[2024-11-27 15:35:10,658] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-11-27 15:35:10,658] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-11-27 15:35:10,658] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-11-27 15:35:10,661] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-11-27 15:35:10,661] 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}} [2024-11-27 15:35:10,661] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-27 15:35:10,692] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-11-27 15:35:10,693] multiqc [INFO ] This is MultiQC v1.9 [2024-11-27 15:35:10,693] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-27 15:35:10,693] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/75/1727282bb952a636dd80e0aa8a142c/1 [2024-11-27 15:35:10,693] multiqc [INFO ] Template : default [2024-11-27 15:35:10,693] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-11-27 15:35:10,693] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/75/1727282bb952a636dd80e0aa8a142c/1 [2024-11-27 15:35:10,693] 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 [2024-11-27 15:35:10,694] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-54066135/tmp49diyynp [2024-11-27 15:35:10,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH35_fastqc.html [2024-11-27 15:35:10,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH35_fastqc.html [2024-11-27 15:35:10,889] multiqc [DEBUG ] File ignored by hicexplorer 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filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH71_fastqc.html [2024-11-27 15:35:11,112] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-27 15:35:11,114] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-27 15:35:11,114] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-27 15:35:11,114] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-27 15:35:11,114] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-27 15:35:11,114] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 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000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH91_fastqc.html [2024-11-27 15:35:18,906] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH91_fastqc.html [2024-11-27 15:35:18,977] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH9_fastqc.html [2024-11-27 15:35:18,979] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH9_fastqc.html [2024-11-27 15:35:19,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH18_fastqc.html [2024-11-27 15:35:19,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH95_fastqc.html [2024-11-27 15:35:19,267] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH95_fastqc.html [2024-11-27 15:35:19,336] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH52_fastqc.html [2024-11-27 15:35:19,338] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH52_fastqc.html [2024-11-27 15:35:19,413] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH55_fastqc.html [2024-11-27 15:35:19,415] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH55_fastqc.html [2024-11-27 15:35:19,486] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH93_fastqc.html [2024-11-27 15:35:19,488] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GNC2B_l01_n01_micro_run2_repeat_GyrBATH93_fastqc.html [2024-11-27 15:35:20,031] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-27 15:35:20,033] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-27 15:35:20,086] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 100 samples (table) [2024-11-27 15:35:20,088] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-11-27 15:35:20,097] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-11-27 15:35:20,103] multiqc [DEBUG ] No samples found: conpair [2024-11-27 15:35:20,108] multiqc [DEBUG ] No samples found: peddy [2024-11-27 15:35:20,113] multiqc [DEBUG ] No samples found: somalier [2024-11-27 15:35:20,118] multiqc [DEBUG ] No samples found: methylQA [2024-11-27 15:35:20,127] multiqc [DEBUG ] No samples found: mosdepth [2024-11-27 15:35:20,132] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-11-27 15:35:20,136] multiqc [DEBUG ] No samples found: qualimap [2024-11-27 15:35:20,141] multiqc [DEBUG ] No samples found: preseq [2024-11-27 15:35:20,146] multiqc [DEBUG ] No samples found: quast [2024-11-27 15:35:20,151] multiqc [DEBUG ] No samples found: qorts [2024-11-27 15:35:20,156] multiqc [DEBUG ] No samples found: rna_seqc [2024-11-27 15:35:20,161] multiqc [DEBUG ] No samples found: rockhopper [2024-11-27 15:35:20,166] multiqc [DEBUG ] No samples found: rsem [2024-11-27 15:35:20,179] multiqc [DEBUG ] No samples found: rseqc [2024-11-27 15:35:20,183] multiqc [DEBUG ] No samples found: busco [2024-11-27 15:35:20,189] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-11-27 15:35:20,193] multiqc [DEBUG ] No samples found: disambiguate [2024-11-27 15:35:20,199] multiqc [DEBUG ] No samples found: supernova [2024-11-27 15:35:20,213] multiqc [DEBUG ] No samples found: deeptools [2024-11-27 15:35:20,219] multiqc [DEBUG ] No samples found: sargasso [2024-11-27 15:35:20,224] multiqc [DEBUG ] No samples found: verifybamid [2024-11-27 15:35:20,229] multiqc [DEBUG ] No samples found: mirtrace [2024-11-27 15:35:20,234] multiqc [DEBUG ] No samples found: happy [2024-11-27 15:35:20,239] multiqc [DEBUG ] No samples found: mirtop [2024-11-27 15:35:20,248] multiqc [DEBUG ] No samples found: homer [2024-11-27 15:35:20,253] multiqc [DEBUG ] No samples found: macs2 [2024-11-27 15:35:20,257] multiqc [DEBUG ] No samples found: theta2 [2024-11-27 15:35:20,263] multiqc [DEBUG ] No samples found: snpeff [2024-11-27 15:35:20,270] multiqc [DEBUG ] No samples found: gatk [2024-11-27 15:35:20,275] multiqc [DEBUG ] No samples found: htseq [2024-11-27 15:35:20,281] multiqc [DEBUG ] No samples found: bcftools [2024-11-27 15:35:20,286] multiqc [DEBUG ] No samples found: featureCounts [2024-11-27 15:35:20,293] multiqc [DEBUG ] No samples found: fgbio [2024-11-27 15:35:20,308] multiqc [DEBUG ] No samples found: dragen [2024-11-27 15:35:20,313] multiqc [DEBUG ] No samples found: dedup [2024-11-27 15:35:20,318] multiqc [DEBUG ] No samples found: damageprofiler [2024-11-27 15:35:20,343] multiqc [DEBUG ] No samples found: biobambam2 [2024-11-27 15:35:20,348] multiqc [DEBUG ] No samples found: mtnucratio [2024-11-27 15:35:20,350] multiqc [DEBUG ] No samples found: picard [2024-11-27 15:35:20,355] multiqc [DEBUG ] No samples found: prokka [2024-11-27 15:35:20,360] multiqc [DEBUG ] No samples found: samblaster [2024-11-27 15:35:20,370] multiqc [DEBUG ] No samples found: samtools [2024-11-27 15:35:20,375] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-11-27 15:35:20,380] multiqc [DEBUG ] No samples found: bamtools [2024-11-27 15:35:20,385] multiqc [DEBUG ] No samples found: jellyfish [2024-11-27 15:35:20,393] multiqc [DEBUG ] No samples found: vcftools [2024-11-27 15:35:20,399] multiqc [DEBUG ] No samples found: longranger [2024-11-27 15:35:20,404] multiqc [DEBUG ] No samples found: stacks [2024-11-27 15:35:20,409] multiqc [DEBUG ] No samples found: varscan2 [2024-11-27 15:35:20,424] multiqc [DEBUG ] No samples found: bbmap [2024-11-27 15:35:20,429] multiqc [DEBUG ] No samples found: bismark [2024-11-27 15:35:20,434] multiqc [DEBUG ] No samples found: biscuit [2024-11-27 15:35:20,440] multiqc [DEBUG ] No samples found: hicexplorer [2024-11-27 15:35:20,445] multiqc [DEBUG ] No samples found: hicup [2024-11-27 15:35:20,450] multiqc [DEBUG ] No samples found: hicpro [2024-11-27 15:35:20,455] multiqc [DEBUG ] No samples found: salmon [2024-11-27 15:35:20,460] multiqc [DEBUG ] No samples found: kallisto [2024-11-27 15:35:20,465] multiqc [DEBUG ] No samples found: slamdunk [2024-11-27 15:35:20,470] multiqc [DEBUG ] No samples found: star [2024-11-27 15:35:20,475] multiqc [DEBUG ] No samples found: hisat2 [2024-11-27 15:35:20,479] multiqc [DEBUG ] No samples found: tophat [2024-11-27 15:35:20,485] multiqc [DEBUG ] No samples found: bowtie2 [2024-11-27 15:35:20,489] multiqc [DEBUG ] No samples found: bowtie1 [2024-11-27 15:35:20,494] multiqc [DEBUG ] No samples found: snpsplit [2024-11-27 15:35:20,499] multiqc [DEBUG ] No samples found: kat [2024-11-27 15:35:20,504] multiqc [DEBUG ] No samples found: leehom [2024-11-27 15:35:20,509] multiqc [DEBUG ] No samples found: adapterRemoval [2024-11-27 15:35:20,514] multiqc [DEBUG ] No samples found: clipandmerge [2024-11-27 15:35:20,519] multiqc [DEBUG ] No samples found: cutadapt [2024-11-27 15:35:20,523] multiqc [DEBUG ] No samples found: flexbar [2024-11-27 15:35:20,528] multiqc [DEBUG ] No samples found: kaiju [2024-11-27 15:35:20,533] multiqc [DEBUG ] No samples found: kraken [2024-11-27 15:35:20,539] multiqc [DEBUG ] No samples found: malt [2024-11-27 15:35:20,544] multiqc [DEBUG ] No samples found: trimmomatic [2024-11-27 15:35:20,548] multiqc [DEBUG ] No samples found: sickle [2024-11-27 15:35:20,553] multiqc [DEBUG ] No samples found: skewer [2024-11-27 15:35:20,558] multiqc [DEBUG ] No samples found: sortmerna [2024-11-27 15:35:20,563] multiqc [DEBUG ] No samples found: biobloomtools [2024-11-27 15:35:20,568] multiqc [DEBUG ] No samples found: fastq_screen [2024-11-27 15:35:20,573] multiqc [DEBUG ] No samples found: afterqc [2024-11-27 15:35:20,578] multiqc [DEBUG ] No samples found: fastp [2024-11-27 15:35:21,281] multiqc.modules.fastqc.fastqc [INFO ] Found 100 reports [2024-11-27 15:35:23,980] multiqc [DEBUG ] No samples found: pycoqc [2024-11-27 15:35:23,985] multiqc [DEBUG ] No samples found: minionqc [2024-11-27 15:35:23,990] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-11-27 15:35:23,996] multiqc [DEBUG ] No samples found: clusterflow [2024-11-27 15:35:24,001] multiqc [DEBUG ] No samples found: bcl2fastq [2024-11-27 15:35:24,006] multiqc [DEBUG ] No samples found: interop [2024-11-27 15:35:24,012] multiqc [DEBUG ] No samples found: ivar [2024-11-27 15:35:24,017] multiqc [DEBUG ] No samples found: flash [2024-11-27 15:35:24,022] multiqc [DEBUG ] No samples found: seqyclean [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-11-27 15:35:24,022] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-11-27 15:35:24,023] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-11-27 15:35:24,023] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-11-27 15:35:24,139] multiqc [INFO ] Compressing plot data [2024-11-27 15:35:25,420] multiqc [INFO ] Report : multiqc_report.html [2024-11-27 15:35:25,420] multiqc [INFO ] Data : multiqc_data [2024-11-27 15:35:25,420] multiqc [DEBUG ] Moving data file from '/state/partition1/job-54066135/tmp49diyynp/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/75/1727282bb952a636dd80e0aa8a142c/1/multiqc_data' [2024-11-27 15:35:25,559] multiqc [INFO ] MultiQC complete