[2025-01-30 18:47:41,179] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-30 18:47:41,179] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-30 18:47:41,180] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-30 18:47:41,182] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-30 18:47:41,182] 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 18:47:41,182] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 18:47:41,217] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-30 18:47:41,218] multiqc [INFO ] This is MultiQC v1.9 [2025-01-30 18:47:41,218] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 18:47:41,218] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/6b/e996b69c82adb5d07100cd78759032/3 [2025-01-30 18:47:41,218] multiqc [INFO ] Template : default [2025-01-30 18:47:41,218] 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 18:47:41,218] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/6b/e996b69c82adb5d07100cd78759032/3 [2025-01-30 18:47:41,218] 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 18:47:41,218] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-56666159/tmp6acg981q [2025-01-30 18:47:41,328] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5220_POOLRET88_fastqc.html [2025-01-30 18:47:41,331] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5220_POOLRET88_fastqc.html [2025-01-30 18:47:41,385] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern 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18:47:59,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n02_ECA3094_POOLRET88_fastqc.html [2025-01-30 18:47:59,348] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n02_ECA3094_POOLRET88_fastqc.html [2025-01-30 18:47:59,394] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_ECA3536_POOLRET88_fastqc.html [2025-01-30 18:47:59,396] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_ECA3536_POOLRET88_fastqc.html [2025-01-30 18:47:59,442] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n02_QG4910_POOLRET88_fastqc.html [2025-01-30 18:47:59,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_ECA3549_POOLRET88_fastqc.html [2025-01-30 18:47:59,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4641_POOLRET88_fastqc.html [2025-01-30 18:47:59,637] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4641_POOLRET88_fastqc.html [2025-01-30 18:47:59,683] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n02_ECA3608_POOLRET88_fastqc.html [2025-01-30 18:47:59,685] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n02_ECA3608_POOLRET88_fastqc.html [2025-01-30 18:47:59,731] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5262_POOLRET88_fastqc.html [2025-01-30 18:47:59,733] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5262_POOLRET88_fastqc.html [2025-01-30 18:47:59,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5008_POOLRET88_fastqc.html [2025-01-30 18:47:59,781] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5008_POOLRET88_fastqc.html [2025-01-30 18:47:59,828] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4780_POOLRET88_fastqc.html [2025-01-30 18:47:59,830] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4780_POOLRET88_fastqc.html [2025-01-30 18:47:59,877] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4924_POOLRET88_fastqc.html [2025-01-30 18:47:59,879] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4924_POOLRET88_fastqc.html [2025-01-30 18:47:59,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4739_POOLRET88_fastqc.html [2025-01-30 18:47:59,926] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4739_POOLRET88_fastqc.html [2025-01-30 18:47:59,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4910_POOLRET88_fastqc.html [2025-01-30 18:47:59,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG4910_POOLRET88_fastqc.html [2025-01-30 18:48:00,021] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5103_POOLRET88_fastqc.html [2025-01-30 18:48:00,023] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_QG5103_POOLRET88_fastqc.html [2025-01-30 18:48:00,069] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_ECA3560_POOLRET88_fastqc.html [2025-01-30 18:48:00,071] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l03_n01_ECA3560_POOLRET88_fastqc.html [2025-01-30 18:48:00,528] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 18:48:00,529] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 18:48:00,539] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-30 18:48:00,626] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 193 samples (table) [2025-01-30 18:48:00,636] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-30 18:48:00,641] multiqc [DEBUG ] No samples found: conpair [2025-01-30 18:48:00,646] multiqc [DEBUG ] No samples found: peddy [2025-01-30 18:48:00,650] multiqc [DEBUG ] No samples found: somalier [2025-01-30 18:48:00,655] multiqc [DEBUG ] No samples found: methylQA [2025-01-30 18:48:00,662] multiqc [DEBUG ] No samples found: mosdepth [2025-01-30 18:48:00,666] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-30 18:48:00,669] multiqc [DEBUG ] No samples found: qualimap [2025-01-30 18:48:00,673] multiqc [DEBUG ] No samples found: preseq [2025-01-30 18:48:00,678] multiqc [DEBUG ] No samples found: quast [2025-01-30 18:48:00,682] multiqc [DEBUG ] No samples found: qorts [2025-01-30 18:48:00,686] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-30 18:48:00,691] multiqc [DEBUG ] No samples found: rockhopper [2025-01-30 18:48:00,695] multiqc [DEBUG ] No samples found: rsem [2025-01-30 18:48:00,705] multiqc [DEBUG ] No samples found: rseqc [2025-01-30 18:48:00,709] multiqc [DEBUG ] No samples found: busco [2025-01-30 18:48:00,713] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-30 18:48:00,717] multiqc [DEBUG ] No samples found: disambiguate [2025-01-30 18:48:00,721] multiqc [DEBUG ] No samples found: supernova [2025-01-30 18:48:00,732] multiqc [DEBUG ] No samples found: deeptools [2025-01-30 18:48:00,737] multiqc [DEBUG ] No samples found: sargasso [2025-01-30 18:48:00,741] multiqc [DEBUG ] No samples found: verifybamid [2025-01-30 18:48:00,745] multiqc [DEBUG ] No samples found: mirtrace [2025-01-30 18:48:00,749] multiqc [DEBUG ] No samples found: happy [2025-01-30 18:48:00,753] multiqc [DEBUG ] No samples found: mirtop [2025-01-30 18:48:00,759] multiqc [DEBUG ] No samples found: homer [2025-01-30 18:48:00,763] multiqc [DEBUG ] No samples found: macs2 [2025-01-30 18:48:00,767] multiqc [DEBUG ] No samples found: theta2 [2025-01-30 18:48:00,771] multiqc [DEBUG ] No samples found: snpeff [2025-01-30 18:48:00,777] multiqc [DEBUG ] No samples found: gatk [2025-01-30 18:48:00,781] multiqc [DEBUG ] No samples found: htseq [2025-01-30 18:48:00,786] multiqc [DEBUG ] No samples found: bcftools [2025-01-30 18:48:00,790] multiqc [DEBUG ] No samples found: featureCounts [2025-01-30 18:48:00,796] multiqc [DEBUG ] No samples found: fgbio [2025-01-30 18:48:00,807] multiqc [DEBUG ] No samples found: dragen [2025-01-30 18:48:00,811] multiqc [DEBUG ] No samples found: dedup [2025-01-30 18:48:00,815] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-30 18:48:00,834] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-30 18:48:00,838] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-30 18:48:00,841] multiqc [DEBUG ] No samples found: picard [2025-01-30 18:48:00,845] multiqc [DEBUG ] No samples found: prokka [2025-01-30 18:48:00,849] multiqc [DEBUG ] No samples found: samblaster [2025-01-30 18:48:00,856] multiqc [DEBUG ] No samples found: samtools [2025-01-30 18:48:00,860] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-30 18:48:00,865] multiqc [DEBUG ] No samples found: bamtools [2025-01-30 18:48:00,869] multiqc [DEBUG ] No samples found: jellyfish [2025-01-30 18:48:00,875] multiqc [DEBUG ] No samples found: vcftools [2025-01-30 18:48:00,880] multiqc [DEBUG ] No samples found: longranger [2025-01-30 18:48:00,884] multiqc [DEBUG ] No samples found: stacks [2025-01-30 18:48:00,888] multiqc [DEBUG ] No samples found: varscan2 [2025-01-30 18:48:00,900] multiqc [DEBUG ] No samples found: bbmap [2025-01-30 18:48:00,904] multiqc [DEBUG ] No samples found: bismark [2025-01-30 18:48:00,909] multiqc [DEBUG ] No samples found: biscuit [2025-01-30 18:48:00,913] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-30 18:48:00,918] multiqc [DEBUG ] No samples found: hicup [2025-01-30 18:48:00,922] multiqc [DEBUG ] No samples found: hicpro [2025-01-30 18:48:00,926] multiqc [DEBUG ] No samples found: salmon [2025-01-30 18:48:00,930] multiqc [DEBUG ] No samples found: kallisto [2025-01-30 18:48:00,935] multiqc [DEBUG ] No samples found: slamdunk [2025-01-30 18:48:00,939] multiqc [DEBUG ] No samples found: star [2025-01-30 18:48:00,944] multiqc [DEBUG ] No samples found: hisat2 [2025-01-30 18:48:00,948] multiqc [DEBUG ] No samples found: tophat [2025-01-30 18:48:00,952] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-30 18:48:00,957] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-30 18:48:00,961] multiqc [DEBUG ] No samples found: snpsplit [2025-01-30 18:48:00,965] multiqc [DEBUG ] No samples found: kat [2025-01-30 18:48:00,969] multiqc [DEBUG ] No samples found: leehom [2025-01-30 18:48:00,973] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-30 18:48:00,977] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-30 18:48:00,982] multiqc [DEBUG ] No samples found: cutadapt [2025-01-30 18:48:00,986] multiqc [DEBUG ] No samples found: flexbar [2025-01-30 18:48:00,990] multiqc [DEBUG ] No samples found: kaiju [2025-01-30 18:48:00,994] multiqc [DEBUG ] No samples found: kraken [2025-01-30 18:48:00,998] multiqc [DEBUG ] No samples found: malt [2025-01-30 18:48:01,003] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-30 18:48:01,007] multiqc [DEBUG ] No samples found: sickle [2025-01-30 18:48:01,011] multiqc [DEBUG ] No samples found: skewer [2025-01-30 18:48:01,015] multiqc [DEBUG ] No samples found: sortmerna [2025-01-30 18:48:01,019] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-30 18:48:01,023] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-30 18:48:01,027] multiqc [DEBUG ] No samples found: afterqc [2025-01-30 18:48:01,032] multiqc [DEBUG ] No samples found: fastp [2025-01-30 18:48:57,975] multiqc.modules.fastqc.fastqc [INFO ] Found 386 reports [2025-01-30 18:49:25,919] multiqc [DEBUG ] No samples found: pycoqc [2025-01-30 18:49:25,924] multiqc [DEBUG ] No samples found: minionqc [2025-01-30 18:49:25,929] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-30 18:49:25,933] multiqc [DEBUG ] No samples found: clusterflow [2025-01-30 18:49:25,937] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-30 18:49:25,942] multiqc [DEBUG ] No samples found: interop [2025-01-30 18:49:25,946] multiqc [DEBUG ] No samples found: ivar [2025-01-30 18:49:25,950] multiqc [DEBUG ] No samples found: flash [2025-01-30 18:49:25,955] multiqc [DEBUG ] No samples found: seqyclean [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-30 18:49:25,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-30 18:49:26,397] multiqc [INFO ] Compressing plot data [2025-01-30 18:49:26,549] multiqc [INFO ] Report : multiqc_report.html [2025-01-30 18:49:26,549] multiqc [INFO ] Data : multiqc_data [2025-01-30 18:49:26,549] multiqc [DEBUG ] Moving data file from '/state/partition1/job-56666159/tmp6acg981q/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/6b/e996b69c82adb5d07100cd78759032/3/multiqc_data' [2025-01-30 18:49:27,046] multiqc [INFO ] MultiQC complete