[2025-02-15 09:18:14,811] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-02-15 09:18:14,811] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-02-15 09:18:14,811] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-02-15 09:18:14,813] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-02-15 09:18:14,813] 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}} [2025-02-15 09:18:14,813] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-15 09:18:14,849] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-02-15 09:18:14,850] multiqc [INFO ] This is MultiQC v1.9 [2025-02-15 09:18:14,850] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-15 09:18:14,850] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/34/6e899badd77ef5de911d8d9a1b91c2/merged [2025-02-15 09:18:14,850] multiqc [INFO ] Template : default [2025-02-15 09:18:14,850] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-02-15 09:18:14,850] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/34/6e899badd77ef5de911d8d9a1b91c2/merged [2025-02-15 09:18:14,850] 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 [2025-02-15 09:18:14,850] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-57290734/tmpmseu9jwv [2025-02-15 09:18:14,969] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_D_e_30_fastqc.html [2025-02-15 09:18:14,972] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_D_e_30_fastqc.html [2025-02-15 09:18:15,048] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H2MGNDMX2_n01_O_D_a_7_fastqc.html [2025-02-15 09:18:16,334] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_D_a_7_fastqc.html [2025-02-15 09:18:16,407] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_D_b_20_fastqc.html [2025-02-15 09:18:16,409] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_D_b_20_fastqc.html [2025-02-15 09:18:16,470] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_undetermined_fastqc.html [2025-02-15 09:18:16,472] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_undetermined_fastqc.html [2025-02-15 09:18:16,540] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_F_b_18_fastqc.html [2025-02-15 09:18:16,542] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_F_b_18_fastqc.html [2025-02-15 09:18:16,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_F_e_32_fastqc.html [2025-02-15 09:18:16,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_F_e_32_fastqc.html [2025-02-15 09:18:16,711] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_P_a_6_fastqc.html [2025-02-15 09:18:16,713] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_P_a_6_fastqc.html [2025-02-15 09:18:16,759] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_D_e_26_fastqc.html [2025-02-15 09:18:16,761] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_D_e_26_fastqc.html [2025-02-15 09:18:16,816] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_P_a_11_fastqc.html [2025-02-15 09:18:16,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_P_a_11_fastqc.html [2025-02-15 09:18:16,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_C_b_15_fastqc.html [2025-02-15 09:18:16,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_W_C_b_15_fastqc.html [2025-02-15 09:18:16,946] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_D_b_19_fastqc.html [2025-02-15 09:18:16,948] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_D_b_19_fastqc.html [2025-02-15 09:18:17,003] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_C_b_22_fastqc.html [2025-02-15 09:18:17,004] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MGNDMX2_n01_O_C_b_22_fastqc.html [2025-02-15 09:18:17,328] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-15 09:18:17,328] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-15 09:18:17,350] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 33 samples (table) [2025-02-15 09:18:17,351] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-02-15 09:18:17,361] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-02-15 09:18:17,364] multiqc [DEBUG ] No samples found: conpair [2025-02-15 09:18:17,367] multiqc [DEBUG ] No samples found: peddy [2025-02-15 09:18:17,370] multiqc [DEBUG ] No samples found: somalier [2025-02-15 09:18:17,373] multiqc [DEBUG ] No samples found: methylQA [2025-02-15 09:18:17,376] multiqc [DEBUG ] No samples found: mosdepth [2025-02-15 09:18:17,379] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-02-15 09:18:17,382] multiqc [DEBUG ] No samples found: qualimap [2025-02-15 09:18:17,384] multiqc [DEBUG ] No samples found: preseq [2025-02-15 09:18:17,387] multiqc [DEBUG ] No samples found: quast [2025-02-15 09:18:17,390] multiqc [DEBUG ] No samples found: qorts [2025-02-15 09:18:17,393] multiqc [DEBUG ] No samples found: rna_seqc [2025-02-15 09:18:17,396] multiqc [DEBUG ] No samples found: rockhopper [2025-02-15 09:18:17,399] multiqc [DEBUG ] No samples found: rsem [2025-02-15 09:18:17,403] multiqc [DEBUG ] No samples found: rseqc [2025-02-15 09:18:17,406] multiqc [DEBUG ] No samples found: busco [2025-02-15 09:18:17,409] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-02-15 09:18:17,412] multiqc [DEBUG ] No samples found: disambiguate [2025-02-15 09:18:17,415] multiqc [DEBUG ] No samples found: supernova [2025-02-15 09:18:17,420] multiqc [DEBUG ] No samples found: deeptools [2025-02-15 09:18:17,423] multiqc [DEBUG ] No samples found: sargasso [2025-02-15 09:18:17,426] multiqc [DEBUG ] No samples found: verifybamid [2025-02-15 09:18:17,429] multiqc [DEBUG ] No samples found: mirtrace [2025-02-15 09:18:17,432] multiqc [DEBUG ] No samples found: happy [2025-02-15 09:18:17,435] multiqc [DEBUG ] No samples found: mirtop [2025-02-15 09:18:17,438] multiqc [DEBUG ] No samples found: homer [2025-02-15 09:18:17,441] multiqc [DEBUG ] No samples found: macs2 [2025-02-15 09:18:17,443] multiqc [DEBUG ] No samples found: theta2 [2025-02-15 09:18:17,446] multiqc [DEBUG ] No samples found: snpeff [2025-02-15 09:18:17,450] multiqc [DEBUG ] No samples found: gatk [2025-02-15 09:18:17,453] multiqc [DEBUG ] No samples found: htseq [2025-02-15 09:18:17,456] multiqc [DEBUG ] No samples found: bcftools [2025-02-15 09:18:17,459] multiqc [DEBUG ] No samples found: featureCounts [2025-02-15 09:18:17,462] multiqc [DEBUG ] No samples found: fgbio [2025-02-15 09:18:17,468] multiqc [DEBUG ] No samples found: dragen [2025-02-15 09:18:17,471] multiqc [DEBUG ] No samples found: dedup [2025-02-15 09:18:17,474] multiqc [DEBUG ] No samples found: damageprofiler [2025-02-15 09:18:17,482] multiqc [DEBUG ] No samples found: biobambam2 [2025-02-15 09:18:17,485] multiqc [DEBUG ] No samples found: mtnucratio [2025-02-15 09:18:17,487] multiqc [DEBUG ] No samples found: picard [2025-02-15 09:18:17,491] multiqc [DEBUG ] No samples found: prokka [2025-02-15 09:18:17,493] multiqc [DEBUG ] No samples found: samblaster [2025-02-15 09:18:17,497] multiqc [DEBUG ] No samples found: samtools [2025-02-15 09:18:17,500] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-02-15 09:18:17,503] multiqc [DEBUG ] No samples found: bamtools [2025-02-15 09:18:17,506] multiqc [DEBUG ] No samples found: jellyfish [2025-02-15 09:18:17,510] multiqc [DEBUG ] No samples found: vcftools [2025-02-15 09:18:17,512] multiqc [DEBUG ] No samples found: longranger [2025-02-15 09:18:17,515] multiqc [DEBUG ] No samples found: stacks [2025-02-15 09:18:17,518] multiqc [DEBUG ] No samples found: varscan2 [2025-02-15 09:18:17,523] multiqc [DEBUG ] No samples found: bbmap [2025-02-15 09:18:17,526] multiqc [DEBUG ] No samples found: bismark [2025-02-15 09:18:17,529] multiqc [DEBUG ] No samples found: biscuit [2025-02-15 09:18:17,532] multiqc [DEBUG ] No samples found: hicexplorer [2025-02-15 09:18:17,535] multiqc [DEBUG ] No samples found: hicup [2025-02-15 09:18:17,538] multiqc [DEBUG ] No samples found: hicpro [2025-02-15 09:18:17,541] multiqc [DEBUG ] No samples found: salmon [2025-02-15 09:18:17,543] multiqc [DEBUG ] No samples found: kallisto [2025-02-15 09:18:17,546] multiqc [DEBUG ] No samples found: slamdunk [2025-02-15 09:18:17,549] multiqc [DEBUG ] No samples found: star [2025-02-15 09:18:17,552] multiqc [DEBUG ] No samples found: hisat2 [2025-02-15 09:18:17,555] multiqc [DEBUG ] No samples found: tophat [2025-02-15 09:18:17,558] multiqc [DEBUG ] No samples found: bowtie2 [2025-02-15 09:18:17,560] multiqc [DEBUG ] No samples found: bowtie1 [2025-02-15 09:18:17,563] multiqc [DEBUG ] No samples found: snpsplit [2025-02-15 09:18:17,566] multiqc [DEBUG ] No samples found: kat [2025-02-15 09:18:17,568] multiqc [DEBUG ] No samples found: leehom [2025-02-15 09:18:17,571] multiqc [DEBUG ] No samples found: adapterRemoval [2025-02-15 09:18:17,574] multiqc [DEBUG ] No samples found: clipandmerge [2025-02-15 09:18:17,577] multiqc [DEBUG ] No samples found: cutadapt [2025-02-15 09:18:17,579] multiqc [DEBUG ] No samples found: flexbar [2025-02-15 09:18:17,582] multiqc [DEBUG ] No samples found: kaiju [2025-02-15 09:18:17,585] multiqc [DEBUG ] No samples found: kraken [2025-02-15 09:18:17,588] multiqc [DEBUG ] No samples found: malt [2025-02-15 09:18:17,590] multiqc [DEBUG ] No samples found: trimmomatic [2025-02-15 09:18:17,593] multiqc [DEBUG ] No samples found: sickle [2025-02-15 09:18:17,596] multiqc [DEBUG ] No samples found: skewer [2025-02-15 09:18:17,599] multiqc [DEBUG ] No samples found: sortmerna [2025-02-15 09:18:17,601] multiqc [DEBUG ] No samples found: biobloomtools [2025-02-15 09:18:17,604] multiqc [DEBUG ] No samples found: fastq_screen [2025-02-15 09:18:17,607] multiqc [DEBUG ] No samples found: afterqc [2025-02-15 09:18:17,610] multiqc [DEBUG ] No samples found: fastp [2025-02-15 09:18:23,347] multiqc.modules.fastqc.fastqc [INFO ] Found 33 reports [2025-02-15 09:18:23,833] multiqc [DEBUG ] No samples found: pycoqc [2025-02-15 09:18:23,836] multiqc [DEBUG ] No samples found: minionqc [2025-02-15 09:18:23,839] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-02-15 09:18:23,842] multiqc [DEBUG ] No samples found: clusterflow [2025-02-15 09:18:23,845] multiqc [DEBUG ] No samples found: bcl2fastq [2025-02-15 09:18:23,847] multiqc [DEBUG ] No samples found: interop [2025-02-15 09:18:23,850] multiqc [DEBUG ] No samples found: ivar [2025-02-15 09:18:23,853] multiqc [DEBUG ] No samples found: flash [2025-02-15 09:18:23,856] multiqc [DEBUG ] No samples found: seqyclean [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 09:18:23,856] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-02-15 09:18:23,857] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-02-15 09:18:23,898] multiqc [INFO ] Compressing plot data [2025-02-15 09:18:24,537] multiqc [INFO ] Report : multiqc_report.html [2025-02-15 09:18:24,537] multiqc [INFO ] Data : multiqc_data [2025-02-15 09:18:24,537] multiqc [DEBUG ] Moving data file from '/state/partition1/job-57290734/tmpmseu9jwv/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/34/6e899badd77ef5de911d8d9a1b91c2/merged/multiqc_data' [2025-02-15 09:18:24,635] multiqc [INFO ] MultiQC complete