[2022-11-23 17:20:53,507] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2022-11-23 17:20:53,507] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2022-11-23 17:20:53,507] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2022-11-23 17:20:53,508] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml
[2022-11-23 17:20:53,508] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}}
[2022-11-23 17:20:53,508] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KPKLT/1
[2022-11-23 17:20:54,016] multiqc [WARNING] MultiQC Version v1.13 now available!
[2022-11-23 17:20:54,016] multiqc [INFO ] This is MultiQC v1.9
[2022-11-23 17:20:54,016] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KPKLT/1
[2022-11-23 17:20:54,017] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KPKLT/1
[2022-11-23 17:20:54,017] multiqc [INFO ] Template : default
[2022-11-23 17:20:54,017] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2022-11-23 17:20:54,017] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KPKLT/1
[2022-11-23 17:20:54,017] 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
[2022-11-23 17:20:54,017] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27276408/tmp0zw38krx
[2022-11-23 17:20:54,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S2-2022-2_fastqc.html
[2022-11-23 17:20:54,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S2-2022-2_fastqc.html
[2022-11-23 17:20:54,155] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_undetermined_fastqc.html
[2022-11-23 17:20:54,157] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_undetermined_fastqc.html
[2022-11-23 17:20:54,177] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S5-2022-2_fastqc.html
[2022-11-23 17:20:54,179] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S5-2022-2_fastqc.html
[2022-11-23 17:20:54,198] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S5-2022-2_fastqc.html
[2022-11-23 17:20:54,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S5-2022-2_fastqc.html
[2022-11-23 17:20:54,219] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S1-2022-2_fastqc.html
[2022-11-23 17:20:54,221] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S1-2022-2_fastqc.html
[2022-11-23 17:20:54,241] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S2-2022-2_fastqc.html
[2022-11-23 17:20:54,243] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S2-2022-2_fastqc.html
[2022-11-23 17:20:54,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_undetermined_fastqc.html
[2022-11-23 17:20:54,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_undetermined_fastqc.html
[2022-11-23 17:20:54,300] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S4-2022-2_fastqc.html
[2022-11-23 17:20:54,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n02_S4-2022-2_fastqc.html
[2022-11-23 17:20:54,322] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S4-2022-2_fastqc.html
[2022-11-23 17:20:54,323] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S4-2022-2_fastqc.html
[2022-11-23 17:20:54,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S1-2022-2_fastqc.html
[2022-11-23 17:20:54,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KPKLT_l01_n01_S1-2022-2_fastqc.html
[2022-11-23 17:20:54,882] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2022-11-23 17:20:54,884] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2022-11-23 17:20:54,893] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt
[2022-11-23 17:20:54,896] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2022-11-23 17:20:54,899] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 5 samples (table)
[2022-11-23 17:20:54,904] multiqc [DEBUG ] No samples found: conpair
[2022-11-23 17:20:54,909] multiqc [DEBUG ] No samples found: peddy
[2022-11-23 17:20:54,914] multiqc [DEBUG ] No samples found: somalier
[2022-11-23 17:20:54,919] multiqc [DEBUG ] No samples found: methylQA
[2022-11-23 17:20:54,928] multiqc [DEBUG ] No samples found: mosdepth
[2022-11-23 17:20:54,933] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2022-11-23 17:20:54,936] multiqc [DEBUG ] No samples found: qualimap
[2022-11-23 17:20:54,941] multiqc [DEBUG ] No samples found: preseq
[2022-11-23 17:20:54,946] multiqc [DEBUG ] No samples found: quast
[2022-11-23 17:20:54,950] multiqc [DEBUG ] No samples found: qorts
[2022-11-23 17:20:54,955] multiqc [DEBUG ] No samples found: rna_seqc
[2022-11-23 17:20:54,959] multiqc [DEBUG ] No samples found: rockhopper
[2022-11-23 17:20:54,967] multiqc [DEBUG ] No samples found: rsem
[2022-11-23 17:20:54,979] multiqc [DEBUG ] No samples found: rseqc
[2022-11-23 17:20:54,983] multiqc [DEBUG ] No samples found: busco
[2022-11-23 17:20:54,987] multiqc [DEBUG ] No samples found: goleft_indexcov
[2022-11-23 17:20:54,992] multiqc [DEBUG ] No samples found: disambiguate
[2022-11-23 17:20:54,996] multiqc [DEBUG ] No samples found: supernova
[2022-11-23 17:20:55,010] multiqc [DEBUG ] No samples found: deeptools
[2022-11-23 17:20:55,015] multiqc [DEBUG ] No samples found: sargasso
[2022-11-23 17:20:55,019] multiqc [DEBUG ] No samples found: verifybamid
[2022-11-23 17:20:55,023] multiqc [DEBUG ] No samples found: mirtrace
[2022-11-23 17:20:55,028] multiqc [DEBUG ] No samples found: happy
[2022-11-23 17:20:55,032] multiqc [DEBUG ] No samples found: mirtop
[2022-11-23 17:20:55,038] multiqc [DEBUG ] No samples found: homer
[2022-11-23 17:20:55,043] multiqc [DEBUG ] No samples found: macs2
[2022-11-23 17:20:55,047] multiqc [DEBUG ] No samples found: theta2
[2022-11-23 17:20:55,051] multiqc [DEBUG ] No samples found: snpeff
[2022-11-23 17:20:55,058] multiqc [DEBUG ] No samples found: gatk
[2022-11-23 17:20:55,062] multiqc [DEBUG ] No samples found: htseq
[2022-11-23 17:20:55,067] multiqc [DEBUG ] No samples found: bcftools
[2022-11-23 17:20:55,071] multiqc [DEBUG ] No samples found: featureCounts
[2022-11-23 17:20:55,077] multiqc [DEBUG ] No samples found: fgbio
[2022-11-23 17:20:55,089] multiqc [DEBUG ] No samples found: dragen
[2022-11-23 17:20:55,094] multiqc [DEBUG ] No samples found: dedup
[2022-11-23 17:20:55,099] multiqc [DEBUG ] No samples found: damageprofiler
[2022-11-23 17:20:55,122] multiqc [DEBUG ] No samples found: biobambam2
[2022-11-23 17:20:55,126] multiqc [DEBUG ] No samples found: mtnucratio
[2022-11-23 17:20:55,128] multiqc [DEBUG ] No samples found: picard
[2022-11-23 17:20:55,133] multiqc [DEBUG ] No samples found: prokka
[2022-11-23 17:20:55,137] multiqc [DEBUG ] No samples found: samblaster
[2022-11-23 17:20:55,144] multiqc [DEBUG ] No samples found: samtools
[2022-11-23 17:20:55,149] multiqc [DEBUG ] No samples found: sexdeterrmine
[2022-11-23 17:20:55,153] multiqc [DEBUG ] No samples found: bamtools
[2022-11-23 17:20:55,157] multiqc [DEBUG ] No samples found: jellyfish
[2022-11-23 17:20:55,164] multiqc [DEBUG ] No samples found: vcftools
[2022-11-23 17:20:55,169] multiqc [DEBUG ] No samples found: longranger
[2022-11-23 17:20:55,173] multiqc [DEBUG ] No samples found: stacks
[2022-11-23 17:20:55,177] multiqc [DEBUG ] No samples found: varscan2
[2022-11-23 17:20:55,190] multiqc [DEBUG ] No samples found: bbmap
[2022-11-23 17:20:55,195] multiqc [DEBUG ] No samples found: bismark
[2022-11-23 17:20:55,199] multiqc [DEBUG ] No samples found: biscuit
[2022-11-23 17:20:55,204] multiqc [DEBUG ] No samples found: hicexplorer
[2022-11-23 17:20:55,208] multiqc [DEBUG ] No samples found: hicup
[2022-11-23 17:20:55,213] multiqc [DEBUG ] No samples found: hicpro
[2022-11-23 17:20:55,217] multiqc [DEBUG ] No samples found: salmon
[2022-11-23 17:20:55,221] multiqc [DEBUG ] No samples found: kallisto
[2022-11-23 17:20:55,225] multiqc [DEBUG ] No samples found: slamdunk
[2022-11-23 17:20:55,230] multiqc [DEBUG ] No samples found: star
[2022-11-23 17:20:55,234] multiqc [DEBUG ] No samples found: hisat2
[2022-11-23 17:20:55,238] multiqc [DEBUG ] No samples found: tophat
[2022-11-23 17:20:55,243] multiqc [DEBUG ] No samples found: bowtie2
[2022-11-23 17:20:55,247] multiqc [DEBUG ] No samples found: bowtie1
[2022-11-23 17:20:55,251] multiqc [DEBUG ] No samples found: snpsplit
[2022-11-23 17:20:55,256] multiqc [DEBUG ] No samples found: kat
[2022-11-23 17:20:55,260] multiqc [DEBUG ] No samples found: leehom
[2022-11-23 17:20:55,264] multiqc [DEBUG ] No samples found: adapterRemoval
[2022-11-23 17:20:55,268] multiqc [DEBUG ] No samples found: clipandmerge
[2022-11-23 17:20:55,272] multiqc [DEBUG ] No samples found: cutadapt
[2022-11-23 17:20:55,276] multiqc [DEBUG ] No samples found: flexbar
[2022-11-23 17:20:55,281] multiqc [DEBUG ] No samples found: kaiju
[2022-11-23 17:20:55,285] multiqc [DEBUG ] No samples found: kraken
[2022-11-23 17:20:55,290] multiqc [DEBUG ] No samples found: malt
[2022-11-23 17:20:55,294] multiqc [DEBUG ] No samples found: trimmomatic
[2022-11-23 17:20:55,298] multiqc [DEBUG ] No samples found: sickle
[2022-11-23 17:20:55,303] multiqc [DEBUG ] No samples found: skewer
[2022-11-23 17:20:55,307] multiqc [DEBUG ] No samples found: sortmerna
[2022-11-23 17:20:55,311] multiqc [DEBUG ] No samples found: biobloomtools
[2022-11-23 17:20:55,315] multiqc [DEBUG ] No samples found: fastq_screen
[2022-11-23 17:20:55,320] multiqc [DEBUG ] No samples found: afterqc
[2022-11-23 17:20:55,324] multiqc [DEBUG ] No samples found: fastp
[2022-11-23 17:20:55,361] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports
[2022-11-23 17:20:55,361] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n01_S2-2022-2'
[2022-11-23 17:20:55,361] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n01_S4-2022-2'
[2022-11-23 17:20:55,361] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n01_S5-2022-2'
[2022-11-23 17:20:55,361] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n01_undetermined'
[2022-11-23 17:20:55,361] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n01_S1-2022-2'
[2022-11-23 17:20:55,362] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n02_undetermined'
[2022-11-23 17:20:55,362] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n02_S4-2022-2'
[2022-11-23 17:20:55,362] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n02_S2-2022-2'
[2022-11-23 17:20:55,362] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n02_S1-2022-2'
[2022-11-23 17:20:55,362] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-KPKLT_l01_n02_S5-2022-2'
[2022-11-23 17:20:55,371] multiqc.modules.fastqc.fastqc [DEBUG ] sequence_quality not found in FastQC reports
[2022-11-23 17:20:55,371] multiqc.modules.fastqc.fastqc [DEBUG ] per_seq_quality not found in FastQC reports
[2022-11-23 17:20:55,388] multiqc.modules.fastqc.fastqc [DEBUG ] adapter_content not found in FastQC reports
[2022-11-23 17:20:55,397] multiqc [DEBUG ] No samples found: pycoqc
[2022-11-23 17:20:55,401] multiqc [DEBUG ] No samples found: minionqc
[2022-11-23 17:20:55,405] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2022-11-23 17:20:55,410] multiqc [DEBUG ] No samples found: clusterflow
[2022-11-23 17:20:55,414] multiqc [DEBUG ] No samples found: bcl2fastq
[2022-11-23 17:20:55,419] multiqc [DEBUG ] No samples found: interop
[2022-11-23 17:20:55,423] multiqc [DEBUG ] No samples found: ivar
[2022-11-23 17:20:55,428] multiqc [DEBUG ] No samples found: flash
[2022-11-23 17:20:55,432] multiqc [DEBUG ] No samples found: seqyclean
[2022-11-23 17:20:55,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found.
[2022-11-23 17:20:55,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'.
[2022-11-23 17:20:55,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'.
[2022-11-23 17:20:55,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2022-11-23 17:20:55,445] multiqc [INFO ] Compressing plot data
[2022-11-23 17:20:55,493] multiqc [INFO ] Report : multiqc_report.html
[2022-11-23 17:20:55,493] multiqc [INFO ] Data : multiqc_data
[2022-11-23 17:20:55,493] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27276408/tmp0zw38krx/multiqc_data' to '/scratch/gencore/logs/html/000000000-KPKLT/1/multiqc_data'
[2022-11-23 17:20:55,633] multiqc [INFO ] MultiQC complete