[2024-02-15 14:14:24,597] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-15 14:14:24,598] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-15 14:14:24,598] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-15 14:14:24,600] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-15 14:14:24,600] 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}} [2024-02-15 14:14:24,601] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-15 14:14:24,754] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-15 14:14:24,754] multiqc [INFO ] This is MultiQC v1.9 [2024-02-15 14:14:24,754] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-15 14:14:24,754] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/30/d8423ffcb6a680bd308aa1ce5b9604/merged [2024-02-15 14:14:24,754] multiqc [INFO ] Template : default [2024-02-15 14:14:24,754] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-15 14:14:24,754] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/30/d8423ffcb6a680bd308aa1ce5b9604/merged [2024-02-15 14:14:24,754] 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 [2024-02-15 14:14:24,755] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43014150/tmpmo86ftuf [2024-02-15 14:14:24,898] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-A1_fastqc.html [2024-02-15 14:14:24,908] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-A1_fastqc.html [2024-02-15 14:14:24,989] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-A2_fastqc.html [2024-02-15 14:14:25,002] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-A2_fastqc.html [2024-02-15 14:14:25,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-A3_fastqc.html [2024-02-15 14:14:25,115] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-A3_fastqc.html [2024-02-15 14:14:25,185] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-B1_fastqc.html [2024-02-15 14:14:25,193] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-B1_fastqc.html [2024-02-15 14:14:25,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-B2_fastqc.html [2024-02-15 14:14:25,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-B2_fastqc.html [2024-02-15 14:14:25,358] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-B3_fastqc.html [2024-02-15 14:14:25,367] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-B3_fastqc.html [2024-02-15 14:14:25,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-C1_fastqc.html [2024-02-15 14:14:25,445] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n01_plasmid758-C1_fastqc.html [2024-02-15 14:14:25,512] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern 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filesize limit: HVGFWAFX5_n02_plasmid758-A1_fastqc.html [2024-02-15 14:14:25,753] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-A1_fastqc.html [2024-02-15 14:14:25,826] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-A2_fastqc.html [2024-02-15 14:14:25,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-A2_fastqc.html [2024-02-15 14:14:25,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-A3_fastqc.html [2024-02-15 14:14:25,918] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-A3_fastqc.html [2024-02-15 14:14:25,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-B1_fastqc.html [2024-02-15 14:14:25,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-B1_fastqc.html [2024-02-15 14:14:26,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-B2_fastqc.html [2024-02-15 14:14:26,071] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-B2_fastqc.html [2024-02-15 14:14:26,175] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-B3_fastqc.html [2024-02-15 14:14:26,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-B3_fastqc.html [2024-02-15 14:14:26,264] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-C1_fastqc.html [2024-02-15 14:14:26,271] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-C1_fastqc.html [2024-02-15 14:14:26,338] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-C2_fastqc.html [2024-02-15 14:14:26,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-C2_fastqc.html [2024-02-15 14:14:26,411] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-C3_fastqc.html [2024-02-15 14:14:26,418] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_plasmid758-C3_fastqc.html [2024-02-15 14:14:26,485] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVGFWAFX5_n02_undetermined_fastqc.html [2024-02-15 14:14:26,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVGFWAFX5_n02_undetermined_fastqc.html [2024-02-15 14:14:26,563] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-15 14:14:26,570] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-15 14:14:27,215] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-15 14:14:27,217] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-15 14:14:27,235] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 10 samples (table) [2024-02-15 14:14:27,236] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-15 14:14:27,247] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-15 14:14:27,254] multiqc [DEBUG ] No samples found: conpair [2024-02-15 14:14:27,260] multiqc [DEBUG ] No samples found: peddy [2024-02-15 14:14:27,267] multiqc [DEBUG ] No samples found: somalier [2024-02-15 14:14:27,277] multiqc [DEBUG ] No samples found: methylQA [2024-02-15 14:14:27,294] multiqc [DEBUG ] No samples found: mosdepth [2024-02-15 14:14:27,300] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-15 14:14:27,308] multiqc [DEBUG ] No samples found: qualimap [2024-02-15 14:14:27,314] multiqc [DEBUG ] No samples found: preseq [2024-02-15 14:14:27,322] multiqc [DEBUG ] No samples found: quast [2024-02-15 14:14:27,334] multiqc [DEBUG ] No samples found: qorts [2024-02-15 14:14:27,340] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-15 14:14:27,346] multiqc [DEBUG ] No samples found: rockhopper [2024-02-15 14:14:27,353] multiqc [DEBUG ] No samples found: rsem [2024-02-15 14:14:27,367] multiqc [DEBUG ] No samples found: rseqc [2024-02-15 14:14:27,373] multiqc [DEBUG ] No samples found: busco [2024-02-15 14:14:27,379] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-15 14:14:27,385] multiqc [DEBUG ] No samples found: disambiguate [2024-02-15 14:14:27,391] multiqc [DEBUG ] No samples found: supernova [2024-02-15 14:14:27,408] multiqc [DEBUG ] No samples found: deeptools [2024-02-15 14:14:27,414] multiqc [DEBUG ] No samples found: sargasso [2024-02-15 14:14:27,421] multiqc [DEBUG ] No samples found: verifybamid [2024-02-15 14:14:27,427] multiqc [DEBUG ] No samples found: mirtrace [2024-02-15 14:14:27,433] multiqc [DEBUG ] No samples found: happy [2024-02-15 14:14:27,439] multiqc [DEBUG ] No samples found: mirtop [2024-02-15 14:14:27,447] multiqc [DEBUG ] No samples found: homer [2024-02-15 14:14:27,453] multiqc [DEBUG ] No samples found: macs2 [2024-02-15 14:14:27,459] multiqc [DEBUG ] No samples found: theta2 [2024-02-15 14:14:27,465] multiqc [DEBUG ] No samples found: snpeff [2024-02-15 14:14:27,475] multiqc [DEBUG ] No samples found: gatk [2024-02-15 14:14:27,481] multiqc [DEBUG ] No samples found: htseq [2024-02-15 14:14:27,488] multiqc [DEBUG ] No samples found: bcftools [2024-02-15 14:14:27,494] multiqc [DEBUG ] No samples found: featureCounts [2024-02-15 14:14:27,503] multiqc [DEBUG ] No samples found: fgbio [2024-02-15 14:14:27,520] multiqc [DEBUG ] No samples found: dragen [2024-02-15 14:14:27,526] multiqc [DEBUG ] No samples found: dedup [2024-02-15 14:14:27,533] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-15 14:14:27,562] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-15 14:14:27,568] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-15 14:14:27,571] multiqc [DEBUG ] No samples found: picard [2024-02-15 14:14:27,576] multiqc [DEBUG ] No samples found: prokka [2024-02-15 14:14:27,582] multiqc [DEBUG ] No samples found: samblaster [2024-02-15 14:14:27,592] multiqc [DEBUG ] No samples found: samtools [2024-02-15 14:14:27,599] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-15 14:14:27,605] multiqc [DEBUG ] No samples found: bamtools [2024-02-15 14:14:27,610] multiqc [DEBUG ] No samples found: jellyfish [2024-02-15 14:14:27,620] multiqc [DEBUG ] No samples found: vcftools [2024-02-15 14:14:27,626] multiqc [DEBUG ] No samples found: longranger [2024-02-15 14:14:27,632] multiqc [DEBUG ] No samples found: stacks [2024-02-15 14:14:27,638] multiqc [DEBUG ] No samples found: varscan2 [2024-02-15 14:14:27,657] multiqc [DEBUG ] No samples found: bbmap [2024-02-15 14:14:27,663] multiqc [DEBUG ] No samples found: bismark [2024-02-15 14:14:27,670] multiqc [DEBUG ] No samples found: biscuit [2024-02-15 14:14:27,676] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-15 14:14:27,682] multiqc [DEBUG ] No samples found: hicup [2024-02-15 14:14:27,688] multiqc [DEBUG ] No samples found: hicpro [2024-02-15 14:14:27,693] multiqc [DEBUG ] No samples found: salmon [2024-02-15 14:14:27,699] multiqc [DEBUG ] No samples found: kallisto [2024-02-15 14:14:27,704] multiqc [DEBUG ] No samples found: slamdunk [2024-02-15 14:14:27,711] multiqc [DEBUG ] No samples found: star [2024-02-15 14:14:27,717] multiqc [DEBUG ] No samples found: hisat2 [2024-02-15 14:14:27,724] multiqc [DEBUG ] No samples found: tophat [2024-02-15 14:14:27,730] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-15 14:14:27,736] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-15 14:14:27,742] multiqc [DEBUG ] No samples found: snpsplit [2024-02-15 14:14:27,748] multiqc [DEBUG ] No samples found: kat [2024-02-15 14:14:27,753] multiqc [DEBUG ] No samples found: leehom [2024-02-15 14:14:27,759] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-15 14:14:27,765] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-15 14:14:27,770] multiqc [DEBUG ] No samples found: cutadapt [2024-02-15 14:14:27,776] multiqc [DEBUG ] No samples found: flexbar [2024-02-15 14:14:27,782] multiqc [DEBUG ] No samples found: kaiju [2024-02-15 14:14:27,788] multiqc [DEBUG ] No samples found: kraken [2024-02-15 14:14:27,794] multiqc [DEBUG ] No samples found: malt [2024-02-15 14:14:27,800] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-15 14:14:27,806] multiqc [DEBUG ] No samples found: sickle [2024-02-15 14:14:27,811] multiqc [DEBUG ] No samples found: skewer [2024-02-15 14:14:27,817] multiqc [DEBUG ] No samples found: sortmerna [2024-02-15 14:14:27,823] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-15 14:14:27,829] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-15 14:14:27,835] multiqc [DEBUG ] No samples found: afterqc [2024-02-15 14:14:27,840] multiqc [DEBUG ] No samples found: fastp [2024-02-15 14:14:28,347] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2024-02-15 14:14:28,562] multiqc [DEBUG ] No samples found: pycoqc [2024-02-15 14:14:28,571] multiqc [DEBUG ] No samples found: minionqc [2024-02-15 14:14:28,578] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-15 14:14:28,584] multiqc [DEBUG ] No samples found: clusterflow [2024-02-15 14:14:28,590] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-15 14:14:28,596] multiqc [DEBUG ] No samples found: interop [2024-02-15 14:14:28,603] multiqc [DEBUG ] No samples found: ivar [2024-02-15 14:14:28,608] multiqc [DEBUG ] No samples found: flash [2024-02-15 14:14:28,614] multiqc [DEBUG ] No samples found: seqyclean [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 14:14:28,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-15 14:14:28,615] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-15 14:14:28,640] multiqc [INFO ] Compressing plot data [2024-02-15 14:14:29,009] multiqc [INFO ] Report : multiqc_report.html [2024-02-15 14:14:29,009] multiqc [INFO ] Data : multiqc_data [2024-02-15 14:14:29,010] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43014150/tmpmo86ftuf/multiqc_data' to '/vast/gencore/GENEFLOW/work/30/d8423ffcb6a680bd308aa1ce5b9604/merged/multiqc_data' [2024-02-15 14:14:29,212] multiqc [INFO ] MultiQC complete