[2022-01-19 05:27:35,976] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-19 05:27:35,976] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-19 05:27:35,976] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-19 05:27:35,977] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-19 05:27:35,977] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-19 05:27:35,977] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWT5YBGXK/merged [2022-01-19 05:27:37,735] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-19 05:27:37,735] multiqc [INFO ] This is MultiQC v1.9 [2022-01-19 05:27:37,735] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWT5YBGXK/merged [2022-01-19 05:27:37,735] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWT5YBGXK/merged [2022-01-19 05:27:37,735] multiqc [INFO ] Template : default [2022-01-19 05:27:37,736] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-19 05:27:37,736] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWT5YBGXK/merged [2022-01-19 05:27:37,736] 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 [2022-01-19 05:27:37,736] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14020447/tmp8_0tvi8i [2022-01-19 05:27:37,847] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-19 05:27:37,850] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-19 05:27:37,893] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:37,894] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:37,894] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:37,895] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:37,895] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:37,895] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:37,895] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:37,937] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-01-19 05:27:39,668] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-19 05:27:39,670] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-19 05:27:39,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-19 05:27:39,714] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-19 05:27:39,756] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-19 05:27:39,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_12hpf_1_MB_fastqc.html [2022-01-19 05:27:39,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-19 05:27:39,801] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-19 05:27:39,842] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-19 05:27:39,844] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-19 05:27:39,887] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-19 05:27:39,889] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_14hpf_1_MB_fastqc.html [2022-01-19 05:27:39,931] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_undetermined_fastqc.html [2022-01-19 05:27:39,933] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_undetermined_fastqc.html [2022-01-19 05:27:39,973] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-19 05:27:39,975] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_2_YB_fastqc.html [2022-01-19 05:27:40,016] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_undetermined_fastqc.html [2022-01-19 05:27:40,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_undetermined_fastqc.html [2022-01-19 05:27:40,060] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-19 05:27:40,062] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_16hpf_1_MB_fastqc.html [2022-01-19 05:27:40,103] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-19 05:27:40,105] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-19 05:27:40,146] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-19 05:27:40,148] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_1_MB_fastqc.html [2022-01-19 05:27:40,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-19 05:27:40,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n01_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-19 05:27:40,233] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-19 05:27:40,235] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_1_YB_fastqc.html [2022-01-19 05:27:40,276] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-19 05:27:40,278] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT5YBGXK_n02_Bulk_ATAC_18hpf_1_UD_YB_fastqc.html [2022-01-19 05:27:40,807] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-19 05:27:40,809] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-19 05:27:40,817] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-19 05:27:40,826] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-19 05:27:40,830] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2022-01-19 05:27:40,835] multiqc [DEBUG ] No samples found: conpair [2022-01-19 05:27:40,841] multiqc [DEBUG ] No samples found: peddy [2022-01-19 05:27:40,846] multiqc [DEBUG ] No samples found: somalier [2022-01-19 05:27:40,851] multiqc [DEBUG ] No samples found: methylQA [2022-01-19 05:27:40,861] multiqc [DEBUG ] No samples found: mosdepth [2022-01-19 05:27:40,865] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-19 05:27:40,869] multiqc [DEBUG ] No samples found: qualimap [2022-01-19 05:27:40,874] multiqc [DEBUG ] No samples found: preseq [2022-01-19 05:27:40,879] multiqc [DEBUG ] No samples found: quast [2022-01-19 05:27:40,884] multiqc [DEBUG ] No samples found: qorts [2022-01-19 05:27:40,890] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-19 05:27:40,895] multiqc [DEBUG ] No samples found: rockhopper [2022-01-19 05:27:40,900] multiqc [DEBUG ] No samples found: rsem [2022-01-19 05:27:40,910] multiqc [DEBUG ] No samples found: rseqc [2022-01-19 05:27:40,915] multiqc [DEBUG ] No samples found: busco [2022-01-19 05:27:40,920] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-19 05:27:40,925] multiqc [DEBUG ] No samples found: disambiguate [2022-01-19 05:27:40,930] multiqc [DEBUG ] No samples found: supernova [2022-01-19 05:27:40,943] multiqc [DEBUG ] No samples found: deeptools [2022-01-19 05:27:40,948] multiqc [DEBUG ] No samples found: sargasso [2022-01-19 05:27:40,953] multiqc [DEBUG ] No samples found: verifybamid [2022-01-19 05:27:40,958] multiqc [DEBUG ] No samples found: mirtrace [2022-01-19 05:27:40,963] multiqc [DEBUG ] No samples found: happy [2022-01-19 05:27:40,968] multiqc [DEBUG ] No samples found: mirtop [2022-01-19 05:27:40,975] multiqc [DEBUG ] No samples found: homer [2022-01-19 05:27:40,980] multiqc [DEBUG ] No samples found: macs2 [2022-01-19 05:27:40,985] multiqc [DEBUG ] No samples found: theta2 [2022-01-19 05:27:40,990] multiqc [DEBUG ] No samples found: snpeff [2022-01-19 05:27:40,997] multiqc [DEBUG ] No samples found: gatk [2022-01-19 05:27:41,003] multiqc [DEBUG ] No samples found: htseq [2022-01-19 05:27:41,008] multiqc [DEBUG ] No samples found: bcftools [2022-01-19 05:27:41,014] multiqc [DEBUG ] No samples found: featureCounts [2022-01-19 05:27:41,020] multiqc [DEBUG ] No samples found: fgbio [2022-01-19 05:27:41,033] multiqc [DEBUG ] No samples found: dragen [2022-01-19 05:27:41,038] multiqc [DEBUG ] No samples found: dedup [2022-01-19 05:27:41,043] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-19 05:27:41,066] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-19 05:27:41,072] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-19 05:27:41,074] multiqc [DEBUG ] No samples found: picard [2022-01-19 05:27:41,079] multiqc [DEBUG ] No samples found: prokka [2022-01-19 05:27:41,084] multiqc [DEBUG ] No samples found: samblaster [2022-01-19 05:27:41,092] multiqc [DEBUG ] No samples found: samtools [2022-01-19 05:27:41,097] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-19 05:27:41,103] multiqc [DEBUG ] No samples found: bamtools [2022-01-19 05:27:41,108] multiqc [DEBUG ] No samples found: jellyfish [2022-01-19 05:27:41,115] multiqc [DEBUG ] No samples found: vcftools [2022-01-19 05:27:41,121] multiqc [DEBUG ] No samples found: longranger [2022-01-19 05:27:41,126] multiqc [DEBUG ] No samples found: stacks [2022-01-19 05:27:41,131] multiqc [DEBUG ] No samples found: varscan2 [2022-01-19 05:27:41,144] multiqc [DEBUG ] No samples found: bbmap [2022-01-19 05:27:41,150] multiqc [DEBUG ] No samples found: bismark [2022-01-19 05:27:41,156] multiqc [DEBUG ] No samples found: biscuit [2022-01-19 05:27:41,161] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-19 05:27:41,167] multiqc [DEBUG ] No samples found: hicup [2022-01-19 05:27:41,172] multiqc [DEBUG ] No samples found: hicpro [2022-01-19 05:27:41,177] multiqc [DEBUG ] No samples found: salmon [2022-01-19 05:27:41,182] multiqc [DEBUG ] No samples found: kallisto [2022-01-19 05:27:41,187] multiqc [DEBUG ] No samples found: slamdunk [2022-01-19 05:27:41,192] multiqc [DEBUG ] No samples found: star [2022-01-19 05:27:41,197] multiqc [DEBUG ] No samples found: hisat2 [2022-01-19 05:27:41,202] multiqc [DEBUG ] No samples found: tophat [2022-01-19 05:27:41,207] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-19 05:27:41,212] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-19 05:27:41,217] multiqc [DEBUG ] No samples found: snpsplit [2022-01-19 05:27:41,221] multiqc [DEBUG ] No samples found: kat [2022-01-19 05:27:41,226] multiqc [DEBUG ] No samples found: leehom [2022-01-19 05:27:41,231] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-19 05:27:41,236] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-19 05:27:41,241] multiqc [DEBUG ] No samples found: cutadapt [2022-01-19 05:27:41,246] multiqc [DEBUG ] No samples found: flexbar [2022-01-19 05:27:41,251] multiqc [DEBUG ] No samples found: kaiju [2022-01-19 05:27:41,255] multiqc [DEBUG ] No samples found: kraken [2022-01-19 05:27:41,261] multiqc [DEBUG ] No samples found: malt [2022-01-19 05:27:41,266] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-19 05:27:41,271] multiqc [DEBUG ] No samples found: sickle [2022-01-19 05:27:41,276] multiqc [DEBUG ] No samples found: skewer [2022-01-19 05:27:41,281] multiqc [DEBUG ] No samples found: sortmerna [2022-01-19 05:27:41,285] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-19 05:27:41,291] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-19 05:27:41,295] multiqc [DEBUG ] No samples found: afterqc [2022-01-19 05:27:41,301] multiqc [DEBUG ] No samples found: fastp [2022-01-19 05:27:41,775] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2022-01-19 05:27:41,885] multiqc [DEBUG ] No samples found: pycoqc [2022-01-19 05:27:41,891] multiqc [DEBUG ] No samples found: minionqc [2022-01-19 05:27:41,895] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-19 05:27:41,901] multiqc [DEBUG ] No samples found: clusterflow [2022-01-19 05:27:41,906] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-19 05:27:41,912] multiqc [DEBUG ] No samples found: interop [2022-01-19 05:27:41,916] multiqc [DEBUG ] No samples found: ivar [2022-01-19 05:27:41,921] multiqc [DEBUG ] No samples found: flash [2022-01-19 05:27:41,926] multiqc [DEBUG ] No samples found: seqyclean [2022-01-19 05:27:41,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-19 05:27:41,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-19 05:27:41,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-19 05:27:41,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-19 05:27:41,945] multiqc [INFO ] Compressing plot data [2022-01-19 05:27:42,163] multiqc [INFO ] Report : multiqc_report.html [2022-01-19 05:27:42,163] multiqc [INFO ] Data : multiqc_data [2022-01-19 05:27:42,163] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14020447/tmp8_0tvi8i/multiqc_data' to '/scratch/gencore/logs/html/HWT5YBGXK/merged/multiqc_data' [2022-01-19 05:27:42,359] multiqc [INFO ] MultiQC complete