[2024-11-09 16:41:43,648] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-11-09 16:41:43,648] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-11-09 16:41:43,648] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-11-09 16:41:43,651] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-11-09 16:41:43,651] 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}} [2024-11-09 16:41:43,651] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-09 16:41:43,703] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-11-09 16:41:43,703] multiqc [INFO ] This is MultiQC v1.9 [2024-11-09 16:41:43,703] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-09 16:41:43,703] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/49/76bfa6be8679e8186cb87f5e9eb73e/1 [2024-11-09 16:41:43,703] multiqc [INFO ] Template : default [2024-11-09 16:41:43,703] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-11-09 16:41:43,703] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/49/76bfa6be8679e8186cb87f5e9eb73e/1 [2024-11-09 16:41:43,704] 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 [2024-11-09 16:41:43,704] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-53237834/tmpjj8cix_k [2024-11-09 16:41:43,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_117_fastqc.html [2024-11-09 16:41:43,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_117_fastqc.html [2024-11-09 16:41:43,863] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_504_fastqc.html [2024-11-09 16:41:43,865] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_504_fastqc.html [2024-11-09 16:41:43,922] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-09 16:41:43,924] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-09 16:41:43,924] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-09 16:41:43,924] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-09 16:41:43,924] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-09 16:41:43,924] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-09 16:41:43,924] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-11-09 16:41:44,577] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_undetermined_fastqc.html [2024-11-09 16:41:44,579] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_undetermined_fastqc.html [2024-11-09 16:41:44,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_504_fastqc.html [2024-11-09 16:41:44,630] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_504_fastqc.html [2024-11-09 16:41:44,688] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_418_fastqc.html [2024-11-09 16:41:44,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_418_fastqc.html [2024-11-09 16:41:44,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_418_fastqc.html [2024-11-09 16:41:44,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_418_fastqc.html [2024-11-09 16:41:44,786] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_203_fastqc.html [2024-11-09 16:41:44,788] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_203_fastqc.html [2024-11-09 16:41:44,833] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_203_fastqc.html [2024-11-09 16:41:44,835] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_203_fastqc.html [2024-11-09 16:41:44,882] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_undetermined_fastqc.html [2024-11-09 16:41:44,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_undetermined_fastqc.html [2024-11-09 16:41:44,932] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_807_fastqc.html [2024-11-09 16:41:44,934] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n01_807_fastqc.html [2024-11-09 16:41:44,979] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_117_fastqc.html [2024-11-09 16:41:44,981] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_117_fastqc.html [2024-11-09 16:41:45,026] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_807_fastqc.html [2024-11-09 16:41:45,028] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJ9RB_l01_n02_807_fastqc.html [2024-11-09 16:41:45,559] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-09 16:41:45,561] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-09 16:41:45,571] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2024-11-09 16:41:45,581] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-11-09 16:41:45,582] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-11-09 16:41:45,587] multiqc [DEBUG ] No samples found: conpair [2024-11-09 16:41:45,592] multiqc [DEBUG ] No samples found: peddy [2024-11-09 16:41:45,597] multiqc [DEBUG ] No samples found: somalier [2024-11-09 16:41:45,602] multiqc [DEBUG ] No samples found: methylQA [2024-11-09 16:41:45,611] multiqc [DEBUG ] No samples found: mosdepth [2024-11-09 16:41:45,615] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-11-09 16:41:45,619] multiqc [DEBUG ] No samples found: qualimap [2024-11-09 16:41:45,624] multiqc [DEBUG ] No samples found: preseq [2024-11-09 16:41:45,629] multiqc [DEBUG ] No samples found: quast [2024-11-09 16:41:45,634] multiqc [DEBUG ] No samples found: qorts [2024-11-09 16:41:45,639] multiqc [DEBUG ] No samples found: rna_seqc [2024-11-09 16:41:45,644] multiqc [DEBUG ] No samples found: rockhopper [2024-11-09 16:41:45,648] multiqc [DEBUG ] No samples found: rsem [2024-11-09 16:41:45,661] multiqc [DEBUG ] No samples found: rseqc [2024-11-09 16:41:45,665] multiqc [DEBUG ] No samples found: busco [2024-11-09 16:41:45,670] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-11-09 16:41:45,675] multiqc [DEBUG ] No samples found: disambiguate [2024-11-09 16:41:45,680] multiqc [DEBUG ] No samples found: supernova [2024-11-09 16:41:45,694] multiqc [DEBUG ] No samples found: deeptools [2024-11-09 16:41:45,700] multiqc [DEBUG ] No samples found: sargasso [2024-11-09 16:41:45,706] multiqc [DEBUG ] No samples found: verifybamid [2024-11-09 16:41:45,711] multiqc [DEBUG ] No samples found: mirtrace [2024-11-09 16:41:45,716] multiqc [DEBUG ] No samples found: happy [2024-11-09 16:41:45,722] multiqc [DEBUG ] No samples found: mirtop [2024-11-09 16:41:45,730] multiqc [DEBUG ] No samples found: homer [2024-11-09 16:41:45,735] multiqc [DEBUG ] No samples found: macs2 [2024-11-09 16:41:45,740] multiqc [DEBUG ] No samples found: theta2 [2024-11-09 16:41:45,745] multiqc [DEBUG ] No samples found: snpeff [2024-11-09 16:41:45,752] multiqc [DEBUG ] No samples found: gatk [2024-11-09 16:41:45,757] multiqc [DEBUG ] No samples found: htseq [2024-11-09 16:41:45,763] multiqc [DEBUG ] No samples found: bcftools [2024-11-09 16:41:45,768] multiqc [DEBUG ] No samples found: featureCounts [2024-11-09 16:41:45,775] multiqc [DEBUG ] No samples found: fgbio [2024-11-09 16:41:45,791] multiqc [DEBUG ] No samples found: dragen [2024-11-09 16:41:45,796] multiqc [DEBUG ] No samples found: dedup [2024-11-09 16:41:45,801] multiqc [DEBUG ] No samples found: damageprofiler [2024-11-09 16:41:45,826] multiqc [DEBUG ] No samples found: biobambam2 [2024-11-09 16:41:45,832] multiqc [DEBUG ] No samples found: mtnucratio [2024-11-09 16:41:45,834] multiqc [DEBUG ] No samples found: picard [2024-11-09 16:41:45,840] multiqc [DEBUG ] No samples found: prokka [2024-11-09 16:41:45,845] multiqc [DEBUG ] No samples found: samblaster [2024-11-09 16:41:45,855] multiqc [DEBUG ] No samples found: samtools [2024-11-09 16:41:45,860] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-11-09 16:41:45,865] multiqc [DEBUG ] No samples found: bamtools [2024-11-09 16:41:45,870] multiqc [DEBUG ] No samples found: jellyfish [2024-11-09 16:41:45,880] multiqc [DEBUG ] No samples found: vcftools [2024-11-09 16:41:45,886] multiqc [DEBUG ] No samples found: longranger [2024-11-09 16:41:45,891] multiqc [DEBUG ] No samples found: stacks [2024-11-09 16:41:45,896] multiqc [DEBUG ] No samples found: varscan2 [2024-11-09 16:41:45,911] multiqc [DEBUG ] No samples found: bbmap [2024-11-09 16:41:45,916] multiqc [DEBUG ] No samples found: bismark [2024-11-09 16:41:45,922] multiqc [DEBUG ] No samples found: biscuit [2024-11-09 16:41:45,927] multiqc [DEBUG ] No samples found: hicexplorer [2024-11-09 16:41:45,933] multiqc [DEBUG ] No samples found: hicup [2024-11-09 16:41:45,938] multiqc [DEBUG ] No samples found: hicpro [2024-11-09 16:41:45,943] multiqc [DEBUG ] No samples found: salmon [2024-11-09 16:41:45,948] multiqc [DEBUG ] No samples found: kallisto [2024-11-09 16:41:45,953] multiqc [DEBUG ] No samples found: slamdunk [2024-11-09 16:41:45,958] multiqc [DEBUG ] No samples found: star [2024-11-09 16:41:45,963] multiqc [DEBUG ] No samples found: hisat2 [2024-11-09 16:41:45,968] multiqc [DEBUG ] No samples found: tophat [2024-11-09 16:41:45,973] multiqc [DEBUG ] No samples found: bowtie2 [2024-11-09 16:41:45,977] multiqc [DEBUG ] No samples found: bowtie1 [2024-11-09 16:41:45,982] multiqc [DEBUG ] No samples found: snpsplit [2024-11-09 16:41:45,987] multiqc [DEBUG ] No samples found: kat [2024-11-09 16:41:45,991] multiqc [DEBUG ] No samples found: leehom [2024-11-09 16:41:45,996] multiqc [DEBUG ] No samples found: adapterRemoval [2024-11-09 16:41:46,000] multiqc [DEBUG ] No samples found: clipandmerge [2024-11-09 16:41:46,005] multiqc [DEBUG ] No samples found: cutadapt [2024-11-09 16:41:46,009] multiqc [DEBUG ] No samples found: flexbar [2024-11-09 16:41:46,014] multiqc [DEBUG ] No samples found: kaiju [2024-11-09 16:41:46,019] multiqc [DEBUG ] No samples found: kraken [2024-11-09 16:41:46,024] multiqc [DEBUG ] No samples found: malt [2024-11-09 16:41:46,028] multiqc [DEBUG ] No samples found: trimmomatic [2024-11-09 16:41:46,033] multiqc [DEBUG ] No samples found: sickle [2024-11-09 16:41:46,037] multiqc [DEBUG ] No samples found: skewer [2024-11-09 16:41:46,042] multiqc [DEBUG ] No samples found: sortmerna [2024-11-09 16:41:46,046] multiqc [DEBUG ] No samples found: biobloomtools [2024-11-09 16:41:46,051] multiqc [DEBUG ] No samples found: fastq_screen [2024-11-09 16:41:46,055] multiqc [DEBUG ] No samples found: afterqc [2024-11-09 16:41:46,060] multiqc [DEBUG ] No samples found: fastp [2024-11-09 16:41:46,143] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2024-11-09 16:41:46,257] multiqc [DEBUG ] No samples found: pycoqc [2024-11-09 16:41:46,261] multiqc [DEBUG ] No samples found: minionqc [2024-11-09 16:41:46,266] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-11-09 16:41:46,270] multiqc [DEBUG ] No samples found: clusterflow [2024-11-09 16:41:46,275] multiqc [DEBUG ] No samples found: bcl2fastq [2024-11-09 16:41:46,280] multiqc [DEBUG ] No samples found: interop [2024-11-09 16:41:46,285] multiqc [DEBUG ] No samples found: ivar [2024-11-09 16:41:46,290] multiqc [DEBUG ] No samples found: flash [2024-11-09 16:41:46,295] multiqc [DEBUG ] No samples found: seqyclean [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-11-09 16:41:46,295] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-11-09 16:41:46,296] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-11-09 16:41:46,311] multiqc [INFO ] Compressing plot data [2024-11-09 16:41:46,506] multiqc [INFO ] Report : multiqc_report.html [2024-11-09 16:41:46,506] multiqc [INFO ] Data : multiqc_data [2024-11-09 16:41:46,506] multiqc [DEBUG ] Moving data file from '/state/partition1/job-53237834/tmpjj8cix_k/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/49/76bfa6be8679e8186cb87f5e9eb73e/1/multiqc_data' [2024-11-09 16:41:46,643] multiqc [INFO ] MultiQC complete