[2022-05-20 10:58:46,893] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-20 10:58:46,893] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-20 10:58:46,893] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-20 10:58:46,895] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-20 10:58:46,895] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-20 10:58:46,895] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLJNGAFX3/merged [2022-05-20 10:58:47,300] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-20 10:58:47,300] multiqc [INFO ] This is MultiQC v1.9 [2022-05-20 10:58:47,300] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLJNGAFX3/merged [2022-05-20 10:58:47,300] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLJNGAFX3/merged [2022-05-20 10:58:47,300] multiqc [INFO ] Template : default [2022-05-20 10:58:47,301] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-20 10:58:47,301] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLJNGAFX3/merged [2022-05-20 10:58:47,301] 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 [2022-05-20 10:58:47,301] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-19866149/tmpsry3ozlv [2022-05-20 10:58:47,418] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:47,420] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:47,421] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:47,421] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:47,421] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:47,421] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:47,421] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:47,441] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 10:58:48,402] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJNGAFX3_n01_FMR1_new_fastqc.html [2022-05-20 10:58:48,404] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJNGAFX3_n01_FMR1_new_fastqc.html [2022-05-20 10:58:48,446] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJNGAFX3_n02_ADARcd_new_fastqc.html [2022-05-20 10:58:48,448] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJNGAFX3_n02_ADARcd_new_fastqc.html [2022-05-20 10:58:48,511] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJNGAFX3_n01_undetermined_fastqc.html [2022-05-20 10:58:48,513] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJNGAFX3_n01_undetermined_fastqc.html [2022-05-20 10:58:48,556] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJNGAFX3_n02_FMR1_new_fastqc.html [2022-05-20 10:58:48,558] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJNGAFX3_n02_FMR1_new_fastqc.html [2022-05-20 10:58:48,616] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJNGAFX3_n02_undetermined_fastqc.html [2022-05-20 10:58:48,618] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJNGAFX3_n02_undetermined_fastqc.html [2022-05-20 10:58:48,673] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJNGAFX3_n01_ADARcd_new_fastqc.html [2022-05-20 10:58:48,675] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJNGAFX3_n01_ADARcd_new_fastqc.html [2022-05-20 10:58:49,095] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-20 10:58:49,098] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-20 10:58:49,107] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-20 10:58:49,117] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-20 10:58:49,119] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2022-05-20 10:58:49,127] multiqc [DEBUG ] No samples found: conpair [2022-05-20 10:58:49,134] multiqc [DEBUG ] No samples found: peddy [2022-05-20 10:58:49,140] multiqc [DEBUG ] No samples found: somalier [2022-05-20 10:58:49,147] multiqc [DEBUG ] No samples found: methylQA [2022-05-20 10:58:49,161] multiqc [DEBUG ] No samples found: mosdepth [2022-05-20 10:58:49,166] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-20 10:58:49,171] multiqc [DEBUG ] No samples found: qualimap [2022-05-20 10:58:49,177] multiqc [DEBUG ] No samples found: preseq [2022-05-20 10:58:49,183] multiqc [DEBUG ] No samples found: quast [2022-05-20 10:58:49,190] multiqc [DEBUG ] No samples found: qorts [2022-05-20 10:58:49,195] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-20 10:58:49,203] multiqc [DEBUG ] No samples found: rockhopper [2022-05-20 10:58:49,211] multiqc [DEBUG ] No samples found: rsem [2022-05-20 10:58:49,233] multiqc [DEBUG ] No samples found: rseqc [2022-05-20 10:58:49,239] multiqc [DEBUG ] No samples found: busco [2022-05-20 10:58:49,248] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-20 10:58:49,254] multiqc [DEBUG ] No samples found: disambiguate [2022-05-20 10:58:49,262] multiqc [DEBUG ] No samples found: supernova [2022-05-20 10:58:49,287] multiqc [DEBUG ] No samples found: deeptools [2022-05-20 10:58:49,296] multiqc [DEBUG ] No samples found: sargasso [2022-05-20 10:58:49,301] multiqc [DEBUG ] No samples found: verifybamid [2022-05-20 10:58:49,307] multiqc [DEBUG ] No samples found: mirtrace [2022-05-20 10:58:49,313] multiqc [DEBUG ] No samples found: happy [2022-05-20 10:58:49,320] multiqc [DEBUG ] No samples found: mirtop [2022-05-20 10:58:49,330] multiqc [DEBUG ] No samples found: homer [2022-05-20 10:58:49,336] multiqc [DEBUG ] No samples found: macs2 [2022-05-20 10:58:49,345] multiqc [DEBUG ] No samples found: theta2 [2022-05-20 10:58:49,354] multiqc [DEBUG ] No samples found: snpeff [2022-05-20 10:58:49,364] multiqc [DEBUG ] No samples found: gatk [2022-05-20 10:58:49,370] multiqc [DEBUG ] No samples found: htseq [2022-05-20 10:58:49,377] multiqc [DEBUG ] No samples found: bcftools [2022-05-20 10:58:49,383] multiqc [DEBUG ] No samples found: featureCounts [2022-05-20 10:58:49,391] multiqc [DEBUG ] No samples found: fgbio [2022-05-20 10:58:49,411] multiqc [DEBUG ] No samples found: dragen [2022-05-20 10:58:49,417] multiqc [DEBUG ] No samples found: dedup [2022-05-20 10:58:49,424] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-20 10:58:49,468] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-20 10:58:49,476] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-20 10:58:49,479] multiqc [DEBUG ] No samples found: picard [2022-05-20 10:58:49,485] multiqc [DEBUG ] No samples found: prokka [2022-05-20 10:58:49,491] multiqc [DEBUG ] No samples found: samblaster [2022-05-20 10:58:49,504] multiqc [DEBUG ] No samples found: samtools [2022-05-20 10:58:49,510] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-20 10:58:49,521] multiqc [DEBUG ] No samples found: bamtools [2022-05-20 10:58:49,528] multiqc [DEBUG ] No samples found: jellyfish [2022-05-20 10:58:49,540] multiqc [DEBUG ] No samples found: vcftools [2022-05-20 10:58:49,546] multiqc [DEBUG ] No samples found: longranger [2022-05-20 10:58:49,555] multiqc [DEBUG ] No samples found: stacks [2022-05-20 10:58:49,575] multiqc [DEBUG ] No samples found: varscan2 [2022-05-20 10:58:49,607] multiqc [DEBUG ] No samples found: bbmap [2022-05-20 10:58:49,613] multiqc [DEBUG ] No samples found: bismark [2022-05-20 10:58:49,622] multiqc [DEBUG ] No samples found: biscuit [2022-05-20 10:58:49,628] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-20 10:58:49,634] multiqc [DEBUG ] No samples found: hicup [2022-05-20 10:58:49,643] multiqc [DEBUG ] No samples found: hicpro [2022-05-20 10:58:49,648] multiqc [DEBUG ] No samples found: salmon [2022-05-20 10:58:49,656] multiqc [DEBUG ] No samples found: kallisto [2022-05-20 10:58:49,661] multiqc [DEBUG ] No samples found: slamdunk [2022-05-20 10:58:49,668] multiqc [DEBUG ] No samples found: star [2022-05-20 10:58:49,674] multiqc [DEBUG ] No samples found: hisat2 [2022-05-20 10:58:49,682] multiqc [DEBUG ] No samples found: tophat [2022-05-20 10:58:49,690] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-20 10:58:49,697] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-20 10:58:49,706] multiqc [DEBUG ] No samples found: snpsplit [2022-05-20 10:58:49,714] multiqc [DEBUG ] No samples found: kat [2022-05-20 10:58:49,720] multiqc [DEBUG ] No samples found: leehom [2022-05-20 10:58:49,728] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-20 10:58:49,734] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-20 10:58:49,740] multiqc [DEBUG ] No samples found: cutadapt [2022-05-20 10:58:49,745] multiqc [DEBUG ] No samples found: flexbar [2022-05-20 10:58:49,753] multiqc [DEBUG ] No samples found: kaiju [2022-05-20 10:58:49,759] multiqc [DEBUG ] No samples found: kraken [2022-05-20 10:58:49,765] multiqc [DEBUG ] No samples found: malt [2022-05-20 10:58:49,772] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-20 10:58:49,779] multiqc [DEBUG ] No samples found: sickle [2022-05-20 10:58:49,786] multiqc [DEBUG ] No samples found: skewer [2022-05-20 10:58:49,792] multiqc [DEBUG ] No samples found: sortmerna [2022-05-20 10:58:49,799] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-20 10:58:49,807] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-20 10:58:49,813] multiqc [DEBUG ] No samples found: afterqc [2022-05-20 10:58:49,820] multiqc [DEBUG ] No samples found: fastp [2022-05-20 10:58:50,049] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2022-05-20 10:58:50,137] multiqc [DEBUG ] No samples found: pycoqc [2022-05-20 10:58:50,144] multiqc [DEBUG ] No samples found: minionqc [2022-05-20 10:58:50,153] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-20 10:58:50,159] multiqc [DEBUG ] No samples found: clusterflow [2022-05-20 10:58:50,168] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-20 10:58:50,176] multiqc [DEBUG ] No samples found: interop [2022-05-20 10:58:50,183] multiqc [DEBUG ] No samples found: ivar [2022-05-20 10:58:50,190] multiqc [DEBUG ] No samples found: flash [2022-05-20 10:58:50,198] multiqc [DEBUG ] No samples found: seqyclean [2022-05-20 10:58:50,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-05-20 10:58:50,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-05-20 10:58:50,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-20 10:58:50,198] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-20 10:58:50,207] multiqc [INFO ] Compressing plot data [2022-05-20 10:58:50,326] multiqc [INFO ] Report : multiqc_report.html [2022-05-20 10:58:50,326] multiqc [INFO ] Data : multiqc_data [2022-05-20 10:58:50,326] multiqc [DEBUG ] Moving data file from '/state/partition1/job-19866149/tmpsry3ozlv/multiqc_data' to '/scratch/gencore/logs/html/HLJNGAFX3/merged/multiqc_data' [2022-05-20 10:58:50,482] multiqc [INFO ] MultiQC complete