[2021-06-15 15:12:46,782] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-15 15:12:46,782] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-15 15:12:46,782] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-15 15:12:46,783] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-15 15:12:46,783] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-15 15:12:46,783] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H533TBGXJ/merged [2021-06-15 15:12:48,142] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-15 15:12:48,142] multiqc [INFO ] This is MultiQC v1.9 [2021-06-15 15:12:48,142] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H533TBGXJ/merged [2021-06-15 15:12:48,143] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H533TBGXJ/merged [2021-06-15 15:12:48,143] multiqc [INFO ] Template : default [2021-06-15 15:12:48,143] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-15 15:12:48,143] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H533TBGXJ/merged [2021-06-15 15:12:48,143] 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 [2021-06-15 15:12:48,143] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7643391/tmp27l8goew [2021-06-15 15:12:48,248] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n02_ADT_D_210615_fastqc.html [2021-06-15 15:12:48,250] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n02_cDNA_A1_210615_fastqc.html [2021-06-15 15:12:51,518] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H533TBGXJ_n02_cDNA_A1_210615_fastqc.html [2021-06-15 15:12:51,564] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n02_HTO_D_210615_fastqc.html [2021-06-15 15:12:51,566] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H533TBGXJ_n02_HTO_D_210615_fastqc.html [2021-06-15 15:12:51,632] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n01_GDO_A_210615_fastqc.html [2021-06-15 15:12:51,634] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H533TBGXJ_n01_GDO_A_210615_fastqc.html [2021-06-15 15:12:51,677] multiqc [DEBUG ] File 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File ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n01_cDNA_B2_210615_fastqc.html [2021-06-15 15:12:51,837] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H533TBGXJ_n01_cDNA_B2_210615_fastqc.html [2021-06-15 15:12:51,879] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n01_cDNA_A3_210615_fastqc.html [2021-06-15 15:12:51,881] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H533TBGXJ_n01_cDNA_A3_210615_fastqc.html [2021-06-15 15:12:51,923] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n01_cDNA_B3_210615_fastqc.html [2021-06-15 15:12:51,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H533TBGXJ_n01_cDNA_B3_210615_fastqc.html [2021-06-15 15:12:51,969] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H533TBGXJ_n01_GDO_D_210615_fastqc.html [2021-06-15 15:12:51,971] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H533TBGXJ_n01_GDO_D_210615_fastqc.html [2021-06-15 15:12:52,678] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-15 15:12:52,680] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-15 15:12:52,696] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-06-15 15:12:52,698] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-15 15:12:52,713] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2021-06-15 15:12:52,717] multiqc [DEBUG ] No samples found: conpair [2021-06-15 15:12:52,722] multiqc [DEBUG ] No samples found: peddy [2021-06-15 15:12:52,726] multiqc [DEBUG ] No samples found: somalier [2021-06-15 15:12:52,731] multiqc [DEBUG ] No samples found: methylQA [2021-06-15 15:12:52,741] multiqc [DEBUG ] No samples found: mosdepth [2021-06-15 15:12:52,745] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-15 15:12:52,749] multiqc [DEBUG ] No samples found: qualimap [2021-06-15 15:12:52,754] multiqc [DEBUG ] No samples found: preseq [2021-06-15 15:12:52,759] multiqc [DEBUG ] No samples found: quast [2021-06-15 15:12:52,763] multiqc [DEBUG ] No samples found: qorts [2021-06-15 15:12:52,768] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-15 15:12:52,774] multiqc [DEBUG ] No samples found: rockhopper [2021-06-15 15:12:52,778] multiqc [DEBUG ] No samples found: rsem [2021-06-15 15:12:52,789] multiqc [DEBUG ] No samples found: rseqc [2021-06-15 15:12:52,793] multiqc [DEBUG ] No samples found: busco [2021-06-15 15:12:52,798] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-15 15:12:52,802] multiqc [DEBUG ] No samples found: disambiguate [2021-06-15 15:12:52,806] multiqc [DEBUG ] No samples found: supernova [2021-06-15 15:12:52,819] multiqc [DEBUG ] No samples found: deeptools [2021-06-15 15:12:52,823] multiqc [DEBUG ] No samples found: sargasso [2021-06-15 15:12:52,828] multiqc [DEBUG ] No samples found: verifybamid [2021-06-15 15:12:52,833] multiqc [DEBUG ] No samples found: mirtrace [2021-06-15 15:12:52,837] multiqc [DEBUG ] No samples found: happy [2021-06-15 15:12:52,842] multiqc [DEBUG ] No samples found: mirtop [2021-06-15 15:12:52,849] multiqc [DEBUG ] No samples found: homer [2021-06-15 15:12:52,854] multiqc [DEBUG ] No samples found: macs2 [2021-06-15 15:12:52,859] multiqc [DEBUG ] No samples found: theta2 [2021-06-15 15:12:52,864] multiqc [DEBUG ] No samples found: snpeff [2021-06-15 15:12:52,872] multiqc [DEBUG ] No samples found: gatk [2021-06-15 15:12:52,876] multiqc [DEBUG ] No samples found: htseq [2021-06-15 15:12:52,882] multiqc [DEBUG ] No samples found: bcftools [2021-06-15 15:12:52,886] multiqc [DEBUG ] No samples found: featureCounts [2021-06-15 15:12:52,892] multiqc [DEBUG ] No samples found: fgbio [2021-06-15 15:12:52,906] multiqc [DEBUG ] No samples found: dragen [2021-06-15 15:12:52,910] multiqc [DEBUG ] No samples found: dedup [2021-06-15 15:12:52,915] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-15 15:12:52,940] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-15 15:12:52,944] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-15 15:12:52,946] multiqc [DEBUG ] No samples found: picard [2021-06-15 15:12:52,951] multiqc [DEBUG ] No samples found: prokka [2021-06-15 15:12:52,955] multiqc [DEBUG ] No samples found: samblaster [2021-06-15 15:12:52,964] multiqc [DEBUG ] No samples found: samtools [2021-06-15 15:12:52,969] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-15 15:12:52,974] multiqc [DEBUG ] No samples found: bamtools [2021-06-15 15:12:52,978] multiqc [DEBUG ] No samples found: jellyfish [2021-06-15 15:12:52,986] multiqc [DEBUG ] No samples found: vcftools [2021-06-15 15:12:52,991] multiqc [DEBUG ] No samples found: longranger [2021-06-15 15:12:52,995] multiqc [DEBUG ] No samples found: stacks [2021-06-15 15:12:53,000] multiqc [DEBUG ] No samples found: varscan2 [2021-06-15 15:12:53,013] multiqc [DEBUG ] No samples found: bbmap [2021-06-15 15:12:53,018] multiqc [DEBUG ] No samples found: bismark [2021-06-15 15:12:53,023] multiqc [DEBUG ] No samples found: biscuit [2021-06-15 15:12:53,028] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-15 15:12:53,033] multiqc [DEBUG ] No samples found: hicup [2021-06-15 15:12:53,038] multiqc [DEBUG ] No samples found: hicpro [2021-06-15 15:12:53,042] multiqc [DEBUG ] No samples found: salmon [2021-06-15 15:12:53,046] multiqc [DEBUG ] No samples found: kallisto [2021-06-15 15:12:53,052] multiqc [DEBUG ] No samples found: slamdunk [2021-06-15 15:12:53,057] multiqc [DEBUG ] No samples found: star [2021-06-15 15:12:53,062] multiqc [DEBUG ] No samples found: hisat2 [2021-06-15 15:12:53,067] multiqc [DEBUG ] No samples found: tophat [2021-06-15 15:12:53,072] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-15 15:12:53,076] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-15 15:12:53,081] multiqc [DEBUG ] No samples found: snpsplit [2021-06-15 15:12:53,086] multiqc [DEBUG ] No samples found: kat [2021-06-15 15:12:53,090] multiqc [DEBUG ] No samples found: leehom [2021-06-15 15:12:53,095] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-15 15:12:53,099] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-15 15:12:53,103] multiqc [DEBUG ] No samples found: cutadapt [2021-06-15 15:12:53,107] multiqc [DEBUG ] No samples found: flexbar [2021-06-15 15:12:53,116] multiqc [DEBUG ] No samples found: kaiju [2021-06-15 15:12:53,121] multiqc [DEBUG ] No samples found: kraken [2021-06-15 15:12:53,126] multiqc [DEBUG ] No samples found: malt [2021-06-15 15:12:53,130] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-15 15:12:53,135] multiqc [DEBUG ] No samples found: sickle [2021-06-15 15:12:53,140] multiqc [DEBUG ] No samples found: skewer [2021-06-15 15:12:53,145] multiqc [DEBUG ] No samples found: sortmerna [2021-06-15 15:12:53,149] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-15 15:12:53,155] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-15 15:12:53,160] multiqc [DEBUG ] No samples found: afterqc [2021-06-15 15:12:53,164] multiqc [DEBUG ] No samples found: fastp [2021-06-15 15:12:56,515] multiqc.modules.fastqc.fastqc [INFO ] Found 58 reports [2021-06-15 15:12:56,890] multiqc [DEBUG ] No samples found: pycoqc [2021-06-15 15:12:56,896] multiqc [DEBUG ] No samples found: minionqc [2021-06-15 15:12:56,901] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-15 15:12:56,906] multiqc [DEBUG ] No samples found: clusterflow [2021-06-15 15:12:56,911] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-15 15:12:56,915] multiqc [DEBUG ] No samples found: interop [2021-06-15 15:12:56,921] multiqc [DEBUG ] No samples found: ivar [2021-06-15 15:12:56,925] multiqc [DEBUG ] No samples found: flash [2021-06-15 15:12:56,930] multiqc [DEBUG ] No samples found: seqyclean [2021-06-15 15:12:56,930] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-06-15 15:12:56,930] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-06-15 15:12:56,930] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-06-15 15:12:56,930] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-15 15:12:57,000] multiqc [INFO ] Compressing plot data [2021-06-15 15:12:57,832] multiqc [INFO ] Report : multiqc_report.html [2021-06-15 15:12:57,832] multiqc [INFO ] Data : multiqc_data [2021-06-15 15:12:57,832] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7643391/tmp27l8goew/multiqc_data' to '/scratch/gencore/logs/html/H533TBGXJ/merged/multiqc_data' [2021-06-15 15:12:57,963] multiqc [INFO ] MultiQC complete