[2024-10-16 18:19:11,041] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-10-16 18:19:11,041] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-10-16 18:19:11,041] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-10-16 18:19:11,044] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-10-16 18:19:11,044] 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}} [2024-10-16 18:19:11,044] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-16 18:19:11,098] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-10-16 18:19:11,098] multiqc [INFO ] This is MultiQC v1.9 [2024-10-16 18:19:11,098] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-16 18:19:11,098] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/f2/b1ac5c5640b4c6d05d2ed4f35e4d7c/2 [2024-10-16 18:19:11,098] multiqc [INFO ] Template : default [2024-10-16 18:19:11,098] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-10-16 18:19:11,098] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/f2/b1ac5c5640b4c6d05d2ed4f35e4d7c/2 [2024-10-16 18:19:11,098] 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 [2024-10-16 18:19:11,098] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-52278942/tmp8brpcr6x [2024-10-16 18:19:11,213] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3004_POOLRET80_fastqc.html [2024-10-16 18:19:11,216] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3004_POOLRET80_fastqc.html [2024-10-16 18:19:11,266] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern 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18:19:29,614] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3519_POOLRET80_fastqc.html [2024-10-16 18:19:29,616] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3519_POOLRET80_fastqc.html [2024-10-16 18:19:29,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3683_POOLRET80_fastqc.html [2024-10-16 18:19:29,664] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3683_POOLRET80_fastqc.html [2024-10-16 18:19:29,710] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA2999_POOLRET80_fastqc.html [2024-10-16 18:19:29,712] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA2999_POOLRET80_fastqc.html [2024-10-16 18:19:29,758] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n02_ECA3134_POOLRET80_fastqc.html [2024-10-16 18:19:29,760] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n02_ECA3134_POOLRET80_fastqc.html [2024-10-16 18:19:29,806] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3602_POOLRET80_fastqc.html [2024-10-16 18:19:29,808] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l02_n01_ECA3602_POOLRET80_fastqc.html [2024-10-16 18:19:30,191] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-16 18:19:30,193] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-16 18:19:30,290] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 193 samples (table) [2024-10-16 18:19:30,300] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-10-16 18:19:30,302] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-10-16 18:19:30,308] multiqc [DEBUG ] No samples found: conpair [2024-10-16 18:19:30,314] multiqc [DEBUG ] No samples found: peddy [2024-10-16 18:19:30,319] multiqc [DEBUG ] No samples found: somalier [2024-10-16 18:19:30,325] multiqc [DEBUG ] No samples found: methylQA [2024-10-16 18:19:30,335] multiqc [DEBUG ] No samples found: mosdepth [2024-10-16 18:19:30,340] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-10-16 18:19:30,343] multiqc [DEBUG ] No samples found: qualimap [2024-10-16 18:19:30,348] multiqc [DEBUG ] No samples found: preseq [2024-10-16 18:19:30,353] multiqc [DEBUG ] No samples found: quast [2024-10-16 18:19:30,358] multiqc [DEBUG ] No samples found: qorts [2024-10-16 18:19:30,363] multiqc [DEBUG ] No samples found: rna_seqc [2024-10-16 18:19:30,368] multiqc [DEBUG ] No samples found: rockhopper [2024-10-16 18:19:30,372] multiqc [DEBUG ] No samples found: rsem [2024-10-16 18:19:30,384] multiqc [DEBUG ] No samples found: rseqc [2024-10-16 18:19:30,389] multiqc [DEBUG ] No samples found: busco [2024-10-16 18:19:30,394] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-10-16 18:19:30,399] multiqc [DEBUG ] No samples found: disambiguate [2024-10-16 18:19:30,405] multiqc [DEBUG ] No samples found: supernova [2024-10-16 18:19:30,420] multiqc [DEBUG ] No samples found: deeptools [2024-10-16 18:19:30,425] multiqc [DEBUG ] No samples found: sargasso [2024-10-16 18:19:30,430] multiqc [DEBUG ] No samples found: verifybamid [2024-10-16 18:19:30,435] multiqc [DEBUG ] No samples found: mirtrace [2024-10-16 18:19:30,440] multiqc [DEBUG ] No samples found: happy [2024-10-16 18:19:30,445] multiqc [DEBUG ] No samples found: mirtop [2024-10-16 18:19:30,451] multiqc [DEBUG ] No samples found: homer [2024-10-16 18:19:30,456] multiqc [DEBUG ] No samples found: macs2 [2024-10-16 18:19:30,460] multiqc [DEBUG ] No samples found: theta2 [2024-10-16 18:19:30,465] multiqc [DEBUG ] No samples found: snpeff [2024-10-16 18:19:30,475] multiqc [DEBUG ] No samples found: gatk [2024-10-16 18:19:30,480] multiqc [DEBUG ] No samples found: htseq [2024-10-16 18:19:30,489] multiqc [DEBUG ] No samples found: bcftools [2024-10-16 18:19:30,495] multiqc [DEBUG ] No samples found: featureCounts [2024-10-16 18:19:30,502] multiqc [DEBUG ] No samples found: fgbio [2024-10-16 18:19:30,518] multiqc [DEBUG ] No samples found: dragen [2024-10-16 18:19:30,523] multiqc [DEBUG ] No samples found: dedup [2024-10-16 18:19:30,528] multiqc [DEBUG ] No samples found: damageprofiler [2024-10-16 18:19:30,553] multiqc [DEBUG ] No samples found: biobambam2 [2024-10-16 18:19:30,557] multiqc [DEBUG ] No samples found: mtnucratio [2024-10-16 18:19:30,560] multiqc [DEBUG ] No samples found: picard [2024-10-16 18:19:30,565] multiqc [DEBUG ] No samples found: prokka [2024-10-16 18:19:30,570] multiqc [DEBUG ] No samples found: samblaster [2024-10-16 18:19:30,579] multiqc [DEBUG ] No samples found: samtools [2024-10-16 18:19:30,585] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-10-16 18:19:30,590] multiqc [DEBUG ] No samples found: bamtools [2024-10-16 18:19:30,596] multiqc [DEBUG ] No samples found: jellyfish [2024-10-16 18:19:30,605] multiqc [DEBUG ] No samples found: vcftools [2024-10-16 18:19:30,610] multiqc [DEBUG ] No samples found: longranger [2024-10-16 18:19:30,615] multiqc [DEBUG ] No samples found: stacks [2024-10-16 18:19:30,621] multiqc [DEBUG ] No samples found: varscan2 [2024-10-16 18:19:30,639] multiqc [DEBUG ] No samples found: bbmap [2024-10-16 18:19:30,645] multiqc [DEBUG ] No samples found: bismark [2024-10-16 18:19:30,650] multiqc [DEBUG ] No samples found: biscuit [2024-10-16 18:19:30,656] multiqc [DEBUG ] No samples found: hicexplorer [2024-10-16 18:19:30,662] multiqc [DEBUG ] No samples found: hicup [2024-10-16 18:19:30,667] multiqc [DEBUG ] No samples found: hicpro [2024-10-16 18:19:30,673] multiqc [DEBUG ] No samples found: salmon [2024-10-16 18:19:30,678] multiqc [DEBUG ] No samples found: kallisto [2024-10-16 18:19:30,684] multiqc [DEBUG ] No samples found: slamdunk [2024-10-16 18:19:30,689] multiqc [DEBUG ] No samples found: star [2024-10-16 18:19:30,694] multiqc [DEBUG ] No samples found: hisat2 [2024-10-16 18:19:30,700] multiqc [DEBUG ] No samples found: tophat [2024-10-16 18:19:30,705] multiqc [DEBUG ] No samples found: bowtie2 [2024-10-16 18:19:30,710] multiqc [DEBUG ] No samples found: bowtie1 [2024-10-16 18:19:30,716] multiqc [DEBUG ] No samples found: snpsplit [2024-10-16 18:19:30,721] multiqc [DEBUG ] No samples found: kat [2024-10-16 18:19:30,725] multiqc [DEBUG ] No samples found: leehom [2024-10-16 18:19:30,730] multiqc [DEBUG ] No samples found: adapterRemoval [2024-10-16 18:19:30,735] multiqc [DEBUG ] No samples found: clipandmerge [2024-10-16 18:19:30,740] multiqc [DEBUG ] No samples found: cutadapt [2024-10-16 18:19:30,745] multiqc [DEBUG ] No samples found: flexbar [2024-10-16 18:19:30,750] multiqc [DEBUG ] No samples found: kaiju [2024-10-16 18:19:30,755] multiqc [DEBUG ] No samples found: kraken [2024-10-16 18:19:30,760] multiqc [DEBUG ] No samples found: malt [2024-10-16 18:19:30,766] multiqc [DEBUG ] No samples found: trimmomatic [2024-10-16 18:19:30,771] multiqc [DEBUG ] No samples found: sickle [2024-10-16 18:19:30,776] multiqc [DEBUG ] No samples found: skewer [2024-10-16 18:19:30,781] multiqc [DEBUG ] No samples found: sortmerna [2024-10-16 18:19:30,785] multiqc [DEBUG ] No samples found: biobloomtools [2024-10-16 18:19:30,790] multiqc [DEBUG ] No samples found: fastq_screen [2024-10-16 18:19:30,796] multiqc [DEBUG ] No samples found: afterqc [2024-10-16 18:19:30,801] multiqc [DEBUG ] No samples found: fastp [2024-10-16 18:20:23,126] multiqc.modules.fastqc.fastqc [INFO ] Found 386 reports [2024-10-16 18:20:52,660] multiqc [DEBUG ] No samples found: pycoqc [2024-10-16 18:20:52,665] multiqc [DEBUG ] No samples found: minionqc [2024-10-16 18:20:52,672] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-10-16 18:20:52,678] multiqc [DEBUG ] No samples found: clusterflow [2024-10-16 18:20:52,684] multiqc [DEBUG ] No samples found: bcl2fastq [2024-10-16 18:20:52,691] multiqc [DEBUG ] No samples found: interop [2024-10-16 18:20:52,696] multiqc [DEBUG ] No samples found: ivar [2024-10-16 18:20:52,704] multiqc [DEBUG ] No samples found: flash [2024-10-16 18:20:52,709] multiqc [DEBUG ] No samples found: seqyclean [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-10-16 18:20:52,710] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-10-16 18:20:53,181] multiqc [INFO ] Compressing plot data [2024-10-16 18:20:53,320] multiqc [INFO ] Report : multiqc_report.html [2024-10-16 18:20:53,320] multiqc [INFO ] Data : multiqc_data [2024-10-16 18:20:53,320] multiqc [DEBUG ] Moving data file from '/state/partition1/job-52278942/tmp8brpcr6x/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/f2/b1ac5c5640b4c6d05d2ed4f35e4d7c/2/multiqc_data' [2024-10-16 18:20:53,880] multiqc [INFO ] MultiQC complete