[2023-09-01 08:55:12,624] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-09-01 08:55:12,624] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-09-01 08:55:12,624] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-09-01 08:55:12,626] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-09-01 08:55:12,626] 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}} [2023-09-01 08:55:12,627] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFLFKDRX3/merged [2023-09-01 08:55:12,819] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-09-01 08:55:12,819] multiqc [INFO ] This is MultiQC v1.9 [2023-09-01 08:55:12,819] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFLFKDRX3/merged [2023-09-01 08:55:12,819] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFLFKDRX3/merged [2023-09-01 08:55:12,819] multiqc [INFO ] Template : default [2023-09-01 08:55:12,819] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-09-01 08:55:12,819] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFLFKDRX3/merged [2023-09-01 08:55:12,820] 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 [2023-09-01 08:55:12,820] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-37112056/tmpdos9o33q [2023-09-01 08:55:12,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLFKDRX3_2_fastqc.html [2023-09-01 08:55:12,960] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLFKDRX3_2_fastqc.html [2023-09-01 08:55:13,000] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLFKDRX3_3_fastqc.html [2023-09-01 08:55:13,002] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLFKDRX3_3_fastqc.html [2023-09-01 08:55:13,047] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLFKDRX3_1_fastqc.html [2023-09-01 08:55:13,049] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLFKDRX3_1_fastqc.html [2023-09-01 08:55:13,387] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-01 08:55:13,389] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-01 08:55:13,393] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-09-01 08:55:13,395] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-09-01 08:55:13,403] multiqc [DEBUG ] No samples found: conpair [2023-09-01 08:55:13,408] multiqc [DEBUG ] No samples found: peddy [2023-09-01 08:55:13,414] multiqc [DEBUG ] No samples found: somalier [2023-09-01 08:55:13,418] multiqc [DEBUG ] No samples found: methylQA [2023-09-01 08:55:13,427] multiqc [DEBUG ] No samples found: mosdepth [2023-09-01 08:55:13,432] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-09-01 08:55:13,435] multiqc [DEBUG ] No samples found: qualimap [2023-09-01 08:55:13,440] multiqc [DEBUG ] No samples found: preseq [2023-09-01 08:55:13,445] multiqc [DEBUG ] No samples found: quast [2023-09-01 08:55:13,450] multiqc [DEBUG ] No samples found: qorts [2023-09-01 08:55:13,456] multiqc [DEBUG ] No samples found: rna_seqc [2023-09-01 08:55:13,460] multiqc [DEBUG ] No samples found: rockhopper [2023-09-01 08:55:13,465] multiqc [DEBUG ] No samples found: rsem [2023-09-01 08:55:13,475] multiqc [DEBUG ] No samples found: rseqc [2023-09-01 08:55:13,480] multiqc [DEBUG ] No samples found: busco [2023-09-01 08:55:13,484] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-09-01 08:55:13,489] multiqc [DEBUG ] No samples found: disambiguate [2023-09-01 08:55:13,494] multiqc [DEBUG ] No samples found: supernova [2023-09-01 08:55:13,506] multiqc [DEBUG ] No samples found: deeptools [2023-09-01 08:55:13,512] multiqc [DEBUG ] No samples found: sargasso [2023-09-01 08:55:13,517] multiqc [DEBUG ] No samples found: verifybamid [2023-09-01 08:55:13,522] multiqc [DEBUG ] No samples found: mirtrace [2023-09-01 08:55:13,527] multiqc [DEBUG ] No samples found: happy [2023-09-01 08:55:13,532] multiqc [DEBUG ] No samples found: mirtop [2023-09-01 08:55:13,538] multiqc [DEBUG ] No samples found: homer [2023-09-01 08:55:13,543] multiqc [DEBUG ] No samples found: macs2 [2023-09-01 08:55:13,548] multiqc [DEBUG ] No samples found: theta2 [2023-09-01 08:55:13,553] multiqc [DEBUG ] No samples found: snpeff [2023-09-01 08:55:13,560] multiqc [DEBUG ] No samples found: gatk [2023-09-01 08:55:13,565] multiqc [DEBUG ] No samples found: htseq [2023-09-01 08:55:13,571] multiqc [DEBUG ] No samples found: bcftools [2023-09-01 08:55:13,576] multiqc [DEBUG ] No samples found: featureCounts [2023-09-01 08:55:13,582] multiqc [DEBUG ] No samples found: fgbio [2023-09-01 08:55:13,595] multiqc [DEBUG ] No samples found: dragen [2023-09-01 08:55:13,600] multiqc [DEBUG ] No samples found: dedup [2023-09-01 08:55:13,605] multiqc [DEBUG ] No samples found: damageprofiler [2023-09-01 08:55:13,627] multiqc [DEBUG ] No samples found: biobambam2 [2023-09-01 08:55:13,633] multiqc [DEBUG ] No samples found: mtnucratio [2023-09-01 08:55:13,636] multiqc [DEBUG ] No samples found: picard [2023-09-01 08:55:13,641] multiqc [DEBUG ] No samples found: prokka [2023-09-01 08:55:13,645] multiqc [DEBUG ] No samples found: samblaster [2023-09-01 08:55:13,654] multiqc [DEBUG ] No samples found: samtools [2023-09-01 08:55:13,661] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-09-01 08:55:13,666] multiqc [DEBUG ] No samples found: bamtools [2023-09-01 08:55:13,670] multiqc [DEBUG ] No samples found: jellyfish [2023-09-01 08:55:13,678] multiqc [DEBUG ] No samples found: vcftools [2023-09-01 08:55:13,683] multiqc [DEBUG ] No samples found: longranger [2023-09-01 08:55:13,688] multiqc [DEBUG ] No samples found: stacks [2023-09-01 08:55:13,694] multiqc [DEBUG ] No samples found: varscan2 [2023-09-01 08:55:13,707] multiqc [DEBUG ] No samples found: bbmap [2023-09-01 08:55:13,712] multiqc [DEBUG ] No samples found: bismark [2023-09-01 08:55:13,717] multiqc [DEBUG ] No samples found: biscuit [2023-09-01 08:55:13,722] multiqc [DEBUG ] No samples found: hicexplorer [2023-09-01 08:55:13,727] multiqc [DEBUG ] No samples found: hicup [2023-09-01 08:55:13,731] multiqc [DEBUG ] No samples found: hicpro [2023-09-01 08:55:13,735] multiqc [DEBUG ] No samples found: salmon [2023-09-01 08:55:13,740] multiqc [DEBUG ] No samples found: kallisto [2023-09-01 08:55:13,745] multiqc [DEBUG ] No samples found: slamdunk [2023-09-01 08:55:13,750] multiqc [DEBUG ] No samples found: star [2023-09-01 08:55:13,755] multiqc [DEBUG ] No samples found: hisat2 [2023-09-01 08:55:13,760] multiqc [DEBUG ] No samples found: tophat [2023-09-01 08:55:13,764] multiqc [DEBUG ] No samples found: bowtie2 [2023-09-01 08:55:13,769] multiqc [DEBUG ] No samples found: bowtie1 [2023-09-01 08:55:13,774] multiqc [DEBUG ] No samples found: snpsplit [2023-09-01 08:55:13,778] multiqc [DEBUG ] No samples found: kat [2023-09-01 08:55:13,782] multiqc [DEBUG ] No samples found: leehom [2023-09-01 08:55:13,787] multiqc [DEBUG ] No samples found: adapterRemoval [2023-09-01 08:55:13,792] multiqc [DEBUG ] No samples found: clipandmerge [2023-09-01 08:55:13,797] multiqc [DEBUG ] No samples found: cutadapt [2023-09-01 08:55:13,801] multiqc [DEBUG ] No samples found: flexbar [2023-09-01 08:55:13,806] multiqc [DEBUG ] No samples found: kaiju [2023-09-01 08:55:13,811] multiqc [DEBUG ] No samples found: kraken [2023-09-01 08:55:13,816] multiqc [DEBUG ] No samples found: malt [2023-09-01 08:55:13,820] multiqc [DEBUG ] No samples found: trimmomatic [2023-09-01 08:55:13,825] multiqc [DEBUG ] No samples found: sickle [2023-09-01 08:55:13,830] multiqc [DEBUG ] No samples found: skewer [2023-09-01 08:55:13,835] multiqc [DEBUG ] No samples found: sortmerna [2023-09-01 08:55:13,840] multiqc [DEBUG ] No samples found: biobloomtools [2023-09-01 08:55:13,845] multiqc [DEBUG ] No samples found: fastq_screen [2023-09-01 08:55:13,849] multiqc [DEBUG ] No samples found: afterqc [2023-09-01 08:55:13,855] multiqc [DEBUG ] No samples found: fastp [2023-09-01 08:55:13,911] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2023-09-01 08:55:13,956] multiqc [DEBUG ] No samples found: pycoqc [2023-09-01 08:55:13,961] multiqc [DEBUG ] No samples found: minionqc [2023-09-01 08:55:13,966] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-09-01 08:55:13,971] multiqc [DEBUG ] No samples found: clusterflow [2023-09-01 08:55:13,975] multiqc [DEBUG ] No samples found: bcl2fastq [2023-09-01 08:55:13,980] multiqc [DEBUG ] No samples found: interop [2023-09-01 08:55:13,985] multiqc [DEBUG ] No samples found: ivar [2023-09-01 08:55:13,990] multiqc [DEBUG ] No samples found: flash [2023-09-01 08:55:13,994] multiqc [DEBUG ] No samples found: seqyclean [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-09-01 08:55:13,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-09-01 08:55:13,995] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-09-01 08:55:13,999] multiqc [INFO ] Compressing plot data [2023-09-01 08:55:14,056] multiqc [INFO ] Report : multiqc_report.html [2023-09-01 08:55:14,057] multiqc [INFO ] Data : multiqc_data [2023-09-01 08:55:14,057] multiqc [DEBUG ] Moving data file from '/state/partition1/job-37112056/tmpdos9o33q/multiqc_data' to '/scratch/gencore/logs/html/HFLFKDRX3/merged/multiqc_data' [2023-09-01 08:55:14,195] multiqc [INFO ] MultiQC complete