[2021-02-12 00:20:39,760] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-02-12 00:20:39,760] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-02-12 00:20:39,760] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-12 00:20:39,761] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-02-12 00:20:39,761] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-02-12 00:20:39,761] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMLGTAFX2/merged [2021-02-12 00:20:41,413] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-12 00:20:41,413] multiqc [INFO ] This is MultiQC v1.9 [2021-02-12 00:20:41,413] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMLGTAFX2/merged [2021-02-12 00:20:41,413] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMLGTAFX2/merged [2021-02-12 00:20:41,413] multiqc [INFO ] Template : default [2021-02-12 00:20:41,413] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-02-12 00:20:41,413] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMLGTAFX2/merged [2021-02-12 00:20:41,414] 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 [2021-02-12 00:20:41,414] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-2670422/tmpascku5k9 [2021-02-12 00:20:41,522] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG4242.mRNA_fastqc.html [2021-02-12 00:20:41,525] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG4242.mRNA_fastqc.html [2021-02-12 00:20:41,571] multiqc [DEBUG ] File ignored by hicexplorer because it 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search pattern filesize limit: HMLGTAFX2_n02_QG2082.mRNA_fastqc.html [2021-02-12 00:20:41,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG2082.mRNA_fastqc.html [2021-02-12 00:20:41,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2082.mRNA_fastqc.html [2021-02-12 00:20:41,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2082.mRNA_fastqc.html [2021-02-12 00:20:41,790] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG3077.mRNA_fastqc.html [2021-02-12 00:20:41,792] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG3077.mRNA_fastqc.html [2021-02-12 00:20:41,834] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2077.mRNA_fastqc.html [2021-02-12 00:20:41,836] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2077.mRNA_fastqc.html [2021-02-12 00:20:41,877] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_undetermined_fastqc.html [2021-02-12 00:20:41,879] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_undetermined_fastqc.html [2021-02-12 00:20:41,918] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG2080.mRNA_fastqc.html [2021-02-12 00:20:41,920] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG2080.mRNA_fastqc.html [2021-02-12 00:20:41,963] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_RS6131.mRNA_fastqc.html [2021-02-12 00:20:41,965] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_RS6131.mRNA_fastqc.html [2021-02-12 00:20:42,007] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG4243.mRNA_fastqc.html [2021-02-12 00:20:42,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG4243.mRNA_fastqc.html [2021-02-12 00:20:42,052] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG4242.mRNA_fastqc.html [2021-02-12 00:20:42,054] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG4242.mRNA_fastqc.html [2021-02-12 00:20:42,096] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG3077.mRNA_fastqc.html [2021-02-12 00:20:42,098] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG3077.mRNA_fastqc.html [2021-02-12 00:20:42,140] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_RS6131.mRNA_fastqc.html [2021-02-12 00:20:42,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_RS6131.mRNA_fastqc.html [2021-02-12 00:20:42,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_undetermined_fastqc.html [2021-02-12 00:20:42,186] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_undetermined_fastqc.html [2021-02-12 00:20:42,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG2935.mRNA_fastqc.html [2021-02-12 00:20:42,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG2935.mRNA_fastqc.html [2021-02-12 00:20:42,269] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG2077.mRNA_fastqc.html [2021-02-12 00:20:42,271] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n02_QG2077.mRNA_fastqc.html [2021-02-12 00:20:42,312] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2935.mRNA_fastqc.html [2021-02-12 00:20:42,314] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2935.mRNA_fastqc.html [2021-02-12 00:20:42,356] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2939.mRNA_fastqc.html [2021-02-12 00:20:42,358] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMLGTAFX2_n01_QG2939.mRNA_fastqc.html [2021-02-12 00:20:42,709] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-12 00:20:42,710] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-12 00:20:42,718] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-02-12 00:20:42,723] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 10 samples (table) [2021-02-12 00:20:42,733] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-02-12 00:20:42,738] multiqc [DEBUG ] No samples found: conpair [2021-02-12 00:20:42,742] multiqc [DEBUG ] No samples found: peddy [2021-02-12 00:20:42,746] multiqc [DEBUG ] No samples found: somalier [2021-02-12 00:20:42,750] multiqc [DEBUG ] No samples found: methylQA [2021-02-12 00:20:42,757] multiqc [DEBUG ] No samples found: mosdepth [2021-02-12 00:20:42,761] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-12 00:20:42,764] multiqc [DEBUG ] No samples found: qualimap [2021-02-12 00:20:42,768] multiqc [DEBUG ] No samples found: preseq [2021-02-12 00:20:42,773] multiqc [DEBUG ] No samples found: quast [2021-02-12 00:20:42,777] multiqc [DEBUG ] No samples found: qorts [2021-02-12 00:20:42,781] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-12 00:20:42,785] multiqc [DEBUG ] No samples found: rockhopper [2021-02-12 00:20:42,790] multiqc [DEBUG ] No samples found: rsem [2021-02-12 00:20:42,799] multiqc [DEBUG ] No samples found: rseqc [2021-02-12 00:20:42,803] multiqc [DEBUG ] No samples found: busco [2021-02-12 00:20:42,807] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-12 00:20:42,811] multiqc [DEBUG ] No samples found: disambiguate [2021-02-12 00:20:42,815] multiqc [DEBUG ] No samples found: supernova [2021-02-12 00:20:42,827] multiqc [DEBUG ] No samples found: deeptools [2021-02-12 00:20:42,831] multiqc [DEBUG ] No samples found: sargasso [2021-02-12 00:20:42,836] multiqc [DEBUG ] No samples found: verifybamid [2021-02-12 00:20:42,840] multiqc [DEBUG ] No samples found: mirtrace [2021-02-12 00:20:42,844] multiqc [DEBUG ] No samples found: happy [2021-02-12 00:20:42,848] multiqc [DEBUG ] No samples found: mirtop [2021-02-12 00:20:42,854] multiqc [DEBUG ] No samples found: homer [2021-02-12 00:20:42,858] multiqc [DEBUG ] No samples found: macs2 [2021-02-12 00:20:42,862] multiqc [DEBUG ] No samples found: theta2 [2021-02-12 00:20:42,867] multiqc [DEBUG ] No samples found: snpeff [2021-02-12 00:20:42,873] multiqc [DEBUG ] No samples found: gatk [2021-02-12 00:20:42,877] multiqc [DEBUG ] No samples found: htseq [2021-02-12 00:20:42,881] multiqc [DEBUG ] No samples found: bcftools [2021-02-12 00:20:42,886] multiqc [DEBUG ] No samples found: featureCounts [2021-02-12 00:20:42,891] multiqc [DEBUG ] No samples found: fgbio [2021-02-12 00:20:42,901] multiqc [DEBUG ] No samples found: dragen [2021-02-12 00:20:42,906] multiqc [DEBUG ] No samples found: dedup [2021-02-12 00:20:42,910] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-12 00:20:42,930] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-12 00:20:42,934] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-12 00:20:42,936] multiqc [DEBUG ] No samples found: picard [2021-02-12 00:20:42,940] multiqc [DEBUG ] No samples found: prokka [2021-02-12 00:20:42,944] multiqc [DEBUG ] No samples found: samblaster [2021-02-12 00:20:42,951] multiqc [DEBUG ] No samples found: samtools [2021-02-12 00:20:42,956] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-12 00:20:42,960] multiqc [DEBUG ] No samples found: bamtools [2021-02-12 00:20:42,964] multiqc [DEBUG ] No samples found: jellyfish [2021-02-12 00:20:42,971] multiqc [DEBUG ] No samples found: vcftools [2021-02-12 00:20:42,975] multiqc [DEBUG ] No samples found: longranger [2021-02-12 00:20:42,980] multiqc [DEBUG ] No samples found: stacks [2021-02-12 00:20:42,984] multiqc [DEBUG ] No samples found: varscan2 [2021-02-12 00:20:42,995] multiqc [DEBUG ] No samples found: bbmap [2021-02-12 00:20:43,000] multiqc [DEBUG ] No samples found: bismark [2021-02-12 00:20:43,004] multiqc [DEBUG ] No samples found: biscuit [2021-02-12 00:20:43,009] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-12 00:20:43,013] multiqc [DEBUG ] No samples found: hicup [2021-02-12 00:20:43,017] multiqc [DEBUG ] No samples found: hicpro [2021-02-12 00:20:43,021] multiqc [DEBUG ] No samples found: salmon [2021-02-12 00:20:43,025] multiqc [DEBUG ] No samples found: kallisto [2021-02-12 00:20:43,029] multiqc [DEBUG ] No samples found: slamdunk [2021-02-12 00:20:43,034] multiqc [DEBUG ] No samples found: star [2021-02-12 00:20:43,038] multiqc [DEBUG ] No samples found: hisat2 [2021-02-12 00:20:43,042] multiqc [DEBUG ] No samples found: tophat [2021-02-12 00:20:43,046] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-12 00:20:43,050] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-12 00:20:43,054] multiqc [DEBUG ] No samples found: snpsplit [2021-02-12 00:20:43,058] multiqc [DEBUG ] No samples found: kat [2021-02-12 00:20:43,062] multiqc [DEBUG ] No samples found: leehom [2021-02-12 00:20:43,066] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-12 00:20:43,070] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-12 00:20:43,074] multiqc [DEBUG ] No samples found: cutadapt [2021-02-12 00:20:43,078] multiqc [DEBUG ] No samples found: flexbar [2021-02-12 00:20:43,082] multiqc [DEBUG ] No samples found: kaiju [2021-02-12 00:20:43,086] multiqc [DEBUG ] No samples found: kraken [2021-02-12 00:20:43,090] multiqc [DEBUG ] No samples found: malt [2021-02-12 00:20:43,094] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-12 00:20:43,098] multiqc [DEBUG ] No samples found: sickle [2021-02-12 00:20:43,102] multiqc [DEBUG ] No samples found: skewer [2021-02-12 00:20:43,107] multiqc [DEBUG ] No samples found: sortmerna [2021-02-12 00:20:43,111] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-12 00:20:43,115] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-12 00:20:43,119] multiqc [DEBUG ] No samples found: afterqc [2021-02-12 00:20:43,123] multiqc [DEBUG ] No samples found: fastp [2021-02-12 00:20:43,558] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2021-02-12 00:20:44,114] multiqc [DEBUG ] No samples found: pycoqc [2021-02-12 00:20:44,119] multiqc [DEBUG ] No samples found: minionqc [2021-02-12 00:20:44,123] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-12 00:20:44,127] multiqc [DEBUG ] No samples found: clusterflow [2021-02-12 00:20:44,132] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-12 00:20:44,137] multiqc [DEBUG ] No samples found: interop [2021-02-12 00:20:44,141] multiqc [DEBUG ] No samples found: ivar [2021-02-12 00:20:44,146] multiqc [DEBUG ] No samples found: flash [2021-02-12 00:20:44,150] multiqc [DEBUG ] No samples found: seqyclean [2021-02-12 00:20:44,150] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-02-12 00:20:44,150] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-02-12 00:20:44,150] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-02-12 00:20:44,151] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-02-12 00:20:44,175] multiqc [INFO ] Compressing plot data [2021-02-12 00:20:44,553] multiqc [INFO ] Report : multiqc_report.html [2021-02-12 00:20:44,553] multiqc [INFO ] Data : multiqc_data [2021-02-12 00:20:44,553] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2670422/tmpascku5k9/multiqc_data' to '/scratch/gencore/logs/html/HMLGTAFX2/merged/multiqc_data' [2021-02-12 00:20:44,670] multiqc [INFO ] MultiQC complete