[2022-02-07 21:53:20,598] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-02-07 21:53:20,599] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-02-07 21:53:20,599] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-07 21:53:20,600] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-02-07 21:53:20,600] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-02-07 21:53:20,600] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H355YBGXL/merged [2022-02-07 21:53:23,182] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-02-07 21:53:23,183] multiqc [INFO ] This is MultiQC v1.9 [2022-02-07 21:53:23,183] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H355YBGXL/merged [2022-02-07 21:53:23,183] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H355YBGXL/merged [2022-02-07 21:53:23,183] multiqc [INFO ] Template : default [2022-02-07 21:53:23,183] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-02-07 21:53:23,183] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H355YBGXL/merged [2022-02-07 21:53:23,183] 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 [2022-02-07 21:53:23,183] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14721618/tmp2pohu9u1 [2022-02-07 21:53:23,316] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-07 21:53:23,319] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-07 21:53:23,418] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_C4_Zmm16_2_fastqc.html [2022-02-07 21:53:23,420] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_C4_Zmm16_2_fastqc.html [2022-02-07 21:53:23,460] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_C1_KN1_1_fastqc.html [2022-02-07 21:53:23,462] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_C1_KN1_1_fastqc.html [2022-02-07 21:53:23,501] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_undetermined_fastqc.html [2022-02-07 21:53:23,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_undetermined_fastqc.html [2022-02-07 21:53:23,540] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_I3_KN1_2_fastqc.html [2022-02-07 21:53:23,542] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_I3_KN1_2_fastqc.html [2022-02-07 21:53:23,582] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_C2_Zmm16_1_fastqc.html [2022-02-07 21:53:23,584] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_C2_Zmm16_1_fastqc.html [2022-02-07 21:53:23,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_I2_Zmm16_1_fastqc.html [2022-02-07 21:53:23,626] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_I2_Zmm16_1_fastqc.html [2022-02-07 21:53:23,666] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_I1_KN1_1_fastqc.html [2022-02-07 21:53:23,668] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_I1_KN1_1_fastqc.html [2022-02-07 21:53:23,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_C3_KN1_2_fastqc.html [2022-02-07 21:53:23,709] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_C3_KN1_2_fastqc.html [2022-02-07 21:53:23,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H355YBGXL_n01_I4_Zmm16_2_fastqc.html [2022-02-07 21:53:23,750] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H355YBGXL_n01_I4_Zmm16_2_fastqc.html [2022-02-07 21:53:24,321] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-07 21:53:24,326] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-07 21:53:24,337] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2022-02-07 21:53:24,347] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-02-07 21:53:24,349] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-02-07 21:53:24,355] multiqc [DEBUG ] No samples found: conpair [2022-02-07 21:53:24,365] multiqc [DEBUG ] No samples found: peddy [2022-02-07 21:53:24,373] multiqc [DEBUG ] No samples found: somalier [2022-02-07 21:53:24,382] multiqc [DEBUG ] No samples found: methylQA [2022-02-07 21:53:24,399] multiqc [DEBUG ] No samples found: mosdepth [2022-02-07 21:53:24,405] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-07 21:53:24,412] multiqc [DEBUG ] No samples found: qualimap [2022-02-07 21:53:24,421] multiqc [DEBUG ] No samples found: preseq [2022-02-07 21:53:24,429] multiqc [DEBUG ] No samples found: quast [2022-02-07 21:53:24,438] multiqc [DEBUG ] No samples found: qorts [2022-02-07 21:53:24,446] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-07 21:53:24,459] multiqc [DEBUG ] No samples found: rockhopper [2022-02-07 21:53:24,467] multiqc [DEBUG ] No samples found: rsem [2022-02-07 21:53:24,490] multiqc [DEBUG ] No samples found: rseqc [2022-02-07 21:53:24,496] multiqc [DEBUG ] No samples found: busco [2022-02-07 21:53:24,505] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-07 21:53:24,509] multiqc [DEBUG ] No samples found: disambiguate [2022-02-07 21:53:24,518] multiqc [DEBUG ] No samples found: supernova [2022-02-07 21:53:24,546] multiqc [DEBUG ] No samples found: deeptools [2022-02-07 21:53:24,551] multiqc [DEBUG ] No samples found: sargasso [2022-02-07 21:53:24,561] multiqc [DEBUG ] No samples found: verifybamid [2022-02-07 21:53:24,570] multiqc [DEBUG ] No samples found: mirtrace [2022-02-07 21:53:24,582] multiqc [DEBUG ] No samples found: happy [2022-02-07 21:53:24,591] multiqc [DEBUG ] No samples found: mirtop [2022-02-07 21:53:24,606] multiqc [DEBUG ] No samples found: homer [2022-02-07 21:53:24,614] multiqc [DEBUG ] No samples found: macs2 [2022-02-07 21:53:24,619] multiqc [DEBUG ] No samples found: theta2 [2022-02-07 21:53:24,629] multiqc [DEBUG ] No samples found: snpeff [2022-02-07 21:53:24,644] multiqc [DEBUG ] No samples found: gatk [2022-02-07 21:53:24,653] multiqc [DEBUG ] No samples found: htseq [2022-02-07 21:53:24,662] multiqc [DEBUG ] No samples found: bcftools [2022-02-07 21:53:24,671] multiqc [DEBUG ] No samples found: featureCounts [2022-02-07 21:53:24,680] multiqc [DEBUG ] No samples found: fgbio [2022-02-07 21:53:24,715] multiqc [DEBUG ] No samples found: dragen [2022-02-07 21:53:24,723] multiqc [DEBUG ] No samples found: dedup [2022-02-07 21:53:24,731] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-07 21:53:24,788] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-07 21:53:24,793] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-07 21:53:24,796] multiqc [DEBUG ] No samples found: picard [2022-02-07 21:53:24,801] multiqc [DEBUG ] No samples found: prokka [2022-02-07 21:53:24,808] multiqc [DEBUG ] No samples found: samblaster [2022-02-07 21:53:24,833] multiqc [DEBUG ] No samples found: samtools [2022-02-07 21:53:24,844] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-07 21:53:24,852] multiqc [DEBUG ] No samples found: bamtools [2022-02-07 21:53:24,857] multiqc [DEBUG ] No samples found: jellyfish [2022-02-07 21:53:24,869] multiqc [DEBUG ] No samples found: vcftools [2022-02-07 21:53:24,879] multiqc [DEBUG ] No samples found: longranger [2022-02-07 21:53:24,885] multiqc [DEBUG ] No samples found: stacks [2022-02-07 21:53:24,895] multiqc [DEBUG ] No samples found: varscan2 [2022-02-07 21:53:24,923] multiqc [DEBUG ] No samples found: bbmap [2022-02-07 21:53:24,932] multiqc [DEBUG ] No samples found: bismark [2022-02-07 21:53:24,942] multiqc [DEBUG ] No samples found: biscuit [2022-02-07 21:53:24,948] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-07 21:53:24,956] multiqc [DEBUG ] No samples found: hicup [2022-02-07 21:53:24,965] multiqc [DEBUG ] No samples found: hicpro [2022-02-07 21:53:24,972] multiqc [DEBUG ] No samples found: salmon [2022-02-07 21:53:24,981] multiqc [DEBUG ] No samples found: kallisto [2022-02-07 21:53:24,991] multiqc [DEBUG ] No samples found: slamdunk [2022-02-07 21:53:24,999] multiqc [DEBUG ] No samples found: star [2022-02-07 21:53:25,006] multiqc [DEBUG ] No samples found: hisat2 [2022-02-07 21:53:25,014] multiqc [DEBUG ] No samples found: tophat [2022-02-07 21:53:25,024] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-07 21:53:25,035] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-07 21:53:25,045] multiqc [DEBUG ] No samples found: snpsplit [2022-02-07 21:53:25,053] multiqc [DEBUG ] No samples found: kat [2022-02-07 21:53:25,057] multiqc [DEBUG ] No samples found: leehom [2022-02-07 21:53:25,062] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-07 21:53:25,068] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-07 21:53:25,078] multiqc [DEBUG ] No samples found: cutadapt [2022-02-07 21:53:25,084] multiqc [DEBUG ] No samples found: flexbar [2022-02-07 21:53:25,094] multiqc [DEBUG ] No samples found: kaiju [2022-02-07 21:53:25,103] multiqc [DEBUG ] No samples found: kraken [2022-02-07 21:53:25,109] multiqc [DEBUG ] No samples found: malt [2022-02-07 21:53:25,117] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-07 21:53:25,127] multiqc [DEBUG ] No samples found: sickle [2022-02-07 21:53:25,133] multiqc [DEBUG ] No samples found: skewer [2022-02-07 21:53:25,139] multiqc [DEBUG ] No samples found: sortmerna [2022-02-07 21:53:25,146] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-07 21:53:25,155] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-07 21:53:25,165] multiqc [DEBUG ] No samples found: afterqc [2022-02-07 21:53:25,173] multiqc [DEBUG ] No samples found: fastp [2022-02-07 21:53:25,801] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports [2022-02-07 21:53:26,001] multiqc [DEBUG ] No samples found: pycoqc [2022-02-07 21:53:26,010] multiqc [DEBUG ] No samples found: minionqc [2022-02-07 21:53:26,018] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-02-07 21:53:26,027] multiqc [DEBUG ] No samples found: clusterflow [2022-02-07 21:53:26,035] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-07 21:53:26,041] multiqc [DEBUG ] No samples found: interop [2022-02-07 21:53:26,046] multiqc [DEBUG ] No samples found: ivar [2022-02-07 21:53:26,055] multiqc [DEBUG ] No samples found: flash [2022-02-07 21:53:26,063] multiqc [DEBUG ] No samples found: seqyclean [2022-02-07 21:53:26,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-02-07 21:53:26,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-02-07 21:53:26,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-02-07 21:53:26,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-02-07 21:53:26,074] multiqc [INFO ] Compressing plot data [2022-02-07 21:53:26,256] multiqc [INFO ] Report : multiqc_report.html [2022-02-07 21:53:26,256] multiqc [INFO ] Data : multiqc_data [2022-02-07 21:53:26,256] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14721618/tmp2pohu9u1/multiqc_data' to '/scratch/gencore/logs/html/H355YBGXL/merged/multiqc_data' [2022-02-07 21:53:26,511] multiqc [INFO ] MultiQC complete