[2024-02-23 06:36:22,870] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-23 06:36:22,871] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-23 06:36:22,871] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-23 06:36:22,874] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-23 06:36:22,874] 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}} [2024-02-23 06:36:22,874] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-23 06:36:23,046] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-23 06:36:23,046] multiqc [INFO ] This is MultiQC v1.9 [2024-02-23 06:36:23,046] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-23 06:36:23,046] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/7f/45a7769c7505b9f718ff9b4cd4777c/merged [2024-02-23 06:36:23,046] multiqc [INFO ] Template : default [2024-02-23 06:36:23,046] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-23 06:36:23,046] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/7f/45a7769c7505b9f718ff9b4cd4777c/merged [2024-02-23 06:36:23,047] 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 [2024-02-23 06:36:23,047] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43307883/tmp62wtocj6 [2024-02-23 06:36:23,208] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n01_AA40_fastqc.html [2024-02-23 06:36:23,217] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n01_AA40_fastqc.html [2024-02-23 06:36:23,288] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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06:36:26,654] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS25_fastqc.html [2024-02-23 06:36:26,661] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS25_fastqc.html [2024-02-23 06:36:26,732] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS26_fastqc.html [2024-02-23 06:36:26,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS26_fastqc.html [2024-02-23 06:36:26,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS27_fastqc.html [2024-02-23 06:36:26,815] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS27_fastqc.html [2024-02-23 06:36:26,884] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS28_fastqc.html [2024-02-23 06:36:26,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS28_fastqc.html [2024-02-23 06:36:26,960] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS29_fastqc.html [2024-02-23 06:36:26,967] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS29_fastqc.html [2024-02-23 06:36:27,054] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS30_fastqc.html [2024-02-23 06:36:27,068] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS30_fastqc.html [2024-02-23 06:36:27,144] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS31_fastqc.html [2024-02-23 06:36:27,151] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_NS31_fastqc.html [2024-02-23 06:36:27,220] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKYGBGXV_n02_undetermined_fastqc.html [2024-02-23 06:36:27,228] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKYGBGXV_n02_undetermined_fastqc.html [2024-02-23 06:36:27,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-23 06:36:27,311] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-23 06:36:27,311] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-23 06:36:27,311] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-23 06:36:27,311] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-23 06:36:27,311] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-23 06:36:27,311] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-23 06:36:29,005] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-23 06:36:29,007] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-23 06:36:29,037] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-02-23 06:36:29,039] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-23 06:36:29,050] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-23 06:36:29,056] multiqc [DEBUG ] No samples found: conpair [2024-02-23 06:36:29,064] multiqc [DEBUG ] No samples found: peddy [2024-02-23 06:36:29,070] multiqc [DEBUG ] No samples found: somalier [2024-02-23 06:36:29,076] multiqc [DEBUG ] No samples found: methylQA [2024-02-23 06:36:29,087] multiqc [DEBUG ] No samples found: mosdepth [2024-02-23 06:36:29,093] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-23 06:36:29,097] multiqc [DEBUG ] No samples found: qualimap [2024-02-23 06:36:29,103] multiqc [DEBUG ] No samples found: preseq [2024-02-23 06:36:29,110] multiqc [DEBUG ] No samples found: quast [2024-02-23 06:36:29,117] multiqc [DEBUG ] No samples found: qorts [2024-02-23 06:36:29,123] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-23 06:36:29,129] multiqc [DEBUG ] No samples found: rockhopper [2024-02-23 06:36:29,135] multiqc [DEBUG ] No samples found: rsem [2024-02-23 06:36:29,150] multiqc [DEBUG ] No samples found: rseqc [2024-02-23 06:36:29,155] multiqc [DEBUG ] No samples found: busco [2024-02-23 06:36:29,161] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-23 06:36:29,167] multiqc [DEBUG ] No samples found: disambiguate [2024-02-23 06:36:29,173] multiqc [DEBUG ] No samples found: supernova [2024-02-23 06:36:29,190] multiqc [DEBUG ] No samples found: deeptools [2024-02-23 06:36:29,196] multiqc [DEBUG ] No samples found: sargasso [2024-02-23 06:36:29,202] multiqc [DEBUG ] No samples found: verifybamid [2024-02-23 06:36:29,208] multiqc [DEBUG ] No samples found: mirtrace [2024-02-23 06:36:29,214] multiqc [DEBUG ] No samples found: happy [2024-02-23 06:36:29,219] multiqc [DEBUG ] No samples found: mirtop [2024-02-23 06:36:29,228] multiqc [DEBUG ] No samples found: homer [2024-02-23 06:36:29,234] multiqc [DEBUG ] No samples found: macs2 [2024-02-23 06:36:29,241] multiqc [DEBUG ] No samples found: theta2 [2024-02-23 06:36:29,247] multiqc [DEBUG ] No samples found: snpeff [2024-02-23 06:36:29,256] multiqc [DEBUG ] No samples found: gatk [2024-02-23 06:36:29,262] multiqc [DEBUG ] No samples found: htseq [2024-02-23 06:36:29,269] multiqc [DEBUG ] No samples found: bcftools [2024-02-23 06:36:29,275] multiqc [DEBUG ] No samples found: featureCounts [2024-02-23 06:36:29,283] multiqc [DEBUG ] No samples found: fgbio [2024-02-23 06:36:29,300] multiqc [DEBUG ] No samples found: dragen [2024-02-23 06:36:29,306] multiqc [DEBUG ] No samples found: dedup [2024-02-23 06:36:29,313] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-23 06:36:29,340] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-23 06:36:29,347] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-23 06:36:29,350] multiqc [DEBUG ] No samples found: picard [2024-02-23 06:36:29,356] multiqc [DEBUG ] No samples found: prokka [2024-02-23 06:36:29,361] multiqc [DEBUG ] No samples found: samblaster [2024-02-23 06:36:29,372] multiqc [DEBUG ] No samples found: samtools [2024-02-23 06:36:29,378] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-23 06:36:29,384] multiqc [DEBUG ] No samples found: bamtools [2024-02-23 06:36:29,390] multiqc [DEBUG ] No samples found: jellyfish [2024-02-23 06:36:29,399] multiqc [DEBUG ] No samples found: vcftools [2024-02-23 06:36:29,405] multiqc [DEBUG ] No samples found: longranger [2024-02-23 06:36:29,411] multiqc [DEBUG ] No samples found: stacks [2024-02-23 06:36:29,418] multiqc [DEBUG ] No samples found: varscan2 [2024-02-23 06:36:29,436] multiqc [DEBUG ] No samples found: bbmap [2024-02-23 06:36:29,442] multiqc [DEBUG ] No samples found: bismark [2024-02-23 06:36:29,448] multiqc [DEBUG ] No samples found: biscuit [2024-02-23 06:36:29,454] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-23 06:36:29,460] multiqc [DEBUG ] No samples found: hicup [2024-02-23 06:36:29,466] multiqc [DEBUG ] No samples found: hicpro [2024-02-23 06:36:29,472] multiqc [DEBUG ] No samples found: salmon [2024-02-23 06:36:29,478] multiqc [DEBUG ] No samples found: kallisto [2024-02-23 06:36:29,484] multiqc [DEBUG ] No samples found: slamdunk [2024-02-23 06:36:29,490] multiqc [DEBUG ] No samples found: star [2024-02-23 06:36:29,496] multiqc [DEBUG ] No samples found: hisat2 [2024-02-23 06:36:29,502] multiqc [DEBUG ] No samples found: tophat [2024-02-23 06:36:29,507] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-23 06:36:29,513] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-23 06:36:29,518] multiqc [DEBUG ] No samples found: snpsplit [2024-02-23 06:36:29,524] multiqc [DEBUG ] No samples found: kat [2024-02-23 06:36:29,529] multiqc [DEBUG ] No samples found: leehom [2024-02-23 06:36:29,542] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-23 06:36:29,548] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-23 06:36:29,554] multiqc [DEBUG ] No samples found: cutadapt [2024-02-23 06:36:29,560] multiqc [DEBUG ] No samples found: flexbar [2024-02-23 06:36:29,567] multiqc [DEBUG ] No samples found: kaiju [2024-02-23 06:36:29,572] multiqc [DEBUG ] No samples found: kraken [2024-02-23 06:36:29,579] multiqc [DEBUG ] No samples found: malt [2024-02-23 06:36:29,585] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-23 06:36:29,591] multiqc [DEBUG ] No samples found: sickle [2024-02-23 06:36:29,597] multiqc [DEBUG ] No samples found: skewer [2024-02-23 06:36:29,602] multiqc [DEBUG ] No samples found: sortmerna [2024-02-23 06:36:29,608] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-23 06:36:29,615] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-23 06:36:29,620] multiqc [DEBUG ] No samples found: afterqc [2024-02-23 06:36:29,626] multiqc [DEBUG ] No samples found: fastp [2024-02-23 06:36:33,914] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2024-02-23 06:36:34,967] multiqc [DEBUG ] No samples found: pycoqc [2024-02-23 06:36:34,973] multiqc [DEBUG ] No samples found: minionqc [2024-02-23 06:36:34,984] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-23 06:36:34,991] multiqc [DEBUG ] No samples found: clusterflow [2024-02-23 06:36:34,997] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-23 06:36:35,014] multiqc [DEBUG ] No samples found: interop [2024-02-23 06:36:35,020] multiqc [DEBUG ] No samples found: ivar [2024-02-23 06:36:35,026] multiqc [DEBUG ] No samples found: flash [2024-02-23 06:36:35,031] multiqc [DEBUG ] No samples found: seqyclean [2024-02-23 06:36:35,031] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-23 06:36:35,031] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-23 06:36:35,032] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-23 06:36:35,093] multiqc [INFO ] Compressing plot data [2024-02-23 06:36:36,099] multiqc [INFO ] Report : multiqc_report.html [2024-02-23 06:36:36,099] multiqc [INFO ] Data : multiqc_data [2024-02-23 06:36:36,099] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43307883/tmp62wtocj6/multiqc_data' to '/vast/gencore/GENEFLOW/work/7f/45a7769c7505b9f718ff9b4cd4777c/merged/multiqc_data' [2024-02-23 06:36:36,343] multiqc [INFO ] MultiQC complete