[2024-12-06 22:19:51,012] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-06 22:19:51,012] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-06 22:19:51,012] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-06 22:19:51,015] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-06 22:19:51,015] 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}} [2024-12-06 22:19:51,015] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-06 22:19:51,035] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-06 22:19:51,035] multiqc [INFO ] This is MultiQC v1.9 [2024-12-06 22:19:51,035] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-06 22:19:51,035] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/ed/68f072ee857eaa29c9d57c0230bcc4/1 [2024-12-06 22:19:51,035] multiqc [INFO ] Template : default [2024-12-06 22:19:51,035] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-06 22:19:51,035] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/ed/68f072ee857eaa29c9d57c0230bcc4/1 [2024-12-06 22:19:51,036] 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 [2024-12-06 22:19:51,036] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-54428485/tmps9mag55n [2024-12-06 22:19:51,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLF5YDRX5_l01_n02_16-R-KL_fastqc.html [2024-12-06 22:19:51,159] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLF5YDRX5_l01_n02_16-R-KL_fastqc.html [2024-12-06 22:19:51,207] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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because it exceeded search pattern filesize limit: HLF5YDRX5_l01_n01_14-R-KL_fastqc.html [2024-12-06 22:20:00,518] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-06 22:20:00,520] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-06 22:20:00,531] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-06 22:20:00,541] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-06 22:20:00,581] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 84 samples (table) [2024-12-06 22:20:00,586] multiqc [DEBUG ] No samples found: conpair [2024-12-06 22:20:00,591] multiqc [DEBUG ] No samples found: peddy [2024-12-06 22:20:00,597] multiqc [DEBUG ] No samples found: somalier [2024-12-06 22:20:00,602] multiqc [DEBUG ] No samples found: methylQA [2024-12-06 22:20:00,611] multiqc [DEBUG ] No samples found: mosdepth [2024-12-06 22:20:00,617] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-06 22:20:00,621] multiqc [DEBUG ] No samples found: qualimap [2024-12-06 22:20:00,626] multiqc [DEBUG ] No samples found: preseq [2024-12-06 22:20:00,631] multiqc [DEBUG ] No samples found: quast [2024-12-06 22:20:00,636] multiqc [DEBUG ] No samples found: qorts [2024-12-06 22:20:00,642] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-06 22:20:00,647] multiqc [DEBUG ] No samples found: rockhopper [2024-12-06 22:20:00,652] multiqc [DEBUG ] No samples found: rsem [2024-12-06 22:20:00,664] multiqc [DEBUG ] No samples found: rseqc [2024-12-06 22:20:00,669] multiqc [DEBUG ] No samples found: busco [2024-12-06 22:20:00,674] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-06 22:20:00,679] multiqc [DEBUG ] No samples found: disambiguate [2024-12-06 22:20:00,686] multiqc [DEBUG ] No samples found: supernova [2024-12-06 22:20:00,699] multiqc [DEBUG ] No samples found: deeptools [2024-12-06 22:20:00,705] multiqc [DEBUG ] No samples found: sargasso [2024-12-06 22:20:00,711] multiqc [DEBUG ] No samples found: verifybamid [2024-12-06 22:20:00,716] multiqc [DEBUG ] No samples found: mirtrace [2024-12-06 22:20:00,721] multiqc [DEBUG ] No samples found: happy [2024-12-06 22:20:00,726] multiqc [DEBUG ] No samples found: mirtop [2024-12-06 22:20:00,733] multiqc [DEBUG ] No samples found: homer [2024-12-06 22:20:00,738] multiqc [DEBUG ] No samples found: macs2 [2024-12-06 22:20:00,743] multiqc [DEBUG ] No samples found: theta2 [2024-12-06 22:20:00,749] multiqc [DEBUG ] No samples found: snpeff [2024-12-06 22:20:00,756] multiqc [DEBUG ] No samples found: gatk [2024-12-06 22:20:00,761] multiqc [DEBUG ] No samples found: htseq [2024-12-06 22:20:00,767] multiqc [DEBUG ] No samples found: bcftools [2024-12-06 22:20:00,774] multiqc [DEBUG ] No samples found: featureCounts [2024-12-06 22:20:00,781] multiqc [DEBUG ] No samples found: fgbio [2024-12-06 22:20:00,794] multiqc [DEBUG ] No samples found: dragen [2024-12-06 22:20:00,800] multiqc [DEBUG ] No samples found: dedup [2024-12-06 22:20:00,805] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-06 22:20:00,829] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-06 22:20:00,834] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-06 22:20:00,837] multiqc [DEBUG ] No samples found: picard [2024-12-06 22:20:00,842] multiqc [DEBUG ] No samples found: prokka [2024-12-06 22:20:00,847] multiqc [DEBUG ] No samples found: samblaster [2024-12-06 22:20:00,856] multiqc [DEBUG ] No samples found: samtools [2024-12-06 22:20:00,861] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-06 22:20:00,867] multiqc [DEBUG ] No samples found: bamtools [2024-12-06 22:20:00,872] multiqc [DEBUG ] No samples found: jellyfish [2024-12-06 22:20:00,879] multiqc [DEBUG ] No samples found: vcftools [2024-12-06 22:20:00,885] multiqc [DEBUG ] No samples found: longranger [2024-12-06 22:20:00,890] multiqc [DEBUG ] No samples found: stacks [2024-12-06 22:20:00,895] multiqc [DEBUG ] No samples found: varscan2 [2024-12-06 22:20:00,910] multiqc [DEBUG ] No samples found: bbmap [2024-12-06 22:20:00,915] multiqc [DEBUG ] No samples found: bismark [2024-12-06 22:20:00,922] multiqc [DEBUG ] No samples found: biscuit [2024-12-06 22:20:00,927] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-06 22:20:00,933] multiqc [DEBUG ] No samples found: hicup [2024-12-06 22:20:00,939] multiqc [DEBUG ] No samples found: hicpro [2024-12-06 22:20:00,944] multiqc [DEBUG ] No samples found: salmon [2024-12-06 22:20:00,949] multiqc [DEBUG ] No samples found: kallisto [2024-12-06 22:20:00,954] multiqc [DEBUG ] No samples found: slamdunk [2024-12-06 22:20:00,959] multiqc [DEBUG ] No samples found: star [2024-12-06 22:20:00,964] multiqc [DEBUG ] No samples found: hisat2 [2024-12-06 22:20:00,969] multiqc [DEBUG ] No samples found: tophat [2024-12-06 22:20:00,975] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-06 22:20:00,980] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-06 22:20:00,985] multiqc [DEBUG ] No samples found: snpsplit [2024-12-06 22:20:00,989] multiqc [DEBUG ] No samples found: kat [2024-12-06 22:20:00,995] multiqc [DEBUG ] No samples found: leehom [2024-12-06 22:20:01,001] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-06 22:20:01,005] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-06 22:20:01,011] multiqc [DEBUG ] No samples found: cutadapt [2024-12-06 22:20:01,015] multiqc [DEBUG ] No samples found: flexbar [2024-12-06 22:20:01,020] multiqc [DEBUG ] No samples found: kaiju [2024-12-06 22:20:01,026] multiqc [DEBUG ] No samples found: kraken [2024-12-06 22:20:01,031] multiqc [DEBUG ] No samples found: malt [2024-12-06 22:20:01,036] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-06 22:20:01,041] multiqc [DEBUG ] No samples found: sickle [2024-12-06 22:20:01,046] multiqc [DEBUG ] No samples found: skewer [2024-12-06 22:20:01,051] multiqc [DEBUG ] No samples found: sortmerna [2024-12-06 22:20:01,056] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-06 22:20:01,061] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-06 22:20:01,066] multiqc [DEBUG ] No samples found: afterqc [2024-12-06 22:20:01,071] multiqc [DEBUG ] No samples found: fastp [2024-12-06 22:20:12,907] multiqc.modules.fastqc.fastqc [INFO ] Found 168 reports [2024-12-06 22:20:33,064] multiqc [DEBUG ] No samples found: pycoqc [2024-12-06 22:20:33,069] multiqc [DEBUG ] No samples found: minionqc [2024-12-06 22:20:33,074] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-06 22:20:33,079] multiqc [DEBUG ] No samples found: clusterflow [2024-12-06 22:20:33,084] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-06 22:20:33,089] multiqc [DEBUG ] No samples found: interop [2024-12-06 22:20:33,094] multiqc [DEBUG ] No samples found: ivar [2024-12-06 22:20:33,099] multiqc [DEBUG ] No samples found: flash [2024-12-06 22:20:33,104] multiqc [DEBUG ] No samples found: seqyclean [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-06 22:20:33,104] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-06 22:20:33,105] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-06 22:20:33,301] multiqc [INFO ] Compressing plot data [2024-12-06 22:20:33,366] multiqc [INFO ] Report : multiqc_report.html [2024-12-06 22:20:33,366] multiqc [INFO ] Data : multiqc_data [2024-12-06 22:20:33,366] multiqc [DEBUG ] Moving data file from '/state/partition1/job-54428485/tmps9mag55n/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/ed/68f072ee857eaa29c9d57c0230bcc4/1/multiqc_data' [2024-12-06 22:20:33,516] multiqc [INFO ] MultiQC complete