[2024-08-30 18:04:39,360] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-30 18:04:39,360] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-30 18:04:39,360] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-30 18:04:39,363] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-30 18:04:39,363] 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}} [2024-08-30 18:04:39,363] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-30 18:04:39,400] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-30 18:04:39,400] multiqc [INFO ] This is MultiQC v1.9 [2024-08-30 18:04:39,400] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-30 18:04:39,400] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/a7/6f8768132be0a990e0383ad2e1caf8/merged [2024-08-30 18:04:39,400] multiqc [INFO ] Template : default [2024-08-30 18:04:39,400] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-30 18:04:39,400] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/a7/6f8768132be0a990e0383ad2e1caf8/merged [2024-08-30 18:04:39,400] 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 [2024-08-30 18:04:39,401] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-50501396/tmpv5txsufq [2024-08-30 18:04:39,499] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:39,502] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 18:04:45,537] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n01_YZ74_fastqc.html [2024-08-30 18:04:45,539] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n01_YZ74_fastqc.html [2024-08-30 18:04:45,584] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n02_DO123_fastqc.html [2024-08-30 18:04:45,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n02_DO123_fastqc.html [2024-08-30 18:04:45,632] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n01_DO123_fastqc.html [2024-08-30 18:04:45,634] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n01_DO123_fastqc.html [2024-08-30 18:04:45,679] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n01_undetermined_fastqc.html [2024-08-30 18:04:45,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n01_undetermined_fastqc.html [2024-08-30 18:04:45,725] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n02_undetermined_fastqc.html [2024-08-30 18:04:45,727] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n02_undetermined_fastqc.html [2024-08-30 18:04:45,771] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n02_YZ74_fastqc.html [2024-08-30 18:04:45,773] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n02_YZ74_fastqc.html [2024-08-30 18:04:45,818] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n01_YZ72_fastqc.html [2024-08-30 18:04:45,820] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n01_YZ72_fastqc.html [2024-08-30 18:04:45,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n02_YZ73_fastqc.html [2024-08-30 18:04:45,868] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n02_YZ73_fastqc.html [2024-08-30 18:04:45,912] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n02_DR10_fastqc.html [2024-08-30 18:04:45,914] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n02_DR10_fastqc.html [2024-08-30 18:04:45,959] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n01_YZ73_fastqc.html [2024-08-30 18:04:45,961] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n01_YZ73_fastqc.html [2024-08-30 18:04:46,006] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n01_DR10_fastqc.html [2024-08-30 18:04:46,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n01_DR10_fastqc.html [2024-08-30 18:04:46,054] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHFMGDRX5_n02_YZ72_fastqc.html [2024-08-30 18:04:46,056] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHFMGDRX5_n02_YZ72_fastqc.html [2024-08-30 18:04:46,402] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-30 18:04:46,402] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-30 18:04:46,410] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-30 18:04:46,414] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2024-08-30 18:04:46,424] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-30 18:04:46,427] multiqc [DEBUG ] No samples found: conpair [2024-08-30 18:04:46,430] multiqc [DEBUG ] No samples found: peddy [2024-08-30 18:04:46,433] multiqc [DEBUG ] No samples found: somalier [2024-08-30 18:04:46,436] multiqc [DEBUG ] No samples found: methylQA [2024-08-30 18:04:46,440] multiqc [DEBUG ] No samples found: mosdepth [2024-08-30 18:04:46,442] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-30 18:04:46,445] multiqc [DEBUG ] No samples found: qualimap [2024-08-30 18:04:46,448] multiqc [DEBUG ] No samples found: preseq [2024-08-30 18:04:46,451] multiqc [DEBUG ] No samples found: quast [2024-08-30 18:04:46,453] multiqc [DEBUG ] No samples found: qorts [2024-08-30 18:04:46,456] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-30 18:04:46,459] multiqc [DEBUG ] No samples found: rockhopper [2024-08-30 18:04:46,462] multiqc [DEBUG ] No samples found: rsem [2024-08-30 18:04:46,467] multiqc [DEBUG ] No samples found: rseqc [2024-08-30 18:04:46,470] multiqc [DEBUG ] No samples found: busco [2024-08-30 18:04:46,473] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-30 18:04:46,475] multiqc [DEBUG ] No samples found: disambiguate [2024-08-30 18:04:46,478] multiqc [DEBUG ] No samples found: supernova [2024-08-30 18:04:46,484] multiqc [DEBUG ] No samples found: deeptools [2024-08-30 18:04:46,487] multiqc [DEBUG ] No samples found: sargasso [2024-08-30 18:04:46,490] multiqc [DEBUG ] No samples found: verifybamid [2024-08-30 18:04:46,493] multiqc [DEBUG ] No samples found: mirtrace [2024-08-30 18:04:46,496] multiqc [DEBUG ] No samples found: happy [2024-08-30 18:04:46,498] multiqc [DEBUG ] No samples found: mirtop [2024-08-30 18:04:46,502] multiqc [DEBUG ] No samples found: homer [2024-08-30 18:04:46,505] multiqc [DEBUG ] No samples found: macs2 [2024-08-30 18:04:46,508] multiqc [DEBUG ] No samples found: theta2 [2024-08-30 18:04:46,511] multiqc [DEBUG ] No samples found: snpeff [2024-08-30 18:04:46,515] multiqc [DEBUG ] No samples found: gatk [2024-08-30 18:04:46,517] multiqc [DEBUG ] No samples found: htseq [2024-08-30 18:04:46,520] multiqc [DEBUG ] No samples found: bcftools [2024-08-30 18:04:46,523] multiqc [DEBUG ] No samples found: featureCounts [2024-08-30 18:04:46,526] multiqc [DEBUG ] No samples found: fgbio [2024-08-30 18:04:46,532] multiqc [DEBUG ] No samples found: dragen [2024-08-30 18:04:46,534] multiqc [DEBUG ] No samples found: dedup [2024-08-30 18:04:46,538] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-30 18:04:46,546] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-30 18:04:46,550] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-30 18:04:46,552] multiqc [DEBUG ] No samples found: picard [2024-08-30 18:04:46,555] multiqc [DEBUG ] No samples found: prokka [2024-08-30 18:04:46,558] multiqc [DEBUG ] No samples found: samblaster [2024-08-30 18:04:46,562] multiqc [DEBUG ] No samples found: samtools [2024-08-30 18:04:46,565] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-30 18:04:46,568] multiqc [DEBUG ] No samples found: bamtools [2024-08-30 18:04:46,571] multiqc [DEBUG ] No samples found: jellyfish [2024-08-30 18:04:46,575] multiqc [DEBUG ] No samples found: vcftools [2024-08-30 18:04:46,578] multiqc [DEBUG ] No samples found: longranger [2024-08-30 18:04:46,581] multiqc [DEBUG ] No samples found: stacks [2024-08-30 18:04:46,583] multiqc [DEBUG ] No samples found: varscan2 [2024-08-30 18:04:46,589] multiqc [DEBUG ] No samples found: bbmap [2024-08-30 18:04:46,592] multiqc [DEBUG ] No samples found: bismark [2024-08-30 18:04:46,595] multiqc [DEBUG ] No samples found: biscuit [2024-08-30 18:04:46,598] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-30 18:04:46,600] multiqc [DEBUG ] No samples found: hicup [2024-08-30 18:04:46,603] multiqc [DEBUG ] No samples found: hicpro [2024-08-30 18:04:46,606] multiqc [DEBUG ] No samples found: salmon [2024-08-30 18:04:46,609] multiqc [DEBUG ] No samples found: kallisto [2024-08-30 18:04:46,612] multiqc [DEBUG ] No samples found: slamdunk [2024-08-30 18:04:46,616] multiqc [DEBUG ] No samples found: star [2024-08-30 18:04:46,619] multiqc [DEBUG ] No samples found: hisat2 [2024-08-30 18:04:46,621] multiqc [DEBUG ] No samples found: tophat [2024-08-30 18:04:46,624] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-30 18:04:46,627] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-30 18:04:46,630] multiqc [DEBUG ] No samples found: snpsplit [2024-08-30 18:04:46,632] multiqc [DEBUG ] No samples found: kat [2024-08-30 18:04:46,635] multiqc [DEBUG ] No samples found: leehom [2024-08-30 18:04:46,638] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-30 18:04:46,641] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-30 18:04:46,644] multiqc [DEBUG ] No samples found: cutadapt [2024-08-30 18:04:46,647] multiqc [DEBUG ] No samples found: flexbar [2024-08-30 18:04:46,650] multiqc [DEBUG ] No samples found: kaiju [2024-08-30 18:04:46,653] multiqc [DEBUG ] No samples found: kraken [2024-08-30 18:04:46,655] multiqc [DEBUG ] No samples found: malt [2024-08-30 18:04:46,658] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-30 18:04:46,662] multiqc [DEBUG ] No samples found: sickle [2024-08-30 18:04:46,664] multiqc [DEBUG ] No samples found: skewer [2024-08-30 18:04:46,667] multiqc [DEBUG ] No samples found: sortmerna [2024-08-30 18:04:46,670] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-30 18:04:46,673] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-30 18:04:46,675] multiqc [DEBUG ] No samples found: afterqc [2024-08-30 18:04:46,678] multiqc [DEBUG ] No samples found: fastp [2024-08-30 18:04:47,102] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2024-08-30 18:04:47,316] multiqc [DEBUG ] No samples found: pycoqc [2024-08-30 18:04:47,320] multiqc [DEBUG ] No samples found: minionqc [2024-08-30 18:04:47,322] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-30 18:04:47,325] multiqc [DEBUG ] No samples found: clusterflow [2024-08-30 18:04:47,329] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-30 18:04:47,331] multiqc [DEBUG ] No samples found: interop [2024-08-30 18:04:47,334] multiqc [DEBUG ] No samples found: ivar [2024-08-30 18:04:47,337] multiqc [DEBUG ] No samples found: flash [2024-08-30 18:04:47,340] multiqc [DEBUG ] No samples found: seqyclean [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-30 18:04:47,340] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-30 18:04:47,341] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-30 18:04:47,356] multiqc [INFO ] Compressing plot data [2024-08-30 18:04:47,577] multiqc [INFO ] Report : multiqc_report.html [2024-08-30 18:04:47,577] multiqc [INFO ] Data : multiqc_data [2024-08-30 18:04:47,577] multiqc [DEBUG ] Moving data file from '/state/partition1/job-50501396/tmpv5txsufq/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/a7/6f8768132be0a990e0383ad2e1caf8/merged/multiqc_data' [2024-08-30 18:04:47,683] multiqc [INFO ] MultiQC complete