[2024-08-13 17:24:08,622] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-13 17:24:08,623] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-13 17:24:08,623] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-13 17:24:08,625] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-13 17:24:08,625] 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}} [2024-08-13 17:24:08,626] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-13 17:24:08,676] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-13 17:24:08,677] multiqc [INFO ] This is MultiQC v1.9 [2024-08-13 17:24:08,677] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-13 17:24:08,677] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/e8/4a909775f900c013a1d7cc432b4a49/merged [2024-08-13 17:24:08,677] multiqc [INFO ] Template : default [2024-08-13 17:24:08,677] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-13 17:24:08,677] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/e8/4a909775f900c013a1d7cc432b4a49/merged [2024-08-13 17:24:08,677] 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 [2024-08-13 17:24:08,678] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49846725/tmpi1rgo0aw [2024-08-13 17:24:08,793] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-13 17:24:08,796] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-08-13 17:24:08,931] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW72_fastqc.html [2024-08-13 17:24:09,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW72_fastqc.html [2024-08-13 17:24:09,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5M5BGXV_n01_DO119_fastqc.html [2024-08-13 17:24:09,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5M5BGXV_n01_DO119_fastqc.html [2024-08-13 17:24:09,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5M5BGXV_n01_DO110_fastqc.html [2024-08-13 17:24:09,921] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5M5BGXV_n01_DO110_fastqc.html [2024-08-13 17:24:09,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW70_fastqc.html [2024-08-13 17:24:09,967] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW70_fastqc.html [2024-08-13 17:24:10,014] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW67_1_fastqc.html [2024-08-13 17:24:10,016] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW67_1_fastqc.html [2024-08-13 17:24:10,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW66_1_fastqc.html [2024-08-13 17:24:10,066] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV5M5BGXV_n01_HW66_1_fastqc.html [2024-08-13 17:24:10,416] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-13 17:24:10,418] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-13 17:24:10,437] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-08-13 17:24:10,439] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-13 17:24:10,449] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-08-13 17:24:10,454] multiqc [DEBUG ] No samples found: conpair [2024-08-13 17:24:10,460] multiqc [DEBUG ] No samples found: peddy [2024-08-13 17:24:10,466] multiqc [DEBUG ] No samples found: somalier [2024-08-13 17:24:10,472] multiqc [DEBUG ] No samples found: methylQA [2024-08-13 17:24:10,483] multiqc [DEBUG ] No samples found: mosdepth [2024-08-13 17:24:10,489] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-13 17:24:10,493] multiqc [DEBUG ] No samples found: qualimap [2024-08-13 17:24:10,499] multiqc [DEBUG ] No samples found: preseq [2024-08-13 17:24:10,505] multiqc [DEBUG ] No samples found: quast [2024-08-13 17:24:10,511] multiqc [DEBUG ] No samples found: qorts [2024-08-13 17:24:10,516] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-13 17:24:10,521] multiqc [DEBUG ] No samples found: rockhopper [2024-08-13 17:24:10,527] multiqc [DEBUG ] No samples found: rsem [2024-08-13 17:24:10,540] multiqc [DEBUG ] No samples found: rseqc [2024-08-13 17:24:10,545] multiqc [DEBUG ] No samples found: busco [2024-08-13 17:24:10,550] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-13 17:24:10,555] multiqc [DEBUG ] No samples found: disambiguate [2024-08-13 17:24:10,561] multiqc [DEBUG ] No samples found: supernova [2024-08-13 17:24:10,576] multiqc [DEBUG ] No samples found: deeptools [2024-08-13 17:24:10,582] multiqc [DEBUG ] No samples found: sargasso [2024-08-13 17:24:10,587] multiqc [DEBUG ] No samples found: verifybamid [2024-08-13 17:24:10,593] multiqc [DEBUG ] No samples found: mirtrace [2024-08-13 17:24:10,599] multiqc [DEBUG ] No samples found: happy [2024-08-13 17:24:10,604] multiqc [DEBUG ] No samples found: mirtop [2024-08-13 17:24:10,613] multiqc [DEBUG ] No samples found: homer [2024-08-13 17:24:10,618] multiqc [DEBUG ] No samples found: macs2 [2024-08-13 17:24:10,623] multiqc [DEBUG ] No samples found: theta2 [2024-08-13 17:24:10,629] multiqc [DEBUG ] No samples found: snpeff [2024-08-13 17:24:10,638] multiqc [DEBUG ] No samples found: gatk [2024-08-13 17:24:10,644] multiqc [DEBUG ] No samples found: htseq [2024-08-13 17:24:10,651] multiqc [DEBUG ] No samples found: bcftools [2024-08-13 17:24:10,656] multiqc [DEBUG ] No samples found: featureCounts [2024-08-13 17:24:10,663] multiqc [DEBUG ] No samples found: fgbio [2024-08-13 17:24:10,678] multiqc [DEBUG ] No samples found: dragen [2024-08-13 17:24:10,683] multiqc [DEBUG ] No samples found: dedup [2024-08-13 17:24:10,688] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-13 17:24:10,714] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-13 17:24:10,719] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-13 17:24:10,721] multiqc [DEBUG ] No samples found: picard [2024-08-13 17:24:10,727] multiqc [DEBUG ] No samples found: prokka [2024-08-13 17:24:10,732] multiqc [DEBUG ] No samples found: samblaster [2024-08-13 17:24:10,741] multiqc [DEBUG ] No samples found: samtools [2024-08-13 17:24:10,747] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-13 17:24:10,755] multiqc [DEBUG ] No samples found: bamtools [2024-08-13 17:24:10,760] multiqc [DEBUG ] No samples found: jellyfish [2024-08-13 17:24:10,768] multiqc [DEBUG ] No samples found: vcftools [2024-08-13 17:24:10,773] multiqc [DEBUG ] No samples found: longranger [2024-08-13 17:24:10,779] multiqc [DEBUG ] No samples found: stacks [2024-08-13 17:24:10,784] multiqc [DEBUG ] No samples found: varscan2 [2024-08-13 17:24:10,800] multiqc [DEBUG ] No samples found: bbmap [2024-08-13 17:24:10,805] multiqc [DEBUG ] No samples found: bismark [2024-08-13 17:24:10,811] multiqc [DEBUG ] No samples found: biscuit [2024-08-13 17:24:10,816] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-13 17:24:10,821] multiqc [DEBUG ] No samples found: hicup [2024-08-13 17:24:10,827] multiqc [DEBUG ] No samples found: hicpro [2024-08-13 17:24:10,831] multiqc [DEBUG ] No samples found: salmon [2024-08-13 17:24:10,836] multiqc [DEBUG ] No samples found: kallisto [2024-08-13 17:24:10,842] multiqc [DEBUG ] No samples found: slamdunk [2024-08-13 17:24:10,847] multiqc [DEBUG ] No samples found: star [2024-08-13 17:24:10,852] multiqc [DEBUG ] No samples found: hisat2 [2024-08-13 17:24:10,857] multiqc [DEBUG ] No samples found: tophat [2024-08-13 17:24:10,862] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-13 17:24:10,867] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-13 17:24:10,872] multiqc [DEBUG ] No samples found: snpsplit [2024-08-13 17:24:10,877] multiqc [DEBUG ] No samples found: kat [2024-08-13 17:24:10,882] multiqc [DEBUG ] No samples found: leehom [2024-08-13 17:24:10,887] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-13 17:24:10,892] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-13 17:24:10,897] multiqc [DEBUG ] No samples found: cutadapt [2024-08-13 17:24:10,902] multiqc [DEBUG ] No samples found: flexbar [2024-08-13 17:24:10,907] multiqc [DEBUG ] No samples found: kaiju [2024-08-13 17:24:10,911] multiqc [DEBUG ] No samples found: kraken [2024-08-13 17:24:10,916] multiqc [DEBUG ] No samples found: malt [2024-08-13 17:24:10,922] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-13 17:24:10,927] multiqc [DEBUG ] No samples found: sickle [2024-08-13 17:24:10,931] multiqc [DEBUG ] No samples found: skewer [2024-08-13 17:24:10,936] multiqc [DEBUG ] No samples found: sortmerna [2024-08-13 17:24:10,941] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-13 17:24:10,946] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-13 17:24:10,951] multiqc [DEBUG ] No samples found: afterqc [2024-08-13 17:24:10,956] multiqc [DEBUG ] No samples found: fastp [2024-08-13 17:24:12,685] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2024-08-13 17:24:13,225] multiqc [DEBUG ] No samples found: pycoqc [2024-08-13 17:24:13,230] multiqc [DEBUG ] No samples found: minionqc [2024-08-13 17:24:13,235] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-13 17:24:13,241] multiqc [DEBUG ] No samples found: clusterflow [2024-08-13 17:24:13,246] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-13 17:24:13,252] multiqc [DEBUG ] No samples found: interop [2024-08-13 17:24:13,257] multiqc [DEBUG ] No samples found: ivar [2024-08-13 17:24:13,262] multiqc [DEBUG ] No samples found: flash [2024-08-13 17:24:13,267] multiqc [DEBUG ] No samples found: seqyclean [2024-08-13 17:24:13,267] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-13 17:24:13,268] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-13 17:24:13,300] multiqc [INFO ] Compressing plot data [2024-08-13 17:24:13,769] multiqc [INFO ] Report : multiqc_report.html [2024-08-13 17:24:13,770] multiqc [INFO ] Data : multiqc_data [2024-08-13 17:24:13,770] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49846725/tmpi1rgo0aw/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/e8/4a909775f900c013a1d7cc432b4a49/merged/multiqc_data' [2024-08-13 17:24:13,896] multiqc [INFO ] MultiQC complete