[2024-11-26 15:07:20,754] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-11-26 15:07:20,754] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-11-26 15:07:20,755] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-11-26 15:07:20,757] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-11-26 15:07:20,757] 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}} [2024-11-26 15:07:20,757] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-26 15:07:20,792] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-11-26 15:07:20,792] multiqc [INFO ] This is MultiQC v1.9 [2024-11-26 15:07:20,792] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-26 15:07:20,792] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/29/3d80584a9f39cedb21fabdfdd482ef/merged [2024-11-26 15:07:20,792] multiqc [INFO ] Template : default [2024-11-26 15:07:20,792] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-11-26 15:07:20,792] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/29/3d80584a9f39cedb21fabdfdd482ef/merged [2024-11-26 15:07:20,792] 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 [2024-11-26 15:07:20,792] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-54033457/tmpotytpg9z [2024-11-26 15:07:20,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHNHYAFX7_n01_undetermined_fastqc.html [2024-11-26 15:07:20,913] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n01_undetermined_fastqc.html [2024-11-26 15:07:20,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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HHNHYAFX7_n01_13014spRed_fastqc.html [2024-11-26 15:07:22,334] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n01_13014spRed_fastqc.html [2024-11-26 15:07:22,379] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13014spIn_fastqc.html [2024-11-26 15:07:22,381] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13014spIn_fastqc.html [2024-11-26 15:07:22,427] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13016in_fastqc.html [2024-11-26 15:07:22,429] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13016in_fastqc.html [2024-11-26 15:07:22,476] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HHNHYAFX7_n01_13014red_fastqc.html [2024-11-26 15:07:22,631] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n01_13014red_fastqc.html [2024-11-26 15:07:22,679] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13013spRed_fastqc.html [2024-11-26 15:07:22,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13013spRed_fastqc.html [2024-11-26 15:07:22,725] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13013spIn_fastqc.html [2024-11-26 15:07:22,727] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13013spIn_fastqc.html [2024-11-26 15:07:22,774] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHNHYAFX7_n01_13015in_fastqc.html [2024-11-26 15:07:22,776] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n01_13015in_fastqc.html [2024-11-26 15:07:22,823] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13016red_fastqc.html [2024-11-26 15:07:22,825] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHNHYAFX7_n02_13016red_fastqc.html [2024-11-26 15:07:23,421] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-26 15:07:23,423] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-26 15:07:23,439] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2024-11-26 15:07:23,449] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-11-26 15:07:23,451] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-11-26 15:07:23,457] multiqc [DEBUG ] No samples found: conpair [2024-11-26 15:07:23,464] multiqc [DEBUG ] No samples found: peddy [2024-11-26 15:07:23,470] multiqc [DEBUG ] No samples found: somalier [2024-11-26 15:07:23,476] multiqc [DEBUG ] No samples found: methylQA [2024-11-26 15:07:23,488] multiqc [DEBUG ] No samples found: mosdepth [2024-11-26 15:07:23,494] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-11-26 15:07:23,498] multiqc [DEBUG ] No samples found: qualimap [2024-11-26 15:07:23,504] multiqc [DEBUG ] No samples found: preseq [2024-11-26 15:07:23,511] multiqc [DEBUG ] No samples found: quast [2024-11-26 15:07:23,517] multiqc [DEBUG ] No samples found: qorts [2024-11-26 15:07:23,524] multiqc [DEBUG ] No samples found: rna_seqc [2024-11-26 15:07:23,530] multiqc [DEBUG ] No samples found: rockhopper [2024-11-26 15:07:23,536] multiqc [DEBUG ] No samples found: rsem [2024-11-26 15:07:23,552] multiqc [DEBUG ] No samples found: rseqc [2024-11-26 15:07:23,557] multiqc [DEBUG ] No samples found: busco [2024-11-26 15:07:23,564] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-11-26 15:07:23,570] multiqc [DEBUG ] No samples found: disambiguate [2024-11-26 15:07:23,576] multiqc [DEBUG ] No samples found: supernova [2024-11-26 15:07:23,595] multiqc [DEBUG ] No samples found: deeptools [2024-11-26 15:07:23,601] multiqc [DEBUG ] No samples found: sargasso [2024-11-26 15:07:23,607] multiqc [DEBUG ] No samples found: verifybamid [2024-11-26 15:07:23,614] multiqc [DEBUG ] No samples found: mirtrace [2024-11-26 15:07:23,620] multiqc [DEBUG ] No samples found: happy [2024-11-26 15:07:23,625] multiqc [DEBUG ] No samples found: mirtop [2024-11-26 15:07:23,634] multiqc [DEBUG ] No samples found: homer [2024-11-26 15:07:23,640] multiqc [DEBUG ] No samples found: macs2 [2024-11-26 15:07:23,646] multiqc [DEBUG ] No samples found: theta2 [2024-11-26 15:07:23,652] multiqc [DEBUG ] No samples found: snpeff [2024-11-26 15:07:23,661] multiqc [DEBUG ] No samples found: gatk [2024-11-26 15:07:23,667] multiqc [DEBUG ] No samples found: htseq [2024-11-26 15:07:23,675] multiqc [DEBUG ] No samples found: bcftools [2024-11-26 15:07:23,681] multiqc [DEBUG ] No samples found: featureCounts [2024-11-26 15:07:23,690] multiqc [DEBUG ] No samples found: fgbio [2024-11-26 15:07:23,706] multiqc [DEBUG ] No samples found: dragen [2024-11-26 15:07:23,712] multiqc [DEBUG ] No samples found: dedup [2024-11-26 15:07:23,718] multiqc [DEBUG ] No samples found: damageprofiler [2024-11-26 15:07:23,750] multiqc [DEBUG ] No samples found: biobambam2 [2024-11-26 15:07:23,755] multiqc [DEBUG ] No samples found: mtnucratio [2024-11-26 15:07:23,758] multiqc [DEBUG ] No samples found: picard [2024-11-26 15:07:23,764] multiqc [DEBUG ] No samples found: prokka [2024-11-26 15:07:23,769] multiqc [DEBUG ] No samples found: samblaster [2024-11-26 15:07:23,780] multiqc [DEBUG ] No samples found: samtools [2024-11-26 15:07:23,786] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-11-26 15:07:23,793] multiqc [DEBUG ] No samples found: bamtools [2024-11-26 15:07:23,799] multiqc [DEBUG ] No samples found: jellyfish [2024-11-26 15:07:23,809] multiqc [DEBUG ] No samples found: vcftools [2024-11-26 15:07:23,815] multiqc [DEBUG ] No samples found: longranger [2024-11-26 15:07:23,821] multiqc [DEBUG ] No samples found: stacks [2024-11-26 15:07:23,827] multiqc [DEBUG ] No samples found: varscan2 [2024-11-26 15:07:23,847] multiqc [DEBUG ] No samples found: bbmap [2024-11-26 15:07:23,853] multiqc [DEBUG ] No samples found: bismark [2024-11-26 15:07:23,859] multiqc [DEBUG ] No samples found: biscuit [2024-11-26 15:07:23,865] multiqc [DEBUG ] No samples found: hicexplorer [2024-11-26 15:07:23,871] multiqc [DEBUG ] No samples found: hicup [2024-11-26 15:07:23,877] multiqc [DEBUG ] No samples found: hicpro [2024-11-26 15:07:23,882] multiqc [DEBUG ] No samples found: salmon [2024-11-26 15:07:23,888] multiqc [DEBUG ] No samples found: kallisto [2024-11-26 15:07:23,894] multiqc [DEBUG ] No samples found: slamdunk [2024-11-26 15:07:23,900] multiqc [DEBUG ] No samples found: star [2024-11-26 15:07:23,905] multiqc [DEBUG ] No samples found: hisat2 [2024-11-26 15:07:23,911] multiqc [DEBUG ] No samples found: tophat [2024-11-26 15:07:23,917] multiqc [DEBUG ] No samples found: bowtie2 [2024-11-26 15:07:23,922] multiqc [DEBUG ] No samples found: bowtie1 [2024-11-26 15:07:23,928] multiqc [DEBUG ] No samples found: snpsplit [2024-11-26 15:07:23,934] multiqc [DEBUG ] No samples found: kat [2024-11-26 15:07:23,939] multiqc [DEBUG ] No samples found: leehom [2024-11-26 15:07:23,945] multiqc [DEBUG ] No samples found: adapterRemoval [2024-11-26 15:07:23,950] multiqc [DEBUG ] No samples found: clipandmerge [2024-11-26 15:07:23,956] multiqc [DEBUG ] No samples found: cutadapt [2024-11-26 15:07:23,962] multiqc [DEBUG ] No samples found: flexbar [2024-11-26 15:07:23,967] multiqc [DEBUG ] No samples found: kaiju [2024-11-26 15:07:23,973] multiqc [DEBUG ] No samples found: kraken [2024-11-26 15:07:23,978] multiqc [DEBUG ] No samples found: malt [2024-11-26 15:07:23,984] multiqc [DEBUG ] No samples found: trimmomatic [2024-11-26 15:07:23,990] multiqc [DEBUG ] No samples found: sickle [2024-11-26 15:07:23,996] multiqc [DEBUG ] No samples found: skewer [2024-11-26 15:07:24,001] multiqc [DEBUG ] No samples found: sortmerna [2024-11-26 15:07:24,007] multiqc [DEBUG ] No samples found: biobloomtools [2024-11-26 15:07:24,012] multiqc [DEBUG ] No samples found: fastq_screen [2024-11-26 15:07:24,018] multiqc [DEBUG ] No samples found: afterqc [2024-11-26 15:07:24,024] multiqc [DEBUG ] No samples found: fastp [2024-11-26 15:07:24,887] multiqc.modules.fastqc.fastqc [INFO ] Found 38 reports [2024-11-26 15:07:25,218] multiqc [DEBUG ] No samples found: pycoqc [2024-11-26 15:07:25,224] multiqc [DEBUG ] No samples found: minionqc [2024-11-26 15:07:25,230] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-11-26 15:07:25,236] multiqc [DEBUG ] No samples found: clusterflow [2024-11-26 15:07:25,243] multiqc [DEBUG ] No samples found: bcl2fastq [2024-11-26 15:07:25,250] multiqc [DEBUG ] No samples found: interop [2024-11-26 15:07:25,256] multiqc [DEBUG ] No samples found: ivar [2024-11-26 15:07:25,262] multiqc [DEBUG ] No samples found: flash [2024-11-26 15:07:25,267] multiqc [DEBUG ] No samples found: seqyclean [2024-11-26 15:07:25,267] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-11-26 15:07:25,267] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-11-26 15:07:25,267] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-11-26 15:07:25,267] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-11-26 15:07:25,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-11-26 15:07:25,314] multiqc [INFO ] Compressing plot data [2024-11-26 15:07:25,978] multiqc [INFO ] Report : multiqc_report.html [2024-11-26 15:07:25,978] multiqc [INFO ] Data : multiqc_data [2024-11-26 15:07:25,978] multiqc [DEBUG ] Moving data file from '/state/partition1/job-54033457/tmpotytpg9z/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/29/3d80584a9f39cedb21fabdfdd482ef/merged/multiqc_data' [2024-11-26 15:07:26,119] multiqc [INFO ] MultiQC complete