[2022-03-15 06:34:30,168] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-15 06:34:30,168] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-15 06:34:30,168] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-15 06:34:30,169] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-15 06:34:30,169] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-15 06:34:30,170] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H722GBGXL/merged [2022-03-15 06:34:30,646] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-15 06:34:30,646] multiqc [INFO ] This is MultiQC v1.9 [2022-03-15 06:34:30,646] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H722GBGXL/merged [2022-03-15 06:34:30,646] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H722GBGXL/merged [2022-03-15 06:34:30,646] multiqc [INFO ] Template : default [2022-03-15 06:34:30,646] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-15 06:34:30,646] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H722GBGXL/merged [2022-03-15 06:34:30,646] 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 [2022-03-15 06:34:30,646] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16055505/tmperfkdacv [2022-03-15 06:34:30,753] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_undetermined_fastqc.html [2022-03-15 06:34:30,756] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_undetermined_fastqc.html [2022-03-15 06:34:30,798] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_16hpf_3_MB_fastqc.html [2022-03-15 06:34:30,800] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_16hpf_3_MB_fastqc.html [2022-03-15 06:34:30,840] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-15 06:34:30,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-15 06:34:31,073] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_14hpf_3_MB_fastqc.html [2022-03-15 06:34:31,074] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_14hpf_3_MB_fastqc.html [2022-03-15 06:34:31,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_3_MB_fastqc.html [2022-03-15 06:34:31,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_3_MB_fastqc.html [2022-03-15 06:34:31,158] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_16hpf_2_MB_fastqc.html [2022-03-15 06:34:31,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_16hpf_2_MB_fastqc.html [2022-03-15 06:34:31,202] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_14hpf_3_MB_fastqc.html [2022-03-15 06:34:31,204] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_14hpf_3_MB_fastqc.html [2022-03-15 06:34:31,246] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,248] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,290] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_3_MB_fastqc.html [2022-03-15 06:34:31,291] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_3_MB_fastqc.html [2022-03-15 06:34:31,332] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_2_MB_fastqc.html [2022-03-15 06:34:31,334] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_2_MB_fastqc.html [2022-03-15 06:34:31,375] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,376] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,418] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_16hpf_3_MB_fastqc.html [2022-03-15 06:34:31,420] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_16hpf_3_MB_fastqc.html [2022-03-15 06:34:31,462] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_2_MB_fastqc.html [2022-03-15 06:34:31,463] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_2_MB_fastqc.html [2022-03-15 06:34:31,504] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_14hpf_2_MB_fastqc.html [2022-03-15 06:34:31,506] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_14hpf_2_MB_fastqc.html [2022-03-15 06:34:31,547] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_14hpf_2_MB_fastqc.html [2022-03-15 06:34:31,549] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_14hpf_2_MB_fastqc.html [2022-03-15 06:34:31,591] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_a_UD_YB_fastqc.html [2022-03-15 06:34:31,592] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_a_UD_YB_fastqc.html [2022-03-15 06:34:31,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_1_YB_fastqc.html [2022-03-15 06:34:31,637] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_12hpf_1_YB_fastqc.html [2022-03-15 06:34:31,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_1_YB_fastqc.html [2022-03-15 06:34:31,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_1_YB_fastqc.html [2022-03-15 06:34:31,721] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_14hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,723] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_14hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,766] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_a_UD_YB_fastqc.html [2022-03-15 06:34:31,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_12hpf_a_UD_YB_fastqc.html [2022-03-15 06:34:31,809] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_undetermined_fastqc.html [2022-03-15 06:34:31,811] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_undetermined_fastqc.html [2022-03-15 06:34:31,849] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_14hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n02_Bulk_ATAC_14hpf_b_UD_YB_fastqc.html [2022-03-15 06:34:31,892] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_16hpf_2_MB_fastqc.html [2022-03-15 06:34:31,894] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H722GBGXL_n01_Bulk_ATAC_16hpf_2_MB_fastqc.html [2022-03-15 06:34:32,239] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-15 06:34:32,241] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-15 06:34:32,253] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2022-03-15 06:34:32,262] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-15 06:34:32,264] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-15 06:34:32,268] multiqc [DEBUG ] No samples found: conpair [2022-03-15 06:34:32,273] multiqc [DEBUG ] No samples found: peddy [2022-03-15 06:34:32,278] multiqc [DEBUG ] No samples found: somalier [2022-03-15 06:34:32,283] multiqc [DEBUG ] No samples found: methylQA [2022-03-15 06:34:32,290] multiqc [DEBUG ] No samples found: mosdepth [2022-03-15 06:34:32,295] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-15 06:34:32,298] multiqc [DEBUG ] No samples found: qualimap [2022-03-15 06:34:32,303] multiqc [DEBUG ] No samples found: preseq [2022-03-15 06:34:32,307] multiqc [DEBUG ] No samples found: quast [2022-03-15 06:34:32,312] multiqc [DEBUG ] No samples found: qorts [2022-03-15 06:34:32,317] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-15 06:34:32,321] multiqc [DEBUG ] No samples found: rockhopper [2022-03-15 06:34:32,326] multiqc [DEBUG ] No samples found: rsem [2022-03-15 06:34:32,336] multiqc [DEBUG ] No samples found: rseqc [2022-03-15 06:34:32,340] multiqc [DEBUG ] No samples found: busco [2022-03-15 06:34:32,345] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-15 06:34:32,349] multiqc [DEBUG ] No samples found: disambiguate [2022-03-15 06:34:32,354] multiqc [DEBUG ] No samples found: supernova [2022-03-15 06:34:32,367] multiqc [DEBUG ] No samples found: deeptools [2022-03-15 06:34:32,372] multiqc [DEBUG ] No samples found: sargasso [2022-03-15 06:34:32,376] multiqc [DEBUG ] No samples found: verifybamid [2022-03-15 06:34:32,381] multiqc [DEBUG ] No samples found: mirtrace [2022-03-15 06:34:32,386] multiqc [DEBUG ] No samples found: happy [2022-03-15 06:34:32,390] multiqc [DEBUG ] No samples found: mirtop [2022-03-15 06:34:32,397] multiqc [DEBUG ] No samples found: homer [2022-03-15 06:34:32,401] multiqc [DEBUG ] No samples found: macs2 [2022-03-15 06:34:32,406] multiqc [DEBUG ] No samples found: theta2 [2022-03-15 06:34:32,410] multiqc [DEBUG ] No samples found: snpeff [2022-03-15 06:34:32,417] multiqc [DEBUG ] No samples found: gatk [2022-03-15 06:34:32,422] multiqc [DEBUG ] No samples found: htseq [2022-03-15 06:34:32,427] multiqc [DEBUG ] No samples found: bcftools [2022-03-15 06:34:32,431] multiqc [DEBUG ] No samples found: featureCounts [2022-03-15 06:34:32,438] multiqc [DEBUG ] No samples found: fgbio [2022-03-15 06:34:32,451] multiqc [DEBUG ] No samples found: dragen [2022-03-15 06:34:32,456] multiqc [DEBUG ] No samples found: dedup [2022-03-15 06:34:32,460] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-15 06:34:32,483] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-15 06:34:32,488] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-15 06:34:32,490] multiqc [DEBUG ] No samples found: picard [2022-03-15 06:34:32,495] multiqc [DEBUG ] No samples found: prokka [2022-03-15 06:34:32,499] multiqc [DEBUG ] No samples found: samblaster [2022-03-15 06:34:32,508] multiqc [DEBUG ] No samples found: samtools [2022-03-15 06:34:32,512] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-15 06:34:32,517] multiqc [DEBUG ] No samples found: bamtools [2022-03-15 06:34:32,522] multiqc [DEBUG ] No samples found: jellyfish [2022-03-15 06:34:32,529] multiqc [DEBUG ] No samples found: vcftools [2022-03-15 06:34:32,534] multiqc [DEBUG ] No samples found: longranger [2022-03-15 06:34:32,538] multiqc [DEBUG ] No samples found: stacks [2022-03-15 06:34:32,543] multiqc [DEBUG ] No samples found: varscan2 [2022-03-15 06:34:32,556] multiqc [DEBUG ] No samples found: bbmap [2022-03-15 06:34:32,561] multiqc [DEBUG ] No samples found: bismark [2022-03-15 06:34:32,566] multiqc [DEBUG ] No samples found: biscuit [2022-03-15 06:34:32,570] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-15 06:34:32,575] multiqc [DEBUG ] No samples found: hicup [2022-03-15 06:34:32,580] multiqc [DEBUG ] No samples found: hicpro [2022-03-15 06:34:32,584] multiqc [DEBUG ] No samples found: salmon [2022-03-15 06:34:32,588] multiqc [DEBUG ] No samples found: kallisto [2022-03-15 06:34:32,593] multiqc [DEBUG ] No samples found: slamdunk [2022-03-15 06:34:32,598] multiqc [DEBUG ] No samples found: star [2022-03-15 06:34:32,602] multiqc [DEBUG ] No samples found: hisat2 [2022-03-15 06:34:32,607] multiqc [DEBUG ] No samples found: tophat [2022-03-15 06:34:32,612] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-15 06:34:32,616] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-15 06:34:32,621] multiqc [DEBUG ] No samples found: snpsplit [2022-03-15 06:34:32,625] multiqc [DEBUG ] No samples found: kat [2022-03-15 06:34:32,629] multiqc [DEBUG ] No samples found: leehom [2022-03-15 06:34:32,634] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-15 06:34:32,639] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-15 06:34:32,643] multiqc [DEBUG ] No samples found: cutadapt [2022-03-15 06:34:32,648] multiqc [DEBUG ] No samples found: flexbar [2022-03-15 06:34:32,652] multiqc [DEBUG ] No samples found: kaiju [2022-03-15 06:34:32,657] multiqc [DEBUG ] No samples found: kraken [2022-03-15 06:34:32,662] multiqc [DEBUG ] No samples found: malt [2022-03-15 06:34:32,666] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-15 06:34:32,671] multiqc [DEBUG ] No samples found: sickle [2022-03-15 06:34:32,675] multiqc [DEBUG ] No samples found: skewer [2022-03-15 06:34:32,680] multiqc [DEBUG ] No samples found: sortmerna [2022-03-15 06:34:32,684] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-15 06:34:32,688] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-15 06:34:32,693] multiqc [DEBUG ] No samples found: afterqc [2022-03-15 06:34:32,698] multiqc [DEBUG ] No samples found: fastp [2022-03-15 06:34:33,945] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2022-03-15 06:34:34,121] multiqc [DEBUG ] No samples found: pycoqc [2022-03-15 06:34:34,126] multiqc [DEBUG ] No samples found: minionqc [2022-03-15 06:34:34,131] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-15 06:34:34,135] multiqc [DEBUG ] No samples found: clusterflow [2022-03-15 06:34:34,140] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-15 06:34:34,145] multiqc [DEBUG ] No samples found: interop [2022-03-15 06:34:34,149] multiqc [DEBUG ] No samples found: ivar [2022-03-15 06:34:34,154] multiqc [DEBUG ] No samples found: flash [2022-03-15 06:34:34,158] multiqc [DEBUG ] No samples found: seqyclean [2022-03-15 06:34:34,158] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-15 06:34:34,158] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-15 06:34:34,158] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-15 06:34:34,158] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-15 06:34:34,185] multiqc [INFO ] Compressing plot data [2022-03-15 06:34:34,533] multiqc [INFO ] Report : multiqc_report.html [2022-03-15 06:34:34,533] multiqc [INFO ] Data : multiqc_data [2022-03-15 06:34:34,533] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16055505/tmperfkdacv/multiqc_data' to '/scratch/gencore/logs/html/H722GBGXL/merged/multiqc_data' [2022-03-15 06:34:34,657] multiqc [INFO ] MultiQC complete