[2024-01-23 21:14:07,739] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-23 21:14:07,739] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-23 21:14:07,739] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-23 21:14:07,741] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2024-01-23 21:14:07,741] 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}} [2024-01-23 21:14:07,741] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVK55DRX3/merged [2024-01-23 21:14:07,906] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-23 21:14:07,907] multiqc [INFO ] This is MultiQC v1.9 [2024-01-23 21:14:07,907] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVK55DRX3/merged [2024-01-23 21:14:07,907] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVK55DRX3/merged [2024-01-23 21:14:07,907] multiqc [INFO ] Template : default [2024-01-23 21:14:07,907] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-23 21:14:07,907] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVK55DRX3/merged [2024-01-23 21:14:07,907] 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 [2024-01-23 21:14:07,907] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42186122/tmp53zxumga [2024-01-23 21:14:08,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVK55DRX3_2_fastqc.html [2024-01-23 21:14:08,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVK55DRX3_2_fastqc.html [2024-01-23 21:14:08,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVK55DRX3_3_fastqc.html [2024-01-23 21:14:08,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVK55DRX3_3_fastqc.html [2024-01-23 21:14:08,277] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVK55DRX3_1_fastqc.html [2024-01-23 21:14:08,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVK55DRX3_1_fastqc.html [2024-01-23 21:14:08,865] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-23 21:14:08,879] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-23 21:14:08,902] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2024-01-23 21:14:08,904] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-23 21:14:08,928] multiqc [DEBUG ] No samples found: conpair [2024-01-23 21:14:08,959] multiqc [DEBUG ] No samples found: peddy [2024-01-23 21:14:08,973] multiqc [DEBUG ] No samples found: somalier [2024-01-23 21:14:08,980] multiqc [DEBUG ] No samples found: methylQA [2024-01-23 21:14:09,029] multiqc [DEBUG ] No samples found: mosdepth [2024-01-23 21:14:09,054] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-23 21:14:09,068] multiqc [DEBUG ] No samples found: qualimap [2024-01-23 21:14:09,101] multiqc [DEBUG ] No samples found: preseq [2024-01-23 21:14:09,106] multiqc [DEBUG ] No samples found: quast [2024-01-23 21:14:09,127] multiqc [DEBUG ] No samples found: qorts [2024-01-23 21:14:09,135] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-23 21:14:09,140] multiqc [DEBUG ] No samples found: rockhopper [2024-01-23 21:14:09,150] multiqc [DEBUG ] No samples found: rsem [2024-01-23 21:14:09,166] multiqc [DEBUG ] No samples found: rseqc [2024-01-23 21:14:09,173] multiqc [DEBUG ] No samples found: busco [2024-01-23 21:14:09,178] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-23 21:14:09,186] multiqc [DEBUG ] No samples found: disambiguate [2024-01-23 21:14:09,192] multiqc [DEBUG ] No samples found: supernova [2024-01-23 21:14:09,211] multiqc [DEBUG ] No samples found: deeptools [2024-01-23 21:14:09,216] multiqc [DEBUG ] No samples found: sargasso [2024-01-23 21:14:09,223] multiqc [DEBUG ] No samples found: verifybamid [2024-01-23 21:14:09,229] multiqc [DEBUG ] No samples found: mirtrace [2024-01-23 21:14:09,234] multiqc [DEBUG ] No samples found: happy [2024-01-23 21:14:09,240] multiqc [DEBUG ] No samples found: mirtop [2024-01-23 21:14:09,248] multiqc [DEBUG ] No samples found: homer [2024-01-23 21:14:09,265] multiqc [DEBUG ] No samples found: macs2 [2024-01-23 21:14:09,281] multiqc [DEBUG ] No samples found: theta2 [2024-01-23 21:14:09,310] multiqc [DEBUG ] No samples found: snpeff [2024-01-23 21:14:09,331] multiqc [DEBUG ] No samples found: gatk [2024-01-23 21:14:09,363] multiqc [DEBUG ] No samples found: htseq [2024-01-23 21:14:09,408] multiqc [DEBUG ] No samples found: bcftools [2024-01-23 21:14:09,439] multiqc [DEBUG ] No samples found: featureCounts [2024-01-23 21:14:09,488] multiqc [DEBUG ] No samples found: fgbio [2024-01-23 21:14:09,536] multiqc [DEBUG ] No samples found: dragen [2024-01-23 21:14:09,555] multiqc [DEBUG ] No samples found: dedup [2024-01-23 21:14:09,560] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-23 21:14:09,730] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-23 21:14:09,755] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-23 21:14:09,758] multiqc [DEBUG ] No samples found: picard [2024-01-23 21:14:09,765] multiqc [DEBUG ] No samples found: prokka [2024-01-23 21:14:09,783] multiqc [DEBUG ] No samples found: samblaster [2024-01-23 21:14:09,792] multiqc [DEBUG ] No samples found: samtools [2024-01-23 21:14:09,797] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-23 21:14:09,804] multiqc [DEBUG ] No samples found: bamtools [2024-01-23 21:14:09,809] multiqc [DEBUG ] No samples found: jellyfish [2024-01-23 21:14:09,819] multiqc [DEBUG ] No samples found: vcftools [2024-01-23 21:14:09,824] multiqc [DEBUG ] No samples found: longranger [2024-01-23 21:14:09,829] multiqc [DEBUG ] No samples found: stacks [2024-01-23 21:14:09,834] multiqc [DEBUG ] No samples found: varscan2 [2024-01-23 21:14:09,849] multiqc [DEBUG ] No samples found: bbmap [2024-01-23 21:14:09,854] multiqc [DEBUG ] No samples found: bismark [2024-01-23 21:14:09,858] multiqc [DEBUG ] No samples found: biscuit [2024-01-23 21:14:09,863] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-23 21:14:09,868] multiqc [DEBUG ] No samples found: hicup [2024-01-23 21:14:09,873] multiqc [DEBUG ] No samples found: hicpro [2024-01-23 21:14:09,877] multiqc [DEBUG ] No samples found: salmon [2024-01-23 21:14:09,882] multiqc [DEBUG ] No samples found: kallisto [2024-01-23 21:14:09,887] multiqc [DEBUG ] No samples found: slamdunk [2024-01-23 21:14:09,892] multiqc [DEBUG ] No samples found: star [2024-01-23 21:14:09,897] multiqc [DEBUG ] No samples found: hisat2 [2024-01-23 21:14:09,902] multiqc [DEBUG ] No samples found: tophat [2024-01-23 21:14:09,907] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-23 21:14:09,911] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-23 21:14:09,946] multiqc [DEBUG ] No samples found: snpsplit [2024-01-23 21:14:09,951] multiqc [DEBUG ] No samples found: kat [2024-01-23 21:14:09,966] multiqc [DEBUG ] No samples found: leehom [2024-01-23 21:14:09,972] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-23 21:14:09,989] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-23 21:14:10,010] multiqc [DEBUG ] No samples found: cutadapt [2024-01-23 21:14:10,024] multiqc [DEBUG ] No samples found: flexbar [2024-01-23 21:14:10,047] multiqc [DEBUG ] No samples found: kaiju [2024-01-23 21:14:10,058] multiqc [DEBUG ] No samples found: kraken [2024-01-23 21:14:10,080] multiqc [DEBUG ] No samples found: malt [2024-01-23 21:14:10,102] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-23 21:14:10,134] multiqc [DEBUG ] No samples found: sickle [2024-01-23 21:14:10,150] multiqc [DEBUG ] No samples found: skewer [2024-01-23 21:14:10,154] multiqc [DEBUG ] No samples found: sortmerna [2024-01-23 21:14:10,166] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-23 21:14:10,194] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-23 21:14:10,208] multiqc [DEBUG ] No samples found: afterqc [2024-01-23 21:14:10,213] multiqc [DEBUG ] No samples found: fastp [2024-01-23 21:14:10,332] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-01-23 21:14:10,409] multiqc [DEBUG ] No samples found: pycoqc [2024-01-23 21:14:10,415] multiqc [DEBUG ] No samples found: minionqc [2024-01-23 21:14:10,432] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-23 21:14:10,438] multiqc [DEBUG ] No samples found: clusterflow [2024-01-23 21:14:10,443] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-23 21:14:10,448] multiqc [DEBUG ] No samples found: interop [2024-01-23 21:14:10,458] multiqc [DEBUG ] No samples found: ivar [2024-01-23 21:14:10,463] multiqc [DEBUG ] No samples found: flash [2024-01-23 21:14:10,468] multiqc [DEBUG ] No samples found: seqyclean [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-23 21:14:10,468] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-23 21:14:10,469] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-23 21:14:10,473] multiqc [INFO ] Compressing plot data [2024-01-23 21:14:10,535] multiqc [INFO ] Report : multiqc_report.html [2024-01-23 21:14:10,535] multiqc [INFO ] Data : multiqc_data [2024-01-23 21:14:10,535] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42186122/tmp53zxumga/multiqc_data' to '/scratch/gencore/logs/html/HVK55DRX3/merged/multiqc_data' [2024-01-23 21:14:18,611] multiqc [INFO ] MultiQC complete