[2025-02-15 00:47:49,069] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-02-15 00:47:49,070] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-02-15 00:47:49,070] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-02-15 00:47:49,072] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-02-15 00:47:49,072] 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 00:47:49,072] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-15 00:47:49,112] multiqc [DEBUG ] Could not connect to multiqc.info for version check: <urlopen error unknown url type: https> [2025-02-15 00:47:49,112] multiqc [INFO ] This is MultiQC v1.9 [2025-02-15 00:47:49,112] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-02-15 00:47:49,113] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/ef/2b9b0d45fdc55680132cc408575cd0/merged [2025-02-15 00:47:49,113] multiqc [INFO ] Template : default [2025-02-15 00:47:49,113] 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 00:47:49,113] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/ef/2b9b0d45fdc55680132cc408575cd0/merged [2025-02-15 00:47:49,113] 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 00:47:49,113] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-57286941/tmpmezu3p2k [2025-02-15 00:47:49,217] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_06_fastqc.html [2025-02-15 00:47:49,220] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_06_fastqc.html [2025-02-15 00:47:49,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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HNTLKDRX5_n01_sr5965_4_13_fastqc.html [2025-02-15 00:47:50,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_13_fastqc.html [2025-02-15 00:47:50,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_02_fastqc.html [2025-02-15 00:47:50,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_02_fastqc.html [2025-02-15 00:47:50,393] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_16_fastqc.html [2025-02-15 00:47:50,394] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_16_fastqc.html [2025-02-15 00:47:50,441] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_03_fastqc.html [2025-02-15 00:47:50,443] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_03_fastqc.html [2025-02-15 00:47:50,490] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_14_fastqc.html [2025-02-15 00:47:50,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_14_fastqc.html [2025-02-15 00:47:50,538] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_16_fastqc.html [2025-02-15 00:47:50,540] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_16_fastqc.html [2025-02-15 00:47:50,607] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_05_fastqc.html [2025-02-15 00:47:50,609] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_05_fastqc.html [2025-02-15 00:47:50,656] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_11_fastqc.html [2025-02-15 00:47:50,658] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_11_fastqc.html [2025-02-15 00:47:50,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_04_fastqc.html [2025-02-15 00:47:50,706] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_04_fastqc.html [2025-02-15 00:47:50,753] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_05_fastqc.html [2025-02-15 00:47:50,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n01_sr5965_4_05_fastqc.html [2025-02-15 00:47:50,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_06_fastqc.html [2025-02-15 00:47:50,803] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_06_fastqc.html [2025-02-15 00:47:50,852] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_09_fastqc.html [2025-02-15 00:47:50,854] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTLKDRX5_n02_sr5965_4_09_fastqc.html [2025-02-15 00:47:51,370] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-15 00:47:51,371] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-02-15 00:47:51,379] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-02-15 00:47:51,388] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2025-02-15 00:47:51,398] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-02-15 00:47:51,402] multiqc [DEBUG ] No samples found: conpair [2025-02-15 00:47:51,407] multiqc [DEBUG ] No samples found: peddy [2025-02-15 00:47:51,412] multiqc [DEBUG ] No samples found: somalier [2025-02-15 00:47:51,416] multiqc [DEBUG ] No samples found: methylQA [2025-02-15 00:47:51,424] multiqc [DEBUG ] No samples found: mosdepth [2025-02-15 00:47:51,428] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-02-15 00:47:51,432] multiqc [DEBUG ] No samples found: qualimap [2025-02-15 00:47:51,436] multiqc [DEBUG ] No samples found: preseq [2025-02-15 00:47:51,441] multiqc [DEBUG ] No samples found: quast [2025-02-15 00:47:51,445] multiqc [DEBUG ] No samples found: qorts [2025-02-15 00:47:51,450] multiqc [DEBUG ] No samples found: rna_seqc [2025-02-15 00:47:51,454] multiqc [DEBUG ] No samples found: rockhopper [2025-02-15 00:47:51,458] multiqc [DEBUG ] No samples found: rsem [2025-02-15 00:47:51,469] multiqc [DEBUG ] No samples found: rseqc [2025-02-15 00:47:51,473] multiqc [DEBUG ] No samples found: busco [2025-02-15 00:47:51,478] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-02-15 00:47:51,482] multiqc [DEBUG ] No samples found: disambiguate [2025-02-15 00:47:51,486] multiqc [DEBUG ] No samples found: supernova [2025-02-15 00:47:51,499] multiqc [DEBUG ] No samples found: deeptools [2025-02-15 00:47:51,503] multiqc [DEBUG ] No samples found: sargasso [2025-02-15 00:47:51,508] multiqc [DEBUG ] No samples found: verifybamid [2025-02-15 00:47:51,513] multiqc [DEBUG ] No samples found: mirtrace [2025-02-15 00:47:51,517] multiqc [DEBUG ] No samples found: happy [2025-02-15 00:47:51,522] multiqc [DEBUG ] No samples found: mirtop [2025-02-15 00:47:51,528] multiqc [DEBUG ] No samples found: homer [2025-02-15 00:47:51,532] multiqc [DEBUG ] No samples found: macs2 [2025-02-15 00:47:51,536] multiqc [DEBUG ] No samples found: theta2 [2025-02-15 00:47:51,541] multiqc [DEBUG ] No samples found: snpeff [2025-02-15 00:47:51,547] multiqc [DEBUG ] No samples found: gatk [2025-02-15 00:47:51,552] multiqc [DEBUG ] No samples found: htseq [2025-02-15 00:47:51,557] multiqc [DEBUG ] No samples found: bcftools [2025-02-15 00:47:51,562] multiqc [DEBUG ] No samples found: featureCounts [2025-02-15 00:47:51,568] multiqc [DEBUG ] No samples found: fgbio [2025-02-15 00:47:51,580] multiqc [DEBUG ] No samples found: dragen [2025-02-15 00:47:51,584] multiqc [DEBUG ] No samples found: dedup [2025-02-15 00:47:51,589] multiqc [DEBUG ] No samples found: damageprofiler [2025-02-15 00:47:51,610] multiqc [DEBUG ] No samples found: biobambam2 [2025-02-15 00:47:51,615] multiqc [DEBUG ] No samples found: mtnucratio [2025-02-15 00:47:51,617] multiqc [DEBUG ] No samples found: picard [2025-02-15 00:47:51,623] multiqc [DEBUG ] No samples found: prokka [2025-02-15 00:47:51,627] multiqc [DEBUG ] No samples found: samblaster [2025-02-15 00:47:51,635] multiqc [DEBUG ] No samples found: samtools [2025-02-15 00:47:51,640] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-02-15 00:47:51,645] multiqc [DEBUG ] No samples found: bamtools [2025-02-15 00:47:51,649] multiqc [DEBUG ] No samples found: jellyfish [2025-02-15 00:47:51,657] multiqc [DEBUG ] No samples found: vcftools [2025-02-15 00:47:51,662] multiqc [DEBUG ] No samples found: longranger [2025-02-15 00:47:51,667] multiqc [DEBUG ] No samples found: stacks [2025-02-15 00:47:51,671] multiqc [DEBUG ] No samples found: varscan2 [2025-02-15 00:47:51,685] multiqc [DEBUG ] No samples found: bbmap [2025-02-15 00:47:51,690] multiqc [DEBUG ] No samples found: bismark [2025-02-15 00:47:51,694] multiqc [DEBUG ] No samples found: biscuit [2025-02-15 00:47:51,699] multiqc [DEBUG ] No samples found: hicexplorer [2025-02-15 00:47:51,703] multiqc [DEBUG ] No samples found: hicup [2025-02-15 00:47:51,708] multiqc [DEBUG ] No samples found: hicpro [2025-02-15 00:47:51,712] multiqc [DEBUG ] No samples found: salmon [2025-02-15 00:47:51,717] multiqc [DEBUG ] No samples found: kallisto [2025-02-15 00:47:51,721] multiqc [DEBUG ] No samples found: slamdunk [2025-02-15 00:47:51,726] multiqc [DEBUG ] No samples found: star [2025-02-15 00:47:51,730] multiqc [DEBUG ] No samples found: hisat2 [2025-02-15 00:47:51,734] multiqc [DEBUG ] No samples found: tophat [2025-02-15 00:47:51,739] multiqc [DEBUG ] No samples found: bowtie2 [2025-02-15 00:47:51,743] multiqc [DEBUG ] No samples found: bowtie1 [2025-02-15 00:47:51,748] multiqc [DEBUG ] No samples found: snpsplit [2025-02-15 00:47:51,752] multiqc [DEBUG ] No samples found: kat [2025-02-15 00:47:51,756] multiqc [DEBUG ] No samples found: leehom [2025-02-15 00:47:51,760] multiqc [DEBUG ] No samples found: adapterRemoval [2025-02-15 00:47:51,764] multiqc [DEBUG ] No samples found: clipandmerge [2025-02-15 00:47:51,769] multiqc [DEBUG ] No samples found: cutadapt [2025-02-15 00:47:51,773] multiqc [DEBUG ] No samples found: flexbar [2025-02-15 00:47:51,777] multiqc [DEBUG ] No samples found: kaiju [2025-02-15 00:47:51,782] multiqc [DEBUG ] No samples found: kraken [2025-02-15 00:47:51,786] multiqc [DEBUG ] No samples found: malt [2025-02-15 00:47:51,790] multiqc [DEBUG ] No samples found: trimmomatic [2025-02-15 00:47:51,795] multiqc [DEBUG ] No samples found: sickle [2025-02-15 00:47:51,799] multiqc [DEBUG ] No samples found: skewer [2025-02-15 00:47:51,803] multiqc [DEBUG ] No samples found: sortmerna [2025-02-15 00:47:51,807] multiqc [DEBUG ] No samples found: biobloomtools [2025-02-15 00:47:51,812] multiqc [DEBUG ] No samples found: fastq_screen [2025-02-15 00:47:51,816] multiqc [DEBUG ] No samples found: afterqc [2025-02-15 00:47:51,821] multiqc [DEBUG ] No samples found: fastp [2025-02-15 00:47:52,713] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2025-02-15 00:47:53,014] multiqc [DEBUG ] No samples found: pycoqc [2025-02-15 00:47:53,018] multiqc [DEBUG ] No samples found: minionqc [2025-02-15 00:47:53,023] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-02-15 00:47:53,028] multiqc [DEBUG ] No samples found: clusterflow [2025-02-15 00:47:53,032] multiqc [DEBUG ] No samples found: bcl2fastq [2025-02-15 00:47:53,036] multiqc [DEBUG ] No samples found: interop [2025-02-15 00:47:53,041] multiqc [DEBUG ] No samples found: ivar [2025-02-15 00:47:53,045] multiqc [DEBUG ] No samples found: flash [2025-02-15 00:47:53,050] multiqc [DEBUG ] No samples found: seqyclean [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-02-15 00:47:53,050] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-02-15 00:47:53,051] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-02-15 00:47:53,093] multiqc [INFO ] Compressing plot data [2025-02-15 00:47:53,670] multiqc [INFO ] Report : multiqc_report.html [2025-02-15 00:47:53,671] multiqc [INFO ] Data : multiqc_data [2025-02-15 00:47:53,671] multiqc [DEBUG ] Moving data file from '/state/partition1/job-57286941/tmpmezu3p2k/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/ef/2b9b0d45fdc55680132cc408575cd0/merged/multiqc_data' [2025-02-15 00:47:53,795] multiqc [INFO ] MultiQC complete