[2023-08-09 14:05:34,417] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-08-09 14:05:34,417] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-08-09 14:05:34,417] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-08-09 14:05:34,419] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-08-09 14:05:34,419] 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}} [2023-08-09 14:05:34,419] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGWKVAFX5/merged [2023-08-09 14:05:34,582] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-08-09 14:05:34,582] multiqc [INFO ] This is MultiQC v1.9 [2023-08-09 14:05:34,582] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGWKVAFX5/merged [2023-08-09 14:05:34,582] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGWKVAFX5/merged [2023-08-09 14:05:34,582] multiqc [INFO ] Template : default [2023-08-09 14:05:34,582] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-08-09 14:05:34,582] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGWKVAFX5/merged [2023-08-09 14:05:34,582] 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 [2023-08-09 14:05:34,582] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-36294941/tmp0xfo2fz6 [2023-08-09 14:05:34,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n02_BARSEQ_0H_fastqc.html [2023-08-09 14:05:34,696] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_12H_0_0_2_fastqc.html [2023-08-09 14:05:37,684] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_12H_0_0_2_fastqc.html [2023-08-09 14:05:37,752] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_undetermined_fastqc.html [2023-08-09 14:05:37,754] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_undetermined_fastqc.html [2023-08-09 14:05:37,803] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_0_0_1_fastqc.html [2023-08-09 14:05:37,805] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_0_0_1_fastqc.html [2023-08-09 14:05:37,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_100_0_1_fastqc.html [2023-08-09 14:05:37,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_100_0_1_fastqc.html [2023-08-09 14:05:37,940] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_0_0_2_fastqc.html [2023-08-09 14:05:37,942] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_0_0_2_fastqc.html [2023-08-09 14:05:38,009] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n02_BARSEQ_48H_0_0_2_fastqc.html [2023-08-09 14:05:38,011] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n02_BARSEQ_48H_0_0_2_fastqc.html [2023-08-09 14:05:38,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_0H_fastqc.html [2023-08-09 14:05:38,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_0H_fastqc.html [2023-08-09 14:05:38,147] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_100_32_1_fastqc.html [2023-08-09 14:05:38,149] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_72H_100_32_1_fastqc.html [2023-08-09 14:05:38,220] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n02_undetermined_fastqc.html [2023-08-09 14:05:38,222] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n02_undetermined_fastqc.html [2023-08-09 14:05:38,273] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_48H_100_32_1_fastqc.html [2023-08-09 14:05:38,275] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGWKVAFX5_n01_BARSEQ_48H_100_32_1_fastqc.html [2023-08-09 14:05:38,687] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-09 14:05:38,689] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-09 14:05:38,708] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 27 samples (table) [2023-08-09 14:05:38,710] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-08-09 14:05:38,719] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-08-09 14:05:38,725] multiqc [DEBUG ] No samples found: conpair [2023-08-09 14:05:38,731] multiqc [DEBUG ] No samples found: peddy [2023-08-09 14:05:38,737] multiqc [DEBUG ] No samples found: somalier [2023-08-09 14:05:38,743] multiqc [DEBUG ] No samples found: methylQA [2023-08-09 14:05:38,753] multiqc [DEBUG ] No samples found: mosdepth [2023-08-09 14:05:38,758] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-08-09 14:05:38,761] multiqc [DEBUG ] No samples found: qualimap [2023-08-09 14:05:38,766] multiqc [DEBUG ] No samples found: preseq [2023-08-09 14:05:38,773] multiqc [DEBUG ] No samples found: quast [2023-08-09 14:05:38,778] multiqc [DEBUG ] No samples found: qorts [2023-08-09 14:05:38,784] multiqc [DEBUG ] No samples found: rna_seqc [2023-08-09 14:05:38,789] multiqc [DEBUG ] No samples found: rockhopper [2023-08-09 14:05:38,794] multiqc [DEBUG ] No samples found: rsem [2023-08-09 14:05:38,808] multiqc [DEBUG ] No samples found: rseqc [2023-08-09 14:05:38,813] multiqc [DEBUG ] No samples found: busco [2023-08-09 14:05:38,818] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-08-09 14:05:38,823] multiqc [DEBUG ] No samples found: disambiguate [2023-08-09 14:05:38,829] multiqc [DEBUG ] No samples found: supernova [2023-08-09 14:05:38,848] multiqc [DEBUG ] No samples found: deeptools [2023-08-09 14:05:38,853] multiqc [DEBUG ] No samples found: sargasso [2023-08-09 14:05:38,859] multiqc [DEBUG ] No samples found: verifybamid [2023-08-09 14:05:38,865] multiqc [DEBUG ] No samples found: mirtrace [2023-08-09 14:05:38,870] multiqc [DEBUG ] No samples found: happy [2023-08-09 14:05:38,876] multiqc [DEBUG ] No samples found: mirtop [2023-08-09 14:05:38,883] multiqc [DEBUG ] No samples found: homer [2023-08-09 14:05:38,890] multiqc [DEBUG ] No samples found: macs2 [2023-08-09 14:05:38,895] multiqc [DEBUG ] No samples found: theta2 [2023-08-09 14:05:38,902] multiqc [DEBUG ] No samples found: snpeff [2023-08-09 14:05:38,909] multiqc [DEBUG ] No samples found: gatk [2023-08-09 14:05:38,915] multiqc [DEBUG ] No samples found: htseq [2023-08-09 14:05:38,921] multiqc [DEBUG ] No samples found: bcftools [2023-08-09 14:05:38,926] multiqc [DEBUG ] No samples found: featureCounts [2023-08-09 14:05:38,934] multiqc [DEBUG ] No samples found: fgbio [2023-08-09 14:05:38,949] multiqc [DEBUG ] No samples found: dragen [2023-08-09 14:05:38,955] multiqc [DEBUG ] No samples found: dedup [2023-08-09 14:05:38,960] multiqc [DEBUG ] No samples found: damageprofiler [2023-08-09 14:05:38,987] multiqc [DEBUG ] No samples found: biobambam2 [2023-08-09 14:05:38,991] multiqc [DEBUG ] No samples found: mtnucratio [2023-08-09 14:05:38,993] multiqc [DEBUG ] No samples found: picard [2023-08-09 14:05:38,998] multiqc [DEBUG ] No samples found: prokka [2023-08-09 14:05:39,004] multiqc [DEBUG ] No samples found: samblaster [2023-08-09 14:05:39,013] multiqc [DEBUG ] No samples found: samtools [2023-08-09 14:05:39,018] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-08-09 14:05:39,024] multiqc [DEBUG ] No samples found: bamtools [2023-08-09 14:05:39,028] multiqc [DEBUG ] No samples found: jellyfish [2023-08-09 14:05:39,037] multiqc [DEBUG ] No samples found: vcftools [2023-08-09 14:05:39,042] multiqc [DEBUG ] No samples found: longranger [2023-08-09 14:05:39,048] multiqc [DEBUG ] No samples found: stacks [2023-08-09 14:05:39,053] multiqc [DEBUG ] No samples found: varscan2 [2023-08-09 14:05:39,071] multiqc [DEBUG ] No samples found: bbmap [2023-08-09 14:05:39,076] multiqc [DEBUG ] No samples found: bismark [2023-08-09 14:05:39,082] multiqc [DEBUG ] No samples found: biscuit [2023-08-09 14:05:39,087] multiqc [DEBUG ] No samples found: hicexplorer [2023-08-09 14:05:39,092] multiqc [DEBUG ] No samples found: hicup [2023-08-09 14:05:39,098] multiqc [DEBUG ] No samples found: hicpro [2023-08-09 14:05:39,102] multiqc [DEBUG ] No samples found: salmon [2023-08-09 14:05:39,108] multiqc [DEBUG ] No samples found: kallisto [2023-08-09 14:05:39,113] multiqc [DEBUG ] No samples found: slamdunk [2023-08-09 14:05:39,119] multiqc [DEBUG ] No samples found: star [2023-08-09 14:05:39,124] multiqc [DEBUG ] No samples found: hisat2 [2023-08-09 14:05:39,130] multiqc [DEBUG ] No samples found: tophat [2023-08-09 14:05:39,135] multiqc [DEBUG ] No samples found: bowtie2 [2023-08-09 14:05:39,141] multiqc [DEBUG ] No samples found: bowtie1 [2023-08-09 14:05:39,146] multiqc [DEBUG ] No samples found: snpsplit [2023-08-09 14:05:39,150] multiqc [DEBUG ] No samples found: kat [2023-08-09 14:05:39,154] multiqc [DEBUG ] No samples found: leehom [2023-08-09 14:05:39,160] multiqc [DEBUG ] No samples found: adapterRemoval [2023-08-09 14:05:39,165] multiqc [DEBUG ] No samples found: clipandmerge [2023-08-09 14:05:39,170] multiqc [DEBUG ] No samples found: cutadapt [2023-08-09 14:05:39,175] multiqc [DEBUG ] No samples found: flexbar [2023-08-09 14:05:39,181] multiqc [DEBUG ] No samples found: kaiju [2023-08-09 14:05:39,187] multiqc [DEBUG ] No samples found: kraken [2023-08-09 14:05:39,192] multiqc [DEBUG ] No samples found: malt [2023-08-09 14:05:39,196] multiqc [DEBUG ] No samples found: trimmomatic [2023-08-09 14:05:39,202] multiqc [DEBUG ] No samples found: sickle [2023-08-09 14:05:39,206] multiqc [DEBUG ] No samples found: skewer [2023-08-09 14:05:39,212] multiqc [DEBUG ] No samples found: sortmerna [2023-08-09 14:05:39,217] multiqc [DEBUG ] No samples found: biobloomtools [2023-08-09 14:05:39,222] multiqc [DEBUG ] No samples found: fastq_screen [2023-08-09 14:05:39,228] multiqc [DEBUG ] No samples found: afterqc [2023-08-09 14:05:39,233] multiqc [DEBUG ] No samples found: fastp [2023-08-09 14:05:40,521] multiqc.modules.fastqc.fastqc [INFO ] Found 54 reports [2023-08-09 14:05:40,994] multiqc [DEBUG ] No samples found: pycoqc [2023-08-09 14:05:40,999] multiqc [DEBUG ] No samples found: minionqc [2023-08-09 14:05:41,005] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-08-09 14:05:41,011] multiqc [DEBUG ] No samples found: clusterflow [2023-08-09 14:05:41,017] multiqc [DEBUG ] No samples found: bcl2fastq [2023-08-09 14:05:41,022] multiqc [DEBUG ] No samples found: interop [2023-08-09 14:05:41,028] multiqc [DEBUG ] No samples found: ivar [2023-08-09 14:05:41,032] multiqc [DEBUG ] No samples found: flash [2023-08-09 14:05:41,037] multiqc [DEBUG ] No samples found: seqyclean [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-08-09 14:05:41,037] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-08-09 14:05:41,038] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-08-09 14:05:41,101] multiqc [INFO ] Compressing plot data [2023-08-09 14:05:42,018] multiqc [INFO ] Report : multiqc_report.html [2023-08-09 14:05:42,018] multiqc [INFO ] Data : multiqc_data [2023-08-09 14:05:42,018] multiqc [DEBUG ] Moving data file from '/state/partition1/job-36294941/tmp0xfo2fz6/multiqc_data' to '/scratch/gencore/logs/html/HGWKVAFX5/merged/multiqc_data' [2023-08-09 14:05:42,167] multiqc [INFO ] MultiQC complete