[2023-10-13 16:15:30,681] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-10-13 16:15:30,681] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-10-13 16:15:30,681] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-10-13 16:15:30,684] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-10-13 16:15:30,684] 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}} [2023-10-13 16:15:30,684] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJMF7AFX5/merged [2023-10-13 16:15:30,857] multiqc [WARNING] MultiQC Version v1.16 now available! [2023-10-13 16:15:30,857] multiqc [INFO ] This is MultiQC v1.9 [2023-10-13 16:15:30,857] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJMF7AFX5/merged [2023-10-13 16:15:30,857] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJMF7AFX5/merged [2023-10-13 16:15:30,857] multiqc [INFO ] Template : default [2023-10-13 16:15:30,857] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-10-13 16:15:30,858] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJMF7AFX5/merged [2023-10-13 16:15:30,858] 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 [2023-10-13 16:15:30,858] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-38855843/tmpoppcpwm1 [2023-10-13 16:15:30,963] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n02_2701_fastqc.html [2023-10-13 16:15:30,966] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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HJMF7AFX5_n01_3227_fastqc.html [2023-10-13 16:15:35,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n01_3230_fastqc.html [2023-10-13 16:15:35,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n01_3230_fastqc.html [2023-10-13 16:15:35,713] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n01_3233_fastqc.html [2023-10-13 16:15:35,715] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n01_3233_fastqc.html [2023-10-13 16:15:35,761] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n02_2349_fastqc.html [2023-10-13 16:15:35,763] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n02_2349_fastqc.html [2023-10-13 16:15:35,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n02_3232_fastqc.html [2023-10-13 16:15:35,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n02_3232_fastqc.html [2023-10-13 16:15:35,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n02_DGY_2543_fastqc.html [2023-10-13 16:15:35,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n02_DGY_2543_fastqc.html [2023-10-13 16:15:36,336] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-13 16:15:36,337] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-13 16:15:36,345] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-10-13 16:15:36,355] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-10-13 16:15:36,369] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2023-10-13 16:15:36,373] multiqc [DEBUG ] No samples found: conpair [2023-10-13 16:15:36,378] multiqc [DEBUG ] No samples found: peddy [2023-10-13 16:15:36,382] multiqc [DEBUG ] No samples found: somalier [2023-10-13 16:15:36,386] multiqc [DEBUG ] No samples found: methylQA [2023-10-13 16:15:36,393] multiqc [DEBUG ] No samples found: mosdepth [2023-10-13 16:15:36,397] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-10-13 16:15:36,400] multiqc [DEBUG ] No samples found: qualimap [2023-10-13 16:15:36,405] multiqc [DEBUG ] No samples found: preseq [2023-10-13 16:15:36,409] multiqc [DEBUG ] No samples found: quast [2023-10-13 16:15:36,413] multiqc [DEBUG ] No samples found: qorts [2023-10-13 16:15:36,418] multiqc [DEBUG ] No samples found: rna_seqc [2023-10-13 16:15:36,422] multiqc [DEBUG ] No samples found: rockhopper [2023-10-13 16:15:36,426] multiqc [DEBUG ] No samples found: rsem [2023-10-13 16:15:36,436] multiqc [DEBUG ] No samples found: rseqc [2023-10-13 16:15:36,440] multiqc [DEBUG ] No samples found: busco [2023-10-13 16:15:36,444] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-10-13 16:15:36,448] multiqc [DEBUG ] No samples found: disambiguate [2023-10-13 16:15:36,453] multiqc [DEBUG ] No samples found: supernova [2023-10-13 16:15:36,464] multiqc [DEBUG ] No samples found: deeptools [2023-10-13 16:15:36,468] multiqc [DEBUG ] No samples found: sargasso [2023-10-13 16:15:36,472] multiqc [DEBUG ] No samples found: verifybamid [2023-10-13 16:15:36,476] multiqc [DEBUG ] No samples found: mirtrace [2023-10-13 16:15:36,481] multiqc [DEBUG ] No samples found: happy [2023-10-13 16:15:36,485] multiqc [DEBUG ] No samples found: mirtop [2023-10-13 16:15:36,490] multiqc [DEBUG ] No samples found: homer [2023-10-13 16:15:36,495] multiqc [DEBUG ] No samples found: macs2 [2023-10-13 16:15:36,499] multiqc [DEBUG ] No samples found: theta2 [2023-10-13 16:15:36,503] multiqc [DEBUG ] No samples found: snpeff [2023-10-13 16:15:36,509] multiqc [DEBUG ] No samples found: gatk [2023-10-13 16:15:36,513] multiqc [DEBUG ] No samples found: htseq [2023-10-13 16:15:36,518] multiqc [DEBUG ] No samples found: bcftools [2023-10-13 16:15:36,522] multiqc [DEBUG ] No samples found: featureCounts [2023-10-13 16:15:36,527] multiqc [DEBUG ] No samples found: fgbio [2023-10-13 16:15:36,539] multiqc [DEBUG ] No samples found: dragen [2023-10-13 16:15:36,543] multiqc [DEBUG ] No samples found: dedup [2023-10-13 16:15:36,547] multiqc [DEBUG ] No samples found: damageprofiler [2023-10-13 16:15:36,567] multiqc [DEBUG ] No samples found: biobambam2 [2023-10-13 16:15:36,571] multiqc [DEBUG ] No samples found: mtnucratio [2023-10-13 16:15:36,573] multiqc [DEBUG ] No samples found: picard [2023-10-13 16:15:36,577] multiqc [DEBUG ] No samples found: prokka [2023-10-13 16:15:36,581] multiqc [DEBUG ] No samples found: samblaster [2023-10-13 16:15:36,588] multiqc [DEBUG ] No samples found: samtools [2023-10-13 16:15:36,593] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-10-13 16:15:36,597] multiqc [DEBUG ] No samples found: bamtools [2023-10-13 16:15:36,601] multiqc [DEBUG ] No samples found: jellyfish [2023-10-13 16:15:36,607] multiqc [DEBUG ] No samples found: vcftools [2023-10-13 16:15:36,612] multiqc [DEBUG ] No samples found: longranger [2023-10-13 16:15:36,616] multiqc [DEBUG ] No samples found: stacks [2023-10-13 16:15:36,620] multiqc [DEBUG ] No samples found: varscan2 [2023-10-13 16:15:36,631] multiqc [DEBUG ] No samples found: bbmap [2023-10-13 16:15:36,636] multiqc [DEBUG ] No samples found: bismark [2023-10-13 16:15:36,640] multiqc [DEBUG ] No samples found: biscuit [2023-10-13 16:15:36,644] multiqc [DEBUG ] No samples found: hicexplorer [2023-10-13 16:15:36,649] multiqc [DEBUG ] No samples found: hicup [2023-10-13 16:15:36,653] multiqc [DEBUG ] No samples found: hicpro [2023-10-13 16:15:36,657] multiqc [DEBUG ] No samples found: salmon [2023-10-13 16:15:36,661] multiqc [DEBUG ] No samples found: kallisto [2023-10-13 16:15:36,666] multiqc [DEBUG ] No samples found: slamdunk [2023-10-13 16:15:36,670] multiqc [DEBUG ] No samples found: star [2023-10-13 16:15:36,674] multiqc [DEBUG ] No samples found: hisat2 [2023-10-13 16:15:36,678] multiqc [DEBUG ] No samples found: tophat [2023-10-13 16:15:36,682] multiqc [DEBUG ] No samples found: bowtie2 [2023-10-13 16:15:36,687] multiqc [DEBUG ] No samples found: bowtie1 [2023-10-13 16:15:36,691] multiqc [DEBUG ] No samples found: snpsplit [2023-10-13 16:15:36,695] multiqc [DEBUG ] No samples found: kat [2023-10-13 16:15:36,699] multiqc [DEBUG ] No samples found: leehom [2023-10-13 16:15:36,703] multiqc [DEBUG ] No samples found: adapterRemoval [2023-10-13 16:15:36,707] multiqc [DEBUG ] No samples found: clipandmerge [2023-10-13 16:15:36,712] multiqc [DEBUG ] No samples found: cutadapt [2023-10-13 16:15:36,715] multiqc [DEBUG ] No samples found: flexbar [2023-10-13 16:15:36,720] multiqc [DEBUG ] No samples found: kaiju [2023-10-13 16:15:36,724] multiqc [DEBUG ] No samples found: kraken [2023-10-13 16:15:36,728] multiqc [DEBUG ] No samples found: malt [2023-10-13 16:15:36,732] multiqc [DEBUG ] No samples found: trimmomatic [2023-10-13 16:15:36,736] multiqc [DEBUG ] No samples found: sickle [2023-10-13 16:15:36,741] multiqc [DEBUG ] No samples found: skewer [2023-10-13 16:15:36,745] multiqc [DEBUG ] No samples found: sortmerna [2023-10-13 16:15:36,748] multiqc [DEBUG ] No samples found: biobloomtools [2023-10-13 16:15:36,753] multiqc [DEBUG ] No samples found: fastq_screen [2023-10-13 16:15:36,757] multiqc [DEBUG ] No samples found: afterqc [2023-10-13 16:15:36,761] multiqc [DEBUG ] No samples found: fastp [2023-10-13 16:15:38,318] multiqc.modules.fastqc.fastqc [INFO ] Found 58 reports [2023-10-13 16:15:38,789] multiqc [DEBUG ] No samples found: pycoqc [2023-10-13 16:15:38,793] multiqc [DEBUG ] No samples found: minionqc [2023-10-13 16:15:38,798] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-10-13 16:15:38,802] multiqc [DEBUG ] No samples found: clusterflow [2023-10-13 16:15:38,806] multiqc [DEBUG ] No samples found: bcl2fastq [2023-10-13 16:15:38,810] multiqc [DEBUG ] No samples found: interop [2023-10-13 16:15:38,815] multiqc [DEBUG ] No samples found: ivar [2023-10-13 16:15:38,819] multiqc [DEBUG ] No samples found: flash [2023-10-13 16:15:38,823] multiqc [DEBUG ] No samples found: seqyclean [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-10-13 16:15:38,823] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-10-13 16:15:38,824] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-10-13 16:15:38,892] multiqc [INFO ] Compressing plot data [2023-10-13 16:15:39,781] multiqc [INFO ] Report : multiqc_report.html [2023-10-13 16:15:39,782] multiqc [INFO ] Data : multiqc_data [2023-10-13 16:15:39,782] multiqc [DEBUG ] Moving data file from '/state/partition1/job-38855843/tmpoppcpwm1/multiqc_data' to '/scratch/gencore/logs/html/HJMF7AFX5/merged/multiqc_data' [2023-10-13 16:15:39,906] multiqc [INFO ] MultiQC complete