[2023-02-05 18:34:22,957] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-02-05 18:34:22,957] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-02-05 18:34:22,957] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-02-05 18:34:22,959] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-02-05 18:34:22,960] 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}} [2023-02-05 18:34:22,960] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN5YJDRX2/merged [2023-02-05 18:34:23,590] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-02-05 18:34:23,590] multiqc [INFO ] This is MultiQC v1.9 [2023-02-05 18:34:23,590] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN5YJDRX2/merged [2023-02-05 18:34:23,590] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HN5YJDRX2/merged [2023-02-05 18:34:23,590] multiqc [INFO ] Template : default [2023-02-05 18:34:23,590] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-02-05 18:34:23,590] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HN5YJDRX2/merged [2023-02-05 18:34:23,591] 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 [2023-02-05 18:34:23,591] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-29862253/tmp9grg3rkz [2023-02-05 18:34:23,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN5YJDRX2_n01_br284a_fastqc.html [2023-02-05 18:34:23,781] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2023-02-05 18:34:32,776] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br261a_fastqc.html [2023-02-05 18:34:32,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br261a_fastqc.html [2023-02-05 18:34:32,835] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br309a_fastqc.html [2023-02-05 18:34:32,837] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br309a_fastqc.html [2023-02-05 18:34:32,909] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN5YJDRX2_n01_br263a_fastqc.html [2023-02-05 18:34:32,911] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN5YJDRX2_n01_br263a_fastqc.html [2023-02-05 18:34:34,370] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br262a_fastqc.html [2023-02-05 18:34:34,372] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br262a_fastqc.html [2023-02-05 18:34:34,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br293a_fastqc.html [2023-02-05 18:34:34,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN5YJDRX2_n02_br293a_fastqc.html [2023-02-05 18:34:36,556] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-05 18:34:36,559] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-05 18:34:36,572] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-02-05 18:34:36,582] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-02-05 18:34:36,611] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 65 samples (table) [2023-02-05 18:34:36,622] multiqc [DEBUG ] No samples found: conpair [2023-02-05 18:34:36,630] multiqc [DEBUG ] No samples found: peddy [2023-02-05 18:34:36,641] multiqc [DEBUG ] No samples found: somalier [2023-02-05 18:34:36,656] multiqc [DEBUG ] No samples found: methylQA [2023-02-05 18:34:36,675] multiqc [DEBUG ] No samples found: mosdepth [2023-02-05 18:34:36,685] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-02-05 18:34:36,691] multiqc [DEBUG ] No samples found: qualimap [2023-02-05 18:34:36,702] multiqc [DEBUG ] No samples found: preseq [2023-02-05 18:34:36,714] multiqc [DEBUG ] No samples found: quast [2023-02-05 18:34:36,725] multiqc [DEBUG ] No samples found: qorts [2023-02-05 18:34:36,733] multiqc [DEBUG ] No samples found: rna_seqc [2023-02-05 18:34:36,747] multiqc [DEBUG ] No samples found: rockhopper [2023-02-05 18:34:36,760] multiqc [DEBUG ] No samples found: rsem [2023-02-05 18:34:36,795] multiqc [DEBUG ] No samples found: rseqc [2023-02-05 18:34:36,803] multiqc [DEBUG ] No samples found: busco [2023-02-05 18:34:36,812] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-02-05 18:34:36,822] multiqc [DEBUG ] No samples found: disambiguate [2023-02-05 18:34:36,836] multiqc [DEBUG ] No samples found: supernova [2023-02-05 18:34:36,871] multiqc [DEBUG ] No samples found: deeptools [2023-02-05 18:34:36,884] multiqc [DEBUG ] No samples found: sargasso [2023-02-05 18:34:36,894] multiqc [DEBUG ] No samples found: verifybamid [2023-02-05 18:34:36,906] multiqc [DEBUG ] No samples found: mirtrace [2023-02-05 18:34:36,921] multiqc [DEBUG ] No samples found: happy [2023-02-05 18:34:36,930] multiqc [DEBUG ] No samples found: mirtop [2023-02-05 18:34:36,950] multiqc [DEBUG ] No samples found: homer [2023-02-05 18:34:36,961] multiqc [DEBUG ] No samples found: macs2 [2023-02-05 18:34:36,971] multiqc [DEBUG ] No samples found: theta2 [2023-02-05 18:34:36,982] multiqc [DEBUG ] No samples found: snpeff [2023-02-05 18:34:37,001] multiqc [DEBUG ] No samples found: gatk [2023-02-05 18:34:37,009] multiqc [DEBUG ] No samples found: htseq [2023-02-05 18:34:37,018] multiqc [DEBUG ] No samples found: bcftools [2023-02-05 18:34:37,026] multiqc [DEBUG ] No samples found: featureCounts [2023-02-05 18:34:37,041] multiqc [DEBUG ] No samples found: fgbio [2023-02-05 18:34:37,075] multiqc [DEBUG ] No samples found: dragen [2023-02-05 18:34:37,085] multiqc [DEBUG ] No samples found: dedup [2023-02-05 18:34:37,096] multiqc [DEBUG ] No samples found: damageprofiler [2023-02-05 18:34:37,188] multiqc [DEBUG ] No samples found: biobambam2 [2023-02-05 18:34:37,196] multiqc [DEBUG ] No samples found: mtnucratio [2023-02-05 18:34:37,198] multiqc [DEBUG ] No samples found: picard [2023-02-05 18:34:37,210] multiqc [DEBUG ] No samples found: prokka [2023-02-05 18:34:37,219] multiqc [DEBUG ] No samples found: samblaster [2023-02-05 18:34:37,248] multiqc [DEBUG ] No samples found: samtools [2023-02-05 18:34:37,255] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-02-05 18:34:37,271] multiqc [DEBUG ] No samples found: bamtools [2023-02-05 18:34:37,281] multiqc [DEBUG ] No samples found: jellyfish [2023-02-05 18:34:37,298] multiqc [DEBUG ] No samples found: vcftools [2023-02-05 18:34:37,311] multiqc [DEBUG ] No samples found: longranger [2023-02-05 18:34:37,325] multiqc [DEBUG ] No samples found: stacks [2023-02-05 18:34:37,337] multiqc [DEBUG ] No samples found: varscan2 [2023-02-05 18:34:37,391] multiqc [DEBUG ] No samples found: bbmap [2023-02-05 18:34:37,405] multiqc [DEBUG ] No samples found: bismark [2023-02-05 18:34:37,413] multiqc [DEBUG ] No samples found: biscuit [2023-02-05 18:34:37,425] multiqc [DEBUG ] No samples found: hicexplorer [2023-02-05 18:34:37,435] multiqc [DEBUG ] No samples found: hicup [2023-02-05 18:34:37,450] multiqc [DEBUG ] No samples found: hicpro [2023-02-05 18:34:37,463] multiqc [DEBUG ] No samples found: salmon [2023-02-05 18:34:37,474] multiqc [DEBUG ] No samples found: kallisto [2023-02-05 18:34:37,486] multiqc [DEBUG ] No samples found: slamdunk [2023-02-05 18:34:37,502] multiqc [DEBUG ] No samples found: star [2023-02-05 18:34:37,514] multiqc [DEBUG ] No samples found: hisat2 [2023-02-05 18:34:37,522] multiqc [DEBUG ] No samples found: tophat [2023-02-05 18:34:37,533] multiqc [DEBUG ] No samples found: bowtie2 [2023-02-05 18:34:37,542] multiqc [DEBUG ] No samples found: bowtie1 [2023-02-05 18:34:37,558] multiqc [DEBUG ] No samples found: snpsplit [2023-02-05 18:34:37,567] multiqc [DEBUG ] No samples found: kat [2023-02-05 18:34:37,574] multiqc [DEBUG ] No samples found: leehom [2023-02-05 18:34:37,580] multiqc [DEBUG ] No samples found: adapterRemoval [2023-02-05 18:34:37,590] multiqc [DEBUG ] No samples found: clipandmerge [2023-02-05 18:34:37,608] multiqc [DEBUG ] No samples found: cutadapt [2023-02-05 18:34:37,618] multiqc [DEBUG ] No samples found: flexbar [2023-02-05 18:34:37,630] multiqc [DEBUG ] No samples found: kaiju [2023-02-05 18:34:37,642] multiqc [DEBUG ] No samples found: kraken [2023-02-05 18:34:37,654] multiqc [DEBUG ] No samples found: malt [2023-02-05 18:34:37,662] multiqc [DEBUG ] No samples found: trimmomatic [2023-02-05 18:34:37,673] multiqc [DEBUG ] No samples found: sickle [2023-02-05 18:34:37,684] multiqc [DEBUG ] No samples found: skewer [2023-02-05 18:34:37,689] multiqc [DEBUG ] No samples found: sortmerna [2023-02-05 18:34:37,698] multiqc [DEBUG ] No samples found: biobloomtools [2023-02-05 18:34:37,711] multiqc [DEBUG ] No samples found: fastq_screen [2023-02-05 18:34:37,722] multiqc [DEBUG ] No samples found: afterqc [2023-02-05 18:34:37,733] multiqc [DEBUG ] No samples found: fastp [2023-02-05 18:34:48,104] multiqc.modules.fastqc.fastqc [INFO ] Found 130 reports [2023-02-05 18:35:10,614] multiqc [DEBUG ] No samples found: pycoqc [2023-02-05 18:35:10,623] multiqc [DEBUG ] No samples found: minionqc [2023-02-05 18:35:10,633] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-02-05 18:35:10,642] multiqc [DEBUG ] No samples found: clusterflow [2023-02-05 18:35:10,653] multiqc [DEBUG ] No samples found: bcl2fastq [2023-02-05 18:35:10,662] multiqc [DEBUG ] No samples found: interop [2023-02-05 18:35:10,671] multiqc [DEBUG ] No samples found: ivar [2023-02-05 18:35:10,683] multiqc [DEBUG ] No samples found: flash [2023-02-05 18:35:10,692] multiqc [DEBUG ] No samples found: seqyclean [2023-02-05 18:35:10,692] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-02-05 18:35:10,693] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-02-05 18:35:10,847] multiqc [INFO ] Compressing plot data [2023-02-05 18:35:10,892] multiqc [INFO ] Report : multiqc_report.html [2023-02-05 18:35:10,892] multiqc [INFO ] Data : multiqc_data [2023-02-05 18:35:10,892] multiqc [DEBUG ] Moving data file from '/state/partition1/job-29862253/tmp9grg3rkz/multiqc_data' to '/scratch/gencore/logs/html/HN5YJDRX2/merged/multiqc_data' [2023-02-05 18:35:11,113] multiqc [INFO ] MultiQC complete