[2024-10-16 18:36:13,174] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-10-16 18:36:13,174] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-10-16 18:36:13,174] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-10-16 18:36:13,177] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-10-16 18:36:13,177] 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}} [2024-10-16 18:36:13,177] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-16 18:36:13,227] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-10-16 18:36:13,228] multiqc [INFO ] This is MultiQC v1.9 [2024-10-16 18:36:13,228] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-16 18:36:13,228] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/c2/69151632c5fc00efda55cbcc3959f4/3 [2024-10-16 18:36:13,228] multiqc [INFO ] Template : default [2024-10-16 18:36:13,228] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-10-16 18:36:13,228] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/c2/69151632c5fc00efda55cbcc3959f4/3 [2024-10-16 18:36:13,228] 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 [2024-10-16 18:36:13,228] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-52279913/tmpv8by6ji_ [2024-10-16 18:36:13,341] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n02_QG4896_POOLRET81_fastqc.html [2024-10-16 18:36:13,343] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n02_QG4896_POOLRET81_fastqc.html [2024-10-16 18:36:13,392] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern 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[DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG5284_POOLRET81_fastqc.html [2024-10-16 18:36:31,105] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG4996_POOLRET81_fastqc.html [2024-10-16 18:36:31,107] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG4996_POOLRET81_fastqc.html [2024-10-16 18:36:31,153] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n02_QG4742_POOLRET81_fastqc.html [2024-10-16 18:36:31,155] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n02_QG4742_POOLRET81_fastqc.html [2024-10-16 18:36:31,201] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_ECA3530_POOLRET81_fastqc.html [2024-10-16 18:36:31,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_ECA3530_POOLRET81_fastqc.html [2024-10-16 18:36:31,541] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG4868_POOLRET81_fastqc.html [2024-10-16 18:36:31,543] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG4868_POOLRET81_fastqc.html [2024-10-16 18:36:31,590] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n02_QG5539_POOLRET81_fastqc.html [2024-10-16 18:36:31,592] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG4867_POOLRET81_fastqc.html [2024-10-16 18:36:31,782] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG5256_POOLRET81_fastqc.html [2024-10-16 18:36:31,784] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG5256_POOLRET81_fastqc.html [2024-10-16 18:36:31,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG5577_POOLRET81_fastqc.html [2024-10-16 18:36:31,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG5577_POOLRET81_fastqc.html [2024-10-16 18:36:31,879] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG4672_POOLRET81_fastqc.html [2024-10-16 18:36:31,881] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG4672_POOLRET81_fastqc.html [2024-10-16 18:36:31,927] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG5502_POOLRET81_fastqc.html [2024-10-16 18:36:31,929] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNJLWDSXC_l03_n01_QG5502_POOLRET81_fastqc.html [2024-10-16 18:36:32,309] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-16 18:36:32,310] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-16 18:36:32,405] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 193 samples (table) [2024-10-16 18:36:32,415] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-10-16 18:36:32,416] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-10-16 18:36:32,422] multiqc [DEBUG ] No samples found: conpair [2024-10-16 18:36:32,427] multiqc [DEBUG ] No samples found: peddy [2024-10-16 18:36:32,432] multiqc [DEBUG ] No samples found: somalier [2024-10-16 18:36:32,436] multiqc [DEBUG ] No samples found: methylQA [2024-10-16 18:36:32,444] multiqc [DEBUG ] No samples found: mosdepth [2024-10-16 18:36:32,448] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-10-16 18:36:32,452] multiqc [DEBUG ] No samples found: qualimap [2024-10-16 18:36:32,457] multiqc [DEBUG ] No samples found: preseq [2024-10-16 18:36:32,462] multiqc [DEBUG ] No samples found: quast [2024-10-16 18:36:32,467] multiqc [DEBUG ] No samples found: qorts [2024-10-16 18:36:32,471] multiqc [DEBUG ] No samples found: rna_seqc [2024-10-16 18:36:32,476] multiqc [DEBUG ] No samples found: rockhopper [2024-10-16 18:36:32,481] multiqc [DEBUG ] No samples found: rsem [2024-10-16 18:36:32,493] multiqc [DEBUG ] No samples found: rseqc [2024-10-16 18:36:32,497] multiqc [DEBUG ] No samples found: busco [2024-10-16 18:36:32,502] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-10-16 18:36:32,507] multiqc [DEBUG ] No samples found: disambiguate [2024-10-16 18:36:32,512] multiqc [DEBUG ] No samples found: supernova [2024-10-16 18:36:32,525] multiqc [DEBUG ] No samples found: deeptools [2024-10-16 18:36:32,530] multiqc [DEBUG ] No samples found: sargasso [2024-10-16 18:36:32,535] multiqc [DEBUG ] No samples found: verifybamid [2024-10-16 18:36:32,539] multiqc [DEBUG ] No samples found: mirtrace [2024-10-16 18:36:32,544] multiqc [DEBUG ] No samples found: happy [2024-10-16 18:36:32,549] multiqc [DEBUG ] No samples found: mirtop [2024-10-16 18:36:32,555] multiqc [DEBUG ] No samples found: homer [2024-10-16 18:36:32,559] multiqc [DEBUG ] No samples found: macs2 [2024-10-16 18:36:32,564] multiqc [DEBUG ] No samples found: theta2 [2024-10-16 18:36:32,568] multiqc [DEBUG ] No samples found: snpeff [2024-10-16 18:36:32,575] multiqc [DEBUG ] No samples found: gatk [2024-10-16 18:36:32,580] multiqc [DEBUG ] No samples found: htseq [2024-10-16 18:36:32,585] multiqc [DEBUG ] No samples found: bcftools [2024-10-16 18:36:32,590] multiqc [DEBUG ] No samples found: featureCounts [2024-10-16 18:36:32,597] multiqc [DEBUG ] No samples found: fgbio [2024-10-16 18:36:32,610] multiqc [DEBUG ] No samples found: dragen [2024-10-16 18:36:32,614] multiqc [DEBUG ] No samples found: dedup [2024-10-16 18:36:32,619] multiqc [DEBUG ] No samples found: damageprofiler [2024-10-16 18:36:32,642] multiqc [DEBUG ] No samples found: biobambam2 [2024-10-16 18:36:32,647] multiqc [DEBUG ] No samples found: mtnucratio [2024-10-16 18:36:32,649] multiqc [DEBUG ] No samples found: picard [2024-10-16 18:36:32,654] multiqc [DEBUG ] No samples found: prokka [2024-10-16 18:36:32,658] multiqc [DEBUG ] No samples found: samblaster [2024-10-16 18:36:32,667] multiqc [DEBUG ] No samples found: samtools [2024-10-16 18:36:32,672] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-10-16 18:36:32,677] multiqc [DEBUG ] No samples found: bamtools [2024-10-16 18:36:32,681] multiqc [DEBUG ] No samples found: jellyfish [2024-10-16 18:36:32,689] multiqc [DEBUG ] No samples found: vcftools [2024-10-16 18:36:32,693] multiqc [DEBUG ] No samples found: longranger [2024-10-16 18:36:32,698] multiqc [DEBUG ] No samples found: stacks [2024-10-16 18:36:32,703] multiqc [DEBUG ] No samples found: varscan2 [2024-10-16 18:36:32,717] multiqc [DEBUG ] No samples found: bbmap [2024-10-16 18:36:32,721] multiqc [DEBUG ] No samples found: bismark [2024-10-16 18:36:32,726] multiqc [DEBUG ] No samples found: biscuit [2024-10-16 18:36:32,731] multiqc [DEBUG ] No samples found: hicexplorer [2024-10-16 18:36:32,735] multiqc [DEBUG ] No samples found: hicup [2024-10-16 18:36:32,740] multiqc [DEBUG ] No samples found: hicpro [2024-10-16 18:36:32,744] multiqc [DEBUG ] No samples found: salmon [2024-10-16 18:36:32,749] multiqc [DEBUG ] No samples found: kallisto [2024-10-16 18:36:32,754] multiqc [DEBUG ] No samples found: slamdunk [2024-10-16 18:36:32,758] multiqc [DEBUG ] No samples found: star [2024-10-16 18:36:32,763] multiqc [DEBUG ] No samples found: hisat2 [2024-10-16 18:36:32,767] multiqc [DEBUG ] No samples found: tophat [2024-10-16 18:36:32,772] multiqc [DEBUG ] No samples found: bowtie2 [2024-10-16 18:36:32,776] multiqc [DEBUG ] No samples found: bowtie1 [2024-10-16 18:36:32,781] multiqc [DEBUG ] No samples found: snpsplit [2024-10-16 18:36:32,785] multiqc [DEBUG ] No samples found: kat [2024-10-16 18:36:32,789] multiqc [DEBUG ] No samples found: leehom [2024-10-16 18:36:32,794] multiqc [DEBUG ] No samples found: adapterRemoval [2024-10-16 18:36:32,798] multiqc [DEBUG ] No samples found: clipandmerge [2024-10-16 18:36:32,803] multiqc [DEBUG ] No samples found: cutadapt [2024-10-16 18:36:32,807] multiqc [DEBUG ] No samples found: flexbar [2024-10-16 18:36:32,812] multiqc [DEBUG ] No samples found: kaiju [2024-10-16 18:36:32,816] multiqc [DEBUG ] No samples found: kraken [2024-10-16 18:36:32,821] multiqc [DEBUG ] No samples found: malt [2024-10-16 18:36:32,826] multiqc [DEBUG ] No samples found: trimmomatic [2024-10-16 18:36:32,830] multiqc [DEBUG ] No samples found: sickle [2024-10-16 18:36:32,835] multiqc [DEBUG ] No samples found: skewer [2024-10-16 18:36:32,839] multiqc [DEBUG ] No samples found: sortmerna [2024-10-16 18:36:32,843] multiqc [DEBUG ] No samples found: biobloomtools [2024-10-16 18:36:32,848] multiqc [DEBUG ] No samples found: fastq_screen [2024-10-16 18:36:32,853] multiqc [DEBUG ] No samples found: afterqc [2024-10-16 18:36:32,857] multiqc [DEBUG ] No samples found: fastp [2024-10-16 18:37:25,242] multiqc.modules.fastqc.fastqc [INFO ] Found 386 reports [2024-10-16 18:38:01,103] multiqc [DEBUG ] No samples found: pycoqc [2024-10-16 18:38:01,108] multiqc [DEBUG ] No samples found: minionqc [2024-10-16 18:38:01,113] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-10-16 18:38:01,118] multiqc [DEBUG ] No samples found: clusterflow [2024-10-16 18:38:01,123] multiqc [DEBUG ] No samples found: bcl2fastq [2024-10-16 18:38:01,128] multiqc [DEBUG ] No samples found: interop [2024-10-16 18:38:01,133] multiqc [DEBUG ] No samples found: ivar [2024-10-16 18:38:01,137] multiqc [DEBUG ] No samples found: flash [2024-10-16 18:38:01,142] multiqc [DEBUG ] No samples found: seqyclean [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-10-16 18:38:01,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-10-16 18:38:01,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-10-16 18:38:01,143] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-10-16 18:38:01,143] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-10-16 18:38:01,143] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-10-16 18:38:01,585] multiqc [INFO ] Compressing plot data [2024-10-16 18:38:01,722] multiqc [INFO ] Report : multiqc_report.html [2024-10-16 18:38:01,722] multiqc [INFO ] Data : multiqc_data [2024-10-16 18:38:01,722] multiqc [DEBUG ] Moving data file from '/state/partition1/job-52279913/tmpv8by6ji_/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/c2/69151632c5fc00efda55cbcc3959f4/3/multiqc_data' [2024-10-16 18:38:01,866] multiqc [INFO ] MultiQC complete