[2025-01-11 04:10:15,319] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-11 04:10:15,319] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-11 04:10:15,319] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-11 04:10:15,322] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-11 04:10:15,322] 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}} [2025-01-11 04:10:15,322] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-11 04:10:15,578] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-11 04:10:15,578] multiqc [INFO ] This is MultiQC v1.9 [2025-01-11 04:10:15,578] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-11 04:10:15,578] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/56/f7d8d4b99f1cacb2aa774c65b86222/merged [2025-01-11 04:10:15,578] multiqc [INFO ] Template : default [2025-01-11 04:10:15,578] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-11 04:10:15,578] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/56/f7d8d4b99f1cacb2aa774c65b86222/merged [2025-01-11 04:10:15,578] 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 [2025-01-11 04:10:15,579] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55755040/tmpo5bttav_ [2025-01-11 04:10:15,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_RNP_NT_fastqc.html [2025-01-11 04:10:15,712] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_RNP_NT_fastqc.html [2025-01-11 04:10:15,764] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_ST_fastqc.html [2025-01-11 04:10:15,766] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_ST_fastqc.html [2025-01-11 04:10:15,766] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_ST_fastqc.html [2025-01-11 04:10:15,766] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_ST_fastqc.html [2025-01-11 04:10:15,766] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_ST_fastqc.html [2025-01-11 04:10:15,767] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_ST_fastqc.html [2025-01-11 04:10:15,767] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_ST_fastqc.html [2025-01-11 04:10:15,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-11 04:10:15,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-11 04:10:15,996] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_RNP_GT1_fastqc.html [2025-01-11 04:10:15,998] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_RNP_GT1_fastqc.html [2025-01-11 04:10:16,053] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n01_undetermined_fastqc.html [2025-01-11 04:10:16,055] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n01_undetermined_fastqc.html [2025-01-11 04:10:16,101] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_MULTI_fastqc.html [2025-01-11 04:10:16,103] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_MULTI_fastqc.html [2025-01-11 04:10:16,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_MULTI_fastqc.html [2025-01-11 04:10:16,153] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_MULTI_fastqc.html [2025-01-11 04:10:16,208] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_RNP_NT_fastqc.html [2025-01-11 04:10:16,210] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_RNP_NT_fastqc.html [2025-01-11 04:10:16,263] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n02_undetermined_fastqc.html [2025-01-11 04:10:16,265] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n02_undetermined_fastqc.html [2025-01-11 04:10:16,312] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_ST_fastqc.html [2025-01-11 04:10:16,314] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n01_GT1_ST_fastqc.html [2025-01-11 04:10:16,378] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_RNP_GT1_fastqc.html [2025-01-11 04:10:16,380] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJW2KDRX5_n02_GT1_RNP_GT1_fastqc.html [2025-01-11 04:10:16,945] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-11 04:10:16,948] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-11 04:10:16,956] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-11 04:10:16,967] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-11 04:10:16,970] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2025-01-11 04:10:16,976] multiqc [DEBUG ] No samples found: conpair [2025-01-11 04:10:16,983] multiqc [DEBUG ] No samples found: peddy [2025-01-11 04:10:16,990] multiqc [DEBUG ] No samples found: somalier [2025-01-11 04:10:16,997] multiqc [DEBUG ] No samples found: methylQA [2025-01-11 04:10:17,008] multiqc [DEBUG ] No samples found: mosdepth [2025-01-11 04:10:17,023] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-11 04:10:17,027] multiqc [DEBUG ] No samples found: qualimap [2025-01-11 04:10:17,034] multiqc [DEBUG ] No samples found: preseq [2025-01-11 04:10:17,041] multiqc [DEBUG ] No samples found: quast [2025-01-11 04:10:17,048] multiqc [DEBUG ] No samples found: qorts [2025-01-11 04:10:17,055] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-11 04:10:17,061] multiqc [DEBUG ] No samples found: rockhopper [2025-01-11 04:10:17,068] multiqc [DEBUG ] No samples found: rsem [2025-01-11 04:10:17,086] multiqc [DEBUG ] No samples found: rseqc [2025-01-11 04:10:17,092] multiqc [DEBUG ] No samples found: busco [2025-01-11 04:10:17,099] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-11 04:10:17,104] multiqc [DEBUG ] No samples found: disambiguate [2025-01-11 04:10:17,111] multiqc [DEBUG ] No samples found: supernova [2025-01-11 04:10:17,132] multiqc [DEBUG ] No samples found: deeptools [2025-01-11 04:10:17,139] multiqc [DEBUG ] No samples found: sargasso [2025-01-11 04:10:17,146] multiqc [DEBUG ] No samples found: verifybamid [2025-01-11 04:10:17,152] multiqc [DEBUG ] No samples found: mirtrace [2025-01-11 04:10:17,159] multiqc [DEBUG ] No samples found: happy [2025-01-11 04:10:17,165] multiqc [DEBUG ] No samples found: mirtop [2025-01-11 04:10:17,174] multiqc [DEBUG ] No samples found: homer [2025-01-11 04:10:17,180] multiqc [DEBUG ] No samples found: macs2 [2025-01-11 04:10:17,187] multiqc [DEBUG ] No samples found: theta2 [2025-01-11 04:10:17,193] multiqc [DEBUG ] No samples found: snpeff [2025-01-11 04:10:17,203] multiqc [DEBUG ] No samples found: gatk [2025-01-11 04:10:17,209] multiqc [DEBUG ] No samples found: htseq [2025-01-11 04:10:17,216] multiqc [DEBUG ] No samples found: bcftools [2025-01-11 04:10:17,223] multiqc [DEBUG ] No samples found: featureCounts [2025-01-11 04:10:17,231] multiqc [DEBUG ] No samples found: fgbio [2025-01-11 04:10:17,249] multiqc [DEBUG ] No samples found: dragen [2025-01-11 04:10:17,256] multiqc [DEBUG ] No samples found: dedup [2025-01-11 04:10:17,262] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-11 04:10:17,291] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-11 04:10:17,298] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-11 04:10:17,300] multiqc [DEBUG ] No samples found: picard [2025-01-11 04:10:17,307] multiqc [DEBUG ] No samples found: prokka [2025-01-11 04:10:17,313] multiqc [DEBUG ] No samples found: samblaster [2025-01-11 04:10:17,326] multiqc [DEBUG ] No samples found: samtools [2025-01-11 04:10:17,332] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-11 04:10:17,340] multiqc [DEBUG ] No samples found: bamtools [2025-01-11 04:10:17,347] multiqc [DEBUG ] No samples found: jellyfish [2025-01-11 04:10:17,359] multiqc [DEBUG ] No samples found: vcftools [2025-01-11 04:10:17,365] multiqc [DEBUG ] No samples found: longranger [2025-01-11 04:10:17,372] multiqc [DEBUG ] No samples found: stacks [2025-01-11 04:10:17,379] multiqc [DEBUG ] No samples found: varscan2 [2025-01-11 04:10:17,404] multiqc [DEBUG ] No samples found: bbmap [2025-01-11 04:10:17,411] multiqc [DEBUG ] No samples found: bismark [2025-01-11 04:10:17,418] multiqc [DEBUG ] No samples found: biscuit [2025-01-11 04:10:17,425] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-11 04:10:17,432] multiqc [DEBUG ] No samples found: hicup [2025-01-11 04:10:17,441] multiqc [DEBUG ] No samples found: hicpro [2025-01-11 04:10:17,446] multiqc [DEBUG ] No samples found: salmon [2025-01-11 04:10:17,453] multiqc [DEBUG ] No samples found: kallisto [2025-01-11 04:10:17,460] multiqc [DEBUG ] No samples found: slamdunk [2025-01-11 04:10:17,466] multiqc [DEBUG ] No samples found: star [2025-01-11 04:10:17,473] multiqc [DEBUG ] No samples found: hisat2 [2025-01-11 04:10:17,479] multiqc [DEBUG ] No samples found: tophat [2025-01-11 04:10:17,486] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-11 04:10:17,491] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-11 04:10:17,497] multiqc [DEBUG ] No samples found: snpsplit [2025-01-11 04:10:17,503] multiqc [DEBUG ] No samples found: kat [2025-01-11 04:10:17,509] multiqc [DEBUG ] No samples found: leehom [2025-01-11 04:10:17,516] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-11 04:10:17,522] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-11 04:10:17,528] multiqc [DEBUG ] No samples found: cutadapt [2025-01-11 04:10:17,534] multiqc [DEBUG ] No samples found: flexbar [2025-01-11 04:10:17,539] multiqc [DEBUG ] No samples found: kaiju [2025-01-11 04:10:17,546] multiqc [DEBUG ] No samples found: kraken [2025-01-11 04:10:17,553] multiqc [DEBUG ] No samples found: malt [2025-01-11 04:10:17,559] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-11 04:10:17,565] multiqc [DEBUG ] No samples found: sickle [2025-01-11 04:10:17,571] multiqc [DEBUG ] No samples found: skewer [2025-01-11 04:10:17,577] multiqc [DEBUG ] No samples found: sortmerna [2025-01-11 04:10:17,584] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-11 04:10:17,591] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-11 04:10:17,598] multiqc [DEBUG ] No samples found: afterqc [2025-01-11 04:10:17,605] multiqc [DEBUG ] No samples found: fastp [2025-01-11 04:10:17,941] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2025-01-11 04:10:18,135] multiqc [DEBUG ] No samples found: pycoqc [2025-01-11 04:10:18,141] multiqc [DEBUG ] No samples found: minionqc [2025-01-11 04:10:18,148] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-11 04:10:18,155] multiqc [DEBUG ] No samples found: clusterflow [2025-01-11 04:10:18,162] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-11 04:10:18,168] multiqc [DEBUG ] No samples found: interop [2025-01-11 04:10:18,174] multiqc [DEBUG ] No samples found: ivar [2025-01-11 04:10:18,180] multiqc [DEBUG ] No samples found: flash [2025-01-11 04:10:18,186] multiqc [DEBUG ] No samples found: seqyclean [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-11 04:10:18,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-11 04:10:18,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-11 04:10:18,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-11 04:10:18,187] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-11 04:10:18,187] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-11 04:10:18,187] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-11 04:10:18,199] multiqc [INFO ] Compressing plot data [2025-01-11 04:10:18,427] multiqc [INFO ] Report : multiqc_report.html [2025-01-11 04:10:18,427] multiqc [INFO ] Data : multiqc_data [2025-01-11 04:10:18,427] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55755040/tmpo5bttav_/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/56/f7d8d4b99f1cacb2aa774c65b86222/merged/multiqc_data' [2025-01-11 04:10:18,586] multiqc [INFO ] MultiQC complete