[2024-07-21 03:16:48,143] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2024-07-21 03:16:48,143] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2024-07-21 03:16:48,144] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2024-07-21 03:16:48,147] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml
[2024-07-21 03:16:48,147] 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}}
[2024-07-21 03:16:48,147] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-07-21 03:16:48,183] multiqc [DEBUG ] Could not connect to multiqc.info for version check: <urlopen error unknown url type: https>
[2024-07-21 03:16:48,183] multiqc [INFO ] This is MultiQC v1.9
[2024-07-21 03:16:48,183] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-07-21 03:16:48,183] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/84/87d518430b31139f3e0a916a2284e3/merged
[2024-07-21 03:16:48,183] multiqc [INFO ] Template : default
[2024-07-21 03:16:48,183] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2024-07-21 03:16:48,183] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/84/87d518430b31139f3e0a916a2284e3/merged
[2024-07-21 03:16:48,183] 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
[2024-07-21 03:16:48,184] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-48764484/tmplhs0ec7f
[2024-07-21 03:16:48,311] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_10_fastqc.html
[2024-07-21 03:16:48,319] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_10_fastqc.html
[2024-07-21 03:16:48,389] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_1_fastqc.html
[2024-07-21 03:16:48,396] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_1_fastqc.html
[2024-07-21 03:16:48,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_20_fastqc.html
[2024-07-21 03:16:48,476] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_20_fastqc.html
[2024-07-21 03:16:48,549] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_5_fastqc.html
[2024-07-21 03:16:48,556] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n01_20240710_InfluenzaMix_5_fastqc.html
[2024-07-21 03:16:48,626] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n01_undetermined_fastqc.html
[2024-07-21 03:16:48,632] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n01_undetermined_fastqc.html
[2024-07-21 03:16:48,694] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_10_fastqc.html
[2024-07-21 03:16:48,700] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_10_fastqc.html
[2024-07-21 03:16:48,769] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_1_fastqc.html
[2024-07-21 03:16:48,777] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_1_fastqc.html
[2024-07-21 03:16:48,845] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_20_fastqc.html
[2024-07-21 03:16:48,852] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_20_fastqc.html
[2024-07-21 03:16:48,921] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_5_fastqc.html
[2024-07-21 03:16:48,927] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n02_20240710_InfluenzaMix_5_fastqc.html
[2024-07-21 03:16:48,995] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFHHKDRX5_n02_undetermined_fastqc.html
[2024-07-21 03:16:49,001] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFHHKDRX5_n02_undetermined_fastqc.html
[2024-07-21 03:16:49,063] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-07-21 03:16:49,069] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-07-21 03:16:49,069] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-07-21 03:16:49,069] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-07-21 03:16:49,069] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-07-21 03:16:49,069] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-07-21 03:16:49,069] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2024-07-21 03:16:50,100] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2024-07-21 03:16:50,102] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2024-07-21 03:16:50,114] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table)
[2024-07-21 03:16:50,115] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2024-07-21 03:16:50,125] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table)
[2024-07-21 03:16:50,131] multiqc [DEBUG ] No samples found: conpair
[2024-07-21 03:16:50,136] multiqc [DEBUG ] No samples found: peddy
[2024-07-21 03:16:50,142] multiqc [DEBUG ] No samples found: somalier
[2024-07-21 03:16:50,148] multiqc [DEBUG ] No samples found: methylQA
[2024-07-21 03:16:50,158] multiqc [DEBUG ] No samples found: mosdepth
[2024-07-21 03:16:50,163] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2024-07-21 03:16:50,166] multiqc [DEBUG ] No samples found: qualimap
[2024-07-21 03:16:50,171] multiqc [DEBUG ] No samples found: preseq
[2024-07-21 03:16:50,177] multiqc [DEBUG ] No samples found: quast
[2024-07-21 03:16:50,183] multiqc [DEBUG ] No samples found: qorts
[2024-07-21 03:16:50,189] multiqc [DEBUG ] No samples found: rna_seqc
[2024-07-21 03:16:50,194] multiqc [DEBUG ] No samples found: rockhopper
[2024-07-21 03:16:50,200] multiqc [DEBUG ] No samples found: rsem
[2024-07-21 03:16:50,212] multiqc [DEBUG ] No samples found: rseqc
[2024-07-21 03:16:50,217] multiqc [DEBUG ] No samples found: busco
[2024-07-21 03:16:50,223] multiqc [DEBUG ] No samples found: goleft_indexcov
[2024-07-21 03:16:50,229] multiqc [DEBUG ] No samples found: disambiguate
[2024-07-21 03:16:50,235] multiqc [DEBUG ] No samples found: supernova
[2024-07-21 03:16:50,250] multiqc [DEBUG ] No samples found: deeptools
[2024-07-21 03:16:50,256] multiqc [DEBUG ] No samples found: sargasso
[2024-07-21 03:16:50,262] multiqc [DEBUG ] No samples found: verifybamid
[2024-07-21 03:16:50,272] multiqc [DEBUG ] No samples found: mirtrace
[2024-07-21 03:16:50,277] multiqc [DEBUG ] No samples found: happy
[2024-07-21 03:16:50,283] multiqc [DEBUG ] No samples found: mirtop
[2024-07-21 03:16:50,290] multiqc [DEBUG ] No samples found: homer
[2024-07-21 03:16:50,296] multiqc [DEBUG ] No samples found: macs2
[2024-07-21 03:16:50,301] multiqc [DEBUG ] No samples found: theta2
[2024-07-21 03:16:50,306] multiqc [DEBUG ] No samples found: snpeff
[2024-07-21 03:16:50,315] multiqc [DEBUG ] No samples found: gatk
[2024-07-21 03:16:50,320] multiqc [DEBUG ] No samples found: htseq
[2024-07-21 03:16:50,327] multiqc [DEBUG ] No samples found: bcftools
[2024-07-21 03:16:50,332] multiqc [DEBUG ] No samples found: featureCounts
[2024-07-21 03:16:50,340] multiqc [DEBUG ] No samples found: fgbio
[2024-07-21 03:16:50,354] multiqc [DEBUG ] No samples found: dragen
[2024-07-21 03:16:50,360] multiqc [DEBUG ] No samples found: dedup
[2024-07-21 03:16:50,365] multiqc [DEBUG ] No samples found: damageprofiler
[2024-07-21 03:16:50,395] multiqc [DEBUG ] No samples found: biobambam2
[2024-07-21 03:16:50,402] multiqc [DEBUG ] No samples found: mtnucratio
[2024-07-21 03:16:50,404] multiqc [DEBUG ] No samples found: picard
[2024-07-21 03:16:50,410] multiqc [DEBUG ] No samples found: prokka
[2024-07-21 03:16:50,415] multiqc [DEBUG ] No samples found: samblaster
[2024-07-21 03:16:50,425] multiqc [DEBUG ] No samples found: samtools
[2024-07-21 03:16:50,431] multiqc [DEBUG ] No samples found: sexdeterrmine
[2024-07-21 03:16:50,436] multiqc [DEBUG ] No samples found: bamtools
[2024-07-21 03:16:50,442] multiqc [DEBUG ] No samples found: jellyfish
[2024-07-21 03:16:50,451] multiqc [DEBUG ] No samples found: vcftools
[2024-07-21 03:16:50,457] multiqc [DEBUG ] No samples found: longranger
[2024-07-21 03:16:50,463] multiqc [DEBUG ] No samples found: stacks
[2024-07-21 03:16:50,469] multiqc [DEBUG ] No samples found: varscan2
[2024-07-21 03:16:50,484] multiqc [DEBUG ] No samples found: bbmap
[2024-07-21 03:16:50,490] multiqc [DEBUG ] No samples found: bismark
[2024-07-21 03:16:50,495] multiqc [DEBUG ] No samples found: biscuit
[2024-07-21 03:16:50,501] multiqc [DEBUG ] No samples found: hicexplorer
[2024-07-21 03:16:50,506] multiqc [DEBUG ] No samples found: hicup
[2024-07-21 03:16:50,512] multiqc [DEBUG ] No samples found: hicpro
[2024-07-21 03:16:50,517] multiqc [DEBUG ] No samples found: salmon
[2024-07-21 03:16:50,523] multiqc [DEBUG ] No samples found: kallisto
[2024-07-21 03:16:50,529] multiqc [DEBUG ] No samples found: slamdunk
[2024-07-21 03:16:50,534] multiqc [DEBUG ] No samples found: star
[2024-07-21 03:16:50,540] multiqc [DEBUG ] No samples found: hisat2
[2024-07-21 03:16:50,545] multiqc [DEBUG ] No samples found: tophat
[2024-07-21 03:16:50,551] multiqc [DEBUG ] No samples found: bowtie2
[2024-07-21 03:16:50,560] multiqc [DEBUG ] No samples found: bowtie1
[2024-07-21 03:16:50,567] multiqc [DEBUG ] No samples found: snpsplit
[2024-07-21 03:16:50,572] multiqc [DEBUG ] No samples found: kat
[2024-07-21 03:16:50,577] multiqc [DEBUG ] No samples found: leehom
[2024-07-21 03:16:50,583] multiqc [DEBUG ] No samples found: adapterRemoval
[2024-07-21 03:16:50,588] multiqc [DEBUG ] No samples found: clipandmerge
[2024-07-21 03:16:50,594] multiqc [DEBUG ] No samples found: cutadapt
[2024-07-21 03:16:50,599] multiqc [DEBUG ] No samples found: flexbar
[2024-07-21 03:16:50,605] multiqc [DEBUG ] No samples found: kaiju
[2024-07-21 03:16:50,610] multiqc [DEBUG ] No samples found: kraken
[2024-07-21 03:16:50,616] multiqc [DEBUG ] No samples found: malt
[2024-07-21 03:16:50,621] multiqc [DEBUG ] No samples found: trimmomatic
[2024-07-21 03:16:50,626] multiqc [DEBUG ] No samples found: sickle
[2024-07-21 03:16:50,632] multiqc [DEBUG ] No samples found: skewer
[2024-07-21 03:16:50,637] multiqc [DEBUG ] No samples found: sortmerna
[2024-07-21 03:16:50,642] multiqc [DEBUG ] No samples found: biobloomtools
[2024-07-21 03:16:50,647] multiqc [DEBUG ] No samples found: fastq_screen
[2024-07-21 03:16:50,652] multiqc [DEBUG ] No samples found: afterqc
[2024-07-21 03:16:50,658] multiqc [DEBUG ] No samples found: fastp
[2024-07-21 03:16:50,922] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports
[2024-07-21 03:16:51,027] multiqc [DEBUG ] No samples found: pycoqc
[2024-07-21 03:16:51,032] multiqc [DEBUG ] No samples found: minionqc
[2024-07-21 03:16:51,038] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2024-07-21 03:16:51,043] multiqc [DEBUG ] No samples found: clusterflow
[2024-07-21 03:16:51,048] multiqc [DEBUG ] No samples found: bcl2fastq
[2024-07-21 03:16:51,055] multiqc [DEBUG ] No samples found: interop
[2024-07-21 03:16:51,060] multiqc [DEBUG ] No samples found: ivar
[2024-07-21 03:16:51,090] multiqc [DEBUG ] No samples found: flash
[2024-07-21 03:16:51,095] multiqc [DEBUG ] No samples found: seqyclean
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'.
[2024-07-21 03:16:51,096] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'.
[2024-07-21 03:16:51,109] multiqc [INFO ] Compressing plot data
[2024-07-21 03:16:51,304] multiqc [INFO ] Report : multiqc_report.html
[2024-07-21 03:16:51,305] multiqc [INFO ] Data : multiqc_data
[2024-07-21 03:16:51,305] multiqc [DEBUG ] Moving data file from '/state/partition1/job-48764484/tmplhs0ec7f/multiqc_data' to '/vast/gencore/GENEFLOW/work/84/87d518430b31139f3e0a916a2284e3/merged/multiqc_data'
[2024-07-21 03:16:51,477] multiqc [INFO ] MultiQC complete