[2024-08-29 09:45:22,328] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-29 09:45:22,328] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-29 09:45:22,328] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-29 09:45:22,331] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-29 09:45:22,331] 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}} [2024-08-29 09:45:22,331] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-29 09:45:22,361] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-29 09:45:22,361] multiqc [INFO ] This is MultiQC v1.9 [2024-08-29 09:45:22,362] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-29 09:45:22,362] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/a1/2683708cec93a30657c40c92a02f7f/merged [2024-08-29 09:45:22,362] multiqc [INFO ] Template : default [2024-08-29 09:45:22,362] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-29 09:45:22,362] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/a1/2683708cec93a30657c40c92a02f7f/merged [2024-08-29 09:45:22,362] 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 [2024-08-29 09:45:22,362] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-50425677/tmptunn8y61 [2024-08-29 09:45:22,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5CNBGXV_n01_DO127_fastqc.html [2024-08-29 09:45:22,472] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5CNBGXV_n01_DO127_fastqc.html [2024-08-29 09:45:22,523] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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09:45:24,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5CNBGXV_n02_HW60_1_fastqc.html [2024-08-29 09:45:24,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5CNBGXV_n02_HW60_1_fastqc.html [2024-08-29 09:45:24,545] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5CNBGXV_n01_DO130_fastqc.html [2024-08-29 09:45:24,546] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5CNBGXV_n01_DO130_fastqc.html [2024-08-29 09:45:24,595] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5CNBGXV_n01_HW62_1_fastqc.html [2024-08-29 09:45:24,596] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5CNBGXV_n01_HW62_1_fastqc.html [2024-08-29 09:45:24,639] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5CNBGXV_n01_HW78_fastqc.html [2024-08-29 09:45:24,641] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5CNBGXV_n01_HW78_fastqc.html [2024-08-29 09:45:24,685] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5CNBGXV_n02_HW75_fastqc.html [2024-08-29 09:45:24,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5CNBGXV_n02_HW75_fastqc.html [2024-08-29 09:45:25,160] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-29 09:45:25,162] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-29 09:45:25,180] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2024-08-29 09:45:25,182] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-29 09:45:25,192] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-29 09:45:25,197] multiqc [DEBUG ] No samples found: conpair [2024-08-29 09:45:25,202] multiqc [DEBUG ] No samples found: peddy [2024-08-29 09:45:25,210] multiqc [DEBUG ] No samples found: somalier [2024-08-29 09:45:25,215] multiqc [DEBUG ] No samples found: methylQA [2024-08-29 09:45:25,225] multiqc [DEBUG ] No samples found: mosdepth [2024-08-29 09:45:25,231] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-29 09:45:25,234] multiqc [DEBUG ] No samples found: qualimap [2024-08-29 09:45:25,240] multiqc [DEBUG ] No samples found: preseq [2024-08-29 09:45:25,245] multiqc [DEBUG ] No samples found: quast [2024-08-29 09:45:25,251] multiqc [DEBUG ] No samples found: qorts [2024-08-29 09:45:25,256] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-29 09:45:25,261] multiqc [DEBUG ] No samples found: rockhopper [2024-08-29 09:45:25,267] multiqc [DEBUG ] No samples found: rsem [2024-08-29 09:45:25,281] multiqc [DEBUG ] No samples found: rseqc [2024-08-29 09:45:25,285] multiqc [DEBUG ] No samples found: busco [2024-08-29 09:45:25,291] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-29 09:45:25,295] multiqc [DEBUG ] No samples found: disambiguate [2024-08-29 09:45:25,301] multiqc [DEBUG ] No samples found: supernova [2024-08-29 09:45:25,315] multiqc [DEBUG ] No samples found: deeptools [2024-08-29 09:45:25,320] multiqc [DEBUG ] No samples found: sargasso [2024-08-29 09:45:25,325] multiqc [DEBUG ] No samples found: verifybamid [2024-08-29 09:45:25,332] multiqc [DEBUG ] No samples found: mirtrace [2024-08-29 09:45:25,337] multiqc [DEBUG ] No samples found: happy [2024-08-29 09:45:25,347] multiqc [DEBUG ] No samples found: mirtop [2024-08-29 09:45:25,353] multiqc [DEBUG ] No samples found: homer [2024-08-29 09:45:25,359] multiqc [DEBUG ] No samples found: macs2 [2024-08-29 09:45:25,363] multiqc [DEBUG ] No samples found: theta2 [2024-08-29 09:45:25,368] multiqc [DEBUG ] No samples found: snpeff [2024-08-29 09:45:25,376] multiqc [DEBUG ] No samples found: gatk [2024-08-29 09:45:25,380] multiqc [DEBUG ] No samples found: htseq [2024-08-29 09:45:25,386] multiqc [DEBUG ] No samples found: bcftools [2024-08-29 09:45:25,391] multiqc [DEBUG ] No samples found: featureCounts [2024-08-29 09:45:25,397] multiqc [DEBUG ] No samples found: fgbio [2024-08-29 09:45:25,411] multiqc [DEBUG ] No samples found: dragen [2024-08-29 09:45:25,416] multiqc [DEBUG ] No samples found: dedup [2024-08-29 09:45:25,421] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-29 09:45:25,448] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-29 09:45:25,452] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-29 09:45:25,455] multiqc [DEBUG ] No samples found: picard [2024-08-29 09:45:25,459] multiqc [DEBUG ] No samples found: prokka [2024-08-29 09:45:25,464] multiqc [DEBUG ] No samples found: samblaster [2024-08-29 09:45:25,473] multiqc [DEBUG ] No samples found: samtools [2024-08-29 09:45:25,478] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-29 09:45:25,483] multiqc [DEBUG ] No samples found: bamtools [2024-08-29 09:45:25,489] multiqc [DEBUG ] No samples found: jellyfish [2024-08-29 09:45:25,497] multiqc [DEBUG ] No samples found: vcftools [2024-08-29 09:45:25,502] multiqc [DEBUG ] No samples found: longranger [2024-08-29 09:45:25,507] multiqc [DEBUG ] No samples found: stacks [2024-08-29 09:45:25,512] multiqc [DEBUG ] No samples found: varscan2 [2024-08-29 09:45:25,526] multiqc [DEBUG ] No samples found: bbmap [2024-08-29 09:45:25,532] multiqc [DEBUG ] No samples found: bismark [2024-08-29 09:45:25,537] multiqc [DEBUG ] No samples found: biscuit [2024-08-29 09:45:25,543] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-29 09:45:25,548] multiqc [DEBUG ] No samples found: hicup [2024-08-29 09:45:25,553] multiqc [DEBUG ] No samples found: hicpro [2024-08-29 09:45:25,558] multiqc [DEBUG ] No samples found: salmon [2024-08-29 09:45:25,563] multiqc [DEBUG ] No samples found: kallisto [2024-08-29 09:45:25,568] multiqc [DEBUG ] No samples found: slamdunk [2024-08-29 09:45:25,573] multiqc [DEBUG ] No samples found: star [2024-08-29 09:45:25,577] multiqc [DEBUG ] No samples found: hisat2 [2024-08-29 09:45:25,582] multiqc [DEBUG ] No samples found: tophat [2024-08-29 09:45:25,587] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-29 09:45:25,592] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-29 09:45:25,597] multiqc [DEBUG ] No samples found: snpsplit [2024-08-29 09:45:25,602] multiqc [DEBUG ] No samples found: kat [2024-08-29 09:45:25,607] multiqc [DEBUG ] No samples found: leehom [2024-08-29 09:45:25,612] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-29 09:45:25,617] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-29 09:45:25,621] multiqc [DEBUG ] No samples found: cutadapt [2024-08-29 09:45:25,626] multiqc [DEBUG ] No samples found: flexbar [2024-08-29 09:45:25,630] multiqc [DEBUG ] No samples found: kaiju [2024-08-29 09:45:25,635] multiqc [DEBUG ] No samples found: kraken [2024-08-29 09:45:25,640] multiqc [DEBUG ] No samples found: malt [2024-08-29 09:45:25,645] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-29 09:45:25,649] multiqc [DEBUG ] No samples found: sickle [2024-08-29 09:45:25,654] multiqc [DEBUG ] No samples found: skewer [2024-08-29 09:45:25,658] multiqc [DEBUG ] No samples found: sortmerna [2024-08-29 09:45:25,663] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-29 09:45:25,669] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-29 09:45:25,673] multiqc [DEBUG ] No samples found: afterqc [2024-08-29 09:45:25,679] multiqc [DEBUG ] No samples found: fastp [2024-08-29 09:45:28,837] multiqc.modules.fastqc.fastqc [INFO ] Found 46 reports [2024-08-29 09:45:29,791] multiqc [DEBUG ] No samples found: pycoqc [2024-08-29 09:45:29,796] multiqc [DEBUG ] No samples found: minionqc [2024-08-29 09:45:29,801] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-29 09:45:29,806] multiqc [DEBUG ] No samples found: clusterflow [2024-08-29 09:45:29,811] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-29 09:45:29,816] multiqc [DEBUG ] No samples found: interop [2024-08-29 09:45:29,822] multiqc [DEBUG ] No samples found: ivar [2024-08-29 09:45:29,827] multiqc [DEBUG ] No samples found: flash [2024-08-29 09:45:29,832] multiqc [DEBUG ] No samples found: seqyclean [2024-08-29 09:45:29,832] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-29 09:45:29,832] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-29 09:45:29,832] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-29 09:45:29,832] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-29 09:45:29,833] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-29 09:45:29,889] multiqc [INFO ] Compressing plot data [2024-08-29 09:45:30,741] multiqc [INFO ] Report : multiqc_report.html [2024-08-29 09:45:30,741] multiqc [INFO ] Data : multiqc_data [2024-08-29 09:45:30,741] multiqc [DEBUG ] Moving data file from '/state/partition1/job-50425677/tmptunn8y61/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/a1/2683708cec93a30657c40c92a02f7f/merged/multiqc_data' [2024-08-29 09:45:30,873] multiqc [INFO ] MultiQC complete