[2025-01-08 14:12:11,151] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-08 14:12:11,151] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-08 14:12:11,151] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-08 14:12:11,154] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-08 14:12:11,154] 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}} [2025-01-08 14:12:11,154] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-08 14:12:11,188] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-08 14:12:11,188] multiqc [INFO ] This is MultiQC v1.9 [2025-01-08 14:12:11,188] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-08 14:12:11,188] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/0c/76f62dbf4600beba3f4ce29214e189/merged [2025-01-08 14:12:11,188] multiqc [INFO ] Template : default [2025-01-08 14:12:11,188] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-08 14:12:11,188] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/0c/76f62dbf4600beba3f4ce29214e189/merged [2025-01-08 14:12:11,189] 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 [2025-01-08 14:12:11,189] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55693662/tmps97u_c8s [2025-01-08 14:12:11,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:11,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:11,309] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:11,309] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:11,309] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:11,309] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:11,310] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:11,343] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-08 14:12:12,780] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5N3DRX5_n01_wy_Petrov_dialout_fastqc.html [2025-01-08 14:12:12,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5N3DRX5_n01_wy_Petrov_dialout_fastqc.html [2025-01-08 14:12:12,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5N3DRX5_n02_wy_Petrov_dialout_fastqc.html [2025-01-08 14:12:12,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5N3DRX5_n02_wy_Petrov_dialout_fastqc.html [2025-01-08 14:12:12,926] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5N3DRX5_n01_wy_Petrov_10X_fastqc.html [2025-01-08 14:12:12,928] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5N3DRX5_n01_wy_Petrov_10X_fastqc.html [2025-01-08 14:12:12,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5N3DRX5_n01_undetermined_fastqc.html [2025-01-08 14:12:12,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5N3DRX5_n01_undetermined_fastqc.html [2025-01-08 14:12:13,038] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5N3DRX5_n02_wy_Petrov_10X_fastqc.html [2025-01-08 14:12:13,040] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5N3DRX5_n02_wy_Petrov_10X_fastqc.html [2025-01-08 14:12:13,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ5N3DRX5_n02_undetermined_fastqc.html [2025-01-08 14:12:13,092] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ5N3DRX5_n02_undetermined_fastqc.html [2025-01-08 14:12:13,630] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-08 14:12:13,632] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-08 14:12:13,641] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2025-01-08 14:12:13,643] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-08 14:12:13,653] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-08 14:12:13,659] multiqc [DEBUG ] No samples found: conpair [2025-01-08 14:12:13,664] multiqc [DEBUG ] No samples found: peddy [2025-01-08 14:12:13,669] multiqc [DEBUG ] No samples found: somalier [2025-01-08 14:12:13,675] multiqc [DEBUG ] No samples found: methylQA [2025-01-08 14:12:13,683] multiqc [DEBUG ] No samples found: mosdepth [2025-01-08 14:12:13,688] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-08 14:12:13,692] multiqc [DEBUG ] No samples found: qualimap [2025-01-08 14:12:13,698] multiqc [DEBUG ] No samples found: preseq [2025-01-08 14:12:13,703] multiqc [DEBUG ] No samples found: quast [2025-01-08 14:12:13,708] multiqc [DEBUG ] No samples found: qorts [2025-01-08 14:12:13,713] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-08 14:12:13,718] multiqc [DEBUG ] No samples found: rockhopper [2025-01-08 14:12:13,723] multiqc [DEBUG ] No samples found: rsem [2025-01-08 14:12:13,736] multiqc [DEBUG ] No samples found: rseqc [2025-01-08 14:12:13,741] multiqc [DEBUG ] No samples found: busco [2025-01-08 14:12:13,746] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-08 14:12:13,750] multiqc [DEBUG ] No samples found: disambiguate [2025-01-08 14:12:13,756] multiqc [DEBUG ] No samples found: supernova [2025-01-08 14:12:13,769] multiqc [DEBUG ] No samples found: deeptools [2025-01-08 14:12:13,775] multiqc [DEBUG ] No samples found: sargasso [2025-01-08 14:12:13,780] multiqc [DEBUG ] No samples found: verifybamid [2025-01-08 14:12:13,786] multiqc [DEBUG ] No samples found: mirtrace [2025-01-08 14:12:13,791] multiqc [DEBUG ] No samples found: happy [2025-01-08 14:12:13,796] multiqc [DEBUG ] No samples found: mirtop [2025-01-08 14:12:13,804] multiqc [DEBUG ] No samples found: homer [2025-01-08 14:12:13,809] multiqc [DEBUG ] No samples found: macs2 [2025-01-08 14:12:13,814] multiqc [DEBUG ] No samples found: theta2 [2025-01-08 14:12:13,819] multiqc [DEBUG ] No samples found: snpeff [2025-01-08 14:12:13,827] multiqc [DEBUG ] No samples found: gatk [2025-01-08 14:12:13,832] multiqc [DEBUG ] No samples found: htseq [2025-01-08 14:12:13,838] multiqc [DEBUG ] No samples found: bcftools [2025-01-08 14:12:13,843] multiqc [DEBUG ] No samples found: featureCounts [2025-01-08 14:12:13,850] multiqc [DEBUG ] No samples found: fgbio [2025-01-08 14:12:13,863] multiqc [DEBUG ] No samples found: dragen [2025-01-08 14:12:13,869] multiqc [DEBUG ] No samples found: dedup [2025-01-08 14:12:13,874] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-08 14:12:13,898] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-08 14:12:13,903] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-08 14:12:13,905] multiqc [DEBUG ] No samples found: picard [2025-01-08 14:12:13,910] multiqc [DEBUG ] No samples found: prokka [2025-01-08 14:12:13,915] multiqc [DEBUG ] No samples found: samblaster [2025-01-08 14:12:13,924] multiqc [DEBUG ] No samples found: samtools [2025-01-08 14:12:13,929] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-08 14:12:13,935] multiqc [DEBUG ] No samples found: bamtools [2025-01-08 14:12:13,940] multiqc [DEBUG ] No samples found: jellyfish [2025-01-08 14:12:13,948] multiqc [DEBUG ] No samples found: vcftools [2025-01-08 14:12:13,953] multiqc [DEBUG ] No samples found: longranger [2025-01-08 14:12:13,958] multiqc [DEBUG ] No samples found: stacks [2025-01-08 14:12:13,963] multiqc [DEBUG ] No samples found: varscan2 [2025-01-08 14:12:13,978] multiqc [DEBUG ] No samples found: bbmap [2025-01-08 14:12:13,984] multiqc [DEBUG ] No samples found: bismark [2025-01-08 14:12:13,989] multiqc [DEBUG ] No samples found: biscuit [2025-01-08 14:12:13,994] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-08 14:12:13,999] multiqc [DEBUG ] No samples found: hicup [2025-01-08 14:12:14,005] multiqc [DEBUG ] No samples found: hicpro [2025-01-08 14:12:14,009] multiqc [DEBUG ] No samples found: salmon [2025-01-08 14:12:14,014] multiqc [DEBUG ] No samples found: kallisto [2025-01-08 14:12:14,020] multiqc [DEBUG ] No samples found: slamdunk [2025-01-08 14:12:14,025] multiqc [DEBUG ] No samples found: star [2025-01-08 14:12:14,030] multiqc [DEBUG ] No samples found: hisat2 [2025-01-08 14:12:14,035] multiqc [DEBUG ] No samples found: tophat [2025-01-08 14:12:14,040] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-08 14:12:14,045] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-08 14:12:14,050] multiqc [DEBUG ] No samples found: snpsplit [2025-01-08 14:12:14,055] multiqc [DEBUG ] No samples found: kat [2025-01-08 14:12:14,060] multiqc [DEBUG ] No samples found: leehom [2025-01-08 14:12:14,065] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-08 14:12:14,070] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-08 14:12:14,076] multiqc [DEBUG ] No samples found: cutadapt [2025-01-08 14:12:14,080] multiqc [DEBUG ] No samples found: flexbar [2025-01-08 14:12:14,086] multiqc [DEBUG ] No samples found: kaiju [2025-01-08 14:12:14,091] multiqc [DEBUG ] No samples found: kraken [2025-01-08 14:12:14,097] multiqc [DEBUG ] No samples found: malt [2025-01-08 14:12:14,103] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-08 14:12:14,108] multiqc [DEBUG ] No samples found: sickle [2025-01-08 14:12:14,113] multiqc [DEBUG ] No samples found: skewer [2025-01-08 14:12:14,118] multiqc [DEBUG ] No samples found: sortmerna [2025-01-08 14:12:14,123] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-08 14:12:14,128] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-08 14:12:14,133] multiqc [DEBUG ] No samples found: afterqc [2025-01-08 14:12:14,138] multiqc [DEBUG ] No samples found: fastp [2025-01-08 14:12:14,321] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2025-01-08 14:12:14,390] multiqc [DEBUG ] No samples found: pycoqc [2025-01-08 14:12:14,395] multiqc [DEBUG ] No samples found: minionqc [2025-01-08 14:12:14,400] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-08 14:12:14,406] multiqc [DEBUG ] No samples found: clusterflow [2025-01-08 14:12:14,411] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-08 14:12:14,416] multiqc [DEBUG ] No samples found: interop [2025-01-08 14:12:14,421] multiqc [DEBUG ] No samples found: ivar [2025-01-08 14:12:14,426] multiqc [DEBUG ] No samples found: flash [2025-01-08 14:12:14,431] multiqc [DEBUG ] No samples found: seqyclean [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-08 14:12:14,432] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-08 14:12:14,441] multiqc [INFO ] Compressing plot data [2025-01-08 14:12:14,548] multiqc [INFO ] Report : multiqc_report.html [2025-01-08 14:12:14,548] multiqc [INFO ] Data : multiqc_data [2025-01-08 14:12:14,548] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55693662/tmps97u_c8s/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/0c/76f62dbf4600beba3f4ce29214e189/merged/multiqc_data' [2025-01-08 14:12:14,678] multiqc [INFO ] MultiQC complete