[2024-10-14 01:09:21,800] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2024-10-14 01:09:21,800] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2024-10-14 01:09:21,800] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2024-10-14 01:09:21,802] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml
[2024-10-14 01:09:21,803] 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}}
[2024-10-14 01:09:21,803] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-10-14 01:09:21,839] multiqc [DEBUG ] Could not connect to multiqc.info for version check: <urlopen error unknown url type: https>
[2024-10-14 01:09:21,839] multiqc [INFO ] This is MultiQC v1.9
[2024-10-14 01:09:21,839] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-10-14 01:09:21,839] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/bc/9538d410f542ce4b6b22dc4b5aaa8d/1
[2024-10-14 01:09:21,839] multiqc [INFO ] Template : default
[2024-10-14 01:09:21,839] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2024-10-14 01:09:21,839] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/bc/9538d410f542ce4b6b22dc4b5aaa8d/1
[2024-10-14 01:09:21,840] 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
[2024-10-14 01:09:21,840] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-52158573/tmp1dezas39
[2024-10-14 01:09:21,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.1_fastqc.html
[2024-10-14 01:09:21,951] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.1_fastqc.html
[2024-10-14 01:09:22,031] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.3_fastqc.html
[2024-10-14 01:09:22,033] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.3_fastqc.html
[2024-10-14 01:09:22,079] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.4_fastqc.html
[2024-10-14 01:09:22,081] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.4_fastqc.html
[2024-10-14 01:09:22,081] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.4_fastqc.html
[2024-10-14 01:09:22,081] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.4_fastqc.html
[2024-10-14 01:09:22,081] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.4_fastqc.html
[2024-10-14 01:09:22,081] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.4_fastqc.html
[2024-10-14 01:09:22,081] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.4_fastqc.html
[2024-10-14 01:09:22,155] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.2_fastqc.html
[2024-10-14 01:09:22,157] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LRD8L_l01.2_fastqc.html
[2024-10-14 01:09:22,737] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2024-10-14 01:09:22,738] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2024-10-14 01:09:22,743] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2024-10-14 01:09:22,750] multiqc [DEBUG ] No samples found: conpair
[2024-10-14 01:09:22,756] multiqc [DEBUG ] No samples found: peddy
[2024-10-14 01:09:22,762] multiqc [DEBUG ] No samples found: somalier
[2024-10-14 01:09:22,768] multiqc [DEBUG ] No samples found: methylQA
[2024-10-14 01:09:22,778] multiqc [DEBUG ] No samples found: mosdepth
[2024-10-14 01:09:22,783] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2024-10-14 01:09:22,787] multiqc [DEBUG ] No samples found: qualimap
[2024-10-14 01:09:22,793] multiqc [DEBUG ] No samples found: preseq
[2024-10-14 01:09:22,799] multiqc [DEBUG ] No samples found: quast
[2024-10-14 01:09:22,804] multiqc [DEBUG ] No samples found: qorts
[2024-10-14 01:09:22,810] multiqc [DEBUG ] No samples found: rna_seqc
[2024-10-14 01:09:22,815] multiqc [DEBUG ] No samples found: rockhopper
[2024-10-14 01:09:22,821] multiqc [DEBUG ] No samples found: rsem
[2024-10-14 01:09:22,835] multiqc [DEBUG ] No samples found: rseqc
[2024-10-14 01:09:22,840] multiqc [DEBUG ] No samples found: busco
[2024-10-14 01:09:22,846] multiqc [DEBUG ] No samples found: goleft_indexcov
[2024-10-14 01:09:22,851] multiqc [DEBUG ] No samples found: disambiguate
[2024-10-14 01:09:22,857] multiqc [DEBUG ] No samples found: supernova
[2024-10-14 01:09:22,873] multiqc [DEBUG ] No samples found: deeptools
[2024-10-14 01:09:22,879] multiqc [DEBUG ] No samples found: sargasso
[2024-10-14 01:09:22,884] multiqc [DEBUG ] No samples found: verifybamid
[2024-10-14 01:09:22,890] multiqc [DEBUG ] No samples found: mirtrace
[2024-10-14 01:09:22,896] multiqc [DEBUG ] No samples found: happy
[2024-10-14 01:09:22,902] multiqc [DEBUG ] No samples found: mirtop
[2024-10-14 01:09:22,911] multiqc [DEBUG ] No samples found: homer
[2024-10-14 01:09:22,916] multiqc [DEBUG ] No samples found: macs2
[2024-10-14 01:09:22,922] multiqc [DEBUG ] No samples found: theta2
[2024-10-14 01:09:22,927] multiqc [DEBUG ] No samples found: snpeff
[2024-10-14 01:09:22,935] multiqc [DEBUG ] No samples found: gatk
[2024-10-14 01:09:22,941] multiqc [DEBUG ] No samples found: htseq
[2024-10-14 01:09:22,947] multiqc [DEBUG ] No samples found: bcftools
[2024-10-14 01:09:22,953] multiqc [DEBUG ] No samples found: featureCounts
[2024-10-14 01:09:22,961] multiqc [DEBUG ] No samples found: fgbio
[2024-10-14 01:09:22,977] multiqc [DEBUG ] No samples found: dragen
[2024-10-14 01:09:22,982] multiqc [DEBUG ] No samples found: dedup
[2024-10-14 01:09:22,987] multiqc [DEBUG ] No samples found: damageprofiler
[2024-10-14 01:09:23,014] multiqc [DEBUG ] No samples found: biobambam2
[2024-10-14 01:09:23,020] multiqc [DEBUG ] No samples found: mtnucratio
[2024-10-14 01:09:23,022] multiqc [DEBUG ] No samples found: picard
[2024-10-14 01:09:23,028] multiqc [DEBUG ] No samples found: prokka
[2024-10-14 01:09:23,033] multiqc [DEBUG ] No samples found: samblaster
[2024-10-14 01:09:23,043] multiqc [DEBUG ] No samples found: samtools
[2024-10-14 01:09:23,048] multiqc [DEBUG ] No samples found: sexdeterrmine
[2024-10-14 01:09:23,055] multiqc [DEBUG ] No samples found: bamtools
[2024-10-14 01:09:23,060] multiqc [DEBUG ] No samples found: jellyfish
[2024-10-14 01:09:23,069] multiqc [DEBUG ] No samples found: vcftools
[2024-10-14 01:09:23,074] multiqc [DEBUG ] No samples found: longranger
[2024-10-14 01:09:23,080] multiqc [DEBUG ] No samples found: stacks
[2024-10-14 01:09:23,086] multiqc [DEBUG ] No samples found: varscan2
[2024-10-14 01:09:23,102] multiqc [DEBUG ] No samples found: bbmap
[2024-10-14 01:09:23,108] multiqc [DEBUG ] No samples found: bismark
[2024-10-14 01:09:23,114] multiqc [DEBUG ] No samples found: biscuit
[2024-10-14 01:09:23,120] multiqc [DEBUG ] No samples found: hicexplorer
[2024-10-14 01:09:23,125] multiqc [DEBUG ] No samples found: hicup
[2024-10-14 01:09:23,130] multiqc [DEBUG ] No samples found: hicpro
[2024-10-14 01:09:23,136] multiqc [DEBUG ] No samples found: salmon
[2024-10-14 01:09:23,141] multiqc [DEBUG ] No samples found: kallisto
[2024-10-14 01:09:23,147] multiqc [DEBUG ] No samples found: slamdunk
[2024-10-14 01:09:23,152] multiqc [DEBUG ] No samples found: star
[2024-10-14 01:09:23,157] multiqc [DEBUG ] No samples found: hisat2
[2024-10-14 01:09:23,162] multiqc [DEBUG ] No samples found: tophat
[2024-10-14 01:09:23,168] multiqc [DEBUG ] No samples found: bowtie2
[2024-10-14 01:09:23,173] multiqc [DEBUG ] No samples found: bowtie1
[2024-10-14 01:09:23,178] multiqc [DEBUG ] No samples found: snpsplit
[2024-10-14 01:09:23,184] multiqc [DEBUG ] No samples found: kat
[2024-10-14 01:09:23,189] multiqc [DEBUG ] No samples found: leehom
[2024-10-14 01:09:23,194] multiqc [DEBUG ] No samples found: adapterRemoval
[2024-10-14 01:09:23,200] multiqc [DEBUG ] No samples found: clipandmerge
[2024-10-14 01:09:23,205] multiqc [DEBUG ] No samples found: cutadapt
[2024-10-14 01:09:23,211] multiqc [DEBUG ] No samples found: flexbar
[2024-10-14 01:09:23,216] multiqc [DEBUG ] No samples found: kaiju
[2024-10-14 01:09:23,221] multiqc [DEBUG ] No samples found: kraken
[2024-10-14 01:09:23,226] multiqc [DEBUG ] No samples found: malt
[2024-10-14 01:09:23,231] multiqc [DEBUG ] No samples found: trimmomatic
[2024-10-14 01:09:23,237] multiqc [DEBUG ] No samples found: sickle
[2024-10-14 01:09:23,242] multiqc [DEBUG ] No samples found: skewer
[2024-10-14 01:09:23,247] multiqc [DEBUG ] No samples found: sortmerna
[2024-10-14 01:09:23,252] multiqc [DEBUG ] No samples found: biobloomtools
[2024-10-14 01:09:23,258] multiqc [DEBUG ] No samples found: fastq_screen
[2024-10-14 01:09:23,263] multiqc [DEBUG ] No samples found: afterqc
[2024-10-14 01:09:23,269] multiqc [DEBUG ] No samples found: fastp
[2024-10-14 01:09:23,319] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports
[2024-10-14 01:09:23,395] multiqc [DEBUG ] No samples found: pycoqc
[2024-10-14 01:09:23,400] multiqc [DEBUG ] No samples found: minionqc
[2024-10-14 01:09:23,406] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2024-10-14 01:09:23,411] multiqc [DEBUG ] No samples found: clusterflow
[2024-10-14 01:09:23,416] multiqc [DEBUG ] No samples found: bcl2fastq
[2024-10-14 01:09:23,422] multiqc [DEBUG ] No samples found: interop
[2024-10-14 01:09:23,427] multiqc [DEBUG ] No samples found: ivar
[2024-10-14 01:09:23,432] multiqc [DEBUG ] No samples found: flash
[2024-10-14 01:09:23,437] multiqc [DEBUG ] No samples found: seqyclean
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'.
[2024-10-14 01:09:23,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2024-10-14 01:09:23,438] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'.
[2024-10-14 01:09:23,438] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'.
[2024-10-14 01:09:23,438] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'.
[2024-10-14 01:09:23,438] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'.
[2024-10-14 01:09:23,438] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'.
[2024-10-14 01:09:23,443] multiqc [INFO ] Compressing plot data
[2024-10-14 01:09:23,532] multiqc [INFO ] Report : multiqc_report.html
[2024-10-14 01:09:23,532] multiqc [INFO ] Data : multiqc_data
[2024-10-14 01:09:23,532] multiqc [DEBUG ] Moving data file from '/state/partition1/job-52158573/tmp1dezas39/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/bc/9538d410f542ce4b6b22dc4b5aaa8d/1/multiqc_data'
[2024-10-14 01:09:23,660] multiqc [INFO ] MultiQC complete