[2022-01-20 01:40:08,535] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-20 01:40:08,535] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-20 01:40:08,535] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-20 01:40:08,536] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-20 01:40:08,536] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-20 01:40:08,536] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWTMCBGXK/merged [2022-01-20 01:40:10,097] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-20 01:40:10,097] multiqc [INFO ] This is MultiQC v1.9 [2022-01-20 01:40:10,097] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWTMCBGXK/merged [2022-01-20 01:40:10,097] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWTMCBGXK/merged [2022-01-20 01:40:10,098] multiqc [INFO ] Template : default [2022-01-20 01:40:10,098] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-20 01:40:10,098] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWTMCBGXK/merged [2022-01-20 01:40:10,099] 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 [2022-01-20 01:40:10,099] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14060649/tmpbi7tud30 [2022-01-20 01:40:10,206] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-20 01:40:10,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-20 01:40:10,747] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_undetermined_fastqc.html [2022-01-20 01:40:10,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_undetermined_fastqc.html [2022-01-20 01:40:10,790] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-20 01:40:10,792] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-20 01:40:10,834] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-20 01:40:10,836] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-20 01:40:10,876] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-20 01:40:10,878] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-20 01:40:10,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-20 01:40:10,921] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-20 01:40:10,962] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-20 01:40:10,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-20 01:40:11,004] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-20 01:40:11,006] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-20 01:40:11,047] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-20 01:40:11,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-20 01:40:11,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_undetermined_fastqc.html [2022-01-20 01:40:11,092] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_undetermined_fastqc.html [2022-01-20 01:40:11,132] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-20 01:40:11,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-20 01:40:11,174] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-20 01:40:11,176] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-20 01:40:11,217] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-20 01:40:11,219] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-20 01:40:11,260] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-20 01:40:11,261] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-20 01:40:11,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-20 01:40:11,304] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n02_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-20 01:40:11,345] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-20 01:40:11,347] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-20 01:40:11,388] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-20 01:40:11,389] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWTMCBGXK_n01_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-20 01:40:11,781] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-20 01:40:11,783] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-20 01:40:11,794] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2022-01-20 01:40:11,796] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-20 01:40:11,805] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-20 01:40:11,810] multiqc [DEBUG ] No samples found: conpair [2022-01-20 01:40:11,816] multiqc [DEBUG ] No samples found: peddy [2022-01-20 01:40:11,821] multiqc [DEBUG ] No samples found: somalier [2022-01-20 01:40:11,826] multiqc [DEBUG ] No samples found: methylQA [2022-01-20 01:40:11,835] multiqc [DEBUG ] No samples found: mosdepth [2022-01-20 01:40:11,840] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-20 01:40:11,844] multiqc [DEBUG ] No samples found: qualimap [2022-01-20 01:40:11,849] multiqc [DEBUG ] No samples found: preseq [2022-01-20 01:40:11,854] multiqc [DEBUG ] No samples found: quast [2022-01-20 01:40:11,860] multiqc [DEBUG ] No samples found: qorts [2022-01-20 01:40:11,865] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-20 01:40:11,870] multiqc [DEBUG ] No samples found: rockhopper [2022-01-20 01:40:11,876] multiqc [DEBUG ] No samples found: rsem [2022-01-20 01:40:11,888] multiqc [DEBUG ] No samples found: rseqc [2022-01-20 01:40:11,893] multiqc [DEBUG ] No samples found: busco [2022-01-20 01:40:11,899] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-20 01:40:11,904] multiqc [DEBUG ] No samples found: disambiguate [2022-01-20 01:40:11,911] multiqc [DEBUG ] No samples found: supernova [2022-01-20 01:40:11,931] multiqc [DEBUG ] No samples found: deeptools [2022-01-20 01:40:11,937] multiqc [DEBUG ] No samples found: sargasso [2022-01-20 01:40:11,943] multiqc [DEBUG ] No samples found: verifybamid [2022-01-20 01:40:11,948] multiqc [DEBUG ] No samples found: mirtrace [2022-01-20 01:40:11,953] multiqc [DEBUG ] No samples found: happy [2022-01-20 01:40:11,958] multiqc [DEBUG ] No samples found: mirtop [2022-01-20 01:40:11,965] multiqc [DEBUG ] No samples found: homer [2022-01-20 01:40:11,971] multiqc [DEBUG ] No samples found: macs2 [2022-01-20 01:40:11,975] multiqc [DEBUG ] No samples found: theta2 [2022-01-20 01:40:11,980] multiqc [DEBUG ] No samples found: snpeff [2022-01-20 01:40:11,988] multiqc [DEBUG ] No samples found: gatk [2022-01-20 01:40:11,993] multiqc [DEBUG ] No samples found: htseq [2022-01-20 01:40:11,999] multiqc [DEBUG ] No samples found: bcftools [2022-01-20 01:40:12,004] multiqc [DEBUG ] No samples found: featureCounts [2022-01-20 01:40:12,011] multiqc [DEBUG ] No samples found: fgbio [2022-01-20 01:40:12,026] multiqc [DEBUG ] No samples found: dragen [2022-01-20 01:40:12,031] multiqc [DEBUG ] No samples found: dedup [2022-01-20 01:40:12,036] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-20 01:40:12,062] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-20 01:40:12,068] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-20 01:40:12,071] multiqc [DEBUG ] No samples found: picard [2022-01-20 01:40:12,076] multiqc [DEBUG ] No samples found: prokka [2022-01-20 01:40:12,080] multiqc [DEBUG ] No samples found: samblaster [2022-01-20 01:40:12,090] multiqc [DEBUG ] No samples found: samtools [2022-01-20 01:40:12,095] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-20 01:40:12,100] multiqc [DEBUG ] No samples found: bamtools [2022-01-20 01:40:12,105] multiqc [DEBUG ] No samples found: jellyfish [2022-01-20 01:40:12,113] multiqc [DEBUG ] No samples found: vcftools [2022-01-20 01:40:12,119] multiqc [DEBUG ] No samples found: longranger [2022-01-20 01:40:12,124] multiqc [DEBUG ] No samples found: stacks [2022-01-20 01:40:12,129] multiqc [DEBUG ] No samples found: varscan2 [2022-01-20 01:40:12,153] multiqc [DEBUG ] No samples found: bbmap [2022-01-20 01:40:12,162] multiqc [DEBUG ] No samples found: bismark [2022-01-20 01:40:12,169] multiqc [DEBUG ] No samples found: biscuit [2022-01-20 01:40:12,175] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-20 01:40:12,181] multiqc [DEBUG ] No samples found: hicup [2022-01-20 01:40:12,187] multiqc [DEBUG ] No samples found: hicpro [2022-01-20 01:40:12,192] multiqc [DEBUG ] No samples found: salmon [2022-01-20 01:40:12,198] multiqc [DEBUG ] No samples found: kallisto [2022-01-20 01:40:12,203] multiqc [DEBUG ] No samples found: slamdunk [2022-01-20 01:40:12,209] multiqc [DEBUG ] No samples found: star [2022-01-20 01:40:12,214] multiqc [DEBUG ] No samples found: hisat2 [2022-01-20 01:40:12,220] multiqc [DEBUG ] No samples found: tophat [2022-01-20 01:40:12,225] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-20 01:40:12,230] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-20 01:40:12,236] multiqc [DEBUG ] No samples found: snpsplit [2022-01-20 01:40:12,241] multiqc [DEBUG ] No samples found: kat [2022-01-20 01:40:12,245] multiqc [DEBUG ] No samples found: leehom [2022-01-20 01:40:12,251] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-20 01:40:12,256] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-20 01:40:12,263] multiqc [DEBUG ] No samples found: cutadapt [2022-01-20 01:40:12,272] multiqc [DEBUG ] No samples found: flexbar [2022-01-20 01:40:12,280] multiqc [DEBUG ] No samples found: kaiju [2022-01-20 01:40:12,285] multiqc [DEBUG ] No samples found: kraken [2022-01-20 01:40:12,291] multiqc [DEBUG ] No samples found: malt [2022-01-20 01:40:12,296] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-20 01:40:12,301] multiqc [DEBUG ] No samples found: sickle [2022-01-20 01:40:12,306] multiqc [DEBUG ] No samples found: skewer [2022-01-20 01:40:12,311] multiqc [DEBUG ] No samples found: sortmerna [2022-01-20 01:40:12,316] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-20 01:40:12,322] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-20 01:40:12,327] multiqc [DEBUG ] No samples found: afterqc [2022-01-20 01:40:12,333] multiqc [DEBUG ] No samples found: fastp [2022-01-20 01:40:13,259] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2022-01-20 01:40:13,373] multiqc [DEBUG ] No samples found: pycoqc [2022-01-20 01:40:13,378] multiqc [DEBUG ] No samples found: minionqc [2022-01-20 01:40:13,383] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-20 01:40:13,391] multiqc [DEBUG ] No samples found: clusterflow [2022-01-20 01:40:13,403] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-20 01:40:13,410] multiqc [DEBUG ] No samples found: interop [2022-01-20 01:40:13,417] multiqc [DEBUG ] No samples found: ivar [2022-01-20 01:40:13,422] multiqc [DEBUG ] No samples found: flash [2022-01-20 01:40:13,427] multiqc [DEBUG ] No samples found: seqyclean [2022-01-20 01:40:13,427] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-20 01:40:13,427] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-20 01:40:13,427] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-20 01:40:13,427] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-20 01:40:13,446] multiqc [INFO ] Compressing plot data [2022-01-20 01:40:13,697] multiqc [INFO ] Report : multiqc_report.html [2022-01-20 01:40:13,697] multiqc [INFO ] Data : multiqc_data [2022-01-20 01:40:13,697] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14060649/tmpbi7tud30/multiqc_data' to '/scratch/gencore/logs/html/HWTMCBGXK/merged/multiqc_data' [2022-01-20 01:40:13,926] multiqc [INFO ] MultiQC complete