[2021-01-15 04:33:31,807] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-01-15 04:33:31,808] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-01-15 04:33:31,808] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-01-15 04:33:31,809] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-01-15 04:33:31,809] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-01-15 04:33:31,809] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHCTDRXX/1 [2021-01-15 04:33:33,186] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-01-15 04:33:33,186] multiqc [INFO ] This is MultiQC v1.9 [2021-01-15 04:33:33,186] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHCTDRXX/1 [2021-01-15 04:33:33,186] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTHCTDRXX/1 [2021-01-15 04:33:33,187] multiqc [INFO ] Template : default [2021-01-15 04:33:33,187] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-01-15 04:33:33,187] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTHCTDRXX/1 [2021-01-15 04:33:33,187] 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 [2021-01-15 04:33:33,187] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-1143371/tmpa8mgwygf [2021-01-15 04:33:33,289] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C18_GFPBFP_R05_fastqc.html [2021-01-15 04:33:33,292] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C18_GFPBFP_R05_fastqc.html [2021-01-15 04:33:33,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-01-15 04:33:33,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-01-15 04:33:33,345] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-01-15 04:33:33,345] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-01-15 04:33:33,345] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-01-15 04:33:33,345] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-01-15 04:33:33,345] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-01-15 04:33:33,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_wt_pre_sort_R01_fastqc.html [2021-01-15 04:33:33,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_wt_pre_sort_R01_fastqc.html [2021-01-15 04:33:33,953] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C22_GFPBFP_R08_fastqc.html [2021-01-15 04:33:33,955] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C22_GFPBFP_R08_fastqc.html [2021-01-15 04:33:34,005] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C22_presort_R07_fastqc.html [2021-01-15 04:33:34,007] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C22_presort_R07_fastqc.html [2021-01-15 04:33:34,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_wt_GFP_BFP_R02_fastqc.html [2021-01-15 04:33:34,058] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_wt_GFP_BFP_R02_fastqc.html [2021-01-15 04:33:34,110] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C22_BFP_R09_fastqc.html [2021-01-15 04:33:34,112] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C22_BFP_R09_fastqc.html [2021-01-15 04:33:34,162] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_undetermined_fastqc.html [2021-01-15 04:33:34,163] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_undetermined_fastqc.html [2021-01-15 04:33:34,207] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_wt_BFP_R03_fastqc.html [2021-01-15 04:33:34,209] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_wt_BFP_R03_fastqc.html [2021-01-15 04:33:34,264] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C18_presort_R04_fastqc.html [2021-01-15 04:33:34,265] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C18_presort_R04_fastqc.html [2021-01-15 04:33:34,315] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C18_BFP_R06_fastqc.html [2021-01-15 04:33:34,317] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l01_n01_optHR_HEK_DNAPK_C18_BFP_R06_fastqc.html [2021-01-15 04:33:34,646] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-15 04:33:34,647] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-15 04:33:34,654] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-01-15 04:33:34,660] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 10 samples (table) [2021-01-15 04:33:34,669] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-01-15 04:33:34,673] multiqc [DEBUG ] No samples found: conpair [2021-01-15 04:33:34,677] multiqc [DEBUG ] No samples found: peddy [2021-01-15 04:33:34,685] multiqc [DEBUG ] No samples found: somalier [2021-01-15 04:33:34,689] multiqc [DEBUG ] No samples found: methylQA [2021-01-15 04:33:34,695] multiqc [DEBUG ] No samples found: mosdepth [2021-01-15 04:33:34,698] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-01-15 04:33:34,701] multiqc [DEBUG ] No samples found: qualimap [2021-01-15 04:33:34,705] multiqc [DEBUG ] No samples found: preseq [2021-01-15 04:33:34,709] multiqc [DEBUG ] No samples found: quast [2021-01-15 04:33:34,712] multiqc [DEBUG ] No samples found: qorts [2021-01-15 04:33:34,716] multiqc [DEBUG ] No samples found: rna_seqc [2021-01-15 04:33:34,720] multiqc [DEBUG ] No samples found: rockhopper [2021-01-15 04:33:34,724] multiqc [DEBUG ] No samples found: rsem [2021-01-15 04:33:34,733] multiqc [DEBUG ] No samples found: rseqc [2021-01-15 04:33:34,737] multiqc [DEBUG ] No samples found: busco [2021-01-15 04:33:34,741] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-01-15 04:33:34,744] multiqc [DEBUG ] No samples found: disambiguate [2021-01-15 04:33:34,748] multiqc [DEBUG ] No samples found: supernova [2021-01-15 04:33:34,759] multiqc [DEBUG ] No samples found: deeptools [2021-01-15 04:33:34,763] multiqc [DEBUG ] No samples found: sargasso [2021-01-15 04:33:34,766] multiqc [DEBUG ] No samples found: verifybamid [2021-01-15 04:33:34,770] multiqc [DEBUG ] No samples found: mirtrace [2021-01-15 04:33:34,774] multiqc [DEBUG ] No samples found: happy [2021-01-15 04:33:34,777] multiqc [DEBUG ] No samples found: mirtop [2021-01-15 04:33:34,782] multiqc [DEBUG ] No samples found: homer [2021-01-15 04:33:34,786] multiqc [DEBUG ] No samples found: macs2 [2021-01-15 04:33:34,789] multiqc [DEBUG ] No samples found: theta2 [2021-01-15 04:33:34,793] multiqc [DEBUG ] No samples found: snpeff [2021-01-15 04:33:34,798] multiqc [DEBUG ] No samples found: gatk [2021-01-15 04:33:34,802] multiqc [DEBUG ] No samples found: htseq [2021-01-15 04:33:34,806] multiqc [DEBUG ] No samples found: bcftools [2021-01-15 04:33:34,810] multiqc [DEBUG ] No samples found: featureCounts [2021-01-15 04:33:34,814] multiqc [DEBUG ] No samples found: fgbio [2021-01-15 04:33:34,825] multiqc [DEBUG ] No samples found: dragen [2021-01-15 04:33:34,829] multiqc [DEBUG ] No samples found: dedup [2021-01-15 04:33:34,833] multiqc [DEBUG ] No samples found: damageprofiler [2021-01-15 04:33:34,850] multiqc [DEBUG ] No samples found: biobambam2 [2021-01-15 04:33:34,853] multiqc [DEBUG ] No samples found: mtnucratio [2021-01-15 04:33:34,856] multiqc [DEBUG ] No samples found: picard [2021-01-15 04:33:34,859] multiqc [DEBUG ] No samples found: prokka [2021-01-15 04:33:34,863] multiqc [DEBUG ] No samples found: samblaster [2021-01-15 04:33:34,871] multiqc [DEBUG ] No samples found: samtools [2021-01-15 04:33:34,875] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-01-15 04:33:34,879] multiqc [DEBUG ] No samples found: bamtools [2021-01-15 04:33:34,882] multiqc [DEBUG ] No samples found: jellyfish [2021-01-15 04:33:34,890] multiqc [DEBUG ] No samples found: vcftools [2021-01-15 04:33:34,894] multiqc [DEBUG ] No samples found: longranger [2021-01-15 04:33:34,898] multiqc [DEBUG ] No samples found: stacks [2021-01-15 04:33:34,901] multiqc [DEBUG ] No samples found: varscan2 [2021-01-15 04:33:34,913] multiqc [DEBUG ] No samples found: bbmap [2021-01-15 04:33:34,916] multiqc [DEBUG ] No samples found: bismark [2021-01-15 04:33:34,920] multiqc [DEBUG ] No samples found: biscuit [2021-01-15 04:33:34,924] multiqc [DEBUG ] No samples found: hicexplorer [2021-01-15 04:33:34,928] multiqc [DEBUG ] No samples found: hicup [2021-01-15 04:33:34,932] multiqc [DEBUG ] No samples found: hicpro [2021-01-15 04:33:34,935] multiqc [DEBUG ] No samples found: salmon [2021-01-15 04:33:34,939] multiqc [DEBUG ] No samples found: kallisto [2021-01-15 04:33:34,943] multiqc [DEBUG ] No samples found: slamdunk [2021-01-15 04:33:34,946] multiqc [DEBUG ] No samples found: star [2021-01-15 04:33:34,950] multiqc [DEBUG ] No samples found: hisat2 [2021-01-15 04:33:34,954] multiqc [DEBUG ] No samples found: tophat [2021-01-15 04:33:34,957] multiqc [DEBUG ] No samples found: bowtie2 [2021-01-15 04:33:34,961] multiqc [DEBUG ] No samples found: bowtie1 [2021-01-15 04:33:34,965] multiqc [DEBUG ] No samples found: snpsplit [2021-01-15 04:33:34,968] multiqc [DEBUG ] No samples found: kat [2021-01-15 04:33:34,972] multiqc [DEBUG ] No samples found: leehom [2021-01-15 04:33:34,976] multiqc [DEBUG ] No samples found: adapterRemoval [2021-01-15 04:33:34,979] multiqc [DEBUG ] No samples found: clipandmerge [2021-01-15 04:33:34,982] multiqc [DEBUG ] No samples found: cutadapt [2021-01-15 04:33:34,986] multiqc [DEBUG ] No samples found: flexbar [2021-01-15 04:33:34,989] multiqc [DEBUG ] No samples found: kaiju [2021-01-15 04:33:34,993] multiqc [DEBUG ] No samples found: kraken [2021-01-15 04:33:34,997] multiqc [DEBUG ] No samples found: malt [2021-01-15 04:33:35,000] multiqc [DEBUG ] No samples found: trimmomatic [2021-01-15 04:33:35,004] multiqc [DEBUG ] No samples found: sickle [2021-01-15 04:33:35,007] multiqc [DEBUG ] No samples found: skewer [2021-01-15 04:33:35,011] multiqc [DEBUG ] No samples found: sortmerna [2021-01-15 04:33:35,014] multiqc [DEBUG ] No samples found: biobloomtools [2021-01-15 04:33:35,018] multiqc [DEBUG ] No samples found: fastq_screen [2021-01-15 04:33:35,022] multiqc [DEBUG ] No samples found: afterqc [2021-01-15 04:33:35,025] multiqc [DEBUG ] No samples found: fastp [2021-01-15 04:33:35,289] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-01-15 04:33:35,503] multiqc [DEBUG ] No samples found: pycoqc [2021-01-15 04:33:35,507] multiqc [DEBUG ] No samples found: minionqc [2021-01-15 04:33:35,510] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-01-15 04:33:35,514] multiqc [DEBUG ] No samples found: clusterflow [2021-01-15 04:33:35,518] multiqc [DEBUG ] No samples found: bcl2fastq [2021-01-15 04:33:35,522] multiqc [DEBUG ] No samples found: interop [2021-01-15 04:33:35,525] multiqc [DEBUG ] No samples found: ivar [2021-01-15 04:33:35,529] multiqc [DEBUG ] No samples found: flash [2021-01-15 04:33:35,533] multiqc [DEBUG ] No samples found: seqyclean [2021-01-15 04:33:35,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-01-15 04:33:35,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-01-15 04:33:35,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-01-15 04:33:35,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-01-15 04:33:35,533] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-01-15 04:33:35,546] multiqc [INFO ] Compressing plot data [2021-01-15 04:33:35,702] multiqc [INFO ] Report : multiqc_report.html [2021-01-15 04:33:35,703] multiqc [INFO ] Data : multiqc_data [2021-01-15 04:33:35,703] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1143371/tmpa8mgwygf/multiqc_data' to '/scratch/gencore/logs/html/HTHCTDRXX/1/multiqc_data' [2021-01-15 04:33:35,853] multiqc [INFO ] MultiQC complete