[2023-03-03 16:19:09,181] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-03-03 16:19:09,181] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-03-03 16:19:09,181] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-03-03 16:19:09,183] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-03-03 16:19:09,183] 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}} [2023-03-03 16:19:09,184] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFFF7AFX5/merged [2023-03-03 16:19:09,612] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-03-03 16:19:09,612] multiqc [INFO ] This is MultiQC v1.9 [2023-03-03 16:19:09,612] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFFF7AFX5/merged [2023-03-03 16:19:09,612] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFFF7AFX5/merged [2023-03-03 16:19:09,612] multiqc [INFO ] Template : default [2023-03-03 16:19:09,613] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-03-03 16:19:09,613] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFFF7AFX5/merged [2023-03-03 16:19:09,613] 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 [2023-03-03 16:19:09,613] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-30729969/tmpue9tnx26 [2023-03-03 16:19:09,713] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_5_fastqc.html [2023-03-03 16:19:09,716] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2023-03-03 16:19:10,898] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n01_dad6A_6_fastqc.html [2023-03-03 16:19:10,900] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n01_dad6A_6_fastqc.html [2023-03-03 16:19:10,949] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n01_dad6A_13_fastqc.html [2023-03-03 16:19:10,951] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n01_dad6A_13_fastqc.html [2023-03-03 16:19:11,001] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n01_undetermined_fastqc.html [2023-03-03 16:19:11,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n01_undetermined_fastqc.html [2023-03-03 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because it exceeded search pattern filesize limit: HFFF7AFX5_n01_dad6A_10_fastqc.html [2023-03-03 16:19:11,364] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n01_dad6A_10_fastqc.html [2023-03-03 16:19:11,407] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_12_fastqc.html [2023-03-03 16:19:11,409] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_12_fastqc.html [2023-03-03 16:19:11,456] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n02_undetermined_fastqc.html [2023-03-03 16:19:11,458] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n02_undetermined_fastqc.html [2023-03-03 16:19:11,504] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_4_fastqc.html [2023-03-03 16:19:11,506] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_4_fastqc.html [2023-03-03 16:19:11,556] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_9_fastqc.html [2023-03-03 16:19:11,558] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_9_fastqc.html [2023-03-03 16:19:11,605] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_10_fastqc.html [2023-03-03 16:19:11,606] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_10_fastqc.html [2023-03-03 16:19:11,668] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_3_fastqc.html [2023-03-03 16:19:11,669] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFF7AFX5_n02_dad6A_3_fastqc.html [2023-03-03 16:19:12,156] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-03 16:19:12,157] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-03 16:19:12,164] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-03-03 16:19:12,172] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 14 samples (table) [2023-03-03 16:19:12,181] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-03-03 16:19:12,185] multiqc [DEBUG ] No samples found: conpair [2023-03-03 16:19:12,190] multiqc [DEBUG ] No samples found: peddy [2023-03-03 16:19:12,194] multiqc [DEBUG ] No samples found: somalier [2023-03-03 16:19:12,198] multiqc [DEBUG ] No samples found: methylQA [2023-03-03 16:19:12,205] multiqc [DEBUG ] No samples found: mosdepth [2023-03-03 16:19:12,209] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-03-03 16:19:12,212] multiqc [DEBUG ] No samples found: qualimap [2023-03-03 16:19:12,216] multiqc [DEBUG ] No samples found: preseq [2023-03-03 16:19:12,220] multiqc [DEBUG ] No samples found: quast [2023-03-03 16:19:12,224] multiqc [DEBUG ] No samples found: qorts [2023-03-03 16:19:12,228] multiqc [DEBUG ] No samples found: rna_seqc [2023-03-03 16:19:12,232] multiqc [DEBUG ] No samples found: rockhopper [2023-03-03 16:19:12,236] multiqc [DEBUG ] No samples found: rsem [2023-03-03 16:19:12,246] multiqc [DEBUG ] No samples found: rseqc [2023-03-03 16:19:12,250] multiqc [DEBUG ] No samples found: busco [2023-03-03 16:19:12,254] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-03-03 16:19:12,257] multiqc [DEBUG ] No samples found: disambiguate [2023-03-03 16:19:12,262] multiqc [DEBUG ] No samples found: supernova [2023-03-03 16:19:12,271] multiqc [DEBUG ] No samples found: deeptools [2023-03-03 16:19:12,275] multiqc [DEBUG ] No samples found: sargasso [2023-03-03 16:19:12,279] multiqc [DEBUG ] No samples found: verifybamid [2023-03-03 16:19:12,284] multiqc [DEBUG ] No samples found: mirtrace [2023-03-03 16:19:12,288] multiqc [DEBUG ] No samples found: happy [2023-03-03 16:19:12,294] multiqc [DEBUG ] No samples found: mirtop [2023-03-03 16:19:12,300] multiqc [DEBUG ] No samples found: homer [2023-03-03 16:19:12,304] multiqc [DEBUG ] No samples found: macs2 [2023-03-03 16:19:12,308] multiqc [DEBUG ] No samples found: theta2 [2023-03-03 16:19:12,312] multiqc [DEBUG ] No samples found: snpeff [2023-03-03 16:19:12,318] multiqc [DEBUG ] No samples found: gatk [2023-03-03 16:19:12,321] multiqc [DEBUG ] No samples found: htseq [2023-03-03 16:19:12,325] multiqc [DEBUG ] No samples found: bcftools [2023-03-03 16:19:12,329] multiqc [DEBUG ] No samples found: featureCounts [2023-03-03 16:19:12,334] multiqc [DEBUG ] No samples found: fgbio [2023-03-03 16:19:12,346] multiqc [DEBUG ] No samples found: dragen [2023-03-03 16:19:12,350] multiqc [DEBUG ] No samples found: dedup [2023-03-03 16:19:12,355] multiqc [DEBUG ] No samples found: damageprofiler [2023-03-03 16:19:12,377] multiqc [DEBUG ] No samples found: biobambam2 [2023-03-03 16:19:12,381] multiqc [DEBUG ] No samples found: mtnucratio [2023-03-03 16:19:12,383] multiqc [DEBUG ] No samples found: picard [2023-03-03 16:19:12,387] multiqc [DEBUG ] No samples found: prokka [2023-03-03 16:19:12,392] multiqc [DEBUG ] No samples found: samblaster [2023-03-03 16:19:12,398] multiqc [DEBUG ] No samples found: samtools [2023-03-03 16:19:12,403] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-03-03 16:19:12,409] multiqc [DEBUG ] No samples found: bamtools [2023-03-03 16:19:12,413] multiqc [DEBUG ] No samples found: jellyfish [2023-03-03 16:19:12,421] multiqc [DEBUG ] No samples found: vcftools [2023-03-03 16:19:12,426] multiqc [DEBUG ] No samples found: longranger [2023-03-03 16:19:12,430] multiqc [DEBUG ] No samples found: stacks [2023-03-03 16:19:12,433] multiqc [DEBUG ] No samples found: varscan2 [2023-03-03 16:19:12,446] multiqc [DEBUG ] No samples found: bbmap [2023-03-03 16:19:12,450] multiqc [DEBUG ] No samples found: bismark [2023-03-03 16:19:12,455] multiqc [DEBUG ] No samples found: biscuit [2023-03-03 16:19:12,459] multiqc [DEBUG ] No samples found: hicexplorer [2023-03-03 16:19:12,463] multiqc [DEBUG ] No samples found: hicup [2023-03-03 16:19:12,467] multiqc [DEBUG ] No samples found: hicpro [2023-03-03 16:19:12,471] multiqc [DEBUG ] No samples found: salmon [2023-03-03 16:19:12,474] multiqc [DEBUG ] No samples found: kallisto [2023-03-03 16:19:12,478] multiqc [DEBUG ] No samples found: slamdunk [2023-03-03 16:19:12,482] multiqc [DEBUG ] No samples found: star [2023-03-03 16:19:12,486] multiqc [DEBUG ] No samples found: hisat2 [2023-03-03 16:19:12,490] multiqc [DEBUG ] No samples found: tophat [2023-03-03 16:19:12,495] multiqc [DEBUG ] No samples found: bowtie2 [2023-03-03 16:19:12,499] multiqc [DEBUG ] No samples found: bowtie1 [2023-03-03 16:19:12,503] multiqc [DEBUG ] No samples found: snpsplit [2023-03-03 16:19:12,507] multiqc [DEBUG ] No samples found: kat [2023-03-03 16:19:12,510] multiqc [DEBUG ] No samples found: leehom [2023-03-03 16:19:12,514] multiqc [DEBUG ] No samples found: adapterRemoval [2023-03-03 16:19:12,518] multiqc [DEBUG ] No samples found: clipandmerge [2023-03-03 16:19:12,522] multiqc [DEBUG ] No samples found: cutadapt [2023-03-03 16:19:12,526] multiqc [DEBUG ] No samples found: flexbar [2023-03-03 16:19:12,531] multiqc [DEBUG ] No samples found: kaiju [2023-03-03 16:19:12,535] multiqc [DEBUG ] No samples found: kraken [2023-03-03 16:19:12,539] multiqc [DEBUG ] No samples found: malt [2023-03-03 16:19:12,543] multiqc [DEBUG ] No samples found: trimmomatic [2023-03-03 16:19:12,547] multiqc [DEBUG ] No samples found: sickle [2023-03-03 16:19:12,552] multiqc [DEBUG ] No samples found: skewer [2023-03-03 16:19:12,556] multiqc [DEBUG ] No samples found: sortmerna [2023-03-03 16:19:12,560] multiqc [DEBUG ] No samples found: biobloomtools [2023-03-03 16:19:12,563] multiqc [DEBUG ] No samples found: fastq_screen [2023-03-03 16:19:12,567] multiqc [DEBUG ] No samples found: afterqc [2023-03-03 16:19:12,571] multiqc [DEBUG ] No samples found: fastp [2023-03-03 16:19:13,486] multiqc.modules.fastqc.fastqc [INFO ] Found 28 reports [2023-03-03 16:19:14,065] multiqc [DEBUG ] No samples found: pycoqc [2023-03-03 16:19:14,070] multiqc [DEBUG ] No samples found: minionqc [2023-03-03 16:19:14,074] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-03-03 16:19:14,078] multiqc [DEBUG ] No samples found: clusterflow [2023-03-03 16:19:14,083] multiqc [DEBUG ] No samples found: bcl2fastq [2023-03-03 16:19:14,086] multiqc [DEBUG ] No samples found: interop [2023-03-03 16:19:14,090] multiqc [DEBUG ] No samples found: ivar [2023-03-03 16:19:14,093] multiqc [DEBUG ] No samples found: flash [2023-03-03 16:19:14,098] multiqc [DEBUG ] No samples found: seqyclean [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-03-03 16:19:14,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-03-03 16:19:14,099] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-03-03 16:19:14,099] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-03-03 16:19:14,099] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-03-03 16:19:14,099] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-03-03 16:19:14,099] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-03-03 16:19:14,132] multiqc [INFO ] Compressing plot data [2023-03-03 16:19:14,636] multiqc [INFO ] Report : multiqc_report.html [2023-03-03 16:19:14,637] multiqc [INFO ] Data : multiqc_data [2023-03-03 16:19:14,637] multiqc [DEBUG ] Moving data file from '/state/partition1/job-30729969/tmpue9tnx26/multiqc_data' to '/scratch/gencore/logs/html/HFFF7AFX5/merged/multiqc_data' [2023-03-03 16:19:14,749] multiqc [INFO ] MultiQC complete