[2022-06-07 20:47:40,225] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2022-06-07 20:47:40,225] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2022-06-07 20:47:40,225] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2022-06-07 20:47:40,226] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml
[2022-06-07 20:47:40,226] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}}
[2022-06-07 20:47:40,226] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMCYCAFX3/merged
[2022-06-07 20:47:40,783] multiqc [WARNING] MultiQC Version v1.12 now available!
[2022-06-07 20:47:40,784] multiqc [INFO ] This is MultiQC v1.9
[2022-06-07 20:47:40,784] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMCYCAFX3/merged
[2022-06-07 20:47:40,784] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMCYCAFX3/merged
[2022-06-07 20:47:40,784] multiqc [INFO ] Template : default
[2022-06-07 20:47:40,784] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2022-06-07 20:47:40,784] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMCYCAFX3/merged
[2022-06-07 20:47:40,784] 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
[2022-06-07 20:47:40,784] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20616092/tmpwdfp8u1m
[2022-06-07 20:47:40,887] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCYCAFX3_n02_undetermined_fastqc.html
[2022-06-07 20:47:40,890] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCYCAFX3_n02_undetermined_fastqc.html
[2022-06-07 20:47:40,918] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCYCAFX3_n01_undetermined_fastqc.html
[2022-06-07 20:47:40,920] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCYCAFX3_n01_undetermined_fastqc.html
[2022-06-07 20:47:40,940] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCYCAFX3_n01_NPB-2__fastqc.html
[2022-06-07 20:47:40,942] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCYCAFX3_n01_NPB-2__fastqc.html
[2022-06-07 20:47:40,983] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCYCAFX3_n02_NPB-2__fastqc.html
[2022-06-07 20:47:40,985] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCYCAFX3_n02_NPB-2__fastqc.html
[2022-06-07 20:47:41,327] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2022-06-07 20:47:41,328] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2022-06-07 20:47:41,333] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt
[2022-06-07 20:47:41,335] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table)
[2022-06-07 20:47:41,337] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2022-06-07 20:47:41,341] multiqc [DEBUG ] No samples found: conpair
[2022-06-07 20:47:41,346] multiqc [DEBUG ] No samples found: peddy
[2022-06-07 20:47:41,350] multiqc [DEBUG ] No samples found: somalier
[2022-06-07 20:47:41,355] multiqc [DEBUG ] No samples found: methylQA
[2022-06-07 20:47:41,363] multiqc [DEBUG ] No samples found: mosdepth
[2022-06-07 20:47:41,367] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2022-06-07 20:47:41,370] multiqc [DEBUG ] No samples found: qualimap
[2022-06-07 20:47:41,374] multiqc [DEBUG ] No samples found: preseq
[2022-06-07 20:47:41,379] multiqc [DEBUG ] No samples found: quast
[2022-06-07 20:47:41,383] multiqc [DEBUG ] No samples found: qorts
[2022-06-07 20:47:41,388] multiqc [DEBUG ] No samples found: rna_seqc
[2022-06-07 20:47:41,392] multiqc [DEBUG ] No samples found: rockhopper
[2022-06-07 20:47:41,396] multiqc [DEBUG ] No samples found: rsem
[2022-06-07 20:47:41,407] multiqc [DEBUG ] No samples found: rseqc
[2022-06-07 20:47:41,411] multiqc [DEBUG ] No samples found: busco
[2022-06-07 20:47:41,415] multiqc [DEBUG ] No samples found: goleft_indexcov
[2022-06-07 20:47:41,419] multiqc [DEBUG ] No samples found: disambiguate
[2022-06-07 20:47:41,424] multiqc [DEBUG ] No samples found: supernova
[2022-06-07 20:47:41,436] multiqc [DEBUG ] No samples found: deeptools
[2022-06-07 20:47:41,441] multiqc [DEBUG ] No samples found: sargasso
[2022-06-07 20:47:41,445] multiqc [DEBUG ] No samples found: verifybamid
[2022-06-07 20:47:41,449] multiqc [DEBUG ] No samples found: mirtrace
[2022-06-07 20:47:41,455] multiqc [DEBUG ] No samples found: happy
[2022-06-07 20:47:41,463] multiqc [DEBUG ] No samples found: mirtop
[2022-06-07 20:47:41,470] multiqc [DEBUG ] No samples found: homer
[2022-06-07 20:47:41,474] multiqc [DEBUG ] No samples found: macs2
[2022-06-07 20:47:41,480] multiqc [DEBUG ] No samples found: theta2
[2022-06-07 20:47:41,484] multiqc [DEBUG ] No samples found: snpeff
[2022-06-07 20:47:41,490] multiqc [DEBUG ] No samples found: gatk
[2022-06-07 20:47:41,494] multiqc [DEBUG ] No samples found: htseq
[2022-06-07 20:47:41,499] multiqc [DEBUG ] No samples found: bcftools
[2022-06-07 20:47:41,504] multiqc [DEBUG ] No samples found: featureCounts
[2022-06-07 20:47:41,510] multiqc [DEBUG ] No samples found: fgbio
[2022-06-07 20:47:41,522] multiqc [DEBUG ] No samples found: dragen
[2022-06-07 20:47:41,526] multiqc [DEBUG ] No samples found: dedup
[2022-06-07 20:47:41,530] multiqc [DEBUG ] No samples found: damageprofiler
[2022-06-07 20:47:41,553] multiqc [DEBUG ] No samples found: biobambam2
[2022-06-07 20:47:41,559] multiqc [DEBUG ] No samples found: mtnucratio
[2022-06-07 20:47:41,561] multiqc [DEBUG ] No samples found: picard
[2022-06-07 20:47:41,567] multiqc [DEBUG ] No samples found: prokka
[2022-06-07 20:47:41,572] multiqc [DEBUG ] No samples found: samblaster
[2022-06-07 20:47:41,580] multiqc [DEBUG ] No samples found: samtools
[2022-06-07 20:47:41,584] multiqc [DEBUG ] No samples found: sexdeterrmine
[2022-06-07 20:47:41,589] multiqc [DEBUG ] No samples found: bamtools
[2022-06-07 20:47:41,596] multiqc [DEBUG ] No samples found: jellyfish
[2022-06-07 20:47:41,604] multiqc [DEBUG ] No samples found: vcftools
[2022-06-07 20:47:41,608] multiqc [DEBUG ] No samples found: longranger
[2022-06-07 20:47:41,612] multiqc [DEBUG ] No samples found: stacks
[2022-06-07 20:47:41,617] multiqc [DEBUG ] No samples found: varscan2
[2022-06-07 20:47:41,629] multiqc [DEBUG ] No samples found: bbmap
[2022-06-07 20:47:41,634] multiqc [DEBUG ] No samples found: bismark
[2022-06-07 20:47:41,638] multiqc [DEBUG ] No samples found: biscuit
[2022-06-07 20:47:41,643] multiqc [DEBUG ] No samples found: hicexplorer
[2022-06-07 20:47:41,648] multiqc [DEBUG ] No samples found: hicup
[2022-06-07 20:47:41,652] multiqc [DEBUG ] No samples found: hicpro
[2022-06-07 20:47:41,656] multiqc [DEBUG ] No samples found: salmon
[2022-06-07 20:47:41,661] multiqc [DEBUG ] No samples found: kallisto
[2022-06-07 20:47:41,665] multiqc [DEBUG ] No samples found: slamdunk
[2022-06-07 20:47:41,671] multiqc [DEBUG ] No samples found: star
[2022-06-07 20:47:41,677] multiqc [DEBUG ] No samples found: hisat2
[2022-06-07 20:47:41,681] multiqc [DEBUG ] No samples found: tophat
[2022-06-07 20:47:41,686] multiqc [DEBUG ] No samples found: bowtie2
[2022-06-07 20:47:41,690] multiqc [DEBUG ] No samples found: bowtie1
[2022-06-07 20:47:41,694] multiqc [DEBUG ] No samples found: snpsplit
[2022-06-07 20:47:41,698] multiqc [DEBUG ] No samples found: kat
[2022-06-07 20:47:41,702] multiqc [DEBUG ] No samples found: leehom
[2022-06-07 20:47:41,706] multiqc [DEBUG ] No samples found: adapterRemoval
[2022-06-07 20:47:41,710] multiqc [DEBUG ] No samples found: clipandmerge
[2022-06-07 20:47:41,715] multiqc [DEBUG ] No samples found: cutadapt
[2022-06-07 20:47:41,719] multiqc [DEBUG ] No samples found: flexbar
[2022-06-07 20:47:41,725] multiqc [DEBUG ] No samples found: kaiju
[2022-06-07 20:47:41,729] multiqc [DEBUG ] No samples found: kraken
[2022-06-07 20:47:41,735] multiqc [DEBUG ] No samples found: malt
[2022-06-07 20:47:41,741] multiqc [DEBUG ] No samples found: trimmomatic
[2022-06-07 20:47:41,747] multiqc [DEBUG ] No samples found: sickle
[2022-06-07 20:47:41,754] multiqc [DEBUG ] No samples found: skewer
[2022-06-07 20:47:41,758] multiqc [DEBUG ] No samples found: sortmerna
[2022-06-07 20:47:41,764] multiqc [DEBUG ] No samples found: biobloomtools
[2022-06-07 20:47:41,772] multiqc [DEBUG ] No samples found: fastq_screen
[2022-06-07 20:47:41,776] multiqc [DEBUG ] No samples found: afterqc
[2022-06-07 20:47:41,781] multiqc [DEBUG ] No samples found: fastp
[2022-06-07 20:47:41,831] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports
[2022-06-07 20:47:41,831] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMCYCAFX3_n02_undetermined'
[2022-06-07 20:47:41,831] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMCYCAFX3_n01_undetermined'
[2022-06-07 20:47:41,876] multiqc [DEBUG ] No samples found: pycoqc
[2022-06-07 20:47:41,880] multiqc [DEBUG ] No samples found: minionqc
[2022-06-07 20:47:41,885] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2022-06-07 20:47:41,889] multiqc [DEBUG ] No samples found: clusterflow
[2022-06-07 20:47:41,895] multiqc [DEBUG ] No samples found: bcl2fastq
[2022-06-07 20:47:41,901] multiqc [DEBUG ] No samples found: interop
[2022-06-07 20:47:41,907] multiqc [DEBUG ] No samples found: ivar
[2022-06-07 20:47:41,913] multiqc [DEBUG ] No samples found: flash
[2022-06-07 20:47:41,918] multiqc [DEBUG ] No samples found: seqyclean
[2022-06-07 20:47:41,918] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'.
[2022-06-07 20:47:41,918] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2022-06-07 20:47:41,918] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2022-06-07 20:47:41,923] multiqc [INFO ] Compressing plot data
[2022-06-07 20:47:41,979] multiqc [INFO ] Report : multiqc_report.html
[2022-06-07 20:47:41,979] multiqc [INFO ] Data : multiqc_data
[2022-06-07 20:47:41,979] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20616092/tmpwdfp8u1m/multiqc_data' to '/scratch/gencore/logs/html/HMCYCAFX3/merged/multiqc_data'
[2022-06-07 20:47:42,099] multiqc [INFO ] MultiQC complete