[2021-09-03 23:48:11,647] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-03 23:48:11,648] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-03 23:48:11,648] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-03 23:48:11,648] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-03 23:48:11,649] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-03 23:48:11,649] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLWNJBGXJ/merged [2021-09-03 23:48:13,112] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-03 23:48:13,112] multiqc [INFO ] This is MultiQC v1.9 [2021-09-03 23:48:13,112] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLWNJBGXJ/merged [2021-09-03 23:48:13,112] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLWNJBGXJ/merged [2021-09-03 23:48:13,112] multiqc [INFO ] Template : default [2021-09-03 23:48:13,112] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-03 23:48:13,112] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLWNJBGXJ/merged [2021-09-03 23:48:13,113] 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 [2021-09-03 23:48:13,113] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9744035/tmpj22gmxym [2021-09-03 23:48:13,235] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_NT_stim_3_fastqc.html [2021-09-03 23:48:13,238] multiqc [DEBUG ] File ignored by longranger/invocation because it 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23:48:16,264] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_RELB_no_stim_1_fastqc.html [2021-09-03 23:48:16,308] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_RELA_no_stim_2_fastqc.html [2021-09-03 23:48:16,310] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_RELA_no_stim_2_fastqc.html [2021-09-03 23:48:16,353] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_RELB_stim_2_fastqc.html [2021-09-03 23:48:16,355] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_RELB_stim_2_fastqc.html [2021-09-03 23:48:16,402] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_RELB_stim_1_fastqc.html [2021-09-03 23:48:16,404] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_RELB_stim_1_fastqc.html [2021-09-03 23:48:16,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELA_no_stim_3_fastqc.html [2021-09-03 23:48:16,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELA_no_stim_3_fastqc.html [2021-09-03 23:48:16,496] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELA_no_stim_1_fastqc.html [2021-09-03 23:48:16,498] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELA_no_stim_1_fastqc.html [2021-09-03 23:48:16,558] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_NT_stim_2_fastqc.html [2021-09-03 23:48:16,560] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_NT_stim_2_fastqc.html [2021-09-03 23:48:16,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_NT_stim_2_fastqc.html [2021-09-03 23:48:16,623] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_NT_stim_2_fastqc.html [2021-09-03 23:48:16,688] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_NT_no_stim_3_fastqc.html [2021-09-03 23:48:16,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_NT_no_stim_3_fastqc.html [2021-09-03 23:48:16,751] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_no_stim_3_fastqc.html [2021-09-03 23:48:16,753] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_no_stim_3_fastqc.html [2021-09-03 23:48:16,795] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELA_stim_1_fastqc.html [2021-09-03 23:48:16,797] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELA_stim_1_fastqc.html [2021-09-03 23:48:16,845] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_NT_stim_1_fastqc.html [2021-09-03 23:48:16,847] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_NT_stim_1_fastqc.html [2021-09-03 23:48:16,894] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_RELB_stim_1_fastqc.html [2021-09-03 23:48:16,896] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_RELB_stim_1_fastqc.html [2021-09-03 23:48:16,942] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_RELA_stim_3_fastqc.html [2021-09-03 23:48:16,944] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_RELA_stim_3_fastqc.html [2021-09-03 23:48:16,987] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELB_stim_3_fastqc.html [2021-09-03 23:48:16,989] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_NGFR_RELB_stim_3_fastqc.html [2021-09-03 23:48:17,035] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_stim_1_fastqc.html [2021-09-03 23:48:17,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_stim_1_fastqc.html [2021-09-03 23:48:17,080] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_RELB_no_stim_3_fastqc.html [2021-09-03 23:48:17,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_LTBR_RELB_no_stim_3_fastqc.html [2021-09-03 23:48:17,125] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_no_stim_1_fastqc.html [2021-09-03 23:48:17,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_no_stim_1_fastqc.html [2021-09-03 23:48:17,234] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_stim_3_fastqc.html [2021-09-03 23:48:17,236] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n02_CD4_NGFR_NT_stim_3_fastqc.html [2021-09-03 23:48:17,291] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_RELB_no_stim_2_fastqc.html [2021-09-03 23:48:17,293] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWNJBGXJ_n01_CD4_LTBR_RELB_no_stim_2_fastqc.html [2021-09-03 23:48:17,628] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-03 23:48:17,629] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-03 23:48:17,637] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-03 23:48:17,647] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-03 23:48:17,665] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 37 samples (table) [2021-09-03 23:48:17,670] multiqc [DEBUG ] No samples found: conpair [2021-09-03 23:48:17,675] multiqc [DEBUG ] No samples found: peddy [2021-09-03 23:48:17,679] multiqc [DEBUG ] No samples found: somalier [2021-09-03 23:48:17,684] multiqc [DEBUG ] No samples found: methylQA [2021-09-03 23:48:17,692] multiqc [DEBUG ] No samples found: mosdepth [2021-09-03 23:48:17,696] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-03 23:48:17,700] multiqc [DEBUG ] No samples found: qualimap [2021-09-03 23:48:17,704] multiqc [DEBUG ] No samples found: preseq [2021-09-03 23:48:17,709] multiqc [DEBUG ] No samples found: quast [2021-09-03 23:48:17,713] multiqc [DEBUG ] No samples found: qorts [2021-09-03 23:48:17,718] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-03 23:48:17,722] multiqc [DEBUG ] No samples found: rockhopper [2021-09-03 23:48:17,727] multiqc [DEBUG ] No samples found: rsem [2021-09-03 23:48:17,737] multiqc [DEBUG ] No samples found: rseqc [2021-09-03 23:48:17,741] multiqc [DEBUG ] No samples found: busco [2021-09-03 23:48:17,746] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-03 23:48:17,750] multiqc [DEBUG ] No samples found: disambiguate [2021-09-03 23:48:17,755] multiqc [DEBUG ] No samples found: supernova [2021-09-03 23:48:17,767] multiqc [DEBUG ] No samples found: deeptools [2021-09-03 23:48:17,771] multiqc [DEBUG ] No samples found: sargasso [2021-09-03 23:48:17,775] multiqc [DEBUG ] No samples found: verifybamid [2021-09-03 23:48:17,780] multiqc [DEBUG ] No samples found: mirtrace [2021-09-03 23:48:17,784] multiqc [DEBUG ] No samples found: happy [2021-09-03 23:48:17,789] multiqc [DEBUG ] No samples found: mirtop [2021-09-03 23:48:17,794] multiqc [DEBUG ] No samples found: homer [2021-09-03 23:48:17,799] multiqc [DEBUG ] No samples found: macs2 [2021-09-03 23:48:17,803] multiqc [DEBUG ] No samples found: theta2 [2021-09-03 23:48:17,807] multiqc [DEBUG ] No samples found: snpeff [2021-09-03 23:48:17,814] multiqc [DEBUG ] No samples found: gatk [2021-09-03 23:48:17,818] multiqc [DEBUG ] No samples found: htseq [2021-09-03 23:48:17,823] multiqc [DEBUG ] No samples found: bcftools [2021-09-03 23:48:17,827] multiqc [DEBUG ] No samples found: featureCounts [2021-09-03 23:48:17,833] multiqc [DEBUG ] No samples found: fgbio [2021-09-03 23:48:17,845] multiqc [DEBUG ] No samples found: dragen [2021-09-03 23:48:17,849] multiqc [DEBUG ] No samples found: dedup [2021-09-03 23:48:17,853] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-03 23:48:17,875] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-03 23:48:17,879] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-03 23:48:17,881] multiqc [DEBUG ] No samples found: picard [2021-09-03 23:48:17,886] multiqc [DEBUG ] No samples found: prokka [2021-09-03 23:48:17,890] multiqc [DEBUG ] No samples found: samblaster [2021-09-03 23:48:17,898] multiqc [DEBUG ] No samples found: samtools [2021-09-03 23:48:17,902] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-03 23:48:17,906] multiqc [DEBUG ] No samples found: bamtools [2021-09-03 23:48:17,910] multiqc [DEBUG ] No samples found: jellyfish [2021-09-03 23:48:17,917] multiqc [DEBUG ] No samples found: vcftools [2021-09-03 23:48:17,921] multiqc [DEBUG ] No samples found: longranger [2021-09-03 23:48:17,926] multiqc [DEBUG ] No samples found: stacks [2021-09-03 23:48:17,930] multiqc [DEBUG ] No samples found: varscan2 [2021-09-03 23:48:17,942] multiqc [DEBUG ] No samples found: bbmap [2021-09-03 23:48:17,947] multiqc [DEBUG ] No samples found: bismark [2021-09-03 23:48:17,951] multiqc [DEBUG ] No samples found: biscuit [2021-09-03 23:48:17,956] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-03 23:48:17,961] multiqc [DEBUG ] No samples found: hicup [2021-09-03 23:48:17,965] multiqc [DEBUG ] No samples found: hicpro [2021-09-03 23:48:17,970] multiqc [DEBUG ] No samples found: salmon [2021-09-03 23:48:17,974] multiqc [DEBUG ] No samples found: kallisto [2021-09-03 23:48:17,978] multiqc [DEBUG ] No samples found: slamdunk [2021-09-03 23:48:17,983] multiqc [DEBUG ] No samples found: star [2021-09-03 23:48:17,988] multiqc [DEBUG ] No samples found: hisat2 [2021-09-03 23:48:17,992] multiqc [DEBUG ] No samples found: tophat [2021-09-03 23:48:18,000] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-03 23:48:18,005] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-03 23:48:18,009] multiqc [DEBUG ] No samples found: snpsplit [2021-09-03 23:48:18,013] multiqc [DEBUG ] No samples found: kat [2021-09-03 23:48:18,017] multiqc [DEBUG ] No samples found: leehom [2021-09-03 23:48:18,022] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-03 23:48:18,026] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-03 23:48:18,030] multiqc [DEBUG ] No samples found: cutadapt [2021-09-03 23:48:18,034] multiqc [DEBUG ] No samples found: flexbar [2021-09-03 23:48:18,039] multiqc [DEBUG ] No samples found: kaiju [2021-09-03 23:48:18,043] multiqc [DEBUG ] No samples found: kraken [2021-09-03 23:48:18,048] multiqc [DEBUG ] No samples found: malt [2021-09-03 23:48:18,052] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-03 23:48:18,056] multiqc [DEBUG ] No samples found: sickle [2021-09-03 23:48:18,060] multiqc [DEBUG ] No samples found: skewer [2021-09-03 23:48:18,064] multiqc [DEBUG ] No samples found: sortmerna [2021-09-03 23:48:18,068] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-03 23:48:18,073] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-03 23:48:18,077] multiqc [DEBUG ] No samples found: afterqc [2021-09-03 23:48:18,082] multiqc [DEBUG ] No samples found: fastp [2021-09-03 23:48:22,804] multiqc.modules.fastqc.fastqc [INFO ] Found 74 reports [2021-09-03 23:48:23,223] multiqc [DEBUG ] No samples found: pycoqc [2021-09-03 23:48:23,227] multiqc [DEBUG ] No samples found: minionqc [2021-09-03 23:48:23,231] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-03 23:48:23,236] multiqc [DEBUG ] No samples found: clusterflow [2021-09-03 23:48:23,240] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-03 23:48:23,245] multiqc [DEBUG ] No samples found: interop [2021-09-03 23:48:23,249] multiqc [DEBUG ] No samples found: ivar [2021-09-03 23:48:23,254] multiqc [DEBUG ] No samples found: flash [2021-09-03 23:48:23,258] multiqc [DEBUG ] No samples found: seqyclean [2021-09-03 23:48:23,258] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-09-03 23:48:23,258] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-09-03 23:48:23,258] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-03 23:48:23,258] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-03 23:48:23,348] multiqc [INFO ] Compressing plot data [2021-09-03 23:48:24,384] multiqc [INFO ] Report : multiqc_report.html [2021-09-03 23:48:24,384] multiqc [INFO ] Data : multiqc_data [2021-09-03 23:48:24,384] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9744035/tmpj22gmxym/multiqc_data' to '/scratch/gencore/logs/html/HLWNJBGXJ/merged/multiqc_data' [2021-09-03 23:48:24,514] multiqc [INFO ] MultiQC complete