[2025-01-28 17:21:38,084] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-28 17:21:38,084] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-28 17:21:38,085] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-28 17:21:38,087] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-28 17:21:38,087] 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 17:21:38,088] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-28 17:21:38,118] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-28 17:21:38,118] multiqc [INFO ] This is MultiQC v1.9 [2025-01-28 17:21:38,118] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-28 17:21:38,118] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/89/bb4fc79e23ba6ee8c869785491f0c8/merged [2025-01-28 17:21:38,118] multiqc [INFO ] Template : default [2025-01-28 17:21:38,118] 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 17:21:38,118] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/89/bb4fc79e23ba6ee8c869785491f0c8/merged [2025-01-28 17:21:38,118] 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 17:21:38,119] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-56561329/tmp7ixz36tf [2025-01-28 17:21:38,235] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n02_undetermined_fastqc.html [2025-01-28 17:21:38,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n02_undetermined_fastqc.html [2025-01-28 17:21:38,288] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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17:21:40,179] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n01_FOXA3_noIFN_rep3_fastqc.html [2025-01-28 17:21:40,181] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n01_FOXA3_noIFN_rep3_fastqc.html [2025-01-28 17:21:40,227] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n01_H3K4me3_plusIFN_rep1_fastqc.html [2025-01-28 17:21:40,229] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n01_H3K4me3_plusIFN_rep1_fastqc.html [2025-01-28 17:21:40,276] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n01_IgG_plusIFN_rep1_fastqc.html [2025-01-28 17:21:40,278] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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search pattern filesize limit: HMMLLDRX5_n01_FOXA3_plusIFN_rep2_fastqc.html [2025-01-28 17:21:40,473] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n02_FOXA3_noIFN_rep2_fastqc.html [2025-01-28 17:21:40,474] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n02_FOXA3_noIFN_rep2_fastqc.html [2025-01-28 17:21:40,521] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n02_IgG_plusIFN_rep1_fastqc.html [2025-01-28 17:21:40,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n02_IgG_plusIFN_rep1_fastqc.html [2025-01-28 17:21:40,572] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n02_H3K27ac_plusIFN_rep3_fastqc.html [2025-01-28 17:21:40,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n02_H3K27ac_plusIFN_rep3_fastqc.html [2025-01-28 17:21:40,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n01_H3K27ac_noIFN_rep3_fastqc.html [2025-01-28 17:21:40,622] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n01_H3K27ac_noIFN_rep3_fastqc.html [2025-01-28 17:21:40,670] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n01_IgG_plusIFN_rep3_fastqc.html [2025-01-28 17:21:40,672] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n01_IgG_plusIFN_rep3_fastqc.html [2025-01-28 17:21:40,719] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMMLLDRX5_n01_FOXA3_noIFN_rep2_fastqc.html [2025-01-28 17:21:40,721] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMMLLDRX5_n01_FOXA3_noIFN_rep2_fastqc.html [2025-01-28 17:21:41,234] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-28 17:21:41,235] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-28 17:21:41,254] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2025-01-28 17:21:41,264] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-28 17:21:41,265] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-28 17:21:41,270] multiqc [DEBUG ] No samples found: conpair [2025-01-28 17:21:41,275] multiqc [DEBUG ] No samples found: peddy [2025-01-28 17:21:41,280] multiqc [DEBUG ] No samples found: somalier [2025-01-28 17:21:41,285] multiqc [DEBUG ] No samples found: methylQA [2025-01-28 17:21:41,293] multiqc [DEBUG ] No samples found: mosdepth [2025-01-28 17:21:41,299] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-28 17:21:41,302] multiqc [DEBUG ] No samples found: qualimap [2025-01-28 17:21:41,308] multiqc [DEBUG ] No samples found: preseq [2025-01-28 17:21:41,313] multiqc [DEBUG ] No samples found: quast [2025-01-28 17:21:41,318] multiqc [DEBUG ] No samples found: qorts [2025-01-28 17:21:41,323] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-28 17:21:41,327] multiqc [DEBUG ] No samples found: rockhopper [2025-01-28 17:21:41,332] multiqc [DEBUG ] No samples found: rsem [2025-01-28 17:21:41,343] multiqc [DEBUG ] No samples found: rseqc [2025-01-28 17:21:41,348] multiqc [DEBUG ] No samples found: busco [2025-01-28 17:21:41,353] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-28 17:21:41,358] multiqc [DEBUG ] No samples found: disambiguate [2025-01-28 17:21:41,363] multiqc [DEBUG ] No samples found: supernova [2025-01-28 17:21:41,376] multiqc [DEBUG ] No samples found: deeptools [2025-01-28 17:21:41,381] multiqc [DEBUG ] No samples found: sargasso [2025-01-28 17:21:41,385] multiqc [DEBUG ] No samples found: verifybamid [2025-01-28 17:21:41,390] multiqc [DEBUG ] No samples found: mirtrace [2025-01-28 17:21:41,395] multiqc [DEBUG ] No samples found: happy [2025-01-28 17:21:41,400] multiqc [DEBUG ] No samples found: mirtop [2025-01-28 17:21:41,406] multiqc [DEBUG ] No samples found: homer [2025-01-28 17:21:41,412] multiqc [DEBUG ] No samples found: macs2 [2025-01-28 17:21:41,416] multiqc [DEBUG ] No samples found: theta2 [2025-01-28 17:21:41,421] multiqc [DEBUG ] No samples found: snpeff [2025-01-28 17:21:41,429] multiqc [DEBUG ] No samples found: gatk [2025-01-28 17:21:41,434] multiqc [DEBUG ] No samples found: htseq [2025-01-28 17:21:41,439] multiqc [DEBUG ] No samples found: bcftools [2025-01-28 17:21:41,445] multiqc [DEBUG ] No samples found: featureCounts [2025-01-28 17:21:41,451] multiqc [DEBUG ] No samples found: fgbio [2025-01-28 17:21:41,464] multiqc [DEBUG ] No samples found: dragen [2025-01-28 17:21:41,469] multiqc [DEBUG ] No samples found: dedup [2025-01-28 17:21:41,474] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-28 17:21:41,496] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-28 17:21:41,501] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-28 17:21:41,504] multiqc [DEBUG ] No samples found: picard [2025-01-28 17:21:41,508] multiqc [DEBUG ] No samples found: prokka [2025-01-28 17:21:41,513] multiqc [DEBUG ] No samples found: samblaster [2025-01-28 17:21:41,521] multiqc [DEBUG ] No samples found: samtools [2025-01-28 17:21:41,526] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-28 17:21:41,531] multiqc [DEBUG ] No samples found: bamtools [2025-01-28 17:21:41,535] multiqc [DEBUG ] No samples found: jellyfish [2025-01-28 17:21:41,543] multiqc [DEBUG ] No samples found: vcftools [2025-01-28 17:21:41,548] multiqc [DEBUG ] No samples found: longranger [2025-01-28 17:21:41,552] multiqc [DEBUG ] No samples found: stacks [2025-01-28 17:21:41,558] multiqc [DEBUG ] No samples found: varscan2 [2025-01-28 17:21:41,572] multiqc [DEBUG ] No samples found: bbmap [2025-01-28 17:21:41,577] multiqc [DEBUG ] No samples found: bismark [2025-01-28 17:21:41,582] multiqc [DEBUG ] No samples found: biscuit [2025-01-28 17:21:41,588] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-28 17:21:41,594] multiqc [DEBUG ] No samples found: hicup [2025-01-28 17:21:41,599] multiqc [DEBUG ] No samples found: hicpro [2025-01-28 17:21:41,604] multiqc [DEBUG ] No samples found: salmon [2025-01-28 17:21:41,608] multiqc [DEBUG ] No samples found: kallisto [2025-01-28 17:21:41,614] multiqc [DEBUG ] No samples found: slamdunk [2025-01-28 17:21:41,619] multiqc [DEBUG ] No samples found: star [2025-01-28 17:21:41,624] multiqc [DEBUG ] No samples found: hisat2 [2025-01-28 17:21:41,628] multiqc [DEBUG ] No samples found: tophat [2025-01-28 17:21:41,635] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-28 17:21:41,640] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-28 17:21:41,645] multiqc [DEBUG ] No samples found: snpsplit [2025-01-28 17:21:41,650] multiqc [DEBUG ] No samples found: kat [2025-01-28 17:21:41,655] multiqc [DEBUG ] No samples found: leehom [2025-01-28 17:21:41,659] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-28 17:21:41,664] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-28 17:21:41,668] multiqc [DEBUG ] No samples found: cutadapt [2025-01-28 17:21:41,673] multiqc [DEBUG ] No samples found: flexbar [2025-01-28 17:21:41,678] multiqc [DEBUG ] No samples found: kaiju [2025-01-28 17:21:41,683] multiqc [DEBUG ] No samples found: kraken [2025-01-28 17:21:41,687] multiqc [DEBUG ] No samples found: malt [2025-01-28 17:21:41,692] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-28 17:21:41,697] multiqc [DEBUG ] No samples found: sickle [2025-01-28 17:21:41,703] multiqc [DEBUG ] No samples found: skewer [2025-01-28 17:21:41,709] multiqc [DEBUG ] No samples found: sortmerna [2025-01-28 17:21:41,713] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-28 17:21:41,718] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-28 17:21:41,723] multiqc [DEBUG ] No samples found: afterqc [2025-01-28 17:21:41,728] multiqc [DEBUG ] No samples found: fastp [2025-01-28 17:21:43,527] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2025-01-28 17:21:44,318] multiqc [DEBUG ] No samples found: pycoqc [2025-01-28 17:21:44,324] multiqc [DEBUG ] No samples found: minionqc [2025-01-28 17:21:44,330] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-28 17:21:44,337] multiqc [DEBUG ] No samples found: clusterflow [2025-01-28 17:21:44,343] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-28 17:21:44,349] multiqc [DEBUG ] No samples found: interop [2025-01-28 17:21:44,355] multiqc [DEBUG ] No samples found: ivar [2025-01-28 17:21:44,362] multiqc [DEBUG ] No samples found: flash [2025-01-28 17:21:44,369] multiqc [DEBUG ] No samples found: seqyclean [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-28 17:21:44,369] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-28 17:21:44,370] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-28 17:21:44,370] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-28 17:21:44,370] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-28 17:21:44,370] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-28 17:21:44,428] multiqc [INFO ] Compressing plot data [2025-01-28 17:21:45,425] multiqc [INFO ] Report : multiqc_report.html [2025-01-28 17:21:45,425] multiqc [INFO ] Data : multiqc_data [2025-01-28 17:21:45,425] multiqc [DEBUG ] Moving data file from '/state/partition1/job-56561329/tmp7ixz36tf/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/89/bb4fc79e23ba6ee8c869785491f0c8/merged/multiqc_data' [2025-01-28 17:21:45,558] multiqc [INFO ] MultiQC complete