[2025-01-30 18:40:03,511] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-30 18:40:03,511] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-30 18:40:03,511] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-30 18:40:03,513] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-30 18:40:03,513] 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 18:40:03,514] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 18:40:03,545] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-30 18:40:03,545] multiqc [INFO ] This is MultiQC v1.9 [2025-01-30 18:40:03,545] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 18:40:03,545] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/30/f779652a946ec8f03c0a799efd3de5/4 [2025-01-30 18:40:03,545] multiqc [INFO ] Template : default [2025-01-30 18:40:03,545] 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 18:40:03,545] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/30/f779652a946ec8f03c0a799efd3de5/4 [2025-01-30 18:40:03,546] 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 18:40:03,546] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-56666123/tmppyywh2mm [2025-01-30 18:40:03,655] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n01_PS9148_POOLRET89_fastqc.html [2025-01-30 18:40:03,658] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n01_PS9148_POOLRET89_fastqc.html [2025-01-30 18:40:03,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern 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File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n01_HPT34_POOLRET89_2_fastqc.html [2025-01-30 18:40:21,037] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_NIC2554_POOLRET89_fastqc.html [2025-01-30 18:40:21,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_NIC2554_POOLRET89_fastqc.html [2025-01-30 18:40:21,085] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_JU4365_POOLRET89_fastqc.html [2025-01-30 18:40:21,087] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_JU4365_POOLRET89_fastqc.html [2025-01-30 18:40:21,132] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H2MF5DSXF_l04_n02_QG4953_POOLRET89_fastqc.html [2025-01-30 18:40:21,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_HPT21_POOLRET89_fastqc.html [2025-01-30 18:40:21,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_HPT21_POOLRET89_fastqc.html [2025-01-30 18:40:21,607] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n01_WN2176_POOLRET89_fastqc.html [2025-01-30 18:40:21,609] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n01_WN2176_POOLRET89_fastqc.html [2025-01-30 18:40:21,654] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n01_QG5643_POOLRET89_fastqc.html [2025-01-30 18:40:21,656] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n01_QG5643_POOLRET89_fastqc.html [2025-01-30 18:40:21,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_BC1983_POOLRET89_fastqc.html [2025-01-30 18:40:21,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l04_n02_BC1983_POOLRET89_fastqc.html [2025-01-30 18:40:22,175] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 18:40:22,176] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 18:40:22,187] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-30 18:40:22,274] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 189 samples (table) [2025-01-30 18:40:22,284] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-30 18:40:22,289] multiqc [DEBUG ] No samples found: conpair [2025-01-30 18:40:22,294] multiqc [DEBUG ] No samples found: peddy [2025-01-30 18:40:22,298] multiqc [DEBUG ] No samples found: somalier [2025-01-30 18:40:22,303] multiqc [DEBUG ] No samples found: methylQA [2025-01-30 18:40:22,311] multiqc [DEBUG ] No samples found: mosdepth [2025-01-30 18:40:22,315] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-30 18:40:22,319] multiqc [DEBUG ] No samples found: qualimap [2025-01-30 18:40:22,323] multiqc [DEBUG ] No samples found: preseq [2025-01-30 18:40:22,328] multiqc [DEBUG ] No samples found: quast [2025-01-30 18:40:22,332] multiqc [DEBUG ] No samples found: qorts [2025-01-30 18:40:22,336] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-30 18:40:22,341] multiqc [DEBUG ] No samples found: rockhopper [2025-01-30 18:40:22,345] multiqc [DEBUG ] No samples found: rsem [2025-01-30 18:40:22,356] multiqc [DEBUG ] No samples found: rseqc [2025-01-30 18:40:22,360] multiqc [DEBUG ] No samples found: busco [2025-01-30 18:40:22,365] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-30 18:40:22,369] multiqc [DEBUG ] No samples found: disambiguate [2025-01-30 18:40:22,374] multiqc [DEBUG ] No samples found: supernova [2025-01-30 18:40:22,386] multiqc [DEBUG ] No samples found: deeptools [2025-01-30 18:40:22,390] multiqc [DEBUG ] No samples found: sargasso [2025-01-30 18:40:22,396] multiqc [DEBUG ] No samples found: verifybamid [2025-01-30 18:40:22,400] multiqc [DEBUG ] No samples found: mirtrace [2025-01-30 18:40:22,405] multiqc [DEBUG ] No samples found: happy [2025-01-30 18:40:22,409] multiqc [DEBUG ] No samples found: mirtop [2025-01-30 18:40:22,415] multiqc [DEBUG ] No samples found: homer [2025-01-30 18:40:22,419] multiqc [DEBUG ] No samples found: macs2 [2025-01-30 18:40:22,424] multiqc [DEBUG ] No samples found: theta2 [2025-01-30 18:40:22,428] multiqc [DEBUG ] No samples found: snpeff [2025-01-30 18:40:22,435] multiqc [DEBUG ] No samples found: gatk [2025-01-30 18:40:22,439] multiqc [DEBUG ] No samples found: htseq [2025-01-30 18:40:22,444] multiqc [DEBUG ] No samples found: bcftools [2025-01-30 18:40:22,448] multiqc [DEBUG ] No samples found: featureCounts [2025-01-30 18:40:22,454] multiqc [DEBUG ] No samples found: fgbio [2025-01-30 18:40:22,466] multiqc [DEBUG ] No samples found: dragen [2025-01-30 18:40:22,471] multiqc [DEBUG ] No samples found: dedup [2025-01-30 18:40:22,475] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-30 18:40:22,496] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-30 18:40:22,501] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-30 18:40:22,503] multiqc [DEBUG ] No samples found: picard [2025-01-30 18:40:22,508] multiqc [DEBUG ] No samples found: prokka [2025-01-30 18:40:22,512] multiqc [DEBUG ] No samples found: samblaster [2025-01-30 18:40:22,520] multiqc [DEBUG ] No samples found: samtools [2025-01-30 18:40:22,524] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-30 18:40:22,529] multiqc [DEBUG ] No samples found: bamtools [2025-01-30 18:40:22,533] multiqc [DEBUG ] No samples found: jellyfish [2025-01-30 18:40:22,541] multiqc [DEBUG ] No samples found: vcftools [2025-01-30 18:40:22,545] multiqc [DEBUG ] No samples found: longranger [2025-01-30 18:40:22,550] multiqc [DEBUG ] No samples found: stacks [2025-01-30 18:40:22,554] multiqc [DEBUG ] No samples found: varscan2 [2025-01-30 18:40:22,567] multiqc [DEBUG ] No samples found: bbmap [2025-01-30 18:40:22,572] multiqc [DEBUG ] No samples found: bismark [2025-01-30 18:40:22,577] multiqc [DEBUG ] No samples found: biscuit [2025-01-30 18:40:22,581] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-30 18:40:22,586] multiqc [DEBUG ] No samples found: hicup [2025-01-30 18:40:22,590] multiqc [DEBUG ] No samples found: hicpro [2025-01-30 18:40:22,595] multiqc [DEBUG ] No samples found: salmon [2025-01-30 18:40:22,599] multiqc [DEBUG ] No samples found: kallisto [2025-01-30 18:40:22,604] multiqc [DEBUG ] No samples found: slamdunk [2025-01-30 18:40:22,608] multiqc [DEBUG ] No samples found: star [2025-01-30 18:40:22,612] multiqc [DEBUG ] No samples found: hisat2 [2025-01-30 18:40:22,617] multiqc [DEBUG ] No samples found: tophat [2025-01-30 18:40:22,621] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-30 18:40:22,626] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-30 18:40:22,630] multiqc [DEBUG ] No samples found: snpsplit [2025-01-30 18:40:22,634] multiqc [DEBUG ] No samples found: kat [2025-01-30 18:40:22,639] multiqc [DEBUG ] No samples found: leehom [2025-01-30 18:40:22,643] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-30 18:40:22,647] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-30 18:40:22,652] multiqc [DEBUG ] No samples found: cutadapt [2025-01-30 18:40:22,656] multiqc [DEBUG ] No samples found: flexbar [2025-01-30 18:40:22,660] multiqc [DEBUG ] No samples found: kaiju [2025-01-30 18:40:22,665] multiqc [DEBUG ] No samples found: kraken [2025-01-30 18:40:22,669] multiqc [DEBUG ] No samples found: malt [2025-01-30 18:40:22,673] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-30 18:40:22,679] multiqc [DEBUG ] No samples found: sickle [2025-01-30 18:40:22,683] multiqc [DEBUG ] No samples found: skewer [2025-01-30 18:40:22,687] multiqc [DEBUG ] No samples found: sortmerna [2025-01-30 18:40:22,692] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-30 18:40:22,696] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-30 18:40:22,700] multiqc [DEBUG ] No samples found: afterqc [2025-01-30 18:40:22,705] multiqc [DEBUG ] No samples found: fastp [2025-01-30 18:41:17,483] multiqc.modules.fastqc.fastqc [INFO ] Found 378 reports [2025-01-30 18:41:53,102] multiqc [DEBUG ] No samples found: pycoqc [2025-01-30 18:41:53,107] multiqc [DEBUG ] No samples found: minionqc [2025-01-30 18:41:53,112] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-30 18:41:53,117] multiqc [DEBUG ] No samples found: clusterflow [2025-01-30 18:41:53,122] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-30 18:41:53,127] multiqc [DEBUG ] No samples found: interop [2025-01-30 18:41:53,132] multiqc [DEBUG ] No samples found: ivar [2025-01-30 18:41:53,137] multiqc [DEBUG ] No samples found: flash [2025-01-30 18:41:53,141] multiqc [DEBUG ] No samples found: seqyclean [2025-01-30 18:41:53,141] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-30 18:41:53,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-30 18:41:53,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-30 18:41:53,598] multiqc [INFO ] Compressing plot data [2025-01-30 18:41:53,732] multiqc [INFO ] Report : multiqc_report.html [2025-01-30 18:41:53,732] multiqc [INFO ] Data : multiqc_data [2025-01-30 18:41:53,732] multiqc [DEBUG ] Moving data file from '/state/partition1/job-56666123/tmppyywh2mm/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/30/f779652a946ec8f03c0a799efd3de5/4/multiqc_data' [2025-01-30 18:41:53,882] multiqc [INFO ] MultiQC complete