[2024-05-09 12:51:54,145] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-05-09 12:51:54,145] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-05-09 12:51:54,146] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-05-09 12:51:54,148] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-05-09 12:51:54,148] 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}} [2024-05-09 12:51:54,149] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-09 12:51:54,185] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-05-09 12:51:54,186] multiqc [INFO ] This is MultiQC v1.9 [2024-05-09 12:51:54,186] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-09 12:51:54,186] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/8e/1d57e76f7405668227c2799e909226/merged [2024-05-09 12:51:54,186] multiqc [INFO ] Template : default [2024-05-09 12:51:54,186] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-05-09 12:51:54,186] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/8e/1d57e76f7405668227c2799e909226/merged [2024-05-09 12:51:54,186] 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 [2024-05-09 12:51:54,186] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-46316302/tmp0sjhk85s [2024-05-09 12:51:54,320] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n01_10G_1-6-NEB_a_fastqc.html [2024-05-09 12:51:54,330] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n01_10G_1-6-NEB_a_fastqc.html [2024-05-09 12:51:54,400] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_8R_1-7-NEB_a_fastqc.html [2024-05-09 12:52:02,421] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_8R_1-7-NEB_a_fastqc.html [2024-05-09 12:52:02,486] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_9G_1-6-NEB_a_fastqc.html [2024-05-09 12:52:02,493] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_9G_1-6-NEB_a_fastqc.html [2024-05-09 12:52:02,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_9G_1-7-NEB_a_fastqc.html [2024-05-09 12:52:02,568] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_9G_1-7-NEB_a_fastqc.html [2024-05-09 12:52:02,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_9R_1-6-NEB_a_fastqc.html [2024-05-09 12:52:02,642] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_9R_1-6-NEB_a_fastqc.html [2024-05-09 12:52:02,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV-1-h-NEB_a_fastqc.html [2024-05-09 12:52:02,716] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV-1-h-NEB_a_fastqc.html [2024-05-09 12:52:02,780] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV-3-h-NEB_a_fastqc.html [2024-05-09 12:52:02,786] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV-3-h-NEB_a_fastqc.html [2024-05-09 12:52:02,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV-exp-1-NEB_a_fastqc.html [2024-05-09 12:52:02,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV-exp-1-NEB_a_fastqc.html [2024-05-09 12:52:02,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV2-h-NEB_a_fastqc.html [2024-05-09 12:52:02,926] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_EV2-h-NEB_a_fastqc.html [2024-05-09 12:52:02,992] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_HMGB1-1_NEB_a_fastqc.html [2024-05-09 12:52:02,999] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_HMGB1-1_NEB_a_fastqc.html [2024-05-09 12:52:03,066] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_HMGB1-2-NEB_a_fastqc.html [2024-05-09 12:52:03,072] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_HMGB1-2-NEB_a_fastqc.html [2024-05-09 12:52:03,135] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_HMGB1-3_NEB_a_fastqc.html [2024-05-09 12:52:03,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_HMGB1-3_NEB_a_fastqc.html [2024-05-09 12:52:03,206] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYLWKDRX3_n02_undetermined_fastqc.html [2024-05-09 12:52:03,212] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYLWKDRX3_n02_undetermined_fastqc.html [2024-05-09 12:52:03,270] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-09 12:52:03,277] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-09 12:52:03,277] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-09 12:52:03,277] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-09 12:52:03,277] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-09 12:52:03,277] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-09 12:52:03,277] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-09 12:52:04,413] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-09 12:52:04,415] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-09 12:52:04,453] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 62 samples (table) [2024-05-09 12:52:04,455] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-05-09 12:52:04,464] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-05-09 12:52:04,470] multiqc [DEBUG ] No samples found: conpair [2024-05-09 12:52:04,478] multiqc [DEBUG ] No samples found: peddy [2024-05-09 12:52:04,486] multiqc [DEBUG ] No samples found: somalier [2024-05-09 12:52:04,492] multiqc [DEBUG ] No samples found: methylQA [2024-05-09 12:52:04,504] multiqc [DEBUG ] No samples found: mosdepth [2024-05-09 12:52:04,510] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-05-09 12:52:04,515] multiqc [DEBUG ] No samples found: qualimap [2024-05-09 12:52:04,521] multiqc [DEBUG ] No samples found: preseq [2024-05-09 12:52:04,526] multiqc [DEBUG ] No samples found: quast [2024-05-09 12:52:04,532] multiqc [DEBUG ] No samples found: qorts [2024-05-09 12:52:04,539] multiqc [DEBUG ] No samples found: rna_seqc [2024-05-09 12:52:04,545] multiqc [DEBUG ] No samples found: rockhopper [2024-05-09 12:52:04,553] multiqc [DEBUG ] No samples found: rsem [2024-05-09 12:52:04,567] multiqc [DEBUG ] No samples found: rseqc [2024-05-09 12:52:04,572] multiqc [DEBUG ] No samples found: busco [2024-05-09 12:52:04,579] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-05-09 12:52:04,584] multiqc [DEBUG ] No samples found: disambiguate [2024-05-09 12:52:04,590] multiqc [DEBUG ] No samples found: supernova [2024-05-09 12:52:04,605] multiqc [DEBUG ] No samples found: deeptools [2024-05-09 12:52:04,611] multiqc [DEBUG ] No samples found: sargasso [2024-05-09 12:52:04,617] multiqc [DEBUG ] No samples found: verifybamid [2024-05-09 12:52:04,624] multiqc [DEBUG ] No samples found: mirtrace [2024-05-09 12:52:04,629] multiqc [DEBUG ] No samples found: happy [2024-05-09 12:52:04,635] multiqc [DEBUG ] No samples found: mirtop [2024-05-09 12:52:04,643] multiqc [DEBUG ] No samples found: homer [2024-05-09 12:52:04,650] multiqc [DEBUG ] No samples found: macs2 [2024-05-09 12:52:04,655] multiqc [DEBUG ] No samples found: theta2 [2024-05-09 12:52:04,661] multiqc [DEBUG ] No samples found: snpeff [2024-05-09 12:52:04,670] multiqc [DEBUG ] No samples found: gatk [2024-05-09 12:52:04,675] multiqc [DEBUG ] No samples found: htseq [2024-05-09 12:52:04,681] multiqc [DEBUG ] No samples found: bcftools [2024-05-09 12:52:04,687] multiqc [DEBUG ] No samples found: featureCounts [2024-05-09 12:52:04,694] multiqc [DEBUG ] No samples found: fgbio [2024-05-09 12:52:04,710] multiqc [DEBUG ] No samples found: dragen [2024-05-09 12:52:04,715] multiqc [DEBUG ] No samples found: dedup [2024-05-09 12:52:04,721] multiqc [DEBUG ] No samples found: damageprofiler [2024-05-09 12:52:04,753] multiqc [DEBUG ] No samples found: biobambam2 [2024-05-09 12:52:04,758] multiqc [DEBUG ] No samples found: mtnucratio [2024-05-09 12:52:04,761] multiqc [DEBUG ] No samples found: picard [2024-05-09 12:52:04,767] multiqc [DEBUG ] No samples found: prokka [2024-05-09 12:52:04,772] multiqc [DEBUG ] No samples found: samblaster [2024-05-09 12:52:04,782] multiqc [DEBUG ] No samples found: samtools [2024-05-09 12:52:04,787] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-05-09 12:52:04,793] multiqc [DEBUG ] No samples found: bamtools [2024-05-09 12:52:04,798] multiqc [DEBUG ] No samples found: jellyfish [2024-05-09 12:52:04,808] multiqc [DEBUG ] No samples found: vcftools [2024-05-09 12:52:04,813] multiqc [DEBUG ] No samples found: longranger [2024-05-09 12:52:04,819] multiqc [DEBUG ] No samples found: stacks [2024-05-09 12:52:04,825] multiqc [DEBUG ] No samples found: varscan2 [2024-05-09 12:52:04,842] multiqc [DEBUG ] No samples found: bbmap [2024-05-09 12:52:04,848] multiqc [DEBUG ] No samples found: bismark [2024-05-09 12:52:04,855] multiqc [DEBUG ] No samples found: biscuit [2024-05-09 12:52:04,861] multiqc [DEBUG ] No samples found: hicexplorer [2024-05-09 12:52:04,867] multiqc [DEBUG ] No samples found: hicup [2024-05-09 12:52:04,873] multiqc [DEBUG ] No samples found: hicpro [2024-05-09 12:52:04,878] multiqc [DEBUG ] No samples found: salmon [2024-05-09 12:52:04,884] multiqc [DEBUG ] No samples found: kallisto [2024-05-09 12:52:04,890] multiqc [DEBUG ] No samples found: slamdunk [2024-05-09 12:52:04,895] multiqc [DEBUG ] No samples found: star [2024-05-09 12:52:04,901] multiqc [DEBUG ] No samples found: hisat2 [2024-05-09 12:52:04,906] multiqc [DEBUG ] No samples found: tophat [2024-05-09 12:52:04,911] multiqc [DEBUG ] No samples found: bowtie2 [2024-05-09 12:52:04,917] multiqc [DEBUG ] No samples found: bowtie1 [2024-05-09 12:52:04,924] multiqc [DEBUG ] No samples found: snpsplit [2024-05-09 12:52:04,930] multiqc [DEBUG ] No samples found: kat [2024-05-09 12:52:04,935] multiqc [DEBUG ] No samples found: leehom [2024-05-09 12:52:04,940] multiqc [DEBUG ] No samples found: adapterRemoval [2024-05-09 12:52:04,946] multiqc [DEBUG ] No samples found: clipandmerge [2024-05-09 12:52:04,951] multiqc [DEBUG ] No samples found: cutadapt [2024-05-09 12:52:04,956] multiqc [DEBUG ] No samples found: flexbar [2024-05-09 12:52:04,962] multiqc [DEBUG ] No samples found: kaiju [2024-05-09 12:52:04,967] multiqc [DEBUG ] No samples found: kraken [2024-05-09 12:52:04,972] multiqc [DEBUG ] No samples found: malt [2024-05-09 12:52:04,977] multiqc [DEBUG ] No samples found: trimmomatic [2024-05-09 12:52:04,983] multiqc [DEBUG ] No samples found: sickle [2024-05-09 12:52:04,989] multiqc [DEBUG ] No samples found: skewer [2024-05-09 12:52:04,994] multiqc [DEBUG ] No samples found: sortmerna [2024-05-09 12:52:04,999] multiqc [DEBUG ] No samples found: biobloomtools [2024-05-09 12:52:05,005] multiqc [DEBUG ] No samples found: fastq_screen [2024-05-09 12:52:05,010] multiqc [DEBUG ] No samples found: afterqc [2024-05-09 12:52:05,016] multiqc [DEBUG ] No samples found: fastp [2024-05-09 12:52:09,475] multiqc.modules.fastqc.fastqc [INFO ] Found 124 reports [2024-05-09 12:52:30,357] multiqc [DEBUG ] No samples found: pycoqc [2024-05-09 12:52:30,363] multiqc [DEBUG ] No samples found: minionqc [2024-05-09 12:52:30,369] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-05-09 12:52:30,375] multiqc [DEBUG ] No samples found: clusterflow [2024-05-09 12:52:30,381] multiqc [DEBUG ] No samples found: bcl2fastq [2024-05-09 12:52:30,387] multiqc [DEBUG ] No samples found: interop [2024-05-09 12:52:30,392] multiqc [DEBUG ] No samples found: ivar [2024-05-09 12:52:30,398] multiqc [DEBUG ] No samples found: flash [2024-05-09 12:52:30,403] multiqc [DEBUG ] No samples found: seqyclean [2024-05-09 12:52:30,403] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-05-09 12:52:30,403] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-05-09 12:52:30,403] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-05-09 12:52:30,403] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-05-09 12:52:30,403] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-05-09 12:52:30,403] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-05-09 12:52:30,403] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-05-09 12:52:30,404] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-05-09 12:52:30,554] multiqc [INFO ] Compressing plot data [2024-05-09 12:52:30,620] multiqc [INFO ] Report : multiqc_report.html [2024-05-09 12:52:30,621] multiqc [INFO ] Data : multiqc_data [2024-05-09 12:52:30,621] multiqc [DEBUG ] Moving data file from '/state/partition1/job-46316302/tmp0sjhk85s/multiqc_data' to '/vast/gencore/GENEFLOW/work/8e/1d57e76f7405668227c2799e909226/merged/multiqc_data' [2024-05-09 12:52:30,862] multiqc [INFO ] MultiQC complete