[2023-12-13 11:46:31,581] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-13 11:46:31,581] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-13 11:46:31,582] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-13 11:46:31,584] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-12-13 11:46:31,584] 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}} [2023-12-13 11:46:31,584] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF3T2DRX3/merged [2023-12-13 11:46:31,795] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-13 11:46:31,795] multiqc [INFO ] This is MultiQC v1.9 [2023-12-13 11:46:31,795] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF3T2DRX3/merged [2023-12-13 11:46:31,795] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HF3T2DRX3/merged [2023-12-13 11:46:31,795] multiqc [INFO ] Template : default [2023-12-13 11:46:31,795] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-13 11:46:31,795] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HF3T2DRX3/merged [2023-12-13 11:46:31,796] 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 [2023-12-13 11:46:31,796] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40811993/tmpuorr3kzt [2023-12-13 11:46:31,913] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n02_SF_01_fastqc.html [2023-12-13 11:46:31,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HF3T2DRX3_n01_NMD_19_fastqc.html [2023-12-13 11:46:37,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n01_NMD_19_fastqc.html [2023-12-13 11:46:37,523] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n01_NMD_02_fastqc.html [2023-12-13 11:46:37,525] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n01_NMD_02_fastqc.html [2023-12-13 11:46:37,672] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n02_NMD_08_fastqc.html [2023-12-13 11:46:37,674] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n02_NMD_08_fastqc.html [2023-12-13 11:46:37,724] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n02_NMD_10_fastqc.html [2023-12-13 11:46:37,726] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n02_NMD_10_fastqc.html [2023-12-13 11:46:37,775] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n01_NMD_10_fastqc.html [2023-12-13 11:46:37,777] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n01_NMD_10_fastqc.html [2023-12-13 11:46:37,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n02_SF_07_fastqc.html [2023-12-13 11:46:37,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n02_SF_07_fastqc.html [2023-12-13 11:46:38,284] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 11:46:38,285] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 11:46:38,302] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-12-13 11:46:38,317] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 31 samples (table) [2023-12-13 11:46:38,319] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-13 11:46:38,323] multiqc [DEBUG ] No samples found: conpair [2023-12-13 11:46:38,328] multiqc [DEBUG ] No samples found: peddy [2023-12-13 11:46:38,332] multiqc [DEBUG ] No samples found: somalier [2023-12-13 11:46:38,337] multiqc [DEBUG ] No samples found: methylQA [2023-12-13 11:46:38,343] multiqc [DEBUG ] No samples found: mosdepth [2023-12-13 11:46:38,347] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-13 11:46:38,351] multiqc [DEBUG ] No samples found: qualimap [2023-12-13 11:46:38,355] multiqc [DEBUG ] No samples found: preseq [2023-12-13 11:46:38,359] multiqc [DEBUG ] No samples found: quast [2023-12-13 11:46:38,363] multiqc [DEBUG ] No samples found: qorts [2023-12-13 11:46:38,367] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-13 11:46:38,371] multiqc [DEBUG ] No samples found: rockhopper [2023-12-13 11:46:38,375] multiqc [DEBUG ] No samples found: rsem [2023-12-13 11:46:38,385] multiqc [DEBUG ] No samples found: rseqc [2023-12-13 11:46:38,389] multiqc [DEBUG ] No samples found: busco [2023-12-13 11:46:38,393] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-13 11:46:38,397] multiqc [DEBUG ] No samples found: disambiguate [2023-12-13 11:46:38,401] multiqc [DEBUG ] No samples found: supernova [2023-12-13 11:46:38,412] multiqc [DEBUG ] No samples found: deeptools [2023-12-13 11:46:38,416] multiqc [DEBUG ] No samples found: sargasso [2023-12-13 11:46:38,421] multiqc [DEBUG ] No samples found: verifybamid [2023-12-13 11:46:38,425] multiqc [DEBUG ] No samples found: mirtrace [2023-12-13 11:46:38,429] multiqc [DEBUG ] No samples found: happy [2023-12-13 11:46:38,433] multiqc [DEBUG ] No samples found: mirtop [2023-12-13 11:46:38,439] multiqc [DEBUG ] No samples found: homer [2023-12-13 11:46:38,443] multiqc [DEBUG ] No samples found: macs2 [2023-12-13 11:46:38,447] multiqc [DEBUG ] No samples found: theta2 [2023-12-13 11:46:38,451] multiqc [DEBUG ] No samples found: snpeff [2023-12-13 11:46:38,457] multiqc [DEBUG ] No samples found: gatk [2023-12-13 11:46:38,461] multiqc [DEBUG ] No samples found: htseq [2023-12-13 11:46:38,466] multiqc [DEBUG ] No samples found: bcftools [2023-12-13 11:46:38,470] multiqc [DEBUG ] No samples found: featureCounts [2023-12-13 11:46:38,477] multiqc [DEBUG ] No samples found: fgbio [2023-12-13 11:46:38,488] multiqc [DEBUG ] No samples found: dragen [2023-12-13 11:46:38,493] multiqc [DEBUG ] No samples found: dedup [2023-12-13 11:46:38,497] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-13 11:46:38,518] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-13 11:46:38,522] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-13 11:46:38,524] multiqc [DEBUG ] No samples found: picard [2023-12-13 11:46:38,532] multiqc [DEBUG ] No samples found: prokka [2023-12-13 11:46:38,536] multiqc [DEBUG ] No samples found: samblaster [2023-12-13 11:46:38,546] multiqc [DEBUG ] No samples found: samtools [2023-12-13 11:46:38,551] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-13 11:46:38,555] multiqc [DEBUG ] No samples found: bamtools [2023-12-13 11:46:38,580] multiqc [DEBUG ] No samples found: jellyfish [2023-12-13 11:46:38,594] multiqc [DEBUG ] No samples found: vcftools [2023-12-13 11:46:38,599] multiqc [DEBUG ] No samples found: longranger [2023-12-13 11:46:38,603] multiqc [DEBUG ] No samples found: stacks [2023-12-13 11:46:38,608] multiqc [DEBUG ] No samples found: varscan2 [2023-12-13 11:46:38,621] multiqc [DEBUG ] No samples found: bbmap [2023-12-13 11:46:38,625] multiqc [DEBUG ] No samples found: bismark [2023-12-13 11:46:38,630] multiqc [DEBUG ] No samples found: biscuit [2023-12-13 11:46:38,634] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-13 11:46:38,638] multiqc [DEBUG ] No samples found: hicup [2023-12-13 11:46:38,642] multiqc [DEBUG ] No samples found: hicpro [2023-12-13 11:46:38,646] multiqc [DEBUG ] No samples found: salmon [2023-12-13 11:46:38,650] multiqc [DEBUG ] No samples found: kallisto [2023-12-13 11:46:38,655] multiqc [DEBUG ] No samples found: slamdunk [2023-12-13 11:46:38,659] multiqc [DEBUG ] No samples found: star [2023-12-13 11:46:38,663] multiqc [DEBUG ] No samples found: hisat2 [2023-12-13 11:46:38,668] multiqc [DEBUG ] No samples found: tophat [2023-12-13 11:46:38,672] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-13 11:46:38,676] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-13 11:46:38,685] multiqc [DEBUG ] No samples found: snpsplit [2023-12-13 11:46:38,692] multiqc [DEBUG ] No samples found: kat [2023-12-13 11:46:38,696] multiqc [DEBUG ] No samples found: leehom [2023-12-13 11:46:38,700] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-13 11:46:38,704] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-13 11:46:38,708] multiqc [DEBUG ] No samples found: cutadapt [2023-12-13 11:46:38,712] multiqc [DEBUG ] No samples found: flexbar [2023-12-13 11:46:38,716] multiqc [DEBUG ] No samples found: kaiju [2023-12-13 11:46:38,720] multiqc [DEBUG ] No samples found: kraken [2023-12-13 11:46:38,724] multiqc [DEBUG ] No samples found: malt [2023-12-13 11:46:38,728] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-13 11:46:38,732] multiqc [DEBUG ] No samples found: sickle [2023-12-13 11:46:38,737] multiqc [DEBUG ] No samples found: skewer [2023-12-13 11:46:38,741] multiqc [DEBUG ] No samples found: sortmerna [2023-12-13 11:46:38,745] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-13 11:46:38,749] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-13 11:46:38,753] multiqc [DEBUG ] No samples found: afterqc [2023-12-13 11:46:38,757] multiqc [DEBUG ] No samples found: fastp [2023-12-13 11:46:43,851] multiqc.modules.fastqc.fastqc [INFO ] Found 62 reports [2023-12-13 11:46:44,728] multiqc [DEBUG ] No samples found: pycoqc [2023-12-13 11:46:44,733] multiqc [DEBUG ] No samples found: minionqc [2023-12-13 11:46:44,737] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-13 11:46:44,742] multiqc [DEBUG ] No samples found: clusterflow [2023-12-13 11:46:44,747] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-13 11:46:44,753] multiqc [DEBUG ] No samples found: interop [2023-12-13 11:46:44,757] multiqc [DEBUG ] No samples found: ivar [2023-12-13 11:46:44,762] multiqc [DEBUG ] No samples found: flash [2023-12-13 11:46:44,767] multiqc [DEBUG ] No samples found: seqyclean [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-13 11:46:44,767] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-13 11:46:44,768] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-13 11:46:44,768] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-13 11:46:44,768] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-13 11:46:44,768] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-13 11:46:44,846] multiqc [INFO ] Compressing plot data [2023-12-13 11:46:46,055] multiqc [INFO ] Report : multiqc_report.html [2023-12-13 11:46:46,055] multiqc [INFO ] Data : multiqc_data [2023-12-13 11:46:46,055] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40811993/tmpuorr3kzt/multiqc_data' to '/scratch/gencore/logs/html/HF3T2DRX3/merged/multiqc_data' [2023-12-13 11:46:46,186] multiqc [INFO ] MultiQC complete