[2024-09-21 01:11:44,089] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-09-21 01:11:44,089] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-09-21 01:11:44,089] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-09-21 01:11:44,092] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-09-21 01:11:44,092] 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}} [2024-09-21 01:11:44,092] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-09-21 01:11:44,140] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-09-21 01:11:44,140] multiqc [INFO ] This is MultiQC v1.9 [2024-09-21 01:11:44,140] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-09-21 01:11:44,140] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/60/d4cb1cb40de43bd2ce3c73ff8454fe/merged [2024-09-21 01:11:44,140] multiqc [INFO ] Template : default [2024-09-21 01:11:44,140] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-09-21 01:11:44,140] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/60/d4cb1cb40de43bd2ce3c73ff8454fe/merged [2024-09-21 01:11:44,141] 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 [2024-09-21 01:11:44,141] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-51224642/tmpper3q1hb [2024-09-21 01:11:44,261] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7LJDRX5_4_fastqc.html [2024-09-21 01:11:44,264] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7LJDRX5_4_fastqc.html [2024-09-21 01:11:44,317] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7LJDRX5_3_fastqc.html [2024-09-21 01:11:44,320] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7LJDRX5_3_fastqc.html [2024-09-21 01:11:44,393] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7LJDRX5_1_fastqc.html [2024-09-21 01:11:44,395] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7LJDRX5_1_fastqc.html [2024-09-21 01:11:44,443] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7LJDRX5_2_fastqc.html [2024-09-21 01:11:44,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7LJDRX5_2_fastqc.html [2024-09-21 01:11:45,038] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-09-21 01:11:45,040] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-09-21 01:11:45,046] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-09-21 01:11:45,053] multiqc [DEBUG ] No samples found: conpair [2024-09-21 01:11:45,059] multiqc [DEBUG ] No samples found: peddy [2024-09-21 01:11:45,064] multiqc [DEBUG ] No samples found: somalier [2024-09-21 01:11:45,071] multiqc [DEBUG ] No samples found: methylQA [2024-09-21 01:11:45,082] multiqc [DEBUG ] No samples found: mosdepth [2024-09-21 01:11:45,088] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-09-21 01:11:45,092] multiqc [DEBUG ] No samples found: qualimap [2024-09-21 01:11:45,098] multiqc [DEBUG ] No samples found: preseq [2024-09-21 01:11:45,105] multiqc [DEBUG ] No samples found: quast [2024-09-21 01:11:45,111] multiqc [DEBUG ] No samples found: qorts [2024-09-21 01:11:45,116] multiqc [DEBUG ] No samples found: rna_seqc [2024-09-21 01:11:45,126] multiqc [DEBUG ] No samples found: rockhopper [2024-09-21 01:11:45,133] multiqc [DEBUG ] No samples found: rsem [2024-09-21 01:11:45,151] multiqc [DEBUG ] No samples found: rseqc [2024-09-21 01:11:45,157] multiqc [DEBUG ] No samples found: busco [2024-09-21 01:11:45,164] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-09-21 01:11:45,170] multiqc [DEBUG ] No samples found: disambiguate [2024-09-21 01:11:45,176] multiqc [DEBUG ] No samples found: supernova [2024-09-21 01:11:45,195] multiqc [DEBUG ] No samples found: deeptools [2024-09-21 01:11:45,201] multiqc [DEBUG ] No samples found: sargasso [2024-09-21 01:11:45,207] multiqc [DEBUG ] No samples found: verifybamid [2024-09-21 01:11:45,214] multiqc [DEBUG ] No samples found: mirtrace [2024-09-21 01:11:45,222] multiqc [DEBUG ] No samples found: happy [2024-09-21 01:11:45,228] multiqc [DEBUG ] No samples found: mirtop [2024-09-21 01:11:45,236] multiqc [DEBUG ] No samples found: homer [2024-09-21 01:11:45,242] multiqc [DEBUG ] No samples found: macs2 [2024-09-21 01:11:45,246] multiqc [DEBUG ] No samples found: theta2 [2024-09-21 01:11:45,252] multiqc [DEBUG ] No samples found: snpeff [2024-09-21 01:11:45,261] multiqc [DEBUG ] No samples found: gatk [2024-09-21 01:11:45,267] multiqc [DEBUG ] No samples found: htseq [2024-09-21 01:11:45,274] multiqc [DEBUG ] No samples found: bcftools [2024-09-21 01:11:45,280] multiqc [DEBUG ] No samples found: featureCounts [2024-09-21 01:11:45,289] multiqc [DEBUG ] No samples found: fgbio [2024-09-21 01:11:45,306] multiqc [DEBUG ] No samples found: dragen [2024-09-21 01:11:45,312] multiqc [DEBUG ] No samples found: dedup [2024-09-21 01:11:45,320] multiqc [DEBUG ] No samples found: damageprofiler [2024-09-21 01:11:45,348] multiqc [DEBUG ] No samples found: biobambam2 [2024-09-21 01:11:45,355] multiqc [DEBUG ] No samples found: mtnucratio [2024-09-21 01:11:45,357] multiqc [DEBUG ] No samples found: picard [2024-09-21 01:11:45,363] multiqc [DEBUG ] No samples found: prokka [2024-09-21 01:11:45,368] multiqc [DEBUG ] No samples found: samblaster [2024-09-21 01:11:45,380] multiqc [DEBUG ] No samples found: samtools [2024-09-21 01:11:45,385] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-09-21 01:11:45,393] multiqc [DEBUG ] No samples found: bamtools [2024-09-21 01:11:45,399] multiqc [DEBUG ] No samples found: jellyfish [2024-09-21 01:11:45,410] multiqc [DEBUG ] No samples found: vcftools [2024-09-21 01:11:45,416] multiqc [DEBUG ] No samples found: longranger [2024-09-21 01:11:45,422] multiqc [DEBUG ] No samples found: stacks [2024-09-21 01:11:45,427] multiqc [DEBUG ] No samples found: varscan2 [2024-09-21 01:11:45,445] multiqc [DEBUG ] No samples found: bbmap [2024-09-21 01:11:45,452] multiqc [DEBUG ] No samples found: bismark [2024-09-21 01:11:45,458] multiqc [DEBUG ] No samples found: biscuit [2024-09-21 01:11:45,464] multiqc [DEBUG ] No samples found: hicexplorer [2024-09-21 01:11:45,471] multiqc [DEBUG ] No samples found: hicup [2024-09-21 01:11:45,478] multiqc [DEBUG ] No samples found: hicpro [2024-09-21 01:11:45,483] multiqc [DEBUG ] No samples found: salmon [2024-09-21 01:11:45,490] multiqc [DEBUG ] No samples found: kallisto [2024-09-21 01:11:45,495] multiqc [DEBUG ] No samples found: slamdunk [2024-09-21 01:11:45,501] multiqc [DEBUG ] No samples found: star [2024-09-21 01:11:45,506] multiqc [DEBUG ] No samples found: hisat2 [2024-09-21 01:11:45,512] multiqc [DEBUG ] No samples found: tophat [2024-09-21 01:11:45,518] multiqc [DEBUG ] No samples found: bowtie2 [2024-09-21 01:11:45,524] multiqc [DEBUG ] No samples found: bowtie1 [2024-09-21 01:11:45,530] multiqc [DEBUG ] No samples found: snpsplit [2024-09-21 01:11:45,536] multiqc [DEBUG ] No samples found: kat [2024-09-21 01:11:45,542] multiqc [DEBUG ] No samples found: leehom [2024-09-21 01:11:45,548] multiqc [DEBUG ] No samples found: adapterRemoval [2024-09-21 01:11:45,554] multiqc [DEBUG ] No samples found: clipandmerge [2024-09-21 01:11:45,561] multiqc [DEBUG ] No samples found: cutadapt [2024-09-21 01:11:45,566] multiqc [DEBUG ] No samples found: flexbar [2024-09-21 01:11:45,572] multiqc [DEBUG ] No samples found: kaiju [2024-09-21 01:11:45,579] multiqc [DEBUG ] No samples found: kraken [2024-09-21 01:11:45,584] multiqc [DEBUG ] No samples found: malt [2024-09-21 01:11:45,590] multiqc [DEBUG ] No samples found: trimmomatic [2024-09-21 01:11:45,596] multiqc [DEBUG ] No samples found: sickle [2024-09-21 01:11:45,601] multiqc [DEBUG ] No samples found: skewer [2024-09-21 01:11:45,607] multiqc [DEBUG ] No samples found: sortmerna [2024-09-21 01:11:45,611] multiqc [DEBUG ] No samples found: biobloomtools [2024-09-21 01:11:45,617] multiqc [DEBUG ] No samples found: fastq_screen [2024-09-21 01:11:45,623] multiqc [DEBUG ] No samples found: afterqc [2024-09-21 01:11:45,629] multiqc [DEBUG ] No samples found: fastp [2024-09-21 01:11:45,818] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-09-21 01:11:45,876] multiqc [DEBUG ] No samples found: pycoqc [2024-09-21 01:11:45,881] multiqc [DEBUG ] No samples found: minionqc [2024-09-21 01:11:45,886] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-09-21 01:11:45,892] multiqc [DEBUG ] No samples found: clusterflow [2024-09-21 01:11:45,898] multiqc [DEBUG ] No samples found: bcl2fastq [2024-09-21 01:11:45,905] multiqc [DEBUG ] No samples found: interop [2024-09-21 01:11:45,911] multiqc [DEBUG ] No samples found: ivar [2024-09-21 01:11:45,916] multiqc [DEBUG ] No samples found: flash [2024-09-21 01:11:45,922] multiqc [DEBUG ] No samples found: seqyclean [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-09-21 01:11:45,922] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-09-21 01:11:45,928] multiqc [INFO ] Compressing plot data [2024-09-21 01:11:46,015] multiqc [INFO ] Report : multiqc_report.html [2024-09-21 01:11:46,016] multiqc [INFO ] Data : multiqc_data [2024-09-21 01:11:46,016] multiqc [DEBUG ] Moving data file from '/state/partition1/job-51224642/tmpper3q1hb/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/60/d4cb1cb40de43bd2ce3c73ff8454fe/merged/multiqc_data' [2024-09-21 01:11:46,160] multiqc [INFO ] MultiQC complete