[2024-09-23 14:55:04,879] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-09-23 14:55:04,879] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-09-23 14:55:04,879] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-09-23 14:55:04,881] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-09-23 14:55:04,882] 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}} [2024-09-23 14:55:04,882] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-09-23 14:55:04,937] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-09-23 14:55:04,937] multiqc [INFO ] This is MultiQC v1.9 [2024-09-23 14:55:04,937] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-09-23 14:55:04,937] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/47/d2071a93ee014fc3c6a6b4e7ed42af/1 [2024-09-23 14:55:04,937] multiqc [INFO ] Template : default [2024-09-23 14:55:04,937] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-09-23 14:55:04,937] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/47/d2071a93ee014fc3c6a6b4e7ed42af/1 [2024-09-23 14:55:04,938] 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 [2024-09-23 14:55:04,938] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-51263310/tmp72mwb36g [2024-09-23 14:55:05,045] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.4_fastqc.html [2024-09-23 14:55:05,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.4_fastqc.html [2024-09-23 14:55:05,119] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.3_fastqc.html [2024-09-23 14:55:05,121] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.3_fastqc.html [2024-09-23 14:55:05,167] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.1_fastqc.html [2024-09-23 14:55:05,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.1_fastqc.html [2024-09-23 14:55:05,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.2_fastqc.html [2024-09-23 14:55:05,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LNMRD_l01.2_fastqc.html [2024-09-23 14:55:05,769] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-09-23 14:55:05,770] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-09-23 14:55:05,775] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-09-23 14:55:05,780] multiqc [DEBUG ] No samples found: conpair [2024-09-23 14:55:05,785] multiqc [DEBUG ] No samples found: peddy [2024-09-23 14:55:05,791] multiqc [DEBUG ] No samples found: somalier [2024-09-23 14:55:05,795] multiqc [DEBUG ] No samples found: methylQA [2024-09-23 14:55:05,803] multiqc [DEBUG ] No samples found: mosdepth [2024-09-23 14:55:05,808] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-09-23 14:55:05,812] multiqc [DEBUG ] No samples found: qualimap [2024-09-23 14:55:05,817] multiqc [DEBUG ] No samples found: preseq [2024-09-23 14:55:05,822] multiqc [DEBUG ] No samples found: quast [2024-09-23 14:55:05,827] multiqc [DEBUG ] No samples found: qorts [2024-09-23 14:55:05,832] multiqc [DEBUG ] No samples found: rna_seqc [2024-09-23 14:55:05,837] multiqc [DEBUG ] No samples found: rockhopper [2024-09-23 14:55:05,842] multiqc [DEBUG ] No samples found: rsem [2024-09-23 14:55:05,854] multiqc [DEBUG ] No samples found: rseqc [2024-09-23 14:55:05,859] multiqc [DEBUG ] No samples found: busco [2024-09-23 14:55:05,865] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-09-23 14:55:05,871] multiqc [DEBUG ] No samples found: disambiguate [2024-09-23 14:55:05,876] multiqc [DEBUG ] No samples found: supernova [2024-09-23 14:55:05,889] multiqc [DEBUG ] No samples found: deeptools [2024-09-23 14:55:05,894] multiqc [DEBUG ] No samples found: sargasso [2024-09-23 14:55:05,899] multiqc [DEBUG ] No samples found: verifybamid [2024-09-23 14:55:05,904] multiqc [DEBUG ] No samples found: mirtrace [2024-09-23 14:55:05,909] multiqc [DEBUG ] No samples found: happy [2024-09-23 14:55:05,915] multiqc [DEBUG ] No samples found: mirtop [2024-09-23 14:55:05,921] multiqc [DEBUG ] No samples found: homer [2024-09-23 14:55:05,927] multiqc [DEBUG ] No samples found: macs2 [2024-09-23 14:55:05,931] multiqc [DEBUG ] No samples found: theta2 [2024-09-23 14:55:05,936] multiqc [DEBUG ] No samples found: snpeff [2024-09-23 14:55:05,944] multiqc [DEBUG ] No samples found: gatk [2024-09-23 14:55:05,949] multiqc [DEBUG ] No samples found: htseq [2024-09-23 14:55:05,954] multiqc [DEBUG ] No samples found: bcftools [2024-09-23 14:55:05,959] multiqc [DEBUG ] No samples found: featureCounts [2024-09-23 14:55:05,966] multiqc [DEBUG ] No samples found: fgbio [2024-09-23 14:55:05,979] multiqc [DEBUG ] No samples found: dragen [2024-09-23 14:55:05,984] multiqc [DEBUG ] No samples found: dedup [2024-09-23 14:55:05,989] multiqc [DEBUG ] No samples found: damageprofiler [2024-09-23 14:55:06,014] multiqc [DEBUG ] No samples found: biobambam2 [2024-09-23 14:55:06,020] multiqc [DEBUG ] No samples found: mtnucratio [2024-09-23 14:55:06,022] multiqc [DEBUG ] No samples found: picard [2024-09-23 14:55:06,027] multiqc [DEBUG ] No samples found: prokka [2024-09-23 14:55:06,032] multiqc [DEBUG ] No samples found: samblaster [2024-09-23 14:55:06,040] multiqc [DEBUG ] No samples found: samtools [2024-09-23 14:55:06,045] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-09-23 14:55:06,050] multiqc [DEBUG ] No samples found: bamtools [2024-09-23 14:55:06,055] multiqc [DEBUG ] No samples found: jellyfish [2024-09-23 14:55:06,063] multiqc [DEBUG ] No samples found: vcftools [2024-09-23 14:55:06,069] multiqc [DEBUG ] No samples found: longranger [2024-09-23 14:55:06,074] multiqc [DEBUG ] No samples found: stacks [2024-09-23 14:55:06,079] multiqc [DEBUG ] No samples found: varscan2 [2024-09-23 14:55:06,093] multiqc [DEBUG ] No samples found: bbmap [2024-09-23 14:55:06,099] multiqc [DEBUG ] No samples found: bismark [2024-09-23 14:55:06,104] multiqc [DEBUG ] No samples found: biscuit [2024-09-23 14:55:06,110] multiqc [DEBUG ] No samples found: hicexplorer [2024-09-23 14:55:06,115] multiqc [DEBUG ] No samples found: hicup [2024-09-23 14:55:06,120] multiqc [DEBUG ] No samples found: hicpro [2024-09-23 14:55:06,124] multiqc [DEBUG ] No samples found: salmon [2024-09-23 14:55:06,129] multiqc [DEBUG ] No samples found: kallisto [2024-09-23 14:55:06,133] multiqc [DEBUG ] No samples found: slamdunk [2024-09-23 14:55:06,138] multiqc [DEBUG ] No samples found: star [2024-09-23 14:55:06,143] multiqc [DEBUG ] No samples found: hisat2 [2024-09-23 14:55:06,148] multiqc [DEBUG ] No samples found: tophat [2024-09-23 14:55:06,154] multiqc [DEBUG ] No samples found: bowtie2 [2024-09-23 14:55:06,158] multiqc [DEBUG ] No samples found: bowtie1 [2024-09-23 14:55:06,163] multiqc [DEBUG ] No samples found: snpsplit [2024-09-23 14:55:06,168] multiqc [DEBUG ] No samples found: kat [2024-09-23 14:55:06,173] multiqc [DEBUG ] No samples found: leehom [2024-09-23 14:55:06,178] multiqc [DEBUG ] No samples found: adapterRemoval [2024-09-23 14:55:06,183] multiqc [DEBUG ] No samples found: clipandmerge [2024-09-23 14:55:06,188] multiqc [DEBUG ] No samples found: cutadapt [2024-09-23 14:55:06,192] multiqc [DEBUG ] No samples found: flexbar [2024-09-23 14:55:06,197] multiqc [DEBUG ] No samples found: kaiju [2024-09-23 14:55:06,201] multiqc [DEBUG ] No samples found: kraken [2024-09-23 14:55:06,206] multiqc [DEBUG ] No samples found: malt [2024-09-23 14:55:06,211] multiqc [DEBUG ] No samples found: trimmomatic [2024-09-23 14:55:06,216] multiqc [DEBUG ] No samples found: sickle [2024-09-23 14:55:06,221] multiqc [DEBUG ] No samples found: skewer [2024-09-23 14:55:06,225] multiqc [DEBUG ] No samples found: sortmerna [2024-09-23 14:55:06,230] multiqc [DEBUG ] No samples found: biobloomtools [2024-09-23 14:55:06,235] multiqc [DEBUG ] No samples found: fastq_screen [2024-09-23 14:55:06,240] multiqc [DEBUG ] No samples found: afterqc [2024-09-23 14:55:06,245] multiqc [DEBUG ] No samples found: fastp [2024-09-23 14:55:06,284] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-09-23 14:55:06,360] multiqc [DEBUG ] No samples found: pycoqc [2024-09-23 14:55:06,365] multiqc [DEBUG ] No samples found: minionqc [2024-09-23 14:55:06,369] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-09-23 14:55:06,374] multiqc [DEBUG ] No samples found: clusterflow [2024-09-23 14:55:06,378] multiqc [DEBUG ] No samples found: bcl2fastq [2024-09-23 14:55:06,383] multiqc [DEBUG ] No samples found: interop [2024-09-23 14:55:06,387] multiqc [DEBUG ] No samples found: ivar [2024-09-23 14:55:06,392] multiqc [DEBUG ] No samples found: flash [2024-09-23 14:55:06,396] multiqc [DEBUG ] No samples found: seqyclean [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-09-23 14:55:06,396] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-09-23 14:55:06,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-09-23 14:55:06,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-09-23 14:55:06,397] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-09-23 14:55:06,397] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-09-23 14:55:06,397] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-09-23 14:55:06,402] multiqc [INFO ] Compressing plot data [2024-09-23 14:55:06,492] multiqc [INFO ] Report : multiqc_report.html [2024-09-23 14:55:06,492] multiqc [INFO ] Data : multiqc_data [2024-09-23 14:55:06,492] multiqc [DEBUG ] Moving data file from '/state/partition1/job-51263310/tmp72mwb36g/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/47/d2071a93ee014fc3c6a6b4e7ed42af/1/multiqc_data' [2024-09-23 14:55:06,618] multiqc [INFO ] MultiQC complete