[2024-08-30 14:37:44,824] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-30 14:37:44,824] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-30 14:37:44,824] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-30 14:37:44,826] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-30 14:37:44,826] 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}} [2024-08-30 14:37:44,827] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-30 14:37:44,850] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-30 14:37:44,850] multiqc [INFO ] This is MultiQC v1.9 [2024-08-30 14:37:44,850] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-30 14:37:44,850] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/99/be746d8f26f5e45ad7eec75a03275e/merged [2024-08-30 14:37:44,850] multiqc [INFO ] Template : default [2024-08-30 14:37:44,850] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-30 14:37:44,850] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/99/be746d8f26f5e45ad7eec75a03275e/merged [2024-08-30 14:37:44,850] 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 [2024-08-30 14:37:44,851] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-50489689/tmpms4skaof [2024-08-30 14:37:44,962] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n01_16fluc_dialout_fastqc.html [2024-08-30 14:37:44,965] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n01_16fluc_dialout_fastqc.html [2024-08-30 14:37:45,016] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:45,018] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-30 14:37:48,581] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n01_16fluc_10X_fastqc.html [2024-08-30 14:37:48,583] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n01_16fluc_10X_fastqc.html [2024-08-30 14:37:48,629] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n02_16fluc_10X_fastqc.html [2024-08-30 14:37:48,631] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n02_16fluc_10X_fastqc.html [2024-08-30 14:37:48,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n01_scgal_dialout_fastqc.html [2024-08-30 14:37:48,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n01_scgal_dialout_fastqc.html [2024-08-30 14:37:48,726] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n01_scgal_10X_fastqc.html [2024-08-30 14:37:48,728] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n01_scgal_10X_fastqc.html [2024-08-30 14:37:48,772] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n01_undetermined_fastqc.html [2024-08-30 14:37:48,774] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n01_undetermined_fastqc.html [2024-08-30 14:37:48,834] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n02_undetermined_fastqc.html [2024-08-30 14:37:48,836] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n02_undetermined_fastqc.html [2024-08-30 14:37:48,882] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n02_scgal_10X_fastqc.html [2024-08-30 14:37:48,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n02_scgal_10X_fastqc.html [2024-08-30 14:37:48,971] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n02_scgal_dialout_fastqc.html [2024-08-30 14:37:48,973] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n02_scgal_dialout_fastqc.html [2024-08-30 14:37:49,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH7YWDRX5_n02_16fluc_dialout_fastqc.html [2024-08-30 14:37:49,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH7YWDRX5_n02_16fluc_dialout_fastqc.html [2024-08-30 14:37:49,616] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-30 14:37:49,618] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-30 14:37:49,634] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-30 14:37:49,637] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2024-08-30 14:37:49,639] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-30 14:37:49,644] multiqc [DEBUG ] No samples found: conpair [2024-08-30 14:37:49,649] multiqc [DEBUG ] No samples found: peddy [2024-08-30 14:37:49,654] multiqc [DEBUG ] No samples found: somalier [2024-08-30 14:37:49,660] multiqc [DEBUG ] No samples found: methylQA [2024-08-30 14:37:49,668] multiqc [DEBUG ] No samples found: mosdepth [2024-08-30 14:37:49,673] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-30 14:37:49,677] multiqc [DEBUG ] No samples found: qualimap [2024-08-30 14:37:49,682] multiqc [DEBUG ] No samples found: preseq [2024-08-30 14:37:49,687] multiqc [DEBUG ] No samples found: quast [2024-08-30 14:37:49,692] multiqc [DEBUG ] No samples found: qorts [2024-08-30 14:37:49,697] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-30 14:37:49,702] multiqc [DEBUG ] No samples found: rockhopper [2024-08-30 14:37:49,707] multiqc [DEBUG ] No samples found: rsem [2024-08-30 14:37:49,719] multiqc [DEBUG ] No samples found: rseqc [2024-08-30 14:37:49,723] multiqc [DEBUG ] No samples found: busco [2024-08-30 14:37:49,728] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-30 14:37:49,733] multiqc [DEBUG ] No samples found: disambiguate [2024-08-30 14:37:49,738] multiqc [DEBUG ] No samples found: supernova [2024-08-30 14:37:49,751] multiqc [DEBUG ] No samples found: deeptools [2024-08-30 14:37:49,756] multiqc [DEBUG ] No samples found: sargasso [2024-08-30 14:37:49,761] multiqc [DEBUG ] No samples found: verifybamid [2024-08-30 14:37:49,766] multiqc [DEBUG ] No samples found: mirtrace [2024-08-30 14:37:49,771] multiqc [DEBUG ] No samples found: happy [2024-08-30 14:37:49,775] multiqc [DEBUG ] No samples found: mirtop [2024-08-30 14:37:49,782] multiqc [DEBUG ] No samples found: homer [2024-08-30 14:37:49,787] multiqc [DEBUG ] No samples found: macs2 [2024-08-30 14:37:49,791] multiqc [DEBUG ] No samples found: theta2 [2024-08-30 14:37:49,796] multiqc [DEBUG ] No samples found: snpeff [2024-08-30 14:37:49,803] multiqc [DEBUG ] No samples found: gatk [2024-08-30 14:37:49,807] multiqc [DEBUG ] No samples found: htseq [2024-08-30 14:37:49,813] multiqc [DEBUG ] No samples found: bcftools [2024-08-30 14:37:49,818] multiqc [DEBUG ] No samples found: featureCounts [2024-08-30 14:37:49,824] multiqc [DEBUG ] No samples found: fgbio [2024-08-30 14:37:49,837] multiqc [DEBUG ] No samples found: dragen [2024-08-30 14:37:49,842] multiqc [DEBUG ] No samples found: dedup [2024-08-30 14:37:49,847] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-30 14:37:49,869] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-30 14:37:49,874] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-30 14:37:49,876] multiqc [DEBUG ] No samples found: picard [2024-08-30 14:37:49,881] multiqc [DEBUG ] No samples found: prokka [2024-08-30 14:37:49,885] multiqc [DEBUG ] No samples found: samblaster [2024-08-30 14:37:49,893] multiqc [DEBUG ] No samples found: samtools [2024-08-30 14:37:49,898] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-30 14:37:49,903] multiqc [DEBUG ] No samples found: bamtools [2024-08-30 14:37:49,907] multiqc [DEBUG ] No samples found: jellyfish [2024-08-30 14:37:49,914] multiqc [DEBUG ] No samples found: vcftools [2024-08-30 14:37:49,919] multiqc [DEBUG ] No samples found: longranger [2024-08-30 14:37:49,923] multiqc [DEBUG ] No samples found: stacks [2024-08-30 14:37:49,928] multiqc [DEBUG ] No samples found: varscan2 [2024-08-30 14:37:49,941] multiqc [DEBUG ] No samples found: bbmap [2024-08-30 14:37:49,946] multiqc [DEBUG ] No samples found: bismark [2024-08-30 14:37:49,951] multiqc [DEBUG ] No samples found: biscuit [2024-08-30 14:37:49,955] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-30 14:37:49,960] multiqc [DEBUG ] No samples found: hicup [2024-08-30 14:37:49,965] multiqc [DEBUG ] No samples found: hicpro [2024-08-30 14:37:49,969] multiqc [DEBUG ] No samples found: salmon [2024-08-30 14:37:49,974] multiqc [DEBUG ] No samples found: kallisto [2024-08-30 14:37:49,978] multiqc [DEBUG ] No samples found: slamdunk [2024-08-30 14:37:49,983] multiqc [DEBUG ] No samples found: star [2024-08-30 14:37:49,988] multiqc [DEBUG ] No samples found: hisat2 [2024-08-30 14:37:49,993] multiqc [DEBUG ] No samples found: tophat [2024-08-30 14:37:49,997] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-30 14:37:50,002] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-30 14:37:50,007] multiqc [DEBUG ] No samples found: snpsplit [2024-08-30 14:37:50,011] multiqc [DEBUG ] No samples found: kat [2024-08-30 14:37:50,016] multiqc [DEBUG ] No samples found: leehom [2024-08-30 14:37:50,021] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-30 14:37:50,025] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-30 14:37:50,030] multiqc [DEBUG ] No samples found: cutadapt [2024-08-30 14:37:50,034] multiqc [DEBUG ] No samples found: flexbar [2024-08-30 14:37:50,039] multiqc [DEBUG ] No samples found: kaiju [2024-08-30 14:37:50,043] multiqc [DEBUG ] No samples found: kraken [2024-08-30 14:37:50,048] multiqc [DEBUG ] No samples found: malt [2024-08-30 14:37:50,053] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-30 14:37:50,058] multiqc [DEBUG ] No samples found: sickle [2024-08-30 14:37:50,062] multiqc [DEBUG ] No samples found: skewer [2024-08-30 14:37:50,067] multiqc [DEBUG ] No samples found: sortmerna [2024-08-30 14:37:50,071] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-30 14:37:50,076] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-30 14:37:50,081] multiqc [DEBUG ] No samples found: afterqc [2024-08-30 14:37:50,086] multiqc [DEBUG ] No samples found: fastp [2024-08-30 14:37:50,327] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2024-08-30 14:37:50,418] multiqc [DEBUG ] No samples found: pycoqc [2024-08-30 14:37:50,424] multiqc [DEBUG ] No samples found: minionqc [2024-08-30 14:37:50,429] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-30 14:37:50,434] multiqc [DEBUG ] No samples found: clusterflow [2024-08-30 14:37:50,439] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-30 14:37:50,444] multiqc [DEBUG ] No samples found: interop [2024-08-30 14:37:50,448] multiqc [DEBUG ] No samples found: ivar [2024-08-30 14:37:50,453] multiqc [DEBUG ] No samples found: flash [2024-08-30 14:37:50,458] multiqc [DEBUG ] No samples found: seqyclean [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 14:37:50,458] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-30 14:37:50,459] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-30 14:37:50,472] multiqc [INFO ] Compressing plot data [2024-08-30 14:37:50,633] multiqc [INFO ] Report : multiqc_report.html [2024-08-30 14:37:50,633] multiqc [INFO ] Data : multiqc_data [2024-08-30 14:37:50,633] multiqc [DEBUG ] Moving data file from '/state/partition1/job-50489689/tmpms4skaof/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/99/be746d8f26f5e45ad7eec75a03275e/merged/multiqc_data' [2024-08-30 14:37:50,790] multiqc [INFO ] MultiQC complete