[2021-10-30 14:16:49,150] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-30 14:16:49,151] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-30 14:16:49,151] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-30 14:16:49,151] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-30 14:16:49,152] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-30 14:16:49,152] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H572WAFX3/merged [2021-10-30 14:16:50,596] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-30 14:16:50,597] multiqc [INFO ] This is MultiQC v1.9 [2021-10-30 14:16:50,597] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H572WAFX3/merged [2021-10-30 14:16:50,597] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H572WAFX3/merged [2021-10-30 14:16:50,597] multiqc [INFO ] Template : default [2021-10-30 14:16:50,597] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-30 14:16:50,597] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H572WAFX3/merged [2021-10-30 14:16:50,597] 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 [2021-10-30 14:16:50,597] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11330455/tmp7_e54ths [2021-10-30 14:16:50,705] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_9251chp4657_fastqc.html [2021-10-30 14:16:50,707] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H572WAFX3_n02_9251chp-red1_fastqc.html [2021-10-30 14:16:51,698] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_10517chp-red1_fastqc.html [2021-10-30 14:16:51,700] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_10517chp-red1_fastqc.html [2021-10-30 14:16:51,739] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_10965chp-red1_fastqc.html [2021-10-30 14:16:51,741] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_10965chp-red1_fastqc.html [2021-10-30 14:16:51,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_undetermined_fastqc.html [2021-10-30 14:16:51,781] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_undetermined_fastqc.html [2021-10-30 14:16:51,822] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_9251in-red1_fastqc.html [2021-10-30 14:16:51,823] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_9251in-red1_fastqc.html [2021-10-30 14:16:51,862] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_5184in_fastqc.html [2021-10-30 14:16:51,864] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_5184in_fastqc.html [2021-10-30 14:16:51,904] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_9251in-red1_fastqc.html [2021-10-30 14:16:51,906] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_9251in-red1_fastqc.html [2021-10-30 14:16:51,945] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_9251in4658_fastqc.html [2021-10-30 14:16:51,947] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_9251in4658_fastqc.html [2021-10-30 14:16:51,986] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_7797chp_fastqc.html [2021-10-30 14:16:51,988] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_7797chp_fastqc.html [2021-10-30 14:16:52,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_10965in-red1_fastqc.html [2021-10-30 14:16:52,031] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_10965in-red1_fastqc.html [2021-10-30 14:16:52,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_9251in4657_fastqc.html [2021-10-30 14:16:52,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_9251in4657_fastqc.html [2021-10-30 14:16:52,115] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_9251chp4658_fastqc.html [2021-10-30 14:16:52,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_9251chp4658_fastqc.html [2021-10-30 14:16:52,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_11617in_fastqc.html [2021-10-30 14:16:52,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_11617in_fastqc.html [2021-10-30 14:16:52,199] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_10517in-red1_fastqc.html [2021-10-30 14:16:52,201] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_10517in-red1_fastqc.html [2021-10-30 14:16:52,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_undetermined_fastqc.html [2021-10-30 14:16:52,241] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_undetermined_fastqc.html [2021-10-30 14:16:52,280] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_9251chp4579_fastqc.html [2021-10-30 14:16:52,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_9251chp4579_fastqc.html [2021-10-30 14:16:52,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n02_5184in_fastqc.html [2021-10-30 14:16:52,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n02_5184in_fastqc.html [2021-10-30 14:16:52,361] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H572WAFX3_n01_9251in4579_fastqc.html [2021-10-30 14:16:52,363] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H572WAFX3_n01_9251in4579_fastqc.html [2021-10-30 14:16:52,849] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-30 14:16:52,851] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-30 14:16:52,866] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-30 14:16:52,876] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2021-10-30 14:16:52,877] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-30 14:16:52,882] multiqc [DEBUG ] No samples found: conpair [2021-10-30 14:16:52,888] multiqc [DEBUG ] No samples found: peddy [2021-10-30 14:16:52,893] multiqc [DEBUG ] No samples found: somalier [2021-10-30 14:16:52,899] multiqc [DEBUG ] No samples found: methylQA [2021-10-30 14:16:52,908] multiqc [DEBUG ] No samples found: mosdepth [2021-10-30 14:16:52,912] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-30 14:16:52,915] multiqc [DEBUG ] No samples found: qualimap [2021-10-30 14:16:52,921] multiqc [DEBUG ] No samples found: preseq [2021-10-30 14:16:52,926] multiqc [DEBUG ] No samples found: quast [2021-10-30 14:16:52,932] multiqc [DEBUG ] No samples found: qorts [2021-10-30 14:16:52,937] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-30 14:16:52,942] multiqc [DEBUG ] No samples found: rockhopper [2021-10-30 14:16:52,947] multiqc [DEBUG ] No samples found: rsem [2021-10-30 14:16:52,957] multiqc [DEBUG ] No samples found: rseqc [2021-10-30 14:16:52,962] multiqc [DEBUG ] No samples found: busco [2021-10-30 14:16:52,968] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-30 14:16:52,974] multiqc [DEBUG ] No samples found: disambiguate [2021-10-30 14:16:52,979] multiqc [DEBUG ] No samples found: supernova [2021-10-30 14:16:52,994] multiqc [DEBUG ] No samples found: deeptools [2021-10-30 14:16:52,999] multiqc [DEBUG ] No samples found: sargasso [2021-10-30 14:16:53,004] multiqc [DEBUG ] No samples found: verifybamid [2021-10-30 14:16:53,009] multiqc [DEBUG ] No samples found: mirtrace [2021-10-30 14:16:53,015] multiqc [DEBUG ] No samples found: happy [2021-10-30 14:16:53,020] multiqc [DEBUG ] No samples found: mirtop [2021-10-30 14:16:53,028] multiqc [DEBUG ] No samples found: homer [2021-10-30 14:16:53,033] multiqc [DEBUG ] No samples found: macs2 [2021-10-30 14:16:53,038] multiqc [DEBUG ] No samples found: theta2 [2021-10-30 14:16:53,043] multiqc [DEBUG ] No samples found: snpeff [2021-10-30 14:16:53,051] multiqc [DEBUG ] No samples found: gatk [2021-10-30 14:16:53,055] multiqc [DEBUG ] No samples found: htseq [2021-10-30 14:16:53,061] multiqc [DEBUG ] No samples found: bcftools [2021-10-30 14:16:53,066] multiqc [DEBUG ] No samples found: featureCounts [2021-10-30 14:16:53,073] multiqc [DEBUG ] No samples found: fgbio [2021-10-30 14:16:53,086] multiqc [DEBUG ] No samples found: dragen [2021-10-30 14:16:53,091] multiqc [DEBUG ] No samples found: dedup [2021-10-30 14:16:53,097] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-30 14:16:53,121] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-30 14:16:53,126] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-30 14:16:53,128] multiqc [DEBUG ] No samples found: picard [2021-10-30 14:16:53,133] multiqc [DEBUG ] No samples found: prokka [2021-10-30 14:16:53,137] multiqc [DEBUG ] No samples found: samblaster [2021-10-30 14:16:53,146] multiqc [DEBUG ] No samples found: samtools [2021-10-30 14:16:53,151] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-30 14:16:53,157] multiqc [DEBUG ] No samples found: bamtools [2021-10-30 14:16:53,161] multiqc [DEBUG ] No samples found: jellyfish [2021-10-30 14:16:53,169] multiqc [DEBUG ] No samples found: vcftools [2021-10-30 14:16:53,174] multiqc [DEBUG ] No samples found: longranger [2021-10-30 14:16:53,180] multiqc [DEBUG ] No samples found: stacks [2021-10-30 14:16:53,185] multiqc [DEBUG ] No samples found: varscan2 [2021-10-30 14:16:53,198] multiqc [DEBUG ] No samples found: bbmap [2021-10-30 14:16:53,203] multiqc [DEBUG ] No samples found: bismark [2021-10-30 14:16:53,208] multiqc [DEBUG ] No samples found: biscuit [2021-10-30 14:16:53,214] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-30 14:16:53,219] multiqc [DEBUG ] No samples found: hicup [2021-10-30 14:16:53,224] multiqc [DEBUG ] No samples found: hicpro [2021-10-30 14:16:53,229] multiqc [DEBUG ] No samples found: salmon [2021-10-30 14:16:53,234] multiqc [DEBUG ] No samples found: kallisto [2021-10-30 14:16:53,239] multiqc [DEBUG ] No samples found: slamdunk [2021-10-30 14:16:53,243] multiqc [DEBUG ] No samples found: star [2021-10-30 14:16:53,248] multiqc [DEBUG ] No samples found: hisat2 [2021-10-30 14:16:53,253] multiqc [DEBUG ] No samples found: tophat [2021-10-30 14:16:53,258] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-30 14:16:53,263] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-30 14:16:53,268] multiqc [DEBUG ] No samples found: snpsplit [2021-10-30 14:16:53,273] multiqc [DEBUG ] No samples found: kat [2021-10-30 14:16:53,277] multiqc [DEBUG ] No samples found: leehom [2021-10-30 14:16:53,282] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-30 14:16:53,286] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-30 14:16:53,291] multiqc [DEBUG ] No samples found: cutadapt [2021-10-30 14:16:53,295] multiqc [DEBUG ] No samples found: flexbar [2021-10-30 14:16:53,300] multiqc [DEBUG ] No samples found: kaiju [2021-10-30 14:16:53,305] multiqc [DEBUG ] No samples found: kraken [2021-10-30 14:16:53,312] multiqc [DEBUG ] No samples found: malt [2021-10-30 14:16:53,317] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-30 14:16:53,321] multiqc [DEBUG ] No samples found: sickle [2021-10-30 14:16:53,326] multiqc [DEBUG ] No samples found: skewer [2021-10-30 14:16:53,330] multiqc [DEBUG ] No samples found: sortmerna [2021-10-30 14:16:53,335] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-30 14:16:53,340] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-30 14:16:53,344] multiqc [DEBUG ] No samples found: afterqc [2021-10-30 14:16:53,350] multiqc [DEBUG ] No samples found: fastp [2021-10-30 14:16:54,186] multiqc.modules.fastqc.fastqc [INFO ] Found 38 reports [2021-10-30 14:16:54,500] multiqc [DEBUG ] No samples found: pycoqc [2021-10-30 14:16:54,504] multiqc [DEBUG ] No samples found: minionqc [2021-10-30 14:16:54,509] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-30 14:16:54,515] multiqc [DEBUG ] No samples found: clusterflow [2021-10-30 14:16:54,520] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-30 14:16:54,525] multiqc [DEBUG ] No samples found: interop [2021-10-30 14:16:54,532] multiqc [DEBUG ] No samples found: ivar [2021-10-30 14:16:54,536] multiqc [DEBUG ] No samples found: flash [2021-10-30 14:16:54,541] multiqc [DEBUG ] No samples found: seqyclean [2021-10-30 14:16:54,541] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-30 14:16:54,541] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-10-30 14:16:54,541] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-30 14:16:54,541] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-30 14:16:54,586] multiqc [INFO ] Compressing plot data [2021-10-30 14:16:55,181] multiqc [INFO ] Report : multiqc_report.html [2021-10-30 14:16:55,181] multiqc [INFO ] Data : multiqc_data [2021-10-30 14:16:55,181] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11330455/tmp7_e54ths/multiqc_data' to '/scratch/gencore/logs/html/H572WAFX3/merged/multiqc_data' [2021-10-30 14:16:55,318] multiqc [INFO ] MultiQC complete