DEBUG ] No samples found: hicup [2025-01-30 13:07:45,596] multiqc [DEBUG ] No samples found: hicpro [2025-01-30 13:07:45,601] multiqc [DEBUG ] No samples found: salmon [2025-01-30 13:07:45,605] multiqc [DEBUG ] No samples found: kallisto [2025-01-30 13:07:45,610] multiqc [DEBUG ] No samples found: slamdunk [2025-01-30 13:07:45,615] multiqc [DEBUG ] No samples found: star [2025-01-30 13:07:45,620] multiqc [DEBUG ] No samples found: hisat2 [2025-01-30 13:07:45,625] multiqc [DEBUG ] No samples found: tophat [2025-01-30 13:07:45,629] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-30 13:07:45,634] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-30 13:07:45,639] multiqc [DEBUG ] No samples found: snpsplit [2025-01-30 13:07:45,643] multiqc [DEBUG ] No samples found: kat [2025-01-30 13:07:45,648] multiqc [DEBUG ] No samples found: leehom [2025-01-30 13:07:45,653] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-30 13:07:45,658] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-30 13:07:45,662] multiqc [DEBUG ] No samples found: cutadapt [2025-01-30 13:07:45,667] multiqc [DEBUG ] No samples found: flexbar [2025-01-30 13:07:45,672] multiqc [DEBUG ] No samples found: kaiju [2025-01-30 13:07:45,677] multiqc [DEBUG ] No samples found: kraken [2025-01-30 13:07:45,682] multiqc [DEBUG ] No samples found: malt [2025-01-30 13:07:45,687] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-30 13:07:45,692] multiqc [DEBUG ] No samples found: sickle [2025-01-30 13:07:45,697] multiqc [DEBUG ] No samples found: skewer [2025-01-30 13:07:45,702] multiqc [DEBUG ] No samples found: sortmerna [2025-01-30 13:07:45,707] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-30 13:07:45,713] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-30 13:07:45,718] multiqc [DEBUG ] No samples found: afterqc [2025-01-30 13:07:45,723] multiqc [DEBUG ] No samples found: fastp [2025-01-30 13:07:46,498] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports [2025-01-30 13:07:46,756] multiqc [DEBUG ] No samples found: pycoqc [2025-01-30 13:07:46,761] multiqc [DEBUG ] No samples found: minionqc [2025-01-30 13:07:46,766] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-30 13:07:46,771] multiqc [DEBUG ] No samples found: clusterflow [2025-01-30 13:07:46,776] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-30 13:07:46,781] multiqc [DEBUG ] No samples found: interop [2025-01-30 13:07:46,786] multiqc [DEBUG ] No samples found: ivar [2025-01-30 13:07:46,791] multiqc [DEBUG ] No samples found: flash [2025-01-30 13:07:46,795] multiqc [DEBUG ] No samples found: seqyclean [2025-01-30 13:07:46,795] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-30 13:07:46,796] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-30 13:07:46,808] multiqc [INFO ] Compressing plot data [2025-01-30 13:07:46,957] multiqc [INFO ] Report : multiqc_report.html [2025-01-30 13:07:46,957] multiqc [INFO ] Data : multiqc_data [2025-01-30 13:07:46,957] multiqc [DEBUG ] Moving data file from '/state/partition1/job-56654485/tmpvaiw_70t/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/b1/0aeabf6406c8a66d66f3584f87f356/merged/multiqc_data' [2025-01-30 13:07:47,100] multiqc [INFO ] MultiQC complete