[2024-12-27 16:07:20,387] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-27 16:07:20,388] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-27 16:07:20,388] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-27 16:07:20,390] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-27 16:07:20,390] 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}} [2024-12-27 16:07:20,391] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-27 16:07:20,428] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-27 16:07:20,428] multiqc [INFO ] This is MultiQC v1.9 [2024-12-27 16:07:20,428] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-27 16:07:20,428] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/b0/05e2779fca5c5a4b76e062ee4d4ab0/merged [2024-12-27 16:07:20,428] multiqc [INFO ] Template : default [2024-12-27 16:07:20,429] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-27 16:07:20,429] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/b0/05e2779fca5c5a4b76e062ee4d4ab0/merged [2024-12-27 16:07:20,429] 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 [2024-12-27 16:07:20,429] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55407927/tmps0smughi [2024-12-27 16:07:20,545] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_R3GEX_fastqc.html [2024-12-27 16:07:20,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_R3GEX_fastqc.html [2024-12-27 16:07:20,602] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-12-27 16:07:22,859] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n02_D4GEX_fastqc.html [2024-12-27 16:07:22,905] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n02_D2CRISPR_fastqc.html [2024-12-27 16:07:22,907] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n02_D2CRISPR_fastqc.html [2024-12-27 16:07:22,986] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_undetermined_fastqc.html [2024-12-27 16:07:22,988] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_undetermined_fastqc.html [2024-12-27 16:07:23,033] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_ES1CRISPR_fastqc.html [2024-12-27 16:07:23,035] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_ES1CRISPR_fastqc.html [2024-12-27 16:07:23,081] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_D2GEX_fastqc.html [2024-12-27 16:07:23,083] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_D2GEX_fastqc.html [2024-12-27 16:07:23,138] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_D4GEX_fastqc.html [2024-12-27 16:07:23,140] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_D4GEX_fastqc.html [2024-12-27 16:07:23,191] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_D1CRISPR_fastqc.html [2024-12-27 16:07:23,193] multiqc [DEBUG ] File 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because it exceeded search pattern filesize limit: H2TFGDSXF_n02_R2CRISPR_fastqc.html [2024-12-27 16:07:23,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_R2CRISPR_fastqc.html [2024-12-27 16:07:23,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_R2CRISPR_fastqc.html [2024-12-27 16:07:23,494] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n02_R3CRISPR_fastqc.html [2024-12-27 16:07:23,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n02_R3CRISPR_fastqc.html [2024-12-27 16:07:23,574] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n02_undetermined_fastqc.html [2024-12-27 16:07:23,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n02_undetermined_fastqc.html [2024-12-27 16:07:23,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_ES2CRISPR_fastqc.html [2024-12-27 16:07:23,626] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_ES2CRISPR_fastqc.html [2024-12-27 16:07:23,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n01_R4GEX_fastqc.html [2024-12-27 16:07:23,678] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n01_R4GEX_fastqc.html [2024-12-27 16:07:23,725] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n02_R3GEX_fastqc.html [2024-12-27 16:07:23,727] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n02_R3GEX_fastqc.html [2024-12-27 16:07:23,773] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2TFGDSXF_n02_R1CRISPR_fastqc.html [2024-12-27 16:07:23,775] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2TFGDSXF_n02_R1CRISPR_fastqc.html [2024-12-27 16:07:24,350] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-27 16:07:24,351] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-27 16:07:24,360] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-27 16:07:24,369] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-27 16:07:24,383] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2024-12-27 16:07:24,389] multiqc [DEBUG ] No samples found: conpair [2024-12-27 16:07:24,394] multiqc [DEBUG ] No samples found: peddy [2024-12-27 16:07:24,399] multiqc [DEBUG ] No samples found: somalier [2024-12-27 16:07:24,404] multiqc [DEBUG ] No samples found: methylQA [2024-12-27 16:07:24,413] multiqc [DEBUG ] No samples found: mosdepth [2024-12-27 16:07:24,418] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-27 16:07:24,421] multiqc [DEBUG ] No samples found: qualimap [2024-12-27 16:07:24,426] multiqc [DEBUG ] No samples found: preseq [2024-12-27 16:07:24,432] multiqc [DEBUG ] No samples found: quast [2024-12-27 16:07:24,437] multiqc [DEBUG ] No samples found: qorts [2024-12-27 16:07:24,442] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-27 16:07:24,447] multiqc [DEBUG ] No samples found: rockhopper [2024-12-27 16:07:24,452] multiqc [DEBUG ] No samples found: rsem [2024-12-27 16:07:24,465] multiqc [DEBUG ] No samples found: rseqc [2024-12-27 16:07:24,470] multiqc [DEBUG ] No samples found: busco [2024-12-27 16:07:24,475] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-27 16:07:24,480] multiqc [DEBUG ] No samples found: disambiguate [2024-12-27 16:07:24,485] multiqc [DEBUG ] No samples found: supernova [2024-12-27 16:07:24,498] multiqc [DEBUG ] No samples found: deeptools [2024-12-27 16:07:24,503] multiqc [DEBUG ] No samples found: sargasso [2024-12-27 16:07:24,509] multiqc [DEBUG ] No samples found: verifybamid [2024-12-27 16:07:24,514] multiqc [DEBUG ] No samples found: mirtrace [2024-12-27 16:07:24,519] multiqc [DEBUG ] No samples found: happy [2024-12-27 16:07:24,524] multiqc [DEBUG ] No samples found: mirtop [2024-12-27 16:07:24,531] multiqc [DEBUG ] No samples found: homer [2024-12-27 16:07:24,536] multiqc [DEBUG ] No samples found: macs2 [2024-12-27 16:07:24,541] multiqc [DEBUG ] No samples found: theta2 [2024-12-27 16:07:24,546] multiqc [DEBUG ] No samples found: snpeff [2024-12-27 16:07:24,553] multiqc [DEBUG ] No samples found: gatk [2024-12-27 16:07:24,558] multiqc [DEBUG ] No samples found: htseq [2024-12-27 16:07:24,564] multiqc [DEBUG ] No samples found: bcftools [2024-12-27 16:07:24,569] multiqc [DEBUG ] No samples found: featureCounts [2024-12-27 16:07:24,576] multiqc [DEBUG ] No samples found: fgbio [2024-12-27 16:07:24,589] multiqc [DEBUG ] No samples found: dragen [2024-12-27 16:07:24,594] multiqc [DEBUG ] No samples found: dedup [2024-12-27 16:07:24,599] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-27 16:07:24,623] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-27 16:07:24,628] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-27 16:07:24,630] multiqc [DEBUG ] No samples found: picard [2024-12-27 16:07:24,635] multiqc [DEBUG ] No samples found: prokka [2024-12-27 16:07:24,640] multiqc [DEBUG ] No samples found: samblaster [2024-12-27 16:07:24,649] multiqc [DEBUG ] No samples found: samtools [2024-12-27 16:07:24,654] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-27 16:07:24,660] multiqc [DEBUG ] No samples found: bamtools [2024-12-27 16:07:24,665] multiqc [DEBUG ] No samples found: jellyfish [2024-12-27 16:07:24,673] multiqc [DEBUG ] No samples found: vcftools [2024-12-27 16:07:24,678] multiqc [DEBUG ] No samples found: longranger [2024-12-27 16:07:24,683] multiqc [DEBUG ] No samples found: stacks [2024-12-27 16:07:24,689] multiqc [DEBUG ] No samples found: varscan2 [2024-12-27 16:07:24,704] multiqc [DEBUG ] No samples found: bbmap [2024-12-27 16:07:24,709] multiqc [DEBUG ] No samples found: bismark [2024-12-27 16:07:24,715] multiqc [DEBUG ] No samples found: biscuit [2024-12-27 16:07:24,720] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-27 16:07:24,724] multiqc [DEBUG ] No samples found: hicup [2024-12-27 16:07:24,729] multiqc [DEBUG ] No samples found: hicpro [2024-12-27 16:07:24,734] multiqc [DEBUG ] No samples found: salmon [2024-12-27 16:07:24,739] multiqc [DEBUG ] No samples found: kallisto [2024-12-27 16:07:24,744] multiqc [DEBUG ] No samples found: slamdunk [2024-12-27 16:07:24,749] multiqc [DEBUG ] No samples found: star [2024-12-27 16:07:24,754] multiqc [DEBUG ] No samples found: hisat2 [2024-12-27 16:07:24,759] multiqc [DEBUG ] No samples found: tophat [2024-12-27 16:07:24,764] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-27 16:07:24,769] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-27 16:07:24,774] multiqc [DEBUG ] No samples found: snpsplit [2024-12-27 16:07:24,779] multiqc [DEBUG ] No samples found: kat [2024-12-27 16:07:24,784] multiqc [DEBUG ] No samples found: leehom [2024-12-27 16:07:24,790] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-27 16:07:24,795] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-27 16:07:24,800] multiqc [DEBUG ] No samples found: cutadapt [2024-12-27 16:07:24,804] multiqc [DEBUG ] No samples found: flexbar [2024-12-27 16:07:24,809] multiqc [DEBUG ] No samples found: kaiju [2024-12-27 16:07:24,814] multiqc [DEBUG ] No samples found: kraken [2024-12-27 16:07:24,819] multiqc [DEBUG ] No samples found: malt [2024-12-27 16:07:24,824] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-27 16:07:24,829] multiqc [DEBUG ] No samples found: sickle [2024-12-27 16:07:24,834] multiqc [DEBUG ] No samples found: skewer [2024-12-27 16:07:24,839] multiqc [DEBUG ] No samples found: sortmerna [2024-12-27 16:07:24,844] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-27 16:07:24,849] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-27 16:07:24,854] multiqc [DEBUG ] No samples found: afterqc [2024-12-27 16:07:24,859] multiqc [DEBUG ] No samples found: fastp [2024-12-27 16:07:32,372] multiqc.modules.fastqc.fastqc [INFO ] Found 58 reports [2024-12-27 16:07:32,744] multiqc [DEBUG ] No samples found: pycoqc [2024-12-27 16:07:32,749] multiqc [DEBUG ] No samples found: minionqc [2024-12-27 16:07:32,755] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-27 16:07:32,760] multiqc [DEBUG ] No samples found: clusterflow [2024-12-27 16:07:32,765] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-27 16:07:32,771] multiqc [DEBUG ] No samples found: interop [2024-12-27 16:07:32,776] multiqc [DEBUG ] No samples found: ivar [2024-12-27 16:07:32,781] multiqc [DEBUG ] No samples found: flash [2024-12-27 16:07:32,786] multiqc [DEBUG ] No samples found: seqyclean [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-27 16:07:32,786] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-27 16:07:32,787] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-27 16:07:32,856] multiqc [INFO ] Compressing plot data [2024-12-27 16:07:33,761] multiqc [INFO ] Report : multiqc_report.html [2024-12-27 16:07:33,761] multiqc [INFO ] Data : multiqc_data [2024-12-27 16:07:33,761] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55407927/tmps0smughi/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/b0/05e2779fca5c5a4b76e062ee4d4ab0/merged/multiqc_data' [2024-12-27 16:07:33,887] multiqc [INFO ] MultiQC complete