[2024-01-22 23:59:59,889] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-22 23:59:59,889] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-22 23:59:59,889] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-22 23:59:59,891] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2024-01-22 23:59:59,892] 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}} [2024-01-22 23:59:59,892] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN2GGAFX5/merged [2024-01-23 00:00:00,079] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-23 00:00:00,079] multiqc [INFO ] This is MultiQC v1.9 [2024-01-23 00:00:00,079] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN2GGAFX5/merged [2024-01-23 00:00:00,079] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HN2GGAFX5/merged [2024-01-23 00:00:00,079] multiqc [INFO ] Template : default [2024-01-23 00:00:00,079] 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 00:00:00,079] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HN2GGAFX5/merged [2024-01-23 00:00:00,079] 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 00:00:00,079] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42171898/tmp1o8lwk45 [2024-01-23 00:00:00,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-2_fastqc.html [2024-01-23 00:00:00,192] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-2_fastqc.html [2024-01-23 00:00:00,244] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-23 00:00:00,245] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-23 00:00:00,604] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_undetermined_fastqc.html [2024-01-23 00:00:00,606] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_undetermined_fastqc.html [2024-01-23 00:00:00,651] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-2_fastqc.html [2024-01-23 00:00:00,653] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-2_fastqc.html [2024-01-23 00:00:00,701] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-2_fastqc.html [2024-01-23 00:00:00,703] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-2_fastqc.html [2024-01-23 00:00:00,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-1_fastqc.html [2024-01-23 00:00:00,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-1_fastqc.html [2024-01-23 00:00:00,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-1_fastqc.html [2024-01-23 00:00:00,801] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-1_fastqc.html [2024-01-23 00:00:00,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-EV_fastqc.html [2024-01-23 00:00:00,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-EV_fastqc.html [2024-01-23 00:00:00,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-1_fastqc.html [2024-01-23 00:00:00,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-1_fastqc.html [2024-01-23 00:00:01,224] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-23 00:00:01,225] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-23 00:00:01,233] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-23 00:00:01,238] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2024-01-23 00:00:01,248] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-23 00:00:01,252] multiqc [DEBUG ] No samples found: conpair [2024-01-23 00:00:01,257] multiqc [DEBUG ] No samples found: peddy [2024-01-23 00:00:01,261] multiqc [DEBUG ] No samples found: somalier [2024-01-23 00:00:01,265] multiqc [DEBUG ] No samples found: methylQA [2024-01-23 00:00:01,273] multiqc [DEBUG ] No samples found: mosdepth [2024-01-23 00:00:01,277] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-23 00:00:01,280] multiqc [DEBUG ] No samples found: qualimap [2024-01-23 00:00:01,285] multiqc [DEBUG ] No samples found: preseq [2024-01-23 00:00:01,318] multiqc [DEBUG ] No samples found: quast [2024-01-23 00:00:01,322] multiqc [DEBUG ] No samples found: qorts [2024-01-23 00:00:01,327] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-23 00:00:01,351] multiqc [DEBUG ] No samples found: rockhopper [2024-01-23 00:00:01,355] multiqc [DEBUG ] No samples found: rsem [2024-01-23 00:00:01,364] multiqc [DEBUG ] No samples found: rseqc [2024-01-23 00:00:01,368] multiqc [DEBUG ] No samples found: busco [2024-01-23 00:00:01,372] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-23 00:00:01,376] multiqc [DEBUG ] No samples found: disambiguate [2024-01-23 00:00:01,380] multiqc [DEBUG ] No samples found: supernova [2024-01-23 00:00:01,390] multiqc [DEBUG ] No samples found: deeptools [2024-01-23 00:00:01,394] multiqc [DEBUG ] No samples found: sargasso [2024-01-23 00:00:01,398] multiqc [DEBUG ] No samples found: verifybamid [2024-01-23 00:00:01,402] multiqc [DEBUG ] No samples found: mirtrace [2024-01-23 00:00:01,407] multiqc [DEBUG ] No samples found: happy [2024-01-23 00:00:01,411] multiqc [DEBUG ] No samples found: mirtop [2024-01-23 00:00:01,416] multiqc [DEBUG ] No samples found: homer [2024-01-23 00:00:01,420] multiqc [DEBUG ] No samples found: macs2 [2024-01-23 00:00:01,424] multiqc [DEBUG ] No samples found: theta2 [2024-01-23 00:00:01,428] multiqc [DEBUG ] No samples found: snpeff [2024-01-23 00:00:01,434] multiqc [DEBUG ] No samples found: gatk [2024-01-23 00:00:01,438] multiqc [DEBUG ] No samples found: htseq [2024-01-23 00:00:01,443] multiqc [DEBUG ] No samples found: bcftools [2024-01-23 00:00:01,447] multiqc [DEBUG ] No samples found: featureCounts [2024-01-23 00:00:01,452] multiqc [DEBUG ] No samples found: fgbio [2024-01-23 00:00:01,463] multiqc [DEBUG ] No samples found: dragen [2024-01-23 00:00:01,467] multiqc [DEBUG ] No samples found: dedup [2024-01-23 00:00:01,471] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-23 00:00:01,490] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-23 00:00:01,508] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-23 00:00:01,511] multiqc [DEBUG ] No samples found: picard [2024-01-23 00:00:01,540] multiqc [DEBUG ] No samples found: prokka [2024-01-23 00:00:01,544] multiqc [DEBUG ] No samples found: samblaster [2024-01-23 00:00:01,551] multiqc [DEBUG ] No samples found: samtools [2024-01-23 00:00:01,555] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-23 00:00:01,560] multiqc [DEBUG ] No samples found: bamtools [2024-01-23 00:00:01,564] multiqc [DEBUG ] No samples found: jellyfish [2024-01-23 00:00:01,570] multiqc [DEBUG ] No samples found: vcftools [2024-01-23 00:00:01,574] multiqc [DEBUG ] No samples found: longranger [2024-01-23 00:00:01,578] multiqc [DEBUG ] No samples found: stacks [2024-01-23 00:00:01,582] multiqc [DEBUG ] No samples found: varscan2 [2024-01-23 00:00:01,593] multiqc [DEBUG ] No samples found: bbmap [2024-01-23 00:00:01,598] multiqc [DEBUG ] No samples found: bismark [2024-01-23 00:00:01,602] multiqc [DEBUG ] No samples found: biscuit [2024-01-23 00:00:01,606] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-23 00:00:01,610] multiqc [DEBUG ] No samples found: hicup [2024-01-23 00:00:01,615] multiqc [DEBUG ] No samples found: hicpro [2024-01-23 00:00:01,618] multiqc [DEBUG ] No samples found: salmon [2024-01-23 00:00:01,622] multiqc [DEBUG ] No samples found: kallisto [2024-01-23 00:00:01,626] multiqc [DEBUG ] No samples found: slamdunk [2024-01-23 00:00:01,631] multiqc [DEBUG ] No samples found: star [2024-01-23 00:00:01,634] multiqc [DEBUG ] No samples found: hisat2 [2024-01-23 00:00:01,638] multiqc [DEBUG ] No samples found: tophat [2024-01-23 00:00:01,642] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-23 00:00:01,646] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-23 00:00:01,651] multiqc [DEBUG ] No samples found: snpsplit [2024-01-23 00:00:01,654] multiqc [DEBUG ] No samples found: kat [2024-01-23 00:00:01,658] multiqc [DEBUG ] No samples found: leehom [2024-01-23 00:00:01,662] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-23 00:00:01,666] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-23 00:00:01,670] multiqc [DEBUG ] No samples found: cutadapt [2024-01-23 00:00:01,674] multiqc [DEBUG ] No samples found: flexbar [2024-01-23 00:00:01,678] multiqc [DEBUG ] No samples found: kaiju [2024-01-23 00:00:01,682] multiqc [DEBUG ] No samples found: kraken [2024-01-23 00:00:01,686] multiqc [DEBUG ] No samples found: malt [2024-01-23 00:00:01,709] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-23 00:00:01,713] multiqc [DEBUG ] No samples found: sickle [2024-01-23 00:00:01,717] multiqc [DEBUG ] No samples found: skewer [2024-01-23 00:00:01,721] multiqc [DEBUG ] No samples found: sortmerna [2024-01-23 00:00:01,724] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-23 00:00:01,729] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-23 00:00:01,733] multiqc [DEBUG ] No samples found: afterqc [2024-01-23 00:00:01,737] multiqc [DEBUG ] No samples found: fastp [2024-01-23 00:00:01,992] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2024-01-23 00:00:02,149] multiqc [DEBUG ] No samples found: pycoqc [2024-01-23 00:00:02,154] multiqc [DEBUG ] No samples found: minionqc [2024-01-23 00:00:02,158] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-23 00:00:02,162] multiqc [DEBUG ] No samples found: clusterflow [2024-01-23 00:00:02,166] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-23 00:00:02,171] multiqc [DEBUG ] No samples found: interop [2024-01-23 00:00:02,175] multiqc [DEBUG ] No samples found: ivar [2024-01-23 00:00:02,180] multiqc [DEBUG ] No samples found: flash [2024-01-23 00:00:02,184] multiqc [DEBUG ] No samples found: seqyclean [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-23 00:00:02,184] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-23 00:00:02,185] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-23 00:00:02,185] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-23 00:00:02,195] multiqc [INFO ] Compressing plot data [2024-01-23 00:00:02,366] multiqc [INFO ] Report : multiqc_report.html [2024-01-23 00:00:02,366] multiqc [INFO ] Data : multiqc_data [2024-01-23 00:00:02,366] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42171898/tmp1o8lwk45/multiqc_data' to '/scratch/gencore/logs/html/HN2GGAFX5/merged/multiqc_data' [2024-01-23 00:00:02,481] multiqc [INFO ] MultiQC complete