[2022-01-22 20:04:24,519] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-22 20:04:24,519] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-22 20:04:24,519] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-22 20:04:24,520] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-22 20:04:24,520] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-22 20:04:24,520] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFLJJAFX3/merged [2022-01-22 20:04:25,794] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-22 20:04:25,794] multiqc [INFO ] This is MultiQC v1.9 [2022-01-22 20:04:25,794] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFLJJAFX3/merged [2022-01-22 20:04:25,794] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFLJJAFX3/merged [2022-01-22 20:04:25,794] multiqc [INFO ] Template : default [2022-01-22 20:04:25,794] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-22 20:04:25,794] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFLJJAFX3/merged [2022-01-22 20:04:25,795] 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 [2022-01-22 20:04:25,795] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14186460/tmp98o622xx [2022-01-22 20:04:25,888] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4_rep3_fastqc.html [2022-01-22 20:04:25,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4_rep3_fastqc.html [2022-01-22 20:04:25,936] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:25,937] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-22 20:04:30,439] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH6.2_rep3_fastqc.html [2022-01-22 20:04:30,441] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH6.2_rep3_fastqc.html [2022-01-22 20:04:30,484] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4_rep1_fastqc.html [2022-01-22 20:04:30,486] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4_rep1_fastqc.html [2022-01-22 20:04:30,530] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH6.2_rep1_fastqc.html [2022-01-22 20:04:30,532] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH6.2_rep1_fastqc.html [2022-01-22 20:04:30,575] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4.5_rep2_fastqc.html [2022-01-22 20:04:30,577] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4.5_rep2_fastqc.html [2022-01-22 20:04:30,620] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4.5_rep1_fastqc.html [2022-01-22 20:04:30,622] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4.5_rep1_fastqc.html [2022-01-22 20:04:30,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4_rep3_fastqc.html [2022-01-22 20:04:30,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4_rep3_fastqc.html [2022-01-22 20:04:30,710] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_undetermined_fastqc.html [2022-01-22 20:04:30,712] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_undetermined_fastqc.html [2022-01-22 20:04:30,754] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH6.2_rep2_fastqc.html [2022-01-22 20:04:30,756] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH6.2_rep2_fastqc.html [2022-01-22 20:04:30,800] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH6.2_rep2_fastqc.html [2022-01-22 20:04:30,801] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH6.2_rep2_fastqc.html [2022-01-22 20:04:30,846] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4.5_rep2_fastqc.html [2022-01-22 20:04:30,848] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4.5_rep2_fastqc.html [2022-01-22 20:04:30,893] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4.5_rep3_fastqc.html [2022-01-22 20:04:30,895] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4.5_rep3_fastqc.html [2022-01-22 20:04:30,937] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4_rep2_fastqc.html [2022-01-22 20:04:30,939] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4_rep2_fastqc.html [2022-01-22 20:04:30,982] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH6.2_rep1_fastqc.html [2022-01-22 20:04:30,984] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH6.2_rep1_fastqc.html [2022-01-22 20:04:31,027] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4.5_rep3_fastqc.html [2022-01-22 20:04:31,029] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4.5_rep3_fastqc.html [2022-01-22 20:04:31,072] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4_rep1_fastqc.html [2022-01-22 20:04:31,074] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_CHAR29_pH4_rep1_fastqc.html [2022-01-22 20:04:31,117] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n02_undetermined_fastqc.html [2022-01-22 20:04:31,119] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n02_undetermined_fastqc.html [2022-01-22 20:04:31,162] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH6.2_rep3_fastqc.html [2022-01-22 20:04:31,164] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH6.2_rep3_fastqc.html [2022-01-22 20:04:31,208] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4.5_rep1_fastqc.html [2022-01-22 20:04:31,210] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4.5_rep1_fastqc.html [2022-01-22 20:04:31,253] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4_rep2_fastqc.html [2022-01-22 20:04:31,255] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFLJJAFX3_n01_CHAR29_pH4_rep2_fastqc.html [2022-01-22 20:04:31,604] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-22 20:04:31,604] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-22 20:04:31,620] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-22 20:04:31,622] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-22 20:04:31,627] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 10 samples (table) [2022-01-22 20:04:31,631] multiqc [DEBUG ] No samples found: conpair [2022-01-22 20:04:31,634] multiqc [DEBUG ] No samples found: peddy [2022-01-22 20:04:31,637] multiqc [DEBUG ] No samples found: somalier [2022-01-22 20:04:31,640] multiqc [DEBUG ] No samples found: methylQA [2022-01-22 20:04:31,645] multiqc [DEBUG ] No samples found: mosdepth [2022-01-22 20:04:31,648] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-22 20:04:31,651] multiqc [DEBUG ] No samples found: qualimap [2022-01-22 20:04:31,654] multiqc [DEBUG ] No samples found: preseq [2022-01-22 20:04:31,657] multiqc [DEBUG ] No samples found: quast [2022-01-22 20:04:31,660] multiqc [DEBUG ] No samples found: qorts [2022-01-22 20:04:31,663] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-22 20:04:31,666] multiqc [DEBUG ] No samples found: rockhopper [2022-01-22 20:04:31,669] multiqc [DEBUG ] No samples found: rsem [2022-01-22 20:04:31,675] multiqc [DEBUG ] No samples found: rseqc [2022-01-22 20:04:31,678] multiqc [DEBUG ] No samples found: busco [2022-01-22 20:04:31,681] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-22 20:04:31,684] multiqc [DEBUG ] No samples found: disambiguate [2022-01-22 20:04:31,687] multiqc [DEBUG ] No samples found: supernova [2022-01-22 20:04:31,693] multiqc [DEBUG ] No samples found: deeptools [2022-01-22 20:04:31,696] multiqc [DEBUG ] No samples found: sargasso [2022-01-22 20:04:31,699] multiqc [DEBUG ] No samples found: verifybamid [2022-01-22 20:04:31,703] multiqc [DEBUG ] No samples found: mirtrace [2022-01-22 20:04:31,706] multiqc [DEBUG ] No samples found: happy [2022-01-22 20:04:31,709] multiqc [DEBUG ] No samples found: mirtop [2022-01-22 20:04:31,713] multiqc [DEBUG ] No samples found: homer [2022-01-22 20:04:31,716] multiqc [DEBUG ] No samples found: macs2 [2022-01-22 20:04:31,719] multiqc [DEBUG ] No samples found: theta2 [2022-01-22 20:04:31,723] multiqc [DEBUG ] No samples found: snpeff [2022-01-22 20:04:31,727] multiqc [DEBUG ] No samples found: gatk [2022-01-22 20:04:31,730] multiqc [DEBUG ] No samples found: htseq [2022-01-22 20:04:31,733] multiqc [DEBUG ] No samples found: bcftools [2022-01-22 20:04:31,736] multiqc [DEBUG ] No samples found: featureCounts [2022-01-22 20:04:31,740] multiqc [DEBUG ] No samples found: fgbio [2022-01-22 20:04:31,746] multiqc [DEBUG ] No samples found: dragen [2022-01-22 20:04:31,749] multiqc [DEBUG ] No samples found: dedup [2022-01-22 20:04:31,752] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-22 20:04:31,762] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-22 20:04:31,765] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-22 20:04:31,767] multiqc [DEBUG ] No samples found: picard [2022-01-22 20:04:31,770] multiqc [DEBUG ] No samples found: prokka [2022-01-22 20:04:31,773] multiqc [DEBUG ] No samples found: samblaster [2022-01-22 20:04:31,777] multiqc [DEBUG ] No samples found: samtools [2022-01-22 20:04:31,780] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-22 20:04:31,783] multiqc [DEBUG ] No samples found: bamtools [2022-01-22 20:04:31,786] multiqc [DEBUG ] No samples found: jellyfish [2022-01-22 20:04:31,791] multiqc [DEBUG ] No samples found: vcftools [2022-01-22 20:04:31,794] multiqc [DEBUG ] No samples found: longranger [2022-01-22 20:04:31,797] multiqc [DEBUG ] No samples found: stacks [2022-01-22 20:04:31,800] multiqc [DEBUG ] No samples found: varscan2 [2022-01-22 20:04:31,807] multiqc [DEBUG ] No samples found: bbmap [2022-01-22 20:04:31,810] multiqc [DEBUG ] No samples found: bismark [2022-01-22 20:04:31,814] multiqc [DEBUG ] No samples found: biscuit [2022-01-22 20:04:31,817] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-22 20:04:31,820] multiqc [DEBUG ] No samples found: hicup [2022-01-22 20:04:31,823] multiqc [DEBUG ] No samples found: hicpro [2022-01-22 20:04:31,826] multiqc [DEBUG ] No samples found: salmon [2022-01-22 20:04:31,829] multiqc [DEBUG ] No samples found: kallisto [2022-01-22 20:04:31,832] multiqc [DEBUG ] No samples found: slamdunk [2022-01-22 20:04:31,835] multiqc [DEBUG ] No samples found: star [2022-01-22 20:04:31,839] multiqc [DEBUG ] No samples found: hisat2 [2022-01-22 20:04:31,842] multiqc [DEBUG ] No samples found: tophat [2022-01-22 20:04:31,844] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-22 20:04:31,847] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-22 20:04:31,851] multiqc [DEBUG ] No samples found: snpsplit [2022-01-22 20:04:31,853] multiqc [DEBUG ] No samples found: kat [2022-01-22 20:04:31,856] multiqc [DEBUG ] No samples found: leehom [2022-01-22 20:04:31,859] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-22 20:04:31,862] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-22 20:04:31,865] multiqc [DEBUG ] No samples found: cutadapt [2022-01-22 20:04:31,868] multiqc [DEBUG ] No samples found: flexbar [2022-01-22 20:04:31,871] multiqc [DEBUG ] No samples found: kaiju [2022-01-22 20:04:31,874] multiqc [DEBUG ] No samples found: kraken [2022-01-22 20:04:31,877] multiqc [DEBUG ] No samples found: malt [2022-01-22 20:04:31,880] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-22 20:04:31,883] multiqc [DEBUG ] No samples found: sickle [2022-01-22 20:04:31,886] multiqc [DEBUG ] No samples found: skewer [2022-01-22 20:04:31,889] multiqc [DEBUG ] No samples found: sortmerna [2022-01-22 20:04:31,892] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-22 20:04:31,895] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-22 20:04:31,898] multiqc [DEBUG ] No samples found: afterqc [2022-01-22 20:04:31,901] multiqc [DEBUG ] No samples found: fastp [2022-01-22 20:04:32,327] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2022-01-22 20:04:32,893] multiqc [DEBUG ] No samples found: pycoqc [2022-01-22 20:04:32,896] multiqc [DEBUG ] No samples found: minionqc [2022-01-22 20:04:32,899] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-22 20:04:32,902] multiqc [DEBUG ] No samples found: clusterflow [2022-01-22 20:04:32,906] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-22 20:04:32,909] multiqc [DEBUG ] No samples found: interop [2022-01-22 20:04:32,912] multiqc [DEBUG ] No samples found: ivar [2022-01-22 20:04:32,915] multiqc [DEBUG ] No samples found: flash [2022-01-22 20:04:32,918] multiqc [DEBUG ] No samples found: seqyclean [2022-01-22 20:04:32,918] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-22 20:04:32,918] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-22 20:04:32,918] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-22 20:04:32,918] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-22 20:04:32,943] multiqc [INFO ] Compressing plot data [2022-01-22 20:04:33,334] multiqc [INFO ] Report : multiqc_report.html [2022-01-22 20:04:33,334] multiqc [INFO ] Data : multiqc_data [2022-01-22 20:04:33,334] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14186460/tmp98o622xx/multiqc_data' to '/scratch/gencore/logs/html/HFLJJAFX3/merged/multiqc_data' [2022-01-22 20:04:33,439] multiqc [INFO ] MultiQC complete