[2021-12-18 05:08:44,260] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-18 05:08:44,260] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-18 05:08:44,260] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-18 05:08:44,261] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-18 05:08:44,261] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-18 05:08:44,261] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWTTHBGXK/merged [2021-12-18 05:08:45,767] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-18 05:08:45,767] multiqc [INFO ] This is MultiQC v1.9 [2021-12-18 05:08:45,767] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWTTHBGXK/merged [2021-12-18 05:08:45,767] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWTTHBGXK/merged [2021-12-18 05:08:45,767] multiqc [INFO ] Template : default [2021-12-18 05:08:45,767] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-18 05:08:45,767] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWTTHBGXK/merged [2021-12-18 05:08:45,768] 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 [2021-12-18 05:08:45,768] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13143165/tmp66ep1dvt [2021-12-18 05:08:45,886] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTTHBGXK_n01_undetermined_fastqc.html [2021-12-18 05:08:45,889] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTTHBGXK_n01_undetermined_fastqc.html [2021-12-18 05:08:45,932] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 05:08:45,934] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 05:08:46,130] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTTHBGXK_n02_undetermined_fastqc.html [2021-12-18 05:08:46,132] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTTHBGXK_n02_undetermined_fastqc.html [2021-12-18 05:08:46,173] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTTHBGXK_n01_A375_2_fastqc.html [2021-12-18 05:08:46,175] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTTHBGXK_n01_A375_2_fastqc.html [2021-12-18 05:08:46,216] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTTHBGXK_n02_A375_2_fastqc.html [2021-12-18 05:08:46,218] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTTHBGXK_n02_A375_2_fastqc.html [2021-12-18 05:08:46,260] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTTHBGXK_n02_A375_1_fastqc.html [2021-12-18 05:08:46,262] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTTHBGXK_n02_A375_1_fastqc.html [2021-12-18 05:08:46,304] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTTHBGXK_n01_A375_1_fastqc.html [2021-12-18 05:08:46,306] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTTHBGXK_n01_A375_1_fastqc.html [2021-12-18 05:08:46,645] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-18 05:08:46,646] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-18 05:08:46,654] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-18 05:08:46,664] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-18 05:08:46,666] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2021-12-18 05:08:46,673] multiqc [DEBUG ] No samples found: conpair [2021-12-18 05:08:46,678] multiqc [DEBUG ] No samples found: peddy [2021-12-18 05:08:46,684] multiqc [DEBUG ] No samples found: somalier [2021-12-18 05:08:46,689] multiqc [DEBUG ] No samples found: methylQA [2021-12-18 05:08:46,700] multiqc [DEBUG ] No samples found: mosdepth [2021-12-18 05:08:46,705] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-18 05:08:46,709] multiqc [DEBUG ] No samples found: qualimap [2021-12-18 05:08:46,714] multiqc [DEBUG ] No samples found: preseq [2021-12-18 05:08:46,719] multiqc [DEBUG ] No samples found: quast [2021-12-18 05:08:46,725] multiqc [DEBUG ] No samples found: qorts [2021-12-18 05:08:46,731] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-18 05:08:46,736] multiqc [DEBUG ] No samples found: rockhopper [2021-12-18 05:08:46,741] multiqc [DEBUG ] No samples found: rsem [2021-12-18 05:08:46,753] multiqc [DEBUG ] No samples found: rseqc [2021-12-18 05:08:46,758] multiqc [DEBUG ] No samples found: busco [2021-12-18 05:08:46,764] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-18 05:08:46,769] multiqc [DEBUG ] No samples found: disambiguate [2021-12-18 05:08:46,775] multiqc [DEBUG ] No samples found: supernova [2021-12-18 05:08:46,787] multiqc [DEBUG ] No samples found: deeptools [2021-12-18 05:08:46,792] multiqc [DEBUG ] No samples found: sargasso [2021-12-18 05:08:46,798] multiqc [DEBUG ] No samples found: verifybamid [2021-12-18 05:08:46,804] multiqc [DEBUG ] No samples found: mirtrace [2021-12-18 05:08:46,809] multiqc [DEBUG ] No samples found: happy [2021-12-18 05:08:46,814] multiqc [DEBUG ] No samples found: mirtop [2021-12-18 05:08:46,821] multiqc [DEBUG ] No samples found: homer [2021-12-18 05:08:46,826] multiqc [DEBUG ] No samples found: macs2 [2021-12-18 05:08:46,832] multiqc [DEBUG ] No samples found: theta2 [2021-12-18 05:08:46,837] multiqc [DEBUG ] No samples found: snpeff [2021-12-18 05:08:46,844] multiqc [DEBUG ] No samples found: gatk [2021-12-18 05:08:46,849] multiqc [DEBUG ] No samples found: htseq [2021-12-18 05:08:46,855] multiqc [DEBUG ] No samples found: bcftools [2021-12-18 05:08:46,860] multiqc [DEBUG ] No samples found: featureCounts [2021-12-18 05:08:46,866] multiqc [DEBUG ] No samples found: fgbio [2021-12-18 05:08:46,878] multiqc [DEBUG ] No samples found: dragen [2021-12-18 05:08:46,885] multiqc [DEBUG ] No samples found: dedup [2021-12-18 05:08:46,891] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-18 05:08:46,913] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-18 05:08:46,919] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-18 05:08:46,921] multiqc [DEBUG ] No samples found: picard [2021-12-18 05:08:46,926] multiqc [DEBUG ] No samples found: prokka [2021-12-18 05:08:46,932] multiqc [DEBUG ] No samples found: samblaster [2021-12-18 05:08:46,940] multiqc [DEBUG ] No samples found: samtools [2021-12-18 05:08:46,945] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-18 05:08:46,951] multiqc [DEBUG ] No samples found: bamtools [2021-12-18 05:08:46,955] multiqc [DEBUG ] No samples found: jellyfish [2021-12-18 05:08:46,962] multiqc [DEBUG ] No samples found: vcftools [2021-12-18 05:08:46,966] multiqc [DEBUG ] No samples found: longranger [2021-12-18 05:08:46,971] multiqc [DEBUG ] No samples found: stacks [2021-12-18 05:08:46,977] multiqc [DEBUG ] No samples found: varscan2 [2021-12-18 05:08:46,990] multiqc [DEBUG ] No samples found: bbmap [2021-12-18 05:08:46,995] multiqc [DEBUG ] No samples found: bismark [2021-12-18 05:08:47,001] multiqc [DEBUG ] No samples found: biscuit [2021-12-18 05:08:47,006] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-18 05:08:47,012] multiqc [DEBUG ] No samples found: hicup [2021-12-18 05:08:47,017] multiqc [DEBUG ] No samples found: hicpro [2021-12-18 05:08:47,023] multiqc [DEBUG ] No samples found: salmon [2021-12-18 05:08:47,028] multiqc [DEBUG ] No samples found: kallisto [2021-12-18 05:08:47,034] multiqc [DEBUG ] No samples found: slamdunk [2021-12-18 05:08:47,039] multiqc [DEBUG ] No samples found: star [2021-12-18 05:08:47,044] multiqc [DEBUG ] No samples found: hisat2 [2021-12-18 05:08:47,049] multiqc [DEBUG ] No samples found: tophat [2021-12-18 05:08:47,054] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-18 05:08:47,059] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-18 05:08:47,064] multiqc [DEBUG ] No samples found: snpsplit [2021-12-18 05:08:47,070] multiqc [DEBUG ] No samples found: kat [2021-12-18 05:08:47,074] multiqc [DEBUG ] No samples found: leehom [2021-12-18 05:08:47,079] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-18 05:08:47,084] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-18 05:08:47,089] multiqc [DEBUG ] No samples found: cutadapt [2021-12-18 05:08:47,094] multiqc [DEBUG ] No samples found: flexbar [2021-12-18 05:08:47,100] multiqc [DEBUG ] No samples found: kaiju [2021-12-18 05:08:47,105] multiqc [DEBUG ] No samples found: kraken [2021-12-18 05:08:47,109] multiqc [DEBUG ] No samples found: malt [2021-12-18 05:08:47,115] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-18 05:08:47,120] multiqc [DEBUG ] No samples found: sickle [2021-12-18 05:08:47,125] multiqc [DEBUG ] No samples found: skewer [2021-12-18 05:08:47,130] multiqc [DEBUG ] No samples found: sortmerna [2021-12-18 05:08:47,134] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-18 05:08:47,144] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-18 05:08:47,152] multiqc [DEBUG ] No samples found: afterqc [2021-12-18 05:08:47,156] multiqc [DEBUG ] No samples found: fastp [2021-12-18 05:08:47,602] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2021-12-18 05:08:47,749] multiqc [DEBUG ] No samples found: pycoqc [2021-12-18 05:08:47,754] multiqc [DEBUG ] No samples found: minionqc [2021-12-18 05:08:47,759] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-18 05:08:47,764] multiqc [DEBUG ] No samples found: clusterflow [2021-12-18 05:08:47,771] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-18 05:08:47,777] multiqc [DEBUG ] No samples found: interop [2021-12-18 05:08:47,782] multiqc [DEBUG ] No samples found: ivar [2021-12-18 05:08:47,786] multiqc [DEBUG ] No samples found: flash [2021-12-18 05:08:47,791] multiqc [DEBUG ] No samples found: seqyclean [2021-12-18 05:08:47,791] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-18 05:08:47,791] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-18 05:08:47,791] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-18 05:08:47,791] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-18 05:08:47,799] multiqc [INFO ] Compressing plot data [2021-12-18 05:08:47,915] multiqc [INFO ] Report : multiqc_report.html [2021-12-18 05:08:47,916] multiqc [INFO ] Data : multiqc_data [2021-12-18 05:08:47,916] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13143165/tmp66ep1dvt/multiqc_data' to '/scratch/gencore/logs/html/HWTTHBGXK/merged/multiqc_data' [2021-12-18 05:08:48,065] multiqc [INFO ] MultiQC complete