[2024-07-24 08:21:09,832] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-07-24 08:21:09,832] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-07-24 08:21:09,835] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-07-24 08:21:09,837] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-07-24 08:21:09,837] 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}} [2024-07-24 08:21:09,837] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-24 08:21:09,873] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-07-24 08:21:09,873] multiqc [INFO ] This is MultiQC v1.9 [2024-07-24 08:21:09,873] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-24 08:21:09,873] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/44/80b815dad0f54a0ec26306c835051f/merged [2024-07-24 08:21:09,873] multiqc [INFO ] Template : default [2024-07-24 08:21:09,873] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-07-24 08:21:09,873] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/44/80b815dad0f54a0ec26306c835051f/merged [2024-07-24 08:21:09,873] 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 [2024-07-24 08:21:09,873] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-48887280/tmpyr2cmsqt [2024-07-24 08:21:10,285] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n01_01_PRMA_fastqc.html [2024-07-24 08:21:10,376] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n01_01_PRMA_fastqc.html [2024-07-24 08:21:10,778] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-07-24 08:21:41,956] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_37_PRMA_fastqc.html [2024-07-24 08:21:42,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_37_PRMA_fastqc.html [2024-07-24 08:21:42,814] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_38_PRMA_fastqc.html [2024-07-24 08:21:42,918] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_38_PRMA_fastqc.html [2024-07-24 08:21:43,565] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_39_PRMA_fastqc.html [2024-07-24 08:21:43,640] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_39_PRMA_fastqc.html [2024-07-24 08:21:44,136] multiqc 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search pattern filesize limit: HFJTJDRX5_n02_46_GTCA_fastqc.html [2024-07-24 08:21:47,021] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_46_GTCA_fastqc.html [2024-07-24 08:21:47,443] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_47_GTCA_fastqc.html [2024-07-24 08:21:47,479] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_47_GTCA_fastqc.html [2024-07-24 08:21:47,851] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_48_GTCA_fastqc.html [2024-07-24 08:21:47,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_48_GTCA_fastqc.html [2024-07-24 08:21:48,358] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_49_GTCA_fastqc.html [2024-07-24 08:21:48,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_49_GTCA_fastqc.html [2024-07-24 08:21:48,848] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_50_GTCA_fastqc.html [2024-07-24 08:21:48,944] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_50_GTCA_fastqc.html [2024-07-24 08:21:49,536] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFJTJDRX5_n02_undetermined_fastqc.html [2024-07-24 08:21:49,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFJTJDRX5_n02_undetermined_fastqc.html [2024-07-24 08:21:50,161] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-24 08:21:50,162] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-24 08:21:50,214] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 39 samples (table) [2024-07-24 08:21:50,216] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-07-24 08:21:50,226] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-07-24 08:21:50,229] multiqc [DEBUG ] No samples found: conpair [2024-07-24 08:21:50,231] multiqc [DEBUG ] No samples found: peddy [2024-07-24 08:21:50,234] multiqc [DEBUG ] No samples found: somalier [2024-07-24 08:21:50,237] multiqc [DEBUG ] No samples found: methylQA [2024-07-24 08:21:50,241] multiqc [DEBUG ] No samples found: mosdepth [2024-07-24 08:21:50,243] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-07-24 08:21:50,246] multiqc [DEBUG ] No samples found: qualimap [2024-07-24 08:21:50,248] multiqc [DEBUG ] No samples found: preseq [2024-07-24 08:21:50,251] multiqc [DEBUG ] No samples found: quast [2024-07-24 08:21:50,254] multiqc [DEBUG ] No samples found: qorts [2024-07-24 08:21:50,257] multiqc [DEBUG ] No samples found: rna_seqc [2024-07-24 08:21:50,259] multiqc [DEBUG ] No samples found: rockhopper [2024-07-24 08:21:50,262] multiqc [DEBUG ] No samples found: rsem [2024-07-24 08:21:50,267] multiqc [DEBUG ] No samples found: rseqc [2024-07-24 08:21:50,269] multiqc [DEBUG ] No samples found: busco [2024-07-24 08:21:50,272] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-07-24 08:21:50,275] multiqc [DEBUG ] No samples found: disambiguate [2024-07-24 08:21:50,278] multiqc [DEBUG ] No samples found: supernova [2024-07-24 08:21:50,282] multiqc [DEBUG ] No samples found: deeptools [2024-07-24 08:21:50,285] multiqc [DEBUG ] No samples found: sargasso [2024-07-24 08:21:50,288] multiqc [DEBUG ] No samples found: verifybamid [2024-07-24 08:21:50,290] multiqc [DEBUG ] No samples found: mirtrace [2024-07-24 08:21:50,293] multiqc [DEBUG ] No samples found: happy [2024-07-24 08:21:50,296] multiqc [DEBUG ] No samples found: mirtop [2024-07-24 08:21:50,299] multiqc [DEBUG ] No samples found: homer [2024-07-24 08:21:50,302] multiqc [DEBUG ] No samples found: macs2 [2024-07-24 08:21:50,304] multiqc [DEBUG ] No samples found: theta2 [2024-07-24 08:21:50,307] multiqc [DEBUG ] No samples found: snpeff [2024-07-24 08:21:50,310] multiqc [DEBUG ] No samples found: gatk [2024-07-24 08:21:50,313] multiqc [DEBUG ] No samples found: htseq [2024-07-24 08:21:50,316] multiqc [DEBUG ] No samples found: bcftools [2024-07-24 08:21:50,318] multiqc [DEBUG ] No samples found: featureCounts [2024-07-24 08:21:50,321] multiqc [DEBUG ] No samples found: fgbio [2024-07-24 08:21:50,326] multiqc [DEBUG ] No samples found: dragen [2024-07-24 08:21:50,329] multiqc [DEBUG ] No samples found: dedup [2024-07-24 08:21:50,332] multiqc [DEBUG ] No samples found: damageprofiler [2024-07-24 08:21:50,339] multiqc [DEBUG ] No samples found: biobambam2 [2024-07-24 08:21:50,342] multiqc [DEBUG ] No samples found: mtnucratio [2024-07-24 08:21:50,344] multiqc [DEBUG ] No samples found: picard [2024-07-24 08:21:50,347] multiqc [DEBUG ] No samples found: prokka [2024-07-24 08:21:50,350] multiqc [DEBUG ] No samples found: samblaster [2024-07-24 08:21:50,353] multiqc [DEBUG ] No samples found: samtools [2024-07-24 08:21:50,356] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-07-24 08:21:50,359] multiqc [DEBUG ] No samples found: bamtools [2024-07-24 08:21:50,361] multiqc [DEBUG ] No samples found: jellyfish [2024-07-24 08:21:50,365] multiqc [DEBUG ] No samples found: vcftools [2024-07-24 08:21:50,367] multiqc [DEBUG ] No samples found: longranger [2024-07-24 08:21:50,370] multiqc [DEBUG ] No samples found: stacks [2024-07-24 08:21:50,373] multiqc [DEBUG ] No samples found: varscan2 [2024-07-24 08:21:50,378] multiqc [DEBUG ] No samples found: bbmap [2024-07-24 08:21:50,381] multiqc [DEBUG ] No samples found: bismark [2024-07-24 08:21:50,384] multiqc [DEBUG ] No samples found: biscuit [2024-07-24 08:21:50,386] multiqc [DEBUG ] No samples found: hicexplorer [2024-07-24 08:21:50,389] multiqc [DEBUG ] No samples found: hicup [2024-07-24 08:21:50,392] multiqc [DEBUG ] No samples found: hicpro [2024-07-24 08:21:50,394] multiqc [DEBUG ] No samples found: salmon [2024-07-24 08:21:50,397] multiqc [DEBUG ] No samples found: kallisto [2024-07-24 08:21:50,400] multiqc [DEBUG ] No samples found: slamdunk [2024-07-24 08:21:50,402] multiqc [DEBUG ] No samples found: star [2024-07-24 08:21:50,405] multiqc [DEBUG ] No samples found: hisat2 [2024-07-24 08:21:50,408] multiqc [DEBUG ] No samples found: tophat [2024-07-24 08:21:50,410] multiqc [DEBUG ] No samples found: bowtie2 [2024-07-24 08:21:50,413] multiqc [DEBUG ] No samples found: bowtie1 [2024-07-24 08:21:50,416] multiqc [DEBUG ] No samples found: snpsplit [2024-07-24 08:21:50,418] multiqc [DEBUG ] No samples found: kat [2024-07-24 08:21:50,421] multiqc [DEBUG ] No samples found: leehom [2024-07-24 08:21:50,424] multiqc [DEBUG ] No samples found: adapterRemoval [2024-07-24 08:21:50,426] multiqc [DEBUG ] No samples found: clipandmerge [2024-07-24 08:21:50,429] multiqc [DEBUG ] No samples found: cutadapt [2024-07-24 08:21:50,432] multiqc [DEBUG ] No samples found: flexbar [2024-07-24 08:21:50,434] multiqc [DEBUG ] No samples found: kaiju [2024-07-24 08:21:50,437] multiqc [DEBUG ] No samples found: kraken [2024-07-24 08:21:50,440] multiqc [DEBUG ] No samples found: malt [2024-07-24 08:21:50,443] multiqc [DEBUG ] No samples found: trimmomatic [2024-07-24 08:21:50,445] multiqc [DEBUG ] No samples found: sickle [2024-07-24 08:21:50,448] multiqc [DEBUG ] No samples found: skewer [2024-07-24 08:21:50,451] multiqc [DEBUG ] No samples found: sortmerna [2024-07-24 08:21:50,453] multiqc [DEBUG ] No samples found: biobloomtools [2024-07-24 08:21:50,456] multiqc [DEBUG ] No samples found: fastq_screen [2024-07-24 08:21:50,459] multiqc [DEBUG ] No samples found: afterqc [2024-07-24 08:21:50,461] multiqc [DEBUG ] No samples found: fastp [2024-07-24 08:21:57,379] multiqc.modules.fastqc.fastqc [INFO ] Found 78 reports [2024-07-24 08:21:57,979] multiqc [DEBUG ] No samples found: pycoqc [2024-07-24 08:21:57,982] multiqc [DEBUG ] No samples found: minionqc [2024-07-24 08:21:57,985] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-07-24 08:21:57,988] multiqc [DEBUG ] No samples found: clusterflow [2024-07-24 08:21:57,991] multiqc [DEBUG ] No samples found: bcl2fastq [2024-07-24 08:21:57,993] multiqc [DEBUG ] No samples found: interop [2024-07-24 08:21:57,996] multiqc [DEBUG ] No samples found: ivar [2024-07-24 08:21:57,999] multiqc [DEBUG ] No samples found: flash [2024-07-24 08:21:58,002] multiqc [DEBUG ] No samples found: seqyclean [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-07-24 08:21:58,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-07-24 08:21:58,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-07-24 08:21:58,003] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-07-24 08:21:58,003] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-07-24 08:21:58,003] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-07-24 08:21:58,094] multiqc [INFO ] Compressing plot data [2024-07-24 08:21:59,365] multiqc [INFO ] Report : multiqc_report.html [2024-07-24 08:21:59,365] multiqc [INFO ] Data : multiqc_data [2024-07-24 08:21:59,365] multiqc [DEBUG ] Moving data file from '/state/partition1/job-48887280/tmpyr2cmsqt/multiqc_data' to '/vast/gencore/GENEFLOW/work/44/80b815dad0f54a0ec26306c835051f/merged/multiqc_data' [2024-07-24 08:22:00,045] multiqc [INFO ] MultiQC complete