[2024-12-22 01:30:08,215] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2024-12-22 01:30:08,215] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2024-12-22 01:30:08,215] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2024-12-22 01:30:08,219] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml
[2024-12-22 01:30:08,219] 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}}
[2024-12-22 01:30:08,219] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-12-22 01:30:08,253] multiqc [DEBUG ] Could not connect to multiqc.info for version check: <urlopen error unknown url type: https>
[2024-12-22 01:30:08,253] multiqc [INFO ] This is MultiQC v1.9
[2024-12-22 01:30:08,253] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-12-22 01:30:08,253] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/fb/f4105bad5c17d0cf330718d5847199/merged
[2024-12-22 01:30:08,253] multiqc [INFO ] Template : default
[2024-12-22 01:30:08,253] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2024-12-22 01:30:08,253] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/fb/f4105bad5c17d0cf330718d5847199/merged
[2024-12-22 01:30:08,254] 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
[2024-12-22 01:30:08,254] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55264672/tmp2x9u3wxu
[2024-12-22 01:30:08,488] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-12-22 01:30:08,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-12-22 01:30:08,543] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D17CD8_fastqc.html
[2024-12-22 01:30:08,546] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D17CD8_fastqc.html
[2024-12-22 01:30:08,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D14CD8_fastqc.html
[2024-12-22 01:30:08,621] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D14CD8_fastqc.html
[2024-12-22 01:30:08,695] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D20CD4_fastqc.html
[2024-12-22 01:30:08,697] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D20CD4_fastqc.html
[2024-12-22 01:30:08,770] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D30CD8_fastqc.html
[2024-12-22 01:30:08,772] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D30CD8_fastqc.html
[2024-12-22 01:30:08,845] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D17CD4_fastqc.html
[2024-12-22 01:30:08,848] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D17CD4_fastqc.html
[2024-12-22 01:30:08,918] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_undetermined_fastqc.html
[2024-12-22 01:30:08,921] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_undetermined_fastqc.html
[2024-12-22 01:30:08,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D14CD4_fastqc.html
[2024-12-22 01:30:08,996] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D14CD4_fastqc.html
[2024-12-22 01:30:09,069] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D20CD8_fastqc.html
[2024-12-22 01:30:09,071] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D20CD8_fastqc.html
[2024-12-22 01:30:09,149] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D30CD4_fastqc.html
[2024-12-22 01:30:09,152] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHJFFBGYW_n01_D30CD4_fastqc.html
[2024-12-22 01:30:09,766] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2024-12-22 01:30:09,776] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2024-12-22 01:30:09,793] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table)
[2024-12-22 01:30:09,806] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table)
[2024-12-22 01:30:09,808] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2024-12-22 01:30:09,829] multiqc [DEBUG ] No samples found: conpair
[2024-12-22 01:30:09,875] multiqc [DEBUG ] No samples found: peddy
[2024-12-22 01:30:09,914] multiqc [DEBUG ] No samples found: somalier
[2024-12-22 01:30:09,948] multiqc [DEBUG ] No samples found: methylQA
[2024-12-22 01:30:09,989] multiqc [DEBUG ] No samples found: mosdepth
[2024-12-22 01:30:10,018] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2024-12-22 01:30:10,024] multiqc [DEBUG ] No samples found: qualimap
[2024-12-22 01:30:10,053] multiqc [DEBUG ] No samples found: preseq
[2024-12-22 01:30:10,082] multiqc [DEBUG ] No samples found: quast
[2024-12-22 01:30:10,131] multiqc [DEBUG ] No samples found: qorts
[2024-12-22 01:30:10,146] multiqc [DEBUG ] No samples found: rna_seqc
[2024-12-22 01:30:10,153] multiqc [DEBUG ] No samples found: rockhopper
[2024-12-22 01:30:10,187] multiqc [DEBUG ] No samples found: rsem
[2024-12-22 01:30:10,240] multiqc [DEBUG ] No samples found: rseqc
[2024-12-22 01:30:10,248] multiqc [DEBUG ] No samples found: busco
[2024-12-22 01:30:10,262] multiqc [DEBUG ] No samples found: goleft_indexcov
[2024-12-22 01:30:10,277] multiqc [DEBUG ] No samples found: disambiguate
[2024-12-22 01:30:10,290] multiqc [DEBUG ] No samples found: supernova
[2024-12-22 01:30:10,348] multiqc [DEBUG ] No samples found: deeptools
[2024-12-22 01:30:10,385] multiqc [DEBUG ] No samples found: sargasso
[2024-12-22 01:30:10,410] multiqc [DEBUG ] No samples found: verifybamid
[2024-12-22 01:30:10,418] multiqc [DEBUG ] No samples found: mirtrace
[2024-12-22 01:30:10,426] multiqc [DEBUG ] No samples found: happy
[2024-12-22 01:30:10,452] multiqc [DEBUG ] No samples found: mirtop
[2024-12-22 01:30:10,524] multiqc [DEBUG ] No samples found: homer
[2024-12-22 01:30:10,544] multiqc [DEBUG ] No samples found: macs2
[2024-12-22 01:30:10,552] multiqc [DEBUG ] No samples found: theta2
[2024-12-22 01:30:10,587] multiqc [DEBUG ] No samples found: snpeff
[2024-12-22 01:30:10,628] multiqc [DEBUG ] No samples found: gatk
[2024-12-22 01:30:10,648] multiqc [DEBUG ] No samples found: htseq
[2024-12-22 01:30:10,661] multiqc [DEBUG ] No samples found: bcftools
[2024-12-22 01:30:10,697] multiqc [DEBUG ] No samples found: featureCounts
[2024-12-22 01:30:10,715] multiqc [DEBUG ] No samples found: fgbio
[2024-12-22 01:30:10,828] multiqc [DEBUG ] No samples found: dragen
[2024-12-22 01:30:10,870] multiqc [DEBUG ] No samples found: dedup
[2024-12-22 01:30:10,900] multiqc [DEBUG ] No samples found: damageprofiler
[2024-12-22 01:30:10,985] multiqc [DEBUG ] No samples found: biobambam2
[2024-12-22 01:30:10,994] multiqc [DEBUG ] No samples found: mtnucratio
[2024-12-22 01:30:10,997] multiqc [DEBUG ] No samples found: picard
[2024-12-22 01:30:11,008] multiqc [DEBUG ] No samples found: prokka
[2024-12-22 01:30:11,019] multiqc [DEBUG ] No samples found: samblaster
[2024-12-22 01:30:11,039] multiqc [DEBUG ] No samples found: samtools
[2024-12-22 01:30:11,069] multiqc [DEBUG ] No samples found: sexdeterrmine
[2024-12-22 01:30:11,089] multiqc [DEBUG ] No samples found: bamtools
[2024-12-22 01:30:11,118] multiqc [DEBUG ] No samples found: jellyfish
[2024-12-22 01:30:11,154] multiqc [DEBUG ] No samples found: vcftools
[2024-12-22 01:30:11,174] multiqc [DEBUG ] No samples found: longranger
[2024-12-22 01:30:11,206] multiqc [DEBUG ] No samples found: stacks
[2024-12-22 01:30:11,253] multiqc [DEBUG ] No samples found: varscan2
[2024-12-22 01:30:11,297] multiqc [DEBUG ] No samples found: bbmap
[2024-12-22 01:30:11,336] multiqc [DEBUG ] No samples found: bismark
[2024-12-22 01:30:11,360] multiqc [DEBUG ] No samples found: biscuit
[2024-12-22 01:30:11,368] multiqc [DEBUG ] No samples found: hicexplorer
[2024-12-22 01:30:11,384] multiqc [DEBUG ] No samples found: hicup
[2024-12-22 01:30:11,404] multiqc [DEBUG ] No samples found: hicpro
[2024-12-22 01:30:11,416] multiqc [DEBUG ] No samples found: salmon
[2024-12-22 01:30:11,429] multiqc [DEBUG ] No samples found: kallisto
[2024-12-22 01:30:11,442] multiqc [DEBUG ] No samples found: slamdunk
[2024-12-22 01:30:11,461] multiqc [DEBUG ] No samples found: star
[2024-12-22 01:30:11,474] multiqc [DEBUG ] No samples found: hisat2
[2024-12-22 01:30:11,482] multiqc [DEBUG ] No samples found: tophat
[2024-12-22 01:30:11,495] multiqc [DEBUG ] No samples found: bowtie2
[2024-12-22 01:30:11,523] multiqc [DEBUG ] No samples found: bowtie1
[2024-12-22 01:30:11,558] multiqc [DEBUG ] No samples found: snpsplit
[2024-12-22 01:30:11,572] multiqc [DEBUG ] No samples found: kat
[2024-12-22 01:30:11,628] multiqc [DEBUG ] No samples found: leehom
[2024-12-22 01:30:11,678] multiqc [DEBUG ] No samples found: adapterRemoval
[2024-12-22 01:30:11,700] multiqc [DEBUG ] No samples found: clipandmerge
[2024-12-22 01:30:11,719] multiqc [DEBUG ] No samples found: cutadapt
[2024-12-22 01:30:11,733] multiqc [DEBUG ] No samples found: flexbar
[2024-12-22 01:30:11,741] multiqc [DEBUG ] No samples found: kaiju
[2024-12-22 01:30:11,749] multiqc [DEBUG ] No samples found: kraken
[2024-12-22 01:30:11,757] multiqc [DEBUG ] No samples found: malt
[2024-12-22 01:30:11,764] multiqc [DEBUG ] No samples found: trimmomatic
[2024-12-22 01:30:11,775] multiqc [DEBUG ] No samples found: sickle
[2024-12-22 01:30:11,783] multiqc [DEBUG ] No samples found: skewer
[2024-12-22 01:30:11,790] multiqc [DEBUG ] No samples found: sortmerna
[2024-12-22 01:30:11,797] multiqc [DEBUG ] No samples found: biobloomtools
[2024-12-22 01:30:11,804] multiqc [DEBUG ] No samples found: fastq_screen
[2024-12-22 01:30:11,811] multiqc [DEBUG ] No samples found: afterqc
[2024-12-22 01:30:11,819] multiqc [DEBUG ] No samples found: fastp
[2024-12-22 01:30:11,868] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports
[2024-12-22 01:30:12,221] multiqc [DEBUG ] No samples found: pycoqc
[2024-12-22 01:30:12,236] multiqc [DEBUG ] No samples found: minionqc
[2024-12-22 01:30:12,246] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2024-12-22 01:30:12,269] multiqc [DEBUG ] No samples found: clusterflow
[2024-12-22 01:30:12,277] multiqc [DEBUG ] No samples found: bcl2fastq
[2024-12-22 01:30:12,360] multiqc [DEBUG ] No samples found: interop
[2024-12-22 01:30:12,372] multiqc [DEBUG ] No samples found: ivar
[2024-12-22 01:30:12,387] multiqc [DEBUG ] No samples found: flash
[2024-12-22 01:30:12,408] multiqc [DEBUG ] No samples found: seqyclean
[2024-12-22 01:30:12,408] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found.
[2024-12-22 01:30:12,408] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found.
[2024-12-22 01:30:12,408] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found.
[2024-12-22 01:30:12,408] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'.
[2024-12-22 01:30:12,408] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'.
[2024-12-22 01:30:12,409] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'.
[2024-12-22 01:30:12,425] multiqc [INFO ] Compressing plot data
[2024-12-22 01:30:12,594] multiqc [INFO ] Report : multiqc_report.html
[2024-12-22 01:30:12,594] multiqc [INFO ] Data : multiqc_data
[2024-12-22 01:30:12,594] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55264672/tmp2x9u3wxu/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/fb/f4105bad5c17d0cf330718d5847199/merged/multiqc_data'
[2024-12-22 01:30:12,819] multiqc [INFO ] MultiQC complete