[2023-12-15 02:44:47,964] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-15 02:44:47,964] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-15 02:44:47,964] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-15 02:44:47,967] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-12-15 02:44:47,967] 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}} [2023-12-15 02:44:47,967] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMJJFAFX5/merged [2023-12-15 02:44:48,127] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-15 02:44:48,127] multiqc [INFO ] This is MultiQC v1.9 [2023-12-15 02:44:48,127] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMJJFAFX5/merged [2023-12-15 02:44:48,127] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMJJFAFX5/merged [2023-12-15 02:44:48,127] multiqc [INFO ] Template : default [2023-12-15 02:44:48,127] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-15 02:44:48,127] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMJJFAFX5/merged [2023-12-15 02:44:48,128] 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 [2023-12-15 02:44:48,128] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40850190/tmpb7_brph3 [2023-12-15 02:44:48,234] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-15 02:44:48,236] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-15 02:44:48,854] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMJJFAFX5_n01_undetermined_fastqc.html [2023-12-15 02:44:48,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMJJFAFX5_n01_undetermined_fastqc.html [2023-12-15 02:44:48,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMJJFAFX5_n01_TopDonor1_fastqc.html [2023-12-15 02:44:48,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMJJFAFX5_n01_TopDonor1_fastqc.html [2023-12-15 02:44:48,978] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMJJFAFX5_n01_PresortDonor1_fastqc.html [2023-12-15 02:44:48,979] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMJJFAFX5_n01_PresortDonor1_fastqc.html [2023-12-15 02:44:49,042] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMJJFAFX5_n01_BotDonor1_fastqc.html [2023-12-15 02:44:49,044] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMJJFAFX5_n01_BotDonor1_fastqc.html [2023-12-15 02:44:49,427] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-15 02:44:49,429] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-15 02:44:49,445] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-12-15 02:44:49,447] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-15 02:44:49,449] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 4 samples (table) [2023-12-15 02:44:49,454] multiqc [DEBUG ] No samples found: conpair [2023-12-15 02:44:49,459] multiqc [DEBUG ] No samples found: peddy [2023-12-15 02:44:49,464] multiqc [DEBUG ] No samples found: somalier [2023-12-15 02:44:49,469] multiqc [DEBUG ] No samples found: methylQA [2023-12-15 02:44:49,476] multiqc [DEBUG ] No samples found: mosdepth [2023-12-15 02:44:49,480] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-15 02:44:49,484] multiqc [DEBUG ] No samples found: qualimap [2023-12-15 02:44:49,488] multiqc [DEBUG ] No samples found: preseq [2023-12-15 02:44:49,493] multiqc [DEBUG ] No samples found: quast [2023-12-15 02:44:49,498] multiqc [DEBUG ] No samples found: qorts [2023-12-15 02:44:49,502] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-15 02:44:49,507] multiqc [DEBUG ] No samples found: rockhopper [2023-12-15 02:44:49,512] multiqc [DEBUG ] No samples found: rsem [2023-12-15 02:44:49,522] multiqc [DEBUG ] No samples found: rseqc [2023-12-15 02:44:49,526] multiqc [DEBUG ] No samples found: busco [2023-12-15 02:44:49,531] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-15 02:44:49,535] multiqc [DEBUG ] No samples found: disambiguate [2023-12-15 02:44:49,539] multiqc [DEBUG ] No samples found: supernova [2023-12-15 02:44:49,551] multiqc [DEBUG ] No samples found: deeptools [2023-12-15 02:44:49,555] multiqc [DEBUG ] No samples found: sargasso [2023-12-15 02:44:49,560] multiqc [DEBUG ] No samples found: verifybamid [2023-12-15 02:44:49,564] multiqc [DEBUG ] No samples found: mirtrace [2023-12-15 02:44:49,569] multiqc [DEBUG ] No samples found: happy [2023-12-15 02:44:49,574] multiqc [DEBUG ] No samples found: mirtop [2023-12-15 02:44:49,580] multiqc [DEBUG ] No samples found: homer [2023-12-15 02:44:49,584] multiqc [DEBUG ] No samples found: macs2 [2023-12-15 02:44:49,588] multiqc [DEBUG ] No samples found: theta2 [2023-12-15 02:44:49,593] multiqc [DEBUG ] No samples found: snpeff [2023-12-15 02:44:49,599] multiqc [DEBUG ] No samples found: gatk [2023-12-15 02:44:49,603] multiqc [DEBUG ] No samples found: htseq [2023-12-15 02:44:49,608] multiqc [DEBUG ] No samples found: bcftools [2023-12-15 02:44:49,613] multiqc [DEBUG ] No samples found: featureCounts [2023-12-15 02:44:49,619] multiqc [DEBUG ] No samples found: fgbio [2023-12-15 02:44:49,631] multiqc [DEBUG ] No samples found: dragen [2023-12-15 02:44:49,636] multiqc [DEBUG ] No samples found: dedup [2023-12-15 02:44:49,640] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-15 02:44:49,661] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-15 02:44:49,666] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-15 02:44:49,669] multiqc [DEBUG ] No samples found: picard [2023-12-15 02:44:49,674] multiqc [DEBUG ] No samples found: prokka [2023-12-15 02:44:49,677] multiqc [DEBUG ] No samples found: samblaster [2023-12-15 02:44:49,685] multiqc [DEBUG ] No samples found: samtools [2023-12-15 02:44:49,690] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-15 02:44:49,694] multiqc [DEBUG ] No samples found: bamtools [2023-12-15 02:44:49,698] multiqc [DEBUG ] No samples found: jellyfish [2023-12-15 02:44:49,705] multiqc [DEBUG ] No samples found: vcftools [2023-12-15 02:44:49,709] multiqc [DEBUG ] No samples found: longranger [2023-12-15 02:44:49,714] multiqc [DEBUG ] No samples found: stacks [2023-12-15 02:44:49,718] multiqc [DEBUG ] No samples found: varscan2 [2023-12-15 02:44:49,731] multiqc [DEBUG ] No samples found: bbmap [2023-12-15 02:44:49,735] multiqc [DEBUG ] No samples found: bismark [2023-12-15 02:44:49,740] multiqc [DEBUG ] No samples found: biscuit [2023-12-15 02:44:49,745] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-15 02:44:49,750] multiqc [DEBUG ] No samples found: hicup [2023-12-15 02:44:49,755] multiqc [DEBUG ] No samples found: hicpro [2023-12-15 02:44:49,759] multiqc [DEBUG ] No samples found: salmon [2023-12-15 02:44:49,764] multiqc [DEBUG ] No samples found: kallisto [2023-12-15 02:44:49,769] multiqc [DEBUG ] No samples found: slamdunk [2023-12-15 02:44:49,773] multiqc [DEBUG ] No samples found: star [2023-12-15 02:44:49,778] multiqc [DEBUG ] No samples found: hisat2 [2023-12-15 02:44:49,782] multiqc [DEBUG ] No samples found: tophat [2023-12-15 02:44:49,787] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-15 02:44:49,791] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-15 02:44:49,796] multiqc [DEBUG ] No samples found: snpsplit [2023-12-15 02:44:49,800] multiqc [DEBUG ] No samples found: kat [2023-12-15 02:44:49,804] multiqc [DEBUG ] No samples found: leehom [2023-12-15 02:44:49,809] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-15 02:44:49,814] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-15 02:44:49,818] multiqc [DEBUG ] No samples found: cutadapt [2023-12-15 02:44:49,822] multiqc [DEBUG ] No samples found: flexbar [2023-12-15 02:44:49,827] multiqc [DEBUG ] No samples found: kaiju [2023-12-15 02:44:49,832] multiqc [DEBUG ] No samples found: kraken [2023-12-15 02:44:49,836] multiqc [DEBUG ] No samples found: malt [2023-12-15 02:44:49,841] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-15 02:44:49,845] multiqc [DEBUG ] No samples found: sickle [2023-12-15 02:44:49,849] multiqc [DEBUG ] No samples found: skewer [2023-12-15 02:44:49,853] multiqc [DEBUG ] No samples found: sortmerna [2023-12-15 02:44:49,857] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-15 02:44:49,865] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-15 02:44:49,870] multiqc [DEBUG ] No samples found: afterqc [2023-12-15 02:44:49,875] multiqc [DEBUG ] No samples found: fastp [2023-12-15 02:44:50,036] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-12-15 02:44:50,095] multiqc [DEBUG ] No samples found: pycoqc [2023-12-15 02:44:50,099] multiqc [DEBUG ] No samples found: minionqc [2023-12-15 02:44:50,103] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-15 02:44:50,108] multiqc [DEBUG ] No samples found: clusterflow [2023-12-15 02:44:50,113] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-15 02:44:50,117] multiqc [DEBUG ] No samples found: interop [2023-12-15 02:44:50,122] multiqc [DEBUG ] No samples found: ivar [2023-12-15 02:44:50,126] multiqc [DEBUG ] No samples found: flash [2023-12-15 02:44:50,130] multiqc [DEBUG ] No samples found: seqyclean [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-15 02:44:50,130] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-15 02:44:50,131] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-15 02:44:50,131] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-15 02:44:50,131] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-15 02:44:50,136] multiqc [INFO ] Compressing plot data [2023-12-15 02:44:50,216] multiqc [INFO ] Report : multiqc_report.html [2023-12-15 02:44:50,217] multiqc [INFO ] Data : multiqc_data [2023-12-15 02:44:50,217] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40850190/tmpb7_brph3/multiqc_data' to '/scratch/gencore/logs/html/HMJJFAFX5/merged/multiqc_data' [2023-12-15 02:44:50,340] multiqc [INFO ] MultiQC complete