[2022-11-28 16:23:18,827] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-28 16:23:18,828] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-28 16:23:18,828] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-28 16:23:18,829] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-28 16:23:18,829] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-28 16:23:18,829] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNF7WDRX2/1 [2022-11-28 16:23:19,381] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-28 16:23:19,381] multiqc [INFO ] This is MultiQC v1.9 [2022-11-28 16:23:19,381] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNF7WDRX2/1 [2022-11-28 16:23:19,381] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNF7WDRX2/1 [2022-11-28 16:23:19,381] multiqc [INFO ] Template : default [2022-11-28 16:23:19,381] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-28 16:23:19,381] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNF7WDRX2/1 [2022-11-28 16:23:19,381] 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 [2022-11-28 16:23:19,381] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27440394/tmpdrve4t5r [2022-11-28 16:23:19,497] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_H9_b_fastqc.html [2022-11-28 16:23:19,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_D9_b_fastqc.html [2022-11-28 16:23:20,066] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_D9_b_fastqc.html [2022-11-28 16:23:20,066] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_D9_b_fastqc.html [2022-11-28 16:23:20,130] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_G4_b_fastqc.html [2022-11-28 16:23:20,132] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_G4_b_fastqc.html [2022-11-28 16:23:20,132] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_G4_b_fastqc.html [2022-11-28 16:23:20,132] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_G4_b_fastqc.html [2022-11-28 16:23:20,132] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_G4_b_fastqc.html [2022-11-28 16:23:20,132] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_G4_b_fastqc.html [2022-11-28 16:23:20,132] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_G4_b_fastqc.html [2022-11-28 16:23:20,197] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_B9_b_fastqc.html [2022-11-28 16:23:20,199] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_B9_b_fastqc.html [2022-11-28 16:23:20,199] multiqc [DEBUG ] File ignored by rockhopper 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rseqc/bam_stat because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_F9_b_fastqc.html [2022-11-28 16:23:20,409] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_F9_b_fastqc.html [2022-11-28 16:23:20,409] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_F9_b_fastqc.html [2022-11-28 16:23:20,409] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_F9_b_fastqc.html [2022-11-28 16:23:20,475] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_D9_b_fastqc.html [2022-11-28 16:23:20,477] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_D9_b_fastqc.html [2022-11-28 16:23:20,547] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_G6_b_fastqc.html [2022-11-28 16:23:20,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_G6_b_fastqc.html [2022-11-28 16:23:20,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_A4_b_fastqc.html [2022-11-28 16:23:20,620] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_A4_b_fastqc.html [2022-11-28 16:23:20,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_A6_b_fastqc.html [2022-11-28 16:23:20,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_A6_b_fastqc.html [2022-11-28 16:23:20,761] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_E4_b_fastqc.html [2022-11-28 16:23:20,763] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_E4_b_fastqc.html [2022-11-28 16:23:20,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_C4_b_fastqc.html [2022-11-28 16:23:20,832] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_C4_b_fastqc.html [2022-11-28 16:23:20,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_undetermined_fastqc.html [2022-11-28 16:23:20,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_undetermined_fastqc.html [2022-11-28 16:23:20,962] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_C4_b_fastqc.html [2022-11-28 16:23:20,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_C4_b_fastqc.html [2022-11-28 16:23:20,964] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_C4_b_fastqc.html [2022-11-28 16:23:20,964] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_C4_b_fastqc.html [2022-11-28 16:23:20,964] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_C4_b_fastqc.html [2022-11-28 16:23:20,964] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_C4_b_fastqc.html [2022-11-28 16:23:20,964] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_C4_b_fastqc.html [2022-11-28 16:23:21,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_H9_b_fastqc.html [2022-11-28 16:23:21,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_H9_b_fastqc.html [2022-11-28 16:23:21,030] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_H9_b_fastqc.html [2022-11-28 16:23:21,030] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_H9_b_fastqc.html [2022-11-28 16:23:21,030] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_H9_b_fastqc.html [2022-11-28 16:23:21,030] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_H9_b_fastqc.html [2022-11-28 16:23:21,030] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_H9_b_fastqc.html [2022-11-28 16:23:21,095] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_A4_b_fastqc.html [2022-11-28 16:23:21,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n02_T14_A4_b_fastqc.html [2022-11-28 16:23:21,166] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_C6_b_fastqc.html [2022-11-28 16:23:21,168] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_C6_b_fastqc.html [2022-11-28 16:23:21,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_B9_b_fastqc.html [2022-11-28 16:23:21,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNF7WDRX2_l01_n01_T14_B9_b_fastqc.html [2022-11-28 16:23:21,895] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-28 16:23:21,897] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-28 16:23:21,904] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-28 16:23:21,914] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-28 16:23:21,920] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 13 samples (table) [2022-11-28 16:23:21,925] multiqc [DEBUG ] No samples found: conpair [2022-11-28 16:23:21,931] multiqc [DEBUG ] No samples found: peddy [2022-11-28 16:23:21,936] multiqc [DEBUG ] No samples found: somalier [2022-11-28 16:23:21,943] multiqc [DEBUG ] No samples found: methylQA [2022-11-28 16:23:21,953] multiqc [DEBUG ] No samples found: mosdepth [2022-11-28 16:23:21,957] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-28 16:23:21,961] multiqc [DEBUG ] No samples found: qualimap [2022-11-28 16:23:21,967] multiqc [DEBUG ] No samples found: preseq [2022-11-28 16:23:21,972] multiqc [DEBUG ] No samples found: quast [2022-11-28 16:23:21,979] multiqc [DEBUG ] No samples found: qorts [2022-11-28 16:23:21,984] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-28 16:23:21,989] multiqc [DEBUG ] No samples found: rockhopper [2022-11-28 16:23:21,994] multiqc [DEBUG ] No samples found: rsem [2022-11-28 16:23:22,009] multiqc [DEBUG ] No samples found: rseqc [2022-11-28 16:23:22,015] multiqc [DEBUG ] No samples found: busco [2022-11-28 16:23:22,020] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-28 16:23:22,025] multiqc [DEBUG ] No samples found: disambiguate [2022-11-28 16:23:22,032] multiqc [DEBUG ] No samples found: supernova [2022-11-28 16:23:22,049] multiqc [DEBUG ] No samples found: deeptools [2022-11-28 16:23:22,055] multiqc [DEBUG ] No samples found: sargasso [2022-11-28 16:23:22,061] multiqc [DEBUG ] No samples found: verifybamid [2022-11-28 16:23:22,069] multiqc [DEBUG ] No samples found: mirtrace [2022-11-28 16:23:22,075] multiqc [DEBUG ] No samples found: happy [2022-11-28 16:23:22,081] multiqc [DEBUG ] No samples found: mirtop [2022-11-28 16:23:22,090] multiqc [DEBUG ] No samples found: homer [2022-11-28 16:23:22,095] multiqc [DEBUG ] No samples found: macs2 [2022-11-28 16:23:22,100] multiqc [DEBUG ] No samples found: theta2 [2022-11-28 16:23:22,107] multiqc [DEBUG ] No samples found: snpeff [2022-11-28 16:23:22,114] multiqc [DEBUG ] No samples found: gatk [2022-11-28 16:23:22,121] multiqc [DEBUG ] No samples found: htseq [2022-11-28 16:23:22,128] multiqc [DEBUG ] No samples found: bcftools [2022-11-28 16:23:22,133] multiqc [DEBUG ] No samples found: featureCounts [2022-11-28 16:23:22,140] multiqc [DEBUG ] No samples found: fgbio [2022-11-28 16:23:22,157] multiqc [DEBUG ] No samples found: dragen [2022-11-28 16:23:22,163] multiqc [DEBUG ] No samples found: dedup [2022-11-28 16:23:22,168] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-28 16:23:22,196] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-28 16:23:22,202] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-28 16:23:22,205] multiqc [DEBUG ] No samples found: picard [2022-11-28 16:23:22,210] multiqc [DEBUG ] No samples found: prokka [2022-11-28 16:23:22,217] multiqc [DEBUG ] No samples found: samblaster [2022-11-28 16:23:22,228] multiqc [DEBUG ] No samples found: samtools [2022-11-28 16:23:22,233] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-28 16:23:22,239] multiqc [DEBUG ] No samples found: bamtools [2022-11-28 16:23:22,246] multiqc [DEBUG ] No samples found: jellyfish [2022-11-28 16:23:22,257] multiqc [DEBUG ] No samples found: vcftools [2022-11-28 16:23:22,264] multiqc [DEBUG ] No samples found: longranger [2022-11-28 16:23:22,271] multiqc [DEBUG ] No samples found: stacks [2022-11-28 16:23:22,276] multiqc [DEBUG ] No samples found: varscan2 [2022-11-28 16:23:22,292] multiqc [DEBUG ] No samples found: bbmap [2022-11-28 16:23:22,298] multiqc [DEBUG ] No samples found: bismark [2022-11-28 16:23:22,303] multiqc [DEBUG ] No samples found: biscuit [2022-11-28 16:23:22,310] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-28 16:23:22,315] multiqc [DEBUG ] No samples found: hicup [2022-11-28 16:23:22,322] multiqc [DEBUG ] No samples found: hicpro [2022-11-28 16:23:22,327] multiqc [DEBUG ] No samples found: salmon [2022-11-28 16:23:22,332] multiqc [DEBUG ] No samples found: kallisto [2022-11-28 16:23:22,338] multiqc [DEBUG ] No samples found: slamdunk [2022-11-28 16:23:22,343] multiqc [DEBUG ] No samples found: star [2022-11-28 16:23:22,348] multiqc [DEBUG ] No samples found: hisat2 [2022-11-28 16:23:22,353] multiqc [DEBUG ] No samples found: tophat [2022-11-28 16:23:22,358] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-28 16:23:22,364] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-28 16:23:22,370] multiqc [DEBUG ] No samples found: snpsplit [2022-11-28 16:23:22,375] multiqc [DEBUG ] No samples found: kat [2022-11-28 16:23:22,380] multiqc [DEBUG ] No samples found: leehom [2022-11-28 16:23:22,385] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-28 16:23:22,390] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-28 16:23:22,396] multiqc [DEBUG ] No samples found: cutadapt [2022-11-28 16:23:22,401] multiqc [DEBUG ] No samples found: flexbar [2022-11-28 16:23:22,406] multiqc [DEBUG ] No samples found: kaiju [2022-11-28 16:23:22,412] multiqc [DEBUG ] No samples found: kraken [2022-11-28 16:23:22,418] multiqc [DEBUG ] No samples found: malt [2022-11-28 16:23:22,422] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-28 16:23:22,427] multiqc [DEBUG ] No samples found: sickle [2022-11-28 16:23:22,432] multiqc [DEBUG ] No samples found: skewer [2022-11-28 16:23:22,437] multiqc [DEBUG ] No samples found: sortmerna [2022-11-28 16:23:22,442] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-28 16:23:22,447] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-28 16:23:22,452] multiqc [DEBUG ] No samples found: afterqc [2022-11-28 16:23:22,457] multiqc [DEBUG ] No samples found: fastp [2022-11-28 16:23:23,302] multiqc.modules.fastqc.fastqc [INFO ] Found 26 reports [2022-11-28 16:23:23,668] multiqc [DEBUG ] No samples found: pycoqc [2022-11-28 16:23:23,675] multiqc [DEBUG ] No samples found: minionqc [2022-11-28 16:23:23,681] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-28 16:23:23,687] multiqc [DEBUG ] No samples found: clusterflow [2022-11-28 16:23:23,695] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-28 16:23:23,703] multiqc [DEBUG ] No samples found: interop [2022-11-28 16:23:23,708] multiqc [DEBUG ] No samples found: ivar [2022-11-28 16:23:23,714] multiqc [DEBUG ] No samples found: flash [2022-11-28 16:23:23,721] multiqc [DEBUG ] No samples found: seqyclean [2022-11-28 16:23:23,721] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-28 16:23:23,722] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-11-28 16:23:23,722] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-28 16:23:23,722] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-11-28 16:23:23,722] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-28 16:23:23,752] multiqc [INFO ] Compressing plot data [2022-11-28 16:23:24,171] multiqc [INFO ] Report : multiqc_report.html [2022-11-28 16:23:24,171] multiqc [INFO ] Data : multiqc_data [2022-11-28 16:23:24,172] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27440394/tmpdrve4t5r/multiqc_data' to '/scratch/gencore/logs/html/HNF7WDRX2/1/multiqc_data' [2022-11-28 16:23:24,306] multiqc [INFO ] MultiQC complete