[2022-02-03 21:37:14,542] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-02-03 21:37:14,542] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-02-03 21:37:14,542] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-03 21:37:14,543] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-02-03 21:37:14,543] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-02-03 21:37:14,544] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWTNGBGXK/merged [2022-02-03 21:37:15,965] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-02-03 21:37:15,965] multiqc [INFO ] This is MultiQC v1.9 [2022-02-03 21:37:15,965] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWTNGBGXK/merged [2022-02-03 21:37:15,965] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWTNGBGXK/merged [2022-02-03 21:37:15,965] multiqc [INFO ] Template : default [2022-02-03 21:37:15,966] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-02-03 21:37:15,966] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWTNGBGXK/merged [2022-02-03 21:37:15,966] 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 [2022-02-03 21:37:15,966] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14645043/tmppiag8km5 [2022-02-03 21:37:16,071] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-03 21:37:16,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-03 21:37:16,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTNGBGXK_n01_undetermined_fastqc.html [2022-02-03 21:37:16,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTNGBGXK_n01_undetermined_fastqc.html [2022-02-03 21:37:16,536] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep2_day21_fastqc.html [2022-02-03 21:37:16,537] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep2_day21_fastqc.html [2022-02-03 21:37:16,591] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep1_day21_fastqc.html [2022-02-03 21:37:16,593] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep1_day21_fastqc.html [2022-02-03 21:37:16,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep2_day0_fastqc.html [2022-02-03 21:37:16,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep2_day0_fastqc.html [2022-02-03 21:37:16,703] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep1_day1_fastqc.html [2022-02-03 21:37:16,705] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTNGBGXK_n01_HCT116_sph_rep1_day1_fastqc.html [2022-02-03 21:37:17,176] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-03 21:37:17,177] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-03 21:37:17,184] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-02-03 21:37:17,194] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-02-03 21:37:17,197] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2022-02-03 21:37:17,202] multiqc [DEBUG ] No samples found: conpair [2022-02-03 21:37:17,207] multiqc [DEBUG ] No samples found: peddy [2022-02-03 21:37:17,213] multiqc [DEBUG ] No samples found: somalier [2022-02-03 21:37:17,218] multiqc [DEBUG ] No samples found: methylQA [2022-02-03 21:37:17,226] multiqc [DEBUG ] No samples found: mosdepth [2022-02-03 21:37:17,232] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-03 21:37:17,236] multiqc [DEBUG ] No samples found: qualimap [2022-02-03 21:37:17,240] multiqc [DEBUG ] No samples found: preseq [2022-02-03 21:37:17,245] multiqc [DEBUG ] No samples found: quast [2022-02-03 21:37:17,250] multiqc [DEBUG ] No samples found: qorts [2022-02-03 21:37:17,255] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-03 21:37:17,259] multiqc [DEBUG ] No samples found: rockhopper [2022-02-03 21:37:17,264] multiqc [DEBUG ] No samples found: rsem [2022-02-03 21:37:17,276] multiqc [DEBUG ] No samples found: rseqc [2022-02-03 21:37:17,281] multiqc [DEBUG ] No samples found: busco [2022-02-03 21:37:17,286] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-03 21:37:17,291] multiqc [DEBUG ] No samples found: disambiguate [2022-02-03 21:37:17,296] multiqc [DEBUG ] No samples found: supernova [2022-02-03 21:37:17,307] multiqc [DEBUG ] No samples found: deeptools [2022-02-03 21:37:17,313] multiqc [DEBUG ] No samples found: sargasso [2022-02-03 21:37:17,317] multiqc [DEBUG ] No samples found: verifybamid [2022-02-03 21:37:17,322] multiqc [DEBUG ] No samples found: mirtrace [2022-02-03 21:37:17,328] multiqc [DEBUG ] No samples found: happy [2022-02-03 21:37:17,333] multiqc [DEBUG ] No samples found: mirtop [2022-02-03 21:37:17,340] multiqc [DEBUG ] No samples found: homer [2022-02-03 21:37:17,345] multiqc [DEBUG ] No samples found: macs2 [2022-02-03 21:37:17,351] multiqc [DEBUG ] No samples found: theta2 [2022-02-03 21:37:17,356] multiqc [DEBUG ] No samples found: snpeff [2022-02-03 21:37:17,363] multiqc [DEBUG ] No samples found: gatk [2022-02-03 21:37:17,368] multiqc [DEBUG ] No samples found: htseq [2022-02-03 21:37:17,374] multiqc [DEBUG ] No samples found: bcftools [2022-02-03 21:37:17,379] multiqc [DEBUG ] No samples found: featureCounts [2022-02-03 21:37:17,385] multiqc [DEBUG ] No samples found: fgbio [2022-02-03 21:37:17,397] multiqc [DEBUG ] No samples found: dragen [2022-02-03 21:37:17,402] multiqc [DEBUG ] No samples found: dedup [2022-02-03 21:37:17,407] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-03 21:37:17,428] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-03 21:37:17,433] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-03 21:37:17,436] multiqc [DEBUG ] No samples found: picard [2022-02-03 21:37:17,440] multiqc [DEBUG ] No samples found: prokka [2022-02-03 21:37:17,445] multiqc [DEBUG ] No samples found: samblaster [2022-02-03 21:37:17,453] multiqc [DEBUG ] No samples found: samtools [2022-02-03 21:37:17,458] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-03 21:37:17,463] multiqc [DEBUG ] No samples found: bamtools [2022-02-03 21:37:17,468] multiqc [DEBUG ] No samples found: jellyfish [2022-02-03 21:37:17,475] multiqc [DEBUG ] No samples found: vcftools [2022-02-03 21:37:17,480] multiqc [DEBUG ] No samples found: longranger [2022-02-03 21:37:17,485] multiqc [DEBUG ] No samples found: stacks [2022-02-03 21:37:17,489] multiqc [DEBUG ] No samples found: varscan2 [2022-02-03 21:37:17,504] multiqc [DEBUG ] No samples found: bbmap [2022-02-03 21:37:17,508] multiqc [DEBUG ] No samples found: bismark [2022-02-03 21:37:17,514] multiqc [DEBUG ] No samples found: biscuit [2022-02-03 21:37:17,520] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-03 21:37:17,525] multiqc [DEBUG ] No samples found: hicup [2022-02-03 21:37:17,530] multiqc [DEBUG ] No samples found: hicpro [2022-02-03 21:37:17,534] multiqc [DEBUG ] No samples found: salmon [2022-02-03 21:37:17,539] multiqc [DEBUG ] No samples found: kallisto [2022-02-03 21:37:17,544] multiqc [DEBUG ] No samples found: slamdunk [2022-02-03 21:37:17,549] multiqc [DEBUG ] No samples found: star [2022-02-03 21:37:17,555] multiqc [DEBUG ] No samples found: hisat2 [2022-02-03 21:37:17,560] multiqc [DEBUG ] No samples found: tophat [2022-02-03 21:37:17,564] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-03 21:37:17,570] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-03 21:37:17,575] multiqc [DEBUG ] No samples found: snpsplit [2022-02-03 21:37:17,580] multiqc [DEBUG ] No samples found: kat [2022-02-03 21:37:17,584] multiqc [DEBUG ] No samples found: leehom [2022-02-03 21:37:17,590] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-03 21:37:17,594] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-03 21:37:17,599] multiqc [DEBUG ] No samples found: cutadapt [2022-02-03 21:37:17,605] multiqc [DEBUG ] No samples found: flexbar [2022-02-03 21:37:17,609] multiqc [DEBUG ] No samples found: kaiju [2022-02-03 21:37:17,614] multiqc [DEBUG ] No samples found: kraken [2022-02-03 21:37:17,619] multiqc [DEBUG ] No samples found: malt [2022-02-03 21:37:17,624] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-03 21:37:17,629] multiqc [DEBUG ] No samples found: sickle [2022-02-03 21:37:17,634] multiqc [DEBUG ] No samples found: skewer [2022-02-03 21:37:17,638] multiqc [DEBUG ] No samples found: sortmerna [2022-02-03 21:37:17,643] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-03 21:37:17,648] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-03 21:37:17,652] multiqc [DEBUG ] No samples found: afterqc [2022-02-03 21:37:17,657] multiqc [DEBUG ] No samples found: fastp [2022-02-03 21:37:18,001] multiqc.modules.fastqc.fastqc [INFO ] Found 5 reports [2022-02-03 21:37:18,125] multiqc [DEBUG ] No samples found: pycoqc [2022-02-03 21:37:18,129] multiqc [DEBUG ] No samples found: minionqc [2022-02-03 21:37:18,134] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-02-03 21:37:18,139] multiqc [DEBUG ] No samples found: clusterflow [2022-02-03 21:37:18,144] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-03 21:37:18,149] multiqc [DEBUG ] No samples found: interop [2022-02-03 21:37:18,155] multiqc [DEBUG ] No samples found: ivar [2022-02-03 21:37:18,160] multiqc [DEBUG ] No samples found: flash [2022-02-03 21:37:18,164] multiqc [DEBUG ] No samples found: seqyclean [2022-02-03 21:37:18,164] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-02-03 21:37:18,164] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-02-03 21:37:18,164] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-02-03 21:37:18,164] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-02-03 21:37:18,171] multiqc [INFO ] Compressing plot data [2022-02-03 21:37:18,253] multiqc [INFO ] Report : multiqc_report.html [2022-02-03 21:37:18,253] multiqc [INFO ] Data : multiqc_data [2022-02-03 21:37:18,253] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14645043/tmppiag8km5/multiqc_data' to '/scratch/gencore/logs/html/HWTNGBGXK/merged/multiqc_data' [2022-02-03 21:37:18,367] multiqc [INFO ] MultiQC complete