[2025-02-20 20:23:03,687] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-02-20 20:23:03,687] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-02-20 20:23:03,687] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-02-20 20:23:03,690] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-02-20 20:23:03,690] 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}} [2025-02-20 20:23:03,690] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-20 20:23:03,728] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-02-20 20:23:03,728] multiqc [INFO ] This is MultiQC v1.9 [2025-02-20 20:23:03,728] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-20 20:23:03,728] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/f3/4fd2911fcb0247a708b774db8c9b1a/merged [2025-02-20 20:23:03,728] multiqc [INFO ] Template : default [2025-02-20 20:23:03,728] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-02-20 20:23:03,728] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/f3/4fd2911fcb0247a708b774db8c9b1a/merged [2025-02-20 20:23:03,728] 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 [2025-02-20 20:23:03,728] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-57467420/tmpp7k61qfr [2025-02-20 20:23:03,833] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_C01_fastqc.html [2025-02-20 20:23:03,836] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_C01_fastqc.html [2025-02-20 20:23:03,885] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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HT2WFDRX5_n02_BS_SMART2_B02_fastqc.html [2025-02-20 20:23:05,431] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2WFDRX5_n02_BS_SMART2_B02_fastqc.html [2025-02-20 20:23:05,477] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2WFDRX5_n02_BS_SMART2_A01_fastqc.html [2025-02-20 20:23:05,479] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2WFDRX5_n02_BS_SMART2_A01_fastqc.html [2025-02-20 20:23:05,500] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_E02_fastqc.html [2025-02-20 20:23:05,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_E02_fastqc.html [2025-02-20 20:23:05,549] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2WFDRX5_n02_BS_SMART2_E01_fastqc.html [2025-02-20 20:23:05,550] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2WFDRX5_n02_BS_SMART2_E01_fastqc.html [2025-02-20 20:23:05,597] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_C02_fastqc.html [2025-02-20 20:23:05,599] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_C02_fastqc.html [2025-02-20 20:23:05,645] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_A01_fastqc.html [2025-02-20 20:23:05,647] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2WFDRX5_n01_BS_SMART2_A01_fastqc.html [2025-02-20 20:23:06,095] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-20 20:23:06,097] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-20 20:23:06,105] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-02-20 20:23:06,115] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 20 samples (table) [2025-02-20 20:23:06,125] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-02-20 20:23:06,129] multiqc [DEBUG ] No samples found: conpair [2025-02-20 20:23:06,134] multiqc [DEBUG ] No samples found: peddy [2025-02-20 20:23:06,139] multiqc [DEBUG ] No samples found: somalier [2025-02-20 20:23:06,144] multiqc [DEBUG ] No samples found: methylQA [2025-02-20 20:23:06,152] multiqc [DEBUG ] No samples found: mosdepth [2025-02-20 20:23:06,156] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-02-20 20:23:06,160] multiqc [DEBUG ] No samples found: qualimap [2025-02-20 20:23:06,164] multiqc [DEBUG ] No samples found: preseq [2025-02-20 20:23:06,169] multiqc [DEBUG ] No samples found: quast [2025-02-20 20:23:06,173] multiqc [DEBUG ] No samples found: qorts [2025-02-20 20:23:06,178] multiqc [DEBUG ] No samples found: rna_seqc [2025-02-20 20:23:06,183] multiqc [DEBUG ] No samples found: rockhopper [2025-02-20 20:23:06,188] multiqc [DEBUG ] No samples found: rsem [2025-02-20 20:23:06,199] multiqc [DEBUG ] No samples found: rseqc [2025-02-20 20:23:06,203] multiqc [DEBUG ] No samples found: busco [2025-02-20 20:23:06,208] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-02-20 20:23:06,212] multiqc [DEBUG ] No samples found: disambiguate [2025-02-20 20:23:06,217] multiqc [DEBUG ] No samples found: supernova [2025-02-20 20:23:06,230] multiqc [DEBUG ] No samples found: deeptools [2025-02-20 20:23:06,234] multiqc [DEBUG ] No samples found: sargasso [2025-02-20 20:23:06,239] multiqc [DEBUG ] No samples found: verifybamid [2025-02-20 20:23:06,246] multiqc [DEBUG ] No samples found: mirtrace [2025-02-20 20:23:06,250] multiqc [DEBUG ] No samples found: happy [2025-02-20 20:23:06,255] multiqc [DEBUG ] No samples found: mirtop [2025-02-20 20:23:06,262] multiqc [DEBUG ] No samples found: homer [2025-02-20 20:23:06,267] multiqc [DEBUG ] No samples found: macs2 [2025-02-20 20:23:06,271] multiqc [DEBUG ] No samples found: theta2 [2025-02-20 20:23:06,276] multiqc [DEBUG ] No samples found: snpeff [2025-02-20 20:23:06,283] multiqc [DEBUG ] No samples found: gatk [2025-02-20 20:23:06,288] multiqc [DEBUG ] No samples found: htseq [2025-02-20 20:23:06,294] multiqc [DEBUG ] No samples found: bcftools [2025-02-20 20:23:06,299] multiqc [DEBUG ] No samples found: featureCounts [2025-02-20 20:23:06,305] multiqc [DEBUG ] No samples found: fgbio [2025-02-20 20:23:06,318] multiqc [DEBUG ] No samples found: dragen [2025-02-20 20:23:06,322] multiqc [DEBUG ] No samples found: dedup [2025-02-20 20:23:06,327] multiqc [DEBUG ] No samples found: damageprofiler [2025-02-20 20:23:06,354] multiqc [DEBUG ] No samples found: biobambam2 [2025-02-20 20:23:06,358] multiqc [DEBUG ] No samples found: mtnucratio [2025-02-20 20:23:06,361] multiqc [DEBUG ] No samples found: picard [2025-02-20 20:23:06,365] multiqc [DEBUG ] No samples found: prokka [2025-02-20 20:23:06,370] multiqc [DEBUG ] No samples found: samblaster [2025-02-20 20:23:06,378] multiqc [DEBUG ] No samples found: samtools [2025-02-20 20:23:06,383] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-02-20 20:23:06,388] multiqc [DEBUG ] No samples found: bamtools [2025-02-20 20:23:06,393] multiqc [DEBUG ] No samples found: jellyfish [2025-02-20 20:23:06,400] multiqc [DEBUG ] No samples found: vcftools [2025-02-20 20:23:06,405] multiqc [DEBUG ] No samples found: longranger [2025-02-20 20:23:06,409] multiqc [DEBUG ] No samples found: stacks [2025-02-20 20:23:06,414] multiqc [DEBUG ] No samples found: varscan2 [2025-02-20 20:23:06,429] multiqc [DEBUG ] No samples found: bbmap [2025-02-20 20:23:06,434] multiqc [DEBUG ] No samples found: bismark [2025-02-20 20:23:06,439] multiqc [DEBUG ] No samples found: biscuit [2025-02-20 20:23:06,444] multiqc [DEBUG ] No samples found: hicexplorer [2025-02-20 20:23:06,449] multiqc [DEBUG ] No samples found: hicup [2025-02-20 20:23:06,453] multiqc [DEBUG ] No samples found: hicpro [2025-02-20 20:23:06,457] multiqc [DEBUG ] No samples found: salmon [2025-02-20 20:23:06,462] multiqc [DEBUG ] No samples found: kallisto [2025-02-20 20:23:06,467] multiqc [DEBUG ] No samples found: slamdunk [2025-02-20 20:23:06,472] multiqc [DEBUG ] No samples found: star [2025-02-20 20:23:06,477] multiqc [DEBUG ] No samples found: hisat2 [2025-02-20 20:23:06,481] multiqc [DEBUG ] No samples found: tophat [2025-02-20 20:23:06,486] multiqc [DEBUG ] No samples found: bowtie2 [2025-02-20 20:23:06,490] multiqc [DEBUG ] No samples found: bowtie1 [2025-02-20 20:23:06,495] multiqc [DEBUG ] No samples found: snpsplit [2025-02-20 20:23:06,499] multiqc [DEBUG ] No samples found: kat [2025-02-20 20:23:06,503] multiqc [DEBUG ] No samples found: leehom [2025-02-20 20:23:06,508] multiqc [DEBUG ] No samples found: adapterRemoval [2025-02-20 20:23:06,513] multiqc [DEBUG ] No samples found: clipandmerge [2025-02-20 20:23:06,517] multiqc [DEBUG ] No samples found: cutadapt [2025-02-20 20:23:06,522] multiqc [DEBUG ] No samples found: flexbar [2025-02-20 20:23:06,526] multiqc [DEBUG ] No samples found: kaiju [2025-02-20 20:23:06,531] multiqc [DEBUG ] No samples found: kraken [2025-02-20 20:23:06,535] multiqc [DEBUG ] No samples found: malt [2025-02-20 20:23:06,540] multiqc [DEBUG ] No samples found: trimmomatic [2025-02-20 20:23:06,544] multiqc [DEBUG ] No samples found: sickle [2025-02-20 20:23:06,549] multiqc [DEBUG ] No samples found: skewer [2025-02-20 20:23:06,553] multiqc [DEBUG ] No samples found: sortmerna [2025-02-20 20:23:06,558] multiqc [DEBUG ] No samples found: biobloomtools [2025-02-20 20:23:06,563] multiqc [DEBUG ] No samples found: fastq_screen [2025-02-20 20:23:06,567] multiqc [DEBUG ] No samples found: afterqc [2025-02-20 20:23:06,572] multiqc [DEBUG ] No samples found: fastp [2025-02-20 20:23:07,788] multiqc.modules.fastqc.fastqc [INFO ] Found 40 reports [2025-02-20 20:23:07,789] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HT2WFDRX5_n01_BS_SMART2_A01' [2025-02-20 20:23:07,789] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HT2WFDRX5_n01_BS_SMART2_B01' [2025-02-20 20:23:07,789] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HT2WFDRX5_n02_BS_SMART2_A01' [2025-02-20 20:23:07,789] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HT2WFDRX5_n02_BS_SMART2_B01' [2025-02-20 20:23:08,297] multiqc [DEBUG ] No samples found: pycoqc [2025-02-20 20:23:08,302] multiqc [DEBUG ] No samples found: minionqc [2025-02-20 20:23:08,306] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-02-20 20:23:08,311] multiqc [DEBUG ] No samples found: clusterflow [2025-02-20 20:23:08,316] multiqc [DEBUG ] No samples found: bcl2fastq [2025-02-20 20:23:08,321] multiqc [DEBUG ] No samples found: interop [2025-02-20 20:23:08,325] multiqc [DEBUG ] No samples found: ivar [2025-02-20 20:23:08,330] multiqc [DEBUG ] No samples found: flash [2025-02-20 20:23:08,334] multiqc [DEBUG ] No samples found: seqyclean [2025-02-20 20:23:08,334] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-02-20 20:23:08,334] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-02-20 20:23:08,334] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-02-20 20:23:08,334] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-02-20 20:23:08,334] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-02-20 20:23:08,335] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-02-20 20:23:08,384] multiqc [INFO ] Compressing plot data [2025-02-20 20:23:09,113] multiqc [INFO ] Report : multiqc_report.html [2025-02-20 20:23:09,113] multiqc [INFO ] Data : multiqc_data [2025-02-20 20:23:09,113] multiqc [DEBUG ] Moving data file from '/state/partition1/job-57467420/tmpp7k61qfr/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/f3/4fd2911fcb0247a708b774db8c9b1a/merged/multiqc_data' [2025-02-20 20:23:09,245] multiqc [INFO ] MultiQC complete