[2021-11-23 10:14:59,535] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2021-11-23 10:14:59,535] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2021-11-23 10:14:59,535] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2021-11-23 10:14:59,536] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml
[2021-11-23 10:14:59,536] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}}
[2021-11-23 10:14:59,536] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMCCLBGXK/merged
[2021-11-23 10:15:01,112] multiqc [WARNING] MultiQC Version v1.11 now available!
[2021-11-23 10:15:01,112] multiqc [INFO ] This is MultiQC v1.9
[2021-11-23 10:15:01,112] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMCCLBGXK/merged
[2021-11-23 10:15:01,112] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMCCLBGXK/merged
[2021-11-23 10:15:01,112] multiqc [INFO ] Template : default
[2021-11-23 10:15:01,112] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2021-11-23 10:15:01,112] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMCCLBGXK/merged
[2021-11-23 10:15:01,113] 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
[2021-11-23 10:15:01,113] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12287838/tmpmq4fs4zw
[2021-11-23 10:15:01,216] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCCLBGXK_n02_CMC_HAP1_2_fastqc.html
[2021-11-23 10:15:01,219] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCCLBGXK_n02_CMC_HAP1_2_fastqc.html
[2021-11-23 10:15:01,258] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2021-11-23 10:15:01,259] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt
[2021-11-23 10:15:01,329] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCCLBGXK_n01_CMC_HAP1_1_fastqc.html
[2021-11-23 10:15:01,331] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCCLBGXK_n01_CMC_HAP1_1_fastqc.html
[2021-11-23 10:15:01,386] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCCLBGXK_n01_undetermined_fastqc.html
[2021-11-23 10:15:01,388] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCCLBGXK_n01_undetermined_fastqc.html
[2021-11-23 10:15:01,426] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCCLBGXK_n02_CMC_HAP1_1_fastqc.html
[2021-11-23 10:15:01,428] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCCLBGXK_n02_CMC_HAP1_1_fastqc.html
[2021-11-23 10:15:01,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCCLBGXK_n01_CMC_HAP1_2_fastqc.html
[2021-11-23 10:15:01,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCCLBGXK_n01_CMC_HAP1_2_fastqc.html
[2021-11-23 10:15:01,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMCCLBGXK_n02_undetermined_fastqc.html
[2021-11-23 10:15:01,527] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMCCLBGXK_n02_undetermined_fastqc.html
[2021-11-23 10:15:02,141] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2021-11-23 10:15:02,142] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2021-11-23 10:15:02,150] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table)
[2021-11-23 10:15:02,151] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2021-11-23 10:15:02,161] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table)
[2021-11-23 10:15:02,165] multiqc [DEBUG ] No samples found: conpair
[2021-11-23 10:15:02,169] multiqc [DEBUG ] No samples found: peddy
[2021-11-23 10:15:02,174] multiqc [DEBUG ] No samples found: somalier
[2021-11-23 10:15:02,178] multiqc [DEBUG ] No samples found: methylQA
[2021-11-23 10:15:02,184] multiqc [DEBUG ] No samples found: mosdepth
[2021-11-23 10:15:02,188] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2021-11-23 10:15:02,191] multiqc [DEBUG ] No samples found: qualimap
[2021-11-23 10:15:02,196] multiqc [DEBUG ] No samples found: preseq
[2021-11-23 10:15:02,200] multiqc [DEBUG ] No samples found: quast
[2021-11-23 10:15:02,204] multiqc [DEBUG ] No samples found: qorts
[2021-11-23 10:15:02,208] multiqc [DEBUG ] No samples found: rna_seqc
[2021-11-23 10:15:02,212] multiqc [DEBUG ] No samples found: rockhopper
[2021-11-23 10:15:02,216] multiqc [DEBUG ] No samples found: rsem
[2021-11-23 10:15:02,224] multiqc [DEBUG ] No samples found: rseqc
[2021-11-23 10:15:02,228] multiqc [DEBUG ] No samples found: busco
[2021-11-23 10:15:02,232] multiqc [DEBUG ] No samples found: goleft_indexcov
[2021-11-23 10:15:02,236] multiqc [DEBUG ] No samples found: disambiguate
[2021-11-23 10:15:02,240] multiqc [DEBUG ] No samples found: supernova
[2021-11-23 10:15:02,250] multiqc [DEBUG ] No samples found: deeptools
[2021-11-23 10:15:02,254] multiqc [DEBUG ] No samples found: sargasso
[2021-11-23 10:15:02,258] multiqc [DEBUG ] No samples found: verifybamid
[2021-11-23 10:15:02,262] multiqc [DEBUG ] No samples found: mirtrace
[2021-11-23 10:15:02,266] multiqc [DEBUG ] No samples found: happy
[2021-11-23 10:15:02,270] multiqc [DEBUG ] No samples found: mirtop
[2021-11-23 10:15:02,275] multiqc [DEBUG ] No samples found: homer
[2021-11-23 10:15:02,279] multiqc [DEBUG ] No samples found: macs2
[2021-11-23 10:15:02,282] multiqc [DEBUG ] No samples found: theta2
[2021-11-23 10:15:02,287] multiqc [DEBUG ] No samples found: snpeff
[2021-11-23 10:15:02,292] multiqc [DEBUG ] No samples found: gatk
[2021-11-23 10:15:02,296] multiqc [DEBUG ] No samples found: htseq
[2021-11-23 10:15:02,300] multiqc [DEBUG ] No samples found: bcftools
[2021-11-23 10:15:02,304] multiqc [DEBUG ] No samples found: featureCounts
[2021-11-23 10:15:02,309] multiqc [DEBUG ] No samples found: fgbio
[2021-11-23 10:15:02,319] multiqc [DEBUG ] No samples found: dragen
[2021-11-23 10:15:02,323] multiqc [DEBUG ] No samples found: dedup
[2021-11-23 10:15:02,327] multiqc [DEBUG ] No samples found: damageprofiler
[2021-11-23 10:15:02,345] multiqc [DEBUG ] No samples found: biobambam2
[2021-11-23 10:15:02,349] multiqc [DEBUG ] No samples found: mtnucratio
[2021-11-23 10:15:02,351] multiqc [DEBUG ] No samples found: picard
[2021-11-23 10:15:02,355] multiqc [DEBUG ] No samples found: prokka
[2021-11-23 10:15:02,359] multiqc [DEBUG ] No samples found: samblaster
[2021-11-23 10:15:02,365] multiqc [DEBUG ] No samples found: samtools
[2021-11-23 10:15:02,369] multiqc [DEBUG ] No samples found: sexdeterrmine
[2021-11-23 10:15:02,374] multiqc [DEBUG ] No samples found: bamtools
[2021-11-23 10:15:02,377] multiqc [DEBUG ] No samples found: jellyfish
[2021-11-23 10:15:02,383] multiqc [DEBUG ] No samples found: vcftools
[2021-11-23 10:15:02,387] multiqc [DEBUG ] No samples found: longranger
[2021-11-23 10:15:02,391] multiqc [DEBUG ] No samples found: stacks
[2021-11-23 10:15:02,395] multiqc [DEBUG ] No samples found: varscan2
[2021-11-23 10:15:02,405] multiqc [DEBUG ] No samples found: bbmap
[2021-11-23 10:15:02,409] multiqc [DEBUG ] No samples found: bismark
[2021-11-23 10:15:02,413] multiqc [DEBUG ] No samples found: biscuit
[2021-11-23 10:15:02,417] multiqc [DEBUG ] No samples found: hicexplorer
[2021-11-23 10:15:02,421] multiqc [DEBUG ] No samples found: hicup
[2021-11-23 10:15:02,425] multiqc [DEBUG ] No samples found: hicpro
[2021-11-23 10:15:02,429] multiqc [DEBUG ] No samples found: salmon
[2021-11-23 10:15:02,433] multiqc [DEBUG ] No samples found: kallisto
[2021-11-23 10:15:02,437] multiqc [DEBUG ] No samples found: slamdunk
[2021-11-23 10:15:02,441] multiqc [DEBUG ] No samples found: star
[2021-11-23 10:15:02,445] multiqc [DEBUG ] No samples found: hisat2
[2021-11-23 10:15:02,449] multiqc [DEBUG ] No samples found: tophat
[2021-11-23 10:15:02,453] multiqc [DEBUG ] No samples found: bowtie2
[2021-11-23 10:15:02,457] multiqc [DEBUG ] No samples found: bowtie1
[2021-11-23 10:15:02,460] multiqc [DEBUG ] No samples found: snpsplit
[2021-11-23 10:15:02,464] multiqc [DEBUG ] No samples found: kat
[2021-11-23 10:15:02,467] multiqc [DEBUG ] No samples found: leehom
[2021-11-23 10:15:02,471] multiqc [DEBUG ] No samples found: adapterRemoval
[2021-11-23 10:15:02,475] multiqc [DEBUG ] No samples found: clipandmerge
[2021-11-23 10:15:02,479] multiqc [DEBUG ] No samples found: cutadapt
[2021-11-23 10:15:02,482] multiqc [DEBUG ] No samples found: flexbar
[2021-11-23 10:15:02,486] multiqc [DEBUG ] No samples found: kaiju
[2021-11-23 10:15:02,490] multiqc [DEBUG ] No samples found: kraken
[2021-11-23 10:15:02,494] multiqc [DEBUG ] No samples found: malt
[2021-11-23 10:15:02,498] multiqc [DEBUG ] No samples found: trimmomatic
[2021-11-23 10:15:02,502] multiqc [DEBUG ] No samples found: sickle
[2021-11-23 10:15:02,506] multiqc [DEBUG ] No samples found: skewer
[2021-11-23 10:15:02,509] multiqc [DEBUG ] No samples found: sortmerna
[2021-11-23 10:15:02,513] multiqc [DEBUG ] No samples found: biobloomtools
[2021-11-23 10:15:02,517] multiqc [DEBUG ] No samples found: fastq_screen
[2021-11-23 10:15:02,521] multiqc [DEBUG ] No samples found: afterqc
[2021-11-23 10:15:02,525] multiqc [DEBUG ] No samples found: fastp
[2021-11-23 10:15:02,989] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports
[2021-11-23 10:15:03,131] multiqc [DEBUG ] No samples found: pycoqc
[2021-11-23 10:15:03,135] multiqc [DEBUG ] No samples found: minionqc
[2021-11-23 10:15:03,139] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2021-11-23 10:15:03,143] multiqc [DEBUG ] No samples found: clusterflow
[2021-11-23 10:15:03,147] multiqc [DEBUG ] No samples found: bcl2fastq
[2021-11-23 10:15:03,151] multiqc [DEBUG ] No samples found: interop
[2021-11-23 10:15:03,155] multiqc [DEBUG ] No samples found: ivar
[2021-11-23 10:15:03,159] multiqc [DEBUG ] No samples found: flash
[2021-11-23 10:15:03,163] multiqc [DEBUG ] No samples found: seqyclean
[2021-11-23 10:15:03,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'.
[2021-11-23 10:15:03,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2021-11-23 10:15:03,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'.
[2021-11-23 10:15:03,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2021-11-23 10:15:03,171] multiqc [INFO ] Compressing plot data
[2021-11-23 10:15:03,281] multiqc [INFO ] Report : multiqc_report.html
[2021-11-23 10:15:03,281] multiqc [INFO ] Data : multiqc_data
[2021-11-23 10:15:03,281] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12287838/tmpmq4fs4zw/multiqc_data' to '/scratch/gencore/logs/html/HMCCLBGXK/merged/multiqc_data'
[2021-11-23 10:15:03,427] multiqc [INFO ] MultiQC complete