[2024-11-01 18:04:42,682] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2024-11-01 18:04:42,682] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2024-11-01 18:04:42,682] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2024-11-01 18:04:42,684] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml
[2024-11-01 18:04:42,684] 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}}
[2024-11-01 18:04:42,685] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-11-01 18:04:42,721] multiqc [DEBUG ] Could not connect to multiqc.info for version check: <urlopen error unknown url type: https>
[2024-11-01 18:04:42,721] multiqc [INFO ] This is MultiQC v1.9
[2024-11-01 18:04:42,721] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-11-01 18:04:42,721] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/ad/9348e52b0db47ed98f47690f507db1/merged
[2024-11-01 18:04:42,721] multiqc [INFO ] Template : default
[2024-11-01 18:04:42,721] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2024-11-01 18:04:42,721] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/ad/9348e52b0db47ed98f47690f507db1/merged
[2024-11-01 18:04:42,722] 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
[2024-11-01 18:04:42,722] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-52930388/tmpmn5yc3u_
[2024-11-01 18:04:42,822] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTWTDRX5_n02_MR_GeneExpression_v2_fastqc.html
[2024-11-01 18:04:42,825] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTWTDRX5_n02_MR_GeneExpression_v2_fastqc.html
[2024-11-01 18:04:42,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:42,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:42,875] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:42,875] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:42,875] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:42,875] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:42,875] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:42,890] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-11-01 18:04:43,548] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTWTDRX5_n02_MR_CMO_v2_fastqc.html
[2024-11-01 18:04:43,550] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTWTDRX5_n02_MR_CMO_v2_fastqc.html
[2024-11-01 18:04:43,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTWTDRX5_n02_undetermined_fastqc.html
[2024-11-01 18:04:43,620] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTWTDRX5_n02_undetermined_fastqc.html
[2024-11-01 18:04:43,666] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTWTDRX5_n01_MR_GeneExpression_v2_fastqc.html
[2024-11-01 18:04:43,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTWTDRX5_n01_MR_GeneExpression_v2_fastqc.html
[2024-11-01 18:04:43,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTWTDRX5_n01_MR_CMO_v2_fastqc.html
[2024-11-01 18:04:43,714] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTWTDRX5_n01_MR_CMO_v2_fastqc.html
[2024-11-01 18:04:43,759] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTWTDRX5_n01_undetermined_fastqc.html
[2024-11-01 18:04:43,760] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTWTDRX5_n01_undetermined_fastqc.html
[2024-11-01 18:04:44,185] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2024-11-01 18:04:44,186] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2024-11-01 18:04:44,194] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table)
[2024-11-01 18:04:44,203] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table)
[2024-11-01 18:04:44,205] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2024-11-01 18:04:44,208] multiqc [DEBUG ] No samples found: conpair
[2024-11-01 18:04:44,212] multiqc [DEBUG ] No samples found: peddy
[2024-11-01 18:04:44,216] multiqc [DEBUG ] No samples found: somalier
[2024-11-01 18:04:44,220] multiqc [DEBUG ] No samples found: methylQA
[2024-11-01 18:04:44,225] multiqc [DEBUG ] No samples found: mosdepth
[2024-11-01 18:04:44,228] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2024-11-01 18:04:44,231] multiqc [DEBUG ] No samples found: qualimap
[2024-11-01 18:04:44,235] multiqc [DEBUG ] No samples found: preseq
[2024-11-01 18:04:44,239] multiqc [DEBUG ] No samples found: quast
[2024-11-01 18:04:44,243] multiqc [DEBUG ] No samples found: qorts
[2024-11-01 18:04:44,247] multiqc [DEBUG ] No samples found: rna_seqc
[2024-11-01 18:04:44,250] multiqc [DEBUG ] No samples found: rockhopper
[2024-11-01 18:04:44,254] multiqc [DEBUG ] No samples found: rsem
[2024-11-01 18:04:44,261] multiqc [DEBUG ] No samples found: rseqc
[2024-11-01 18:04:44,264] multiqc [DEBUG ] No samples found: busco
[2024-11-01 18:04:44,268] multiqc [DEBUG ] No samples found: goleft_indexcov
[2024-11-01 18:04:44,271] multiqc [DEBUG ] No samples found: disambiguate
[2024-11-01 18:04:44,275] multiqc [DEBUG ] No samples found: supernova
[2024-11-01 18:04:44,284] multiqc [DEBUG ] No samples found: deeptools
[2024-11-01 18:04:44,287] multiqc [DEBUG ] No samples found: sargasso
[2024-11-01 18:04:44,291] multiqc [DEBUG ] No samples found: verifybamid
[2024-11-01 18:04:44,294] multiqc [DEBUG ] No samples found: mirtrace
[2024-11-01 18:04:44,297] multiqc [DEBUG ] No samples found: happy
[2024-11-01 18:04:44,301] multiqc [DEBUG ] No samples found: mirtop
[2024-11-01 18:04:44,306] multiqc [DEBUG ] No samples found: homer
[2024-11-01 18:04:44,309] multiqc [DEBUG ] No samples found: macs2
[2024-11-01 18:04:44,312] multiqc [DEBUG ] No samples found: theta2
[2024-11-01 18:04:44,316] multiqc [DEBUG ] No samples found: snpeff
[2024-11-01 18:04:44,321] multiqc [DEBUG ] No samples found: gatk
[2024-11-01 18:04:44,325] multiqc [DEBUG ] No samples found: htseq
[2024-11-01 18:04:44,328] multiqc [DEBUG ] No samples found: bcftools
[2024-11-01 18:04:44,332] multiqc [DEBUG ] No samples found: featureCounts
[2024-11-01 18:04:44,336] multiqc [DEBUG ] No samples found: fgbio
[2024-11-01 18:04:44,344] multiqc [DEBUG ] No samples found: dragen
[2024-11-01 18:04:44,348] multiqc [DEBUG ] No samples found: dedup
[2024-11-01 18:04:44,352] multiqc [DEBUG ] No samples found: damageprofiler
[2024-11-01 18:04:44,366] multiqc [DEBUG ] No samples found: biobambam2
[2024-11-01 18:04:44,369] multiqc [DEBUG ] No samples found: mtnucratio
[2024-11-01 18:04:44,372] multiqc [DEBUG ] No samples found: picard
[2024-11-01 18:04:44,375] multiqc [DEBUG ] No samples found: prokka
[2024-11-01 18:04:44,379] multiqc [DEBUG ] No samples found: samblaster
[2024-11-01 18:04:44,385] multiqc [DEBUG ] No samples found: samtools
[2024-11-01 18:04:44,388] multiqc [DEBUG ] No samples found: sexdeterrmine
[2024-11-01 18:04:44,392] multiqc [DEBUG ] No samples found: bamtools
[2024-11-01 18:04:44,395] multiqc [DEBUG ] No samples found: jellyfish
[2024-11-01 18:04:44,400] multiqc [DEBUG ] No samples found: vcftools
[2024-11-01 18:04:44,404] multiqc [DEBUG ] No samples found: longranger
[2024-11-01 18:04:44,408] multiqc [DEBUG ] No samples found: stacks
[2024-11-01 18:04:44,411] multiqc [DEBUG ] No samples found: varscan2
[2024-11-01 18:04:44,420] multiqc [DEBUG ] No samples found: bbmap
[2024-11-01 18:04:44,424] multiqc [DEBUG ] No samples found: bismark
[2024-11-01 18:04:44,428] multiqc [DEBUG ] No samples found: biscuit
[2024-11-01 18:04:44,432] multiqc [DEBUG ] No samples found: hicexplorer
[2024-11-01 18:04:44,436] multiqc [DEBUG ] No samples found: hicup
[2024-11-01 18:04:44,440] multiqc [DEBUG ] No samples found: hicpro
[2024-11-01 18:04:44,443] multiqc [DEBUG ] No samples found: salmon
[2024-11-01 18:04:44,447] multiqc [DEBUG ] No samples found: kallisto
[2024-11-01 18:04:44,450] multiqc [DEBUG ] No samples found: slamdunk
[2024-11-01 18:04:44,454] multiqc [DEBUG ] No samples found: star
[2024-11-01 18:04:44,458] multiqc [DEBUG ] No samples found: hisat2
[2024-11-01 18:04:44,461] multiqc [DEBUG ] No samples found: tophat
[2024-11-01 18:04:44,465] multiqc [DEBUG ] No samples found: bowtie2
[2024-11-01 18:04:44,468] multiqc [DEBUG ] No samples found: bowtie1
[2024-11-01 18:04:44,472] multiqc [DEBUG ] No samples found: snpsplit
[2024-11-01 18:04:44,475] multiqc [DEBUG ] No samples found: kat
[2024-11-01 18:04:44,478] multiqc [DEBUG ] No samples found: leehom
[2024-11-01 18:04:44,482] multiqc [DEBUG ] No samples found: adapterRemoval
[2024-11-01 18:04:44,485] multiqc [DEBUG ] No samples found: clipandmerge
[2024-11-01 18:04:44,488] multiqc [DEBUG ] No samples found: cutadapt
[2024-11-01 18:04:44,491] multiqc [DEBUG ] No samples found: flexbar
[2024-11-01 18:04:44,495] multiqc [DEBUG ] No samples found: kaiju
[2024-11-01 18:04:44,498] multiqc [DEBUG ] No samples found: kraken
[2024-11-01 18:04:44,501] multiqc [DEBUG ] No samples found: malt
[2024-11-01 18:04:44,505] multiqc [DEBUG ] No samples found: trimmomatic
[2024-11-01 18:04:44,508] multiqc [DEBUG ] No samples found: sickle
[2024-11-01 18:04:44,512] multiqc [DEBUG ] No samples found: skewer
[2024-11-01 18:04:44,515] multiqc [DEBUG ] No samples found: sortmerna
[2024-11-01 18:04:44,518] multiqc [DEBUG ] No samples found: biobloomtools
[2024-11-01 18:04:44,522] multiqc [DEBUG ] No samples found: fastq_screen
[2024-11-01 18:04:44,525] multiqc [DEBUG ] No samples found: afterqc
[2024-11-01 18:04:44,529] multiqc [DEBUG ] No samples found: fastp
[2024-11-01 18:04:44,677] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports
[2024-11-01 18:04:44,742] multiqc [DEBUG ] No samples found: pycoqc
[2024-11-01 18:04:44,746] multiqc [DEBUG ] No samples found: minionqc
[2024-11-01 18:04:44,749] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2024-11-01 18:04:44,753] multiqc [DEBUG ] No samples found: clusterflow
[2024-11-01 18:04:44,756] multiqc [DEBUG ] No samples found: bcl2fastq
[2024-11-01 18:04:44,760] multiqc [DEBUG ] No samples found: interop
[2024-11-01 18:04:44,763] multiqc [DEBUG ] No samples found: ivar
[2024-11-01 18:04:44,767] multiqc [DEBUG ] No samples found: flash
[2024-11-01 18:04:44,770] multiqc [DEBUG ] No samples found: seqyclean
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'.
[2024-11-01 18:04:44,770] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'.
[2024-11-01 18:04:44,771] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'.
[2024-11-01 18:04:44,779] multiqc [INFO ] Compressing plot data
[2024-11-01 18:04:44,891] multiqc [INFO ] Report : multiqc_report.html
[2024-11-01 18:04:44,891] multiqc [INFO ] Data : multiqc_data
[2024-11-01 18:04:44,891] multiqc [DEBUG ] Moving data file from '/state/partition1/job-52930388/tmpmn5yc3u_/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/ad/9348e52b0db47ed98f47690f507db1/merged/multiqc_data'
[2024-11-01 18:04:45,008] multiqc [INFO ] MultiQC complete