[2024-06-04 18:03:57,495] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-04 18:03:57,495] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-04 18:03:57,496] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-04 18:03:57,498] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-04 18:03:57,498] 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}} [2024-06-04 18:03:57,499] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-04 18:03:57,534] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-04 18:03:57,534] multiqc [INFO ] This is MultiQC v1.9 [2024-06-04 18:03:57,534] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-04 18:03:57,534] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/87/af2582e50d417b28421afa6cbf0bd9/merged [2024-06-04 18:03:57,534] multiqc [INFO ] Template : default [2024-06-04 18:03:57,534] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-04 18:03:57,534] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/87/af2582e50d417b28421afa6cbf0bd9/merged [2024-06-04 18:03:57,535] 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 [2024-06-04 18:03:57,535] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47247264/tmpnizld9mk [2024-06-04 18:03:57,666] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57WGDRX5_n01_C01.Head_fastqc.html [2024-06-04 18:03:57,674] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57WGDRX5_n01_C01.Head_fastqc.html [2024-06-04 18:03:57,741] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H57WGDRX5_n02_R02.Leg_fastqc.html [2024-06-04 18:04:01,182] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57WGDRX5_n02_R02.Leg_fastqc.html [2024-06-04 18:04:01,247] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57WGDRX5_n02_R03.Head_fastqc.html [2024-06-04 18:04:01,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57WGDRX5_n02_R03.Head_fastqc.html [2024-06-04 18:04:01,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57WGDRX5_n02_R03.Leg_fastqc.html [2024-06-04 18:04:01,358] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57WGDRX5_n02_R03.Leg_fastqc.html [2024-06-04 18:04:01,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57WGDRX5_n02_R04.Head_fastqc.html [2024-06-04 18:04:01,456] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57WGDRX5_n02_R04.Head_fastqc.html [2024-06-04 18:04:01,523] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57WGDRX5_n02_R04.Leg_fastqc.html [2024-06-04 18:04:01,530] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57WGDRX5_n02_R04.Leg_fastqc.html [2024-06-04 18:04:01,596] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57WGDRX5_n02_undetermined_fastqc.html [2024-06-04 18:04:01,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57WGDRX5_n02_undetermined_fastqc.html [2024-06-04 18:04:02,193] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-04 18:04:02,196] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-04 18:04:02,218] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-06-04 18:04:02,219] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-04 18:04:02,229] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-04 18:04:02,235] multiqc [DEBUG ] No samples found: conpair [2024-06-04 18:04:02,241] multiqc [DEBUG ] No samples found: peddy [2024-06-04 18:04:02,247] multiqc [DEBUG ] No samples found: somalier [2024-06-04 18:04:02,253] multiqc [DEBUG ] No samples found: methylQA [2024-06-04 18:04:02,264] multiqc [DEBUG ] No samples found: mosdepth [2024-06-04 18:04:02,269] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-04 18:04:02,272] multiqc [DEBUG ] No samples found: qualimap [2024-06-04 18:04:02,278] multiqc [DEBUG ] No samples found: preseq [2024-06-04 18:04:02,284] multiqc [DEBUG ] No samples found: quast [2024-06-04 18:04:02,290] multiqc [DEBUG ] No samples found: qorts [2024-06-04 18:04:02,296] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-04 18:04:02,301] multiqc [DEBUG ] No samples found: rockhopper [2024-06-04 18:04:02,307] multiqc [DEBUG ] No samples found: rsem [2024-06-04 18:04:02,321] multiqc [DEBUG ] No samples found: rseqc [2024-06-04 18:04:02,326] multiqc [DEBUG ] No samples found: busco [2024-06-04 18:04:02,332] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-04 18:04:02,337] multiqc [DEBUG ] No samples found: disambiguate [2024-06-04 18:04:02,343] multiqc [DEBUG ] No samples found: supernova [2024-06-04 18:04:02,361] multiqc [DEBUG ] No samples found: deeptools [2024-06-04 18:04:02,366] multiqc [DEBUG ] No samples found: sargasso [2024-06-04 18:04:02,372] multiqc [DEBUG ] No samples found: verifybamid [2024-06-04 18:04:02,378] multiqc [DEBUG ] No samples found: mirtrace [2024-06-04 18:04:02,384] multiqc [DEBUG ] No samples found: happy [2024-06-04 18:04:02,389] multiqc [DEBUG ] No samples found: mirtop [2024-06-04 18:04:02,397] multiqc [DEBUG ] No samples found: homer [2024-06-04 18:04:02,402] multiqc [DEBUG ] No samples found: macs2 [2024-06-04 18:04:02,408] multiqc [DEBUG ] No samples found: theta2 [2024-06-04 18:04:02,414] multiqc [DEBUG ] No samples found: snpeff [2024-06-04 18:04:02,422] multiqc [DEBUG ] No samples found: gatk [2024-06-04 18:04:02,427] multiqc [DEBUG ] No samples found: htseq [2024-06-04 18:04:02,434] multiqc [DEBUG ] No samples found: bcftools [2024-06-04 18:04:02,440] multiqc [DEBUG ] No samples found: featureCounts [2024-06-04 18:04:02,447] multiqc [DEBUG ] No samples found: fgbio [2024-06-04 18:04:02,464] multiqc [DEBUG ] No samples found: dragen [2024-06-04 18:04:02,470] multiqc [DEBUG ] No samples found: dedup [2024-06-04 18:04:02,476] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-04 18:04:02,502] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-04 18:04:02,509] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-04 18:04:02,511] multiqc [DEBUG ] No samples found: picard [2024-06-04 18:04:02,516] multiqc [DEBUG ] No samples found: prokka [2024-06-04 18:04:02,522] multiqc [DEBUG ] No samples found: samblaster [2024-06-04 18:04:02,534] multiqc [DEBUG ] No samples found: samtools [2024-06-04 18:04:02,539] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-04 18:04:02,546] multiqc [DEBUG ] No samples found: bamtools [2024-06-04 18:04:02,551] multiqc [DEBUG ] No samples found: jellyfish [2024-06-04 18:04:02,562] multiqc [DEBUG ] No samples found: vcftools [2024-06-04 18:04:02,568] multiqc [DEBUG ] No samples found: longranger [2024-06-04 18:04:02,574] multiqc [DEBUG ] No samples found: stacks [2024-06-04 18:04:02,580] multiqc [DEBUG ] No samples found: varscan2 [2024-06-04 18:04:02,598] multiqc [DEBUG ] No samples found: bbmap [2024-06-04 18:04:02,604] multiqc [DEBUG ] No samples found: bismark [2024-06-04 18:04:02,610] multiqc [DEBUG ] No samples found: biscuit [2024-06-04 18:04:02,615] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-04 18:04:02,621] multiqc [DEBUG ] No samples found: hicup [2024-06-04 18:04:02,627] multiqc [DEBUG ] No samples found: hicpro [2024-06-04 18:04:02,631] multiqc [DEBUG ] No samples found: salmon [2024-06-04 18:04:02,637] multiqc [DEBUG ] No samples found: kallisto [2024-06-04 18:04:02,643] multiqc [DEBUG ] No samples found: slamdunk [2024-06-04 18:04:02,648] multiqc [DEBUG ] No samples found: star [2024-06-04 18:04:02,654] multiqc [DEBUG ] No samples found: hisat2 [2024-06-04 18:04:02,659] multiqc [DEBUG ] No samples found: tophat [2024-06-04 18:04:02,665] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-04 18:04:02,670] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-04 18:04:02,676] multiqc [DEBUG ] No samples found: snpsplit [2024-06-04 18:04:02,681] multiqc [DEBUG ] No samples found: kat [2024-06-04 18:04:02,686] multiqc [DEBUG ] No samples found: leehom [2024-06-04 18:04:02,691] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-04 18:04:02,696] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-04 18:04:02,702] multiqc [DEBUG ] No samples found: cutadapt [2024-06-04 18:04:02,706] multiqc [DEBUG ] No samples found: flexbar [2024-06-04 18:04:02,712] multiqc [DEBUG ] No samples found: kaiju [2024-06-04 18:04:02,717] multiqc [DEBUG ] No samples found: kraken [2024-06-04 18:04:02,723] multiqc [DEBUG ] No samples found: malt [2024-06-04 18:04:02,728] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-04 18:04:02,733] multiqc [DEBUG ] No samples found: sickle [2024-06-04 18:04:02,738] multiqc [DEBUG ] No samples found: skewer [2024-06-04 18:04:02,743] multiqc [DEBUG ] No samples found: sortmerna [2024-06-04 18:04:02,748] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-04 18:04:02,754] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-04 18:04:02,760] multiqc [DEBUG ] No samples found: afterqc [2024-06-04 18:04:02,765] multiqc [DEBUG ] No samples found: fastp [2024-06-04 18:04:04,100] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2024-06-04 18:04:04,519] multiqc [DEBUG ] No samples found: pycoqc [2024-06-04 18:04:04,524] multiqc [DEBUG ] No samples found: minionqc [2024-06-04 18:04:04,529] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-04 18:04:04,535] multiqc [DEBUG ] No samples found: clusterflow [2024-06-04 18:04:04,541] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-04 18:04:04,547] multiqc [DEBUG ] No samples found: interop [2024-06-04 18:04:04,552] multiqc [DEBUG ] No samples found: ivar [2024-06-04 18:04:04,558] multiqc [DEBUG ] No samples found: flash [2024-06-04 18:04:04,563] multiqc [DEBUG ] No samples found: seqyclean [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-04 18:04:04,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-04 18:04:04,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-04 18:04:04,623] multiqc [INFO ] Compressing plot data [2024-06-04 18:04:05,453] multiqc [INFO ] Report : multiqc_report.html [2024-06-04 18:04:05,453] multiqc [INFO ] Data : multiqc_data [2024-06-04 18:04:05,453] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47247264/tmpnizld9mk/multiqc_data' to '/vast/gencore/GENEFLOW/work/87/af2582e50d417b28421afa6cbf0bd9/merged/multiqc_data' [2024-06-04 18:04:05,658] multiqc [INFO ] MultiQC complete