[2025-02-06 19:53:09,447] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2025-02-06 19:53:09,447] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2025-02-06 19:53:09,447] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2025-02-06 19:53:09,450] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml
[2025-02-06 19:53:09,450] 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}}
[2025-02-06 19:53:09,450] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2025-02-06 19:53:09,486] multiqc [DEBUG ] Could not connect to multiqc.info for version check: <urlopen error unknown url type: https>
[2025-02-06 19:53:09,486] multiqc [INFO ] This is MultiQC v1.9
[2025-02-06 19:53:09,486] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2025-02-06 19:53:09,486] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/9b/ca678bf354dce97c50ff3b531467b6/merged
[2025-02-06 19:53:09,486] multiqc [INFO ] Template : default
[2025-02-06 19:53:09,486] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2025-02-06 19:53:09,486] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/9b/ca678bf354dce97c50ff3b531467b6/merged
[2025-02-06 19:53:09,487] 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
[2025-02-06 19:53:09,487] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-57017700/tmpbcqgllcw
[2025-02-06 19:53:09,599] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:09,601] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:09,601] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:09,602] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:09,602] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:09,602] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:09,602] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:09,643] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2025-02-06 19:53:11,397] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5N7DRX5_n02_wy_flu1_10X_fastqc.html
[2025-02-06 19:53:11,399] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5N7DRX5_n02_wy_flu1_10X_fastqc.html
[2025-02-06 19:53:11,449] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5N7DRX5_n01_wy_flu1_10X_fastqc.html
[2025-02-06 19:53:11,451] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5N7DRX5_n01_wy_flu1_10X_fastqc.html
[2025-02-06 19:53:11,497] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5N7DRX5_n01_wy_flu1_dialout_fastqc.html
[2025-02-06 19:53:11,499] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5N7DRX5_n01_wy_flu1_dialout_fastqc.html
[2025-02-06 19:53:11,547] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5N7DRX5_n02_wy_flu1_dialout_fastqc.html
[2025-02-06 19:53:11,549] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5N7DRX5_n02_wy_flu1_dialout_fastqc.html
[2025-02-06 19:53:11,625] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5N7DRX5_n02_undetermined_fastqc.html
[2025-02-06 19:53:11,627] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5N7DRX5_n02_undetermined_fastqc.html
[2025-02-06 19:53:11,674] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT5N7DRX5_n01_undetermined_fastqc.html
[2025-02-06 19:53:11,676] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT5N7DRX5_n01_undetermined_fastqc.html
[2025-02-06 19:53:12,200] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2025-02-06 19:53:12,201] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2025-02-06 19:53:12,212] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2025-02-06 19:53:12,222] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table)
[2025-02-06 19:53:12,224] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table)
[2025-02-06 19:53:12,229] multiqc [DEBUG ] No samples found: conpair
[2025-02-06 19:53:12,234] multiqc [DEBUG ] No samples found: peddy
[2025-02-06 19:53:12,240] multiqc [DEBUG ] No samples found: somalier
[2025-02-06 19:53:12,245] multiqc [DEBUG ] No samples found: methylQA
[2025-02-06 19:53:12,255] multiqc [DEBUG ] No samples found: mosdepth
[2025-02-06 19:53:12,260] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2025-02-06 19:53:12,263] multiqc [DEBUG ] No samples found: qualimap
[2025-02-06 19:53:12,269] multiqc [DEBUG ] No samples found: preseq
[2025-02-06 19:53:12,274] multiqc [DEBUG ] No samples found: quast
[2025-02-06 19:53:12,279] multiqc [DEBUG ] No samples found: qorts
[2025-02-06 19:53:12,284] multiqc [DEBUG ] No samples found: rna_seqc
[2025-02-06 19:53:12,289] multiqc [DEBUG ] No samples found: rockhopper
[2025-02-06 19:53:12,294] multiqc [DEBUG ] No samples found: rsem
[2025-02-06 19:53:12,306] multiqc [DEBUG ] No samples found: rseqc
[2025-02-06 19:53:12,311] multiqc [DEBUG ] No samples found: busco
[2025-02-06 19:53:12,317] multiqc [DEBUG ] No samples found: goleft_indexcov
[2025-02-06 19:53:12,322] multiqc [DEBUG ] No samples found: disambiguate
[2025-02-06 19:53:12,327] multiqc [DEBUG ] No samples found: supernova
[2025-02-06 19:53:12,342] multiqc [DEBUG ] No samples found: deeptools
[2025-02-06 19:53:12,348] multiqc [DEBUG ] No samples found: sargasso
[2025-02-06 19:53:12,353] multiqc [DEBUG ] No samples found: verifybamid
[2025-02-06 19:53:12,358] multiqc [DEBUG ] No samples found: mirtrace
[2025-02-06 19:53:12,364] multiqc [DEBUG ] No samples found: happy
[2025-02-06 19:53:12,369] multiqc [DEBUG ] No samples found: mirtop
[2025-02-06 19:53:12,376] multiqc [DEBUG ] No samples found: homer
[2025-02-06 19:53:12,381] multiqc [DEBUG ] No samples found: macs2
[2025-02-06 19:53:12,386] multiqc [DEBUG ] No samples found: theta2
[2025-02-06 19:53:12,391] multiqc [DEBUG ] No samples found: snpeff
[2025-02-06 19:53:12,398] multiqc [DEBUG ] No samples found: gatk
[2025-02-06 19:53:12,404] multiqc [DEBUG ] No samples found: htseq
[2025-02-06 19:53:12,409] multiqc [DEBUG ] No samples found: bcftools
[2025-02-06 19:53:12,415] multiqc [DEBUG ] No samples found: featureCounts
[2025-02-06 19:53:12,421] multiqc [DEBUG ] No samples found: fgbio
[2025-02-06 19:53:12,435] multiqc [DEBUG ] No samples found: dragen
[2025-02-06 19:53:12,440] multiqc [DEBUG ] No samples found: dedup
[2025-02-06 19:53:12,445] multiqc [DEBUG ] No samples found: damageprofiler
[2025-02-06 19:53:12,470] multiqc [DEBUG ] No samples found: biobambam2
[2025-02-06 19:53:12,475] multiqc [DEBUG ] No samples found: mtnucratio
[2025-02-06 19:53:12,477] multiqc [DEBUG ] No samples found: picard
[2025-02-06 19:53:12,482] multiqc [DEBUG ] No samples found: prokka
[2025-02-06 19:53:12,487] multiqc [DEBUG ] No samples found: samblaster
[2025-02-06 19:53:12,496] multiqc [DEBUG ] No samples found: samtools
[2025-02-06 19:53:12,501] multiqc [DEBUG ] No samples found: sexdeterrmine
[2025-02-06 19:53:12,506] multiqc [DEBUG ] No samples found: bamtools
[2025-02-06 19:53:12,511] multiqc [DEBUG ] No samples found: jellyfish
[2025-02-06 19:53:12,519] multiqc [DEBUG ] No samples found: vcftools
[2025-02-06 19:53:12,524] multiqc [DEBUG ] No samples found: longranger
[2025-02-06 19:53:12,529] multiqc [DEBUG ] No samples found: stacks
[2025-02-06 19:53:12,534] multiqc [DEBUG ] No samples found: varscan2
[2025-02-06 19:53:12,549] multiqc [DEBUG ] No samples found: bbmap
[2025-02-06 19:53:12,554] multiqc [DEBUG ] No samples found: bismark
[2025-02-06 19:53:12,559] multiqc [DEBUG ] No samples found: biscuit
[2025-02-06 19:53:12,565] multiqc [DEBUG ] No samples found: hicexplorer
[2025-02-06 19:53:12,570] multiqc [DEBUG ] No samples found: hicup
[2025-02-06 19:53:12,575] multiqc [DEBUG ] No samples found: hicpro
[2025-02-06 19:53:12,580] multiqc [DEBUG ] No samples found: salmon
[2025-02-06 19:53:12,585] multiqc [DEBUG ] No samples found: kallisto
[2025-02-06 19:53:12,590] multiqc [DEBUG ] No samples found: slamdunk
[2025-02-06 19:53:12,596] multiqc [DEBUG ] No samples found: star
[2025-02-06 19:53:12,601] multiqc [DEBUG ] No samples found: hisat2
[2025-02-06 19:53:12,606] multiqc [DEBUG ] No samples found: tophat
[2025-02-06 19:53:12,611] multiqc [DEBUG ] No samples found: bowtie2
[2025-02-06 19:53:12,617] multiqc [DEBUG ] No samples found: bowtie1
[2025-02-06 19:53:12,622] multiqc [DEBUG ] No samples found: snpsplit
[2025-02-06 19:53:12,626] multiqc [DEBUG ] No samples found: kat
[2025-02-06 19:53:12,631] multiqc [DEBUG ] No samples found: leehom
[2025-02-06 19:53:12,636] multiqc [DEBUG ] No samples found: adapterRemoval
[2025-02-06 19:53:12,641] multiqc [DEBUG ] No samples found: clipandmerge
[2025-02-06 19:53:12,646] multiqc [DEBUG ] No samples found: cutadapt
[2025-02-06 19:53:12,650] multiqc [DEBUG ] No samples found: flexbar
[2025-02-06 19:53:12,656] multiqc [DEBUG ] No samples found: kaiju
[2025-02-06 19:53:12,661] multiqc [DEBUG ] No samples found: kraken
[2025-02-06 19:53:12,666] multiqc [DEBUG ] No samples found: malt
[2025-02-06 19:53:12,672] multiqc [DEBUG ] No samples found: trimmomatic
[2025-02-06 19:53:12,678] multiqc [DEBUG ] No samples found: sickle
[2025-02-06 19:53:12,683] multiqc [DEBUG ] No samples found: skewer
[2025-02-06 19:53:12,688] multiqc [DEBUG ] No samples found: sortmerna
[2025-02-06 19:53:12,693] multiqc [DEBUG ] No samples found: biobloomtools
[2025-02-06 19:53:12,698] multiqc [DEBUG ] No samples found: fastq_screen
[2025-02-06 19:53:12,704] multiqc [DEBUG ] No samples found: afterqc
[2025-02-06 19:53:12,710] multiqc [DEBUG ] No samples found: fastp
[2025-02-06 19:53:12,860] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports
[2025-02-06 19:53:12,930] multiqc [DEBUG ] No samples found: pycoqc
[2025-02-06 19:53:12,936] multiqc [DEBUG ] No samples found: minionqc
[2025-02-06 19:53:12,941] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2025-02-06 19:53:12,946] multiqc [DEBUG ] No samples found: clusterflow
[2025-02-06 19:53:12,952] multiqc [DEBUG ] No samples found: bcl2fastq
[2025-02-06 19:53:12,957] multiqc [DEBUG ] No samples found: interop
[2025-02-06 19:53:12,962] multiqc [DEBUG ] No samples found: ivar
[2025-02-06 19:53:12,967] multiqc [DEBUG ] No samples found: flash
[2025-02-06 19:53:12,973] multiqc [DEBUG ] No samples found: seqyclean
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'.
[2025-02-06 19:53:12,973] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'.
[2025-02-06 19:53:12,974] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'.
[2025-02-06 19:53:12,982] multiqc [INFO ] Compressing plot data
[2025-02-06 19:53:13,094] multiqc [INFO ] Report : multiqc_report.html
[2025-02-06 19:53:13,094] multiqc [INFO ] Data : multiqc_data
[2025-02-06 19:53:13,095] multiqc [DEBUG ] Moving data file from '/state/partition1/job-57017700/tmpbcqgllcw/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/9b/ca678bf354dce97c50ff3b531467b6/merged/multiqc_data'
[2025-02-06 19:53:13,232] multiqc [INFO ] MultiQC complete