[2024-11-28 03:46:41,782] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-11-28 03:46:41,782] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-11-28 03:46:41,782] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-11-28 03:46:41,785] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-11-28 03:46:41,785] 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}} [2024-11-28 03:46:41,785] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-28 03:46:41,816] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-11-28 03:46:41,816] multiqc [INFO ] This is MultiQC v1.9 [2024-11-28 03:46:41,816] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-28 03:46:41,816] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/9e/0906b16148e36fe18ce541784fbd98/merged [2024-11-28 03:46:41,816] multiqc [INFO ] Template : default [2024-11-28 03:46:41,816] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-11-28 03:46:41,816] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/9e/0906b16148e36fe18ce541784fbd98/merged [2024-11-28 03:46:41,816] 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 [2024-11-28 03:46:41,817] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-54089289/tmp8rjmbroc [2024-11-28 03:46:41,934] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKN5LAFX7_n01_jz7340_2_14_fastqc.html [2024-11-28 03:46:41,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKN5LAFX7_n01_jz7340_2_14_fastqc.html [2024-11-28 03:46:41,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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HKN5LAFX7_n02_jz7340_2_11_fastqc.html [2024-11-28 03:46:43,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKN5LAFX7_n02_jz7340_2_11_fastqc.html [2024-11-28 03:46:43,697] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKN5LAFX7_n01_jz7340_2_05_fastqc.html [2024-11-28 03:46:43,699] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKN5LAFX7_n01_jz7340_2_05_fastqc.html [2024-11-28 03:46:43,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKN5LAFX7_n02_jz7340_2_14_fastqc.html [2024-11-28 03:46:43,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKN5LAFX7_n02_jz7340_2_14_fastqc.html [2024-11-28 03:46:43,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKN5LAFX7_n01_jz7340_2_01_fastqc.html [2024-11-28 03:46:43,800] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKN5LAFX7_n01_jz7340_2_01_fastqc.html [2024-11-28 03:46:44,361] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-28 03:46:44,363] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-28 03:46:44,379] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-11-28 03:46:44,381] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-11-28 03:46:44,389] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2024-11-28 03:46:44,404] multiqc [DEBUG ] No samples found: conpair [2024-11-28 03:46:44,410] multiqc [DEBUG ] No samples found: peddy [2024-11-28 03:46:44,416] multiqc [DEBUG ] No samples found: somalier [2024-11-28 03:46:44,423] multiqc [DEBUG ] No samples found: methylQA [2024-11-28 03:46:44,435] multiqc [DEBUG ] No samples found: mosdepth [2024-11-28 03:46:44,441] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-11-28 03:46:44,445] multiqc [DEBUG ] No samples found: qualimap [2024-11-28 03:46:44,451] multiqc [DEBUG ] No samples found: preseq [2024-11-28 03:46:44,458] multiqc [DEBUG ] No samples found: quast [2024-11-28 03:46:44,465] multiqc [DEBUG ] No samples found: qorts [2024-11-28 03:46:44,471] multiqc [DEBUG ] No samples found: rna_seqc [2024-11-28 03:46:44,477] multiqc [DEBUG ] No samples found: rockhopper [2024-11-28 03:46:44,482] multiqc [DEBUG ] No samples found: rsem [2024-11-28 03:46:44,498] multiqc [DEBUG ] No samples found: rseqc [2024-11-28 03:46:44,504] multiqc [DEBUG ] No samples found: busco [2024-11-28 03:46:44,510] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-11-28 03:46:44,517] multiqc [DEBUG ] No samples found: disambiguate [2024-11-28 03:46:44,523] multiqc [DEBUG ] No samples found: supernova [2024-11-28 03:46:44,541] multiqc [DEBUG ] No samples found: deeptools [2024-11-28 03:46:44,549] multiqc [DEBUG ] No samples found: sargasso [2024-11-28 03:46:44,555] multiqc [DEBUG ] No samples found: verifybamid [2024-11-28 03:46:44,562] multiqc [DEBUG ] No samples found: mirtrace [2024-11-28 03:46:44,567] multiqc [DEBUG ] No samples found: happy [2024-11-28 03:46:44,575] multiqc [DEBUG ] No samples found: mirtop [2024-11-28 03:46:44,586] multiqc [DEBUG ] No samples found: homer [2024-11-28 03:46:44,594] multiqc [DEBUG ] No samples found: macs2 [2024-11-28 03:46:44,599] multiqc [DEBUG ] No samples found: theta2 [2024-11-28 03:46:44,606] multiqc [DEBUG ] No samples found: snpeff [2024-11-28 03:46:44,615] multiqc [DEBUG ] No samples found: gatk [2024-11-28 03:46:44,620] multiqc [DEBUG ] No samples found: htseq [2024-11-28 03:46:44,627] multiqc [DEBUG ] No samples found: bcftools [2024-11-28 03:46:44,633] multiqc [DEBUG ] No samples found: featureCounts [2024-11-28 03:46:44,641] multiqc [DEBUG ] No samples found: fgbio [2024-11-28 03:46:44,660] multiqc [DEBUG ] No samples found: dragen [2024-11-28 03:46:44,666] multiqc [DEBUG ] No samples found: dedup [2024-11-28 03:46:44,673] multiqc [DEBUG ] No samples found: damageprofiler [2024-11-28 03:46:44,700] multiqc [DEBUG ] No samples found: biobambam2 [2024-11-28 03:46:44,706] multiqc [DEBUG ] No samples found: mtnucratio [2024-11-28 03:46:44,708] multiqc [DEBUG ] No samples found: picard [2024-11-28 03:46:44,715] multiqc [DEBUG ] No samples found: prokka [2024-11-28 03:46:44,720] multiqc [DEBUG ] No samples found: samblaster [2024-11-28 03:46:44,733] multiqc [DEBUG ] No samples found: samtools [2024-11-28 03:46:44,738] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-11-28 03:46:44,747] multiqc [DEBUG ] No samples found: bamtools [2024-11-28 03:46:44,752] multiqc [DEBUG ] No samples found: jellyfish [2024-11-28 03:46:44,764] multiqc [DEBUG ] No samples found: vcftools [2024-11-28 03:46:44,770] multiqc [DEBUG ] No samples found: longranger [2024-11-28 03:46:44,777] multiqc [DEBUG ] No samples found: stacks [2024-11-28 03:46:44,783] multiqc [DEBUG ] No samples found: varscan2 [2024-11-28 03:46:44,800] multiqc [DEBUG ] No samples found: bbmap [2024-11-28 03:46:44,805] multiqc [DEBUG ] No samples found: bismark [2024-11-28 03:46:44,812] multiqc [DEBUG ] No samples found: biscuit [2024-11-28 03:46:44,818] multiqc [DEBUG ] No samples found: hicexplorer [2024-11-28 03:46:44,825] multiqc [DEBUG ] No samples found: hicup [2024-11-28 03:46:44,831] multiqc [DEBUG ] No samples found: hicpro [2024-11-28 03:46:44,837] multiqc [DEBUG ] No samples found: salmon [2024-11-28 03:46:44,843] multiqc [DEBUG ] No samples found: kallisto [2024-11-28 03:46:44,849] multiqc [DEBUG ] No samples found: slamdunk [2024-11-28 03:46:44,855] multiqc [DEBUG ] No samples found: star [2024-11-28 03:46:44,861] multiqc [DEBUG ] No samples found: hisat2 [2024-11-28 03:46:44,866] multiqc [DEBUG ] No samples found: tophat [2024-11-28 03:46:44,873] multiqc [DEBUG ] No samples found: bowtie2 [2024-11-28 03:46:44,879] multiqc [DEBUG ] No samples found: bowtie1 [2024-11-28 03:46:44,885] multiqc [DEBUG ] No samples found: snpsplit [2024-11-28 03:46:44,891] multiqc [DEBUG ] No samples found: kat [2024-11-28 03:46:44,897] multiqc [DEBUG ] No samples found: leehom [2024-11-28 03:46:44,904] multiqc [DEBUG ] No samples found: adapterRemoval [2024-11-28 03:46:44,910] multiqc [DEBUG ] No samples found: clipandmerge [2024-11-28 03:46:44,915] multiqc [DEBUG ] No samples found: cutadapt [2024-11-28 03:46:44,920] multiqc [DEBUG ] No samples found: flexbar [2024-11-28 03:46:44,927] multiqc [DEBUG ] No samples found: kaiju [2024-11-28 03:46:44,932] multiqc [DEBUG ] No samples found: kraken [2024-11-28 03:46:44,938] multiqc [DEBUG ] No samples found: malt [2024-11-28 03:46:44,944] multiqc [DEBUG ] No samples found: trimmomatic [2024-11-28 03:46:44,951] multiqc [DEBUG ] No samples found: sickle [2024-11-28 03:46:44,957] multiqc [DEBUG ] No samples found: skewer [2024-11-28 03:46:44,962] multiqc [DEBUG ] No samples found: sortmerna [2024-11-28 03:46:44,969] multiqc [DEBUG ] No samples found: biobloomtools [2024-11-28 03:46:44,975] multiqc [DEBUG ] No samples found: fastq_screen [2024-11-28 03:46:44,981] multiqc [DEBUG ] No samples found: afterqc [2024-11-28 03:46:44,988] multiqc [DEBUG ] No samples found: fastp [2024-11-28 03:46:45,879] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2024-11-28 03:46:46,588] multiqc [DEBUG ] No samples found: pycoqc [2024-11-28 03:46:46,594] multiqc [DEBUG ] No samples found: minionqc [2024-11-28 03:46:46,599] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-11-28 03:46:46,606] multiqc [DEBUG ] No samples found: clusterflow [2024-11-28 03:46:46,612] multiqc [DEBUG ] No samples found: bcl2fastq [2024-11-28 03:46:46,619] multiqc [DEBUG ] No samples found: interop [2024-11-28 03:46:46,625] multiqc [DEBUG ] No samples found: ivar [2024-11-28 03:46:46,631] multiqc [DEBUG ] No samples found: flash [2024-11-28 03:46:46,637] multiqc [DEBUG ] No samples found: seqyclean [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-28 03:46:46,637] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-11-28 03:46:46,638] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-11-28 03:46:46,688] multiqc [INFO ] Compressing plot data [2024-11-28 03:46:47,340] multiqc [INFO ] Report : multiqc_report.html [2024-11-28 03:46:47,340] multiqc [INFO ] Data : multiqc_data [2024-11-28 03:46:47,340] multiqc [DEBUG ] Moving data file from '/state/partition1/job-54089289/tmp8rjmbroc/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/9e/0906b16148e36fe18ce541784fbd98/merged/multiqc_data' [2024-11-28 03:46:47,488] multiqc [INFO ] MultiQC complete