[2025-01-03 14:17:52,960] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-03 14:17:52,960] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-03 14:17:52,960] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-03 14:17:52,963] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-03 14:17:52,963] 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}} [2025-01-03 14:17:52,963] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-03 14:17:52,999] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-03 14:17:52,999] multiqc [INFO ] This is MultiQC v1.9 [2025-01-03 14:17:53,000] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-03 14:17:53,000] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/ec/abff51df9e194e34270f5579cf6450/merged [2025-01-03 14:17:53,000] multiqc [INFO ] Template : default [2025-01-03 14:17:53,000] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-03 14:17:53,000] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/ec/abff51df9e194e34270f5579cf6450/merged [2025-01-03 14:17:53,000] 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 [2025-01-03 14:17:53,000] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55547260/tmpwzwtdxg1 [2025-01-03 14:17:53,121] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2TNDRX5_3_fastqc.html [2025-01-03 14:17:53,124] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2TNDRX5_3_fastqc.html [2025-01-03 14:17:53,190] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2TNDRX5_4_fastqc.html [2025-01-03 14:17:53,192] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2TNDRX5_4_fastqc.html [2025-01-03 14:17:53,242] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2TNDRX5_1_fastqc.html [2025-01-03 14:17:53,244] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2TNDRX5_1_fastqc.html [2025-01-03 14:17:53,289] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ2TNDRX5_2_fastqc.html [2025-01-03 14:17:53,291] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ2TNDRX5_2_fastqc.html [2025-01-03 14:17:53,874] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-03 14:17:53,876] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-03 14:17:53,881] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-03 14:17:53,888] multiqc [DEBUG ] No samples found: conpair [2025-01-03 14:17:53,894] multiqc [DEBUG ] No samples found: peddy [2025-01-03 14:17:53,901] multiqc [DEBUG ] No samples found: somalier [2025-01-03 14:17:53,908] multiqc [DEBUG ] No samples found: methylQA [2025-01-03 14:17:53,920] multiqc [DEBUG ] No samples found: mosdepth [2025-01-03 14:17:53,926] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-03 14:17:53,930] multiqc [DEBUG ] No samples found: qualimap [2025-01-03 14:17:53,936] multiqc [DEBUG ] No samples found: preseq [2025-01-03 14:17:53,942] multiqc [DEBUG ] No samples found: quast [2025-01-03 14:17:53,949] multiqc [DEBUG ] No samples found: qorts [2025-01-03 14:17:53,956] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-03 14:17:53,962] multiqc [DEBUG ] No samples found: rockhopper [2025-01-03 14:17:53,968] multiqc [DEBUG ] No samples found: rsem [2025-01-03 14:17:53,984] multiqc [DEBUG ] No samples found: rseqc [2025-01-03 14:17:53,990] multiqc [DEBUG ] No samples found: busco [2025-01-03 14:17:53,997] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-03 14:17:54,004] multiqc [DEBUG ] No samples found: disambiguate [2025-01-03 14:17:54,010] multiqc [DEBUG ] No samples found: supernova [2025-01-03 14:17:54,034] multiqc [DEBUG ] No samples found: deeptools [2025-01-03 14:17:54,041] multiqc [DEBUG ] No samples found: sargasso [2025-01-03 14:17:54,047] multiqc [DEBUG ] No samples found: verifybamid [2025-01-03 14:17:54,054] multiqc [DEBUG ] No samples found: mirtrace [2025-01-03 14:17:54,061] multiqc [DEBUG ] No samples found: happy [2025-01-03 14:17:54,068] multiqc [DEBUG ] No samples found: mirtop [2025-01-03 14:17:54,076] multiqc [DEBUG ] No samples found: homer [2025-01-03 14:17:54,083] multiqc [DEBUG ] No samples found: macs2 [2025-01-03 14:17:54,089] multiqc [DEBUG ] No samples found: theta2 [2025-01-03 14:17:54,096] multiqc [DEBUG ] No samples found: snpeff [2025-01-03 14:17:54,105] multiqc [DEBUG ] No samples found: gatk [2025-01-03 14:17:54,111] multiqc [DEBUG ] No samples found: htseq [2025-01-03 14:17:54,119] multiqc [DEBUG ] No samples found: bcftools [2025-01-03 14:17:54,125] multiqc [DEBUG ] No samples found: featureCounts [2025-01-03 14:17:54,134] multiqc [DEBUG ] No samples found: fgbio [2025-01-03 14:17:54,151] multiqc [DEBUG ] No samples found: dragen [2025-01-03 14:17:54,158] multiqc [DEBUG ] No samples found: dedup [2025-01-03 14:17:54,164] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-03 14:17:54,196] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-03 14:17:54,203] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-03 14:17:54,205] multiqc [DEBUG ] No samples found: picard [2025-01-03 14:17:54,212] multiqc [DEBUG ] No samples found: prokka [2025-01-03 14:17:54,217] multiqc [DEBUG ] No samples found: samblaster [2025-01-03 14:17:54,228] multiqc [DEBUG ] No samples found: samtools [2025-01-03 14:17:54,235] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-03 14:17:54,242] multiqc [DEBUG ] No samples found: bamtools [2025-01-03 14:17:54,248] multiqc [DEBUG ] No samples found: jellyfish [2025-01-03 14:17:54,259] multiqc [DEBUG ] No samples found: vcftools [2025-01-03 14:17:54,265] multiqc [DEBUG ] No samples found: longranger [2025-01-03 14:17:54,272] multiqc [DEBUG ] No samples found: stacks [2025-01-03 14:17:54,278] multiqc [DEBUG ] No samples found: varscan2 [2025-01-03 14:17:54,298] multiqc [DEBUG ] No samples found: bbmap [2025-01-03 14:17:54,305] multiqc [DEBUG ] No samples found: bismark [2025-01-03 14:17:54,312] multiqc [DEBUG ] No samples found: biscuit [2025-01-03 14:17:54,318] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-03 14:17:54,325] multiqc [DEBUG ] No samples found: hicup [2025-01-03 14:17:54,331] multiqc [DEBUG ] No samples found: hicpro [2025-01-03 14:17:54,337] multiqc [DEBUG ] No samples found: salmon [2025-01-03 14:17:54,343] multiqc [DEBUG ] No samples found: kallisto [2025-01-03 14:17:54,350] multiqc [DEBUG ] No samples found: slamdunk [2025-01-03 14:17:54,356] multiqc [DEBUG ] No samples found: star [2025-01-03 14:17:54,362] multiqc [DEBUG ] No samples found: hisat2 [2025-01-03 14:17:54,368] multiqc [DEBUG ] No samples found: tophat [2025-01-03 14:17:54,374] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-03 14:17:54,383] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-03 14:17:54,389] multiqc [DEBUG ] No samples found: snpsplit [2025-01-03 14:17:54,396] multiqc [DEBUG ] No samples found: kat [2025-01-03 14:17:54,401] multiqc [DEBUG ] No samples found: leehom [2025-01-03 14:17:54,407] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-03 14:17:54,413] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-03 14:17:54,419] multiqc [DEBUG ] No samples found: cutadapt [2025-01-03 14:17:54,425] multiqc [DEBUG ] No samples found: flexbar [2025-01-03 14:17:54,431] multiqc [DEBUG ] No samples found: kaiju [2025-01-03 14:17:54,437] multiqc [DEBUG ] No samples found: kraken [2025-01-03 14:17:54,444] multiqc [DEBUG ] No samples found: malt [2025-01-03 14:17:54,450] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-03 14:17:54,456] multiqc [DEBUG ] No samples found: sickle [2025-01-03 14:17:54,462] multiqc [DEBUG ] No samples found: skewer [2025-01-03 14:17:54,468] multiqc [DEBUG ] No samples found: sortmerna [2025-01-03 14:17:54,473] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-03 14:17:54,480] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-03 14:17:54,486] multiqc [DEBUG ] No samples found: afterqc [2025-01-03 14:17:54,493] multiqc [DEBUG ] No samples found: fastp [2025-01-03 14:17:54,580] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2025-01-03 14:17:54,635] multiqc [DEBUG ] No samples found: pycoqc [2025-01-03 14:17:54,641] multiqc [DEBUG ] No samples found: minionqc [2025-01-03 14:17:54,647] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-03 14:17:54,654] multiqc [DEBUG ] No samples found: clusterflow [2025-01-03 14:17:54,660] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-03 14:17:54,667] multiqc [DEBUG ] No samples found: interop [2025-01-03 14:17:54,673] multiqc [DEBUG ] No samples found: ivar [2025-01-03 14:17:54,678] multiqc [DEBUG ] No samples found: flash [2025-01-03 14:17:54,684] multiqc [DEBUG ] No samples found: seqyclean [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-03 14:17:54,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-03 14:17:54,685] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-03 14:17:54,691] multiqc [INFO ] Compressing plot data [2025-01-03 14:17:54,771] multiqc [INFO ] Report : multiqc_report.html [2025-01-03 14:17:54,771] multiqc [INFO ] Data : multiqc_data [2025-01-03 14:17:54,771] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55547260/tmpwzwtdxg1/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/ec/abff51df9e194e34270f5579cf6450/merged/multiqc_data' [2025-01-03 14:17:54,912] multiqc [INFO ] MultiQC complete