[2021-07-07 02:28:17,674] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-07-07 02:28:17,674] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-07-07 02:28:17,675] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-07-07 02:28:17,675] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-07-07 02:28:17,675] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-07-07 02:28:17,676] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGTNGBGXJ/merged [2021-07-07 02:28:19,186] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-07-07 02:28:19,186] multiqc [INFO ] This is MultiQC v1.9 [2021-07-07 02:28:19,186] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGTNGBGXJ/merged [2021-07-07 02:28:19,186] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGTNGBGXJ/merged [2021-07-07 02:28:19,186] multiqc [INFO ] Template : default [2021-07-07 02:28:19,187] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-07-07 02:28:19,187] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGTNGBGXJ/merged [2021-07-07 02:28:19,187] 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 [2021-07-07 02:28:19,187] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8429305/tmpej366e6p [2021-07-07 02:28:19,290] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_Halo_ampCol-B_s_fastqc.html [2021-07-07 02:28:19,292] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_Halo_ampCol-B_s_fastqc.html [2021-07-07 02:28:19,338] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_ps-bZIP11..ph-bZIP1_Col..s-B..h-B_s_fastqc.html [2021-07-07 02:28:19,339] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_ps-bZIP11..ph-bZIP1_Col..s-B..h-B_s_fastqc.html [2021-07-07 02:28:19,380] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvMYB135_PN94-B_s2_fastqc.html [2021-07-07 02:28:19,382] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvMYB135_PN94-B_s2_fastqc.html [2021-07-07 02:28:19,422] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-07 02:28:19,423] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-07 02:28:19,423] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-07 02:28:19,423] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-07 02:28:19,423] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-07 02:28:19,423] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-07 02:28:19,423] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-07 02:28:19,442] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern 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[2021-07-07 02:28:20,922] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_MdPS82_Md-B_s2_fastqc.html [2021-07-07 02:28:20,924] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_MdPS82_Md-B_s2_fastqc.html [2021-07-07 02:28:20,965] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_Halo_3351.27-B_s_fastqc.html [2021-07-07 02:28:20,967] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_Halo_3351.27-B_s_fastqc.html [2021-07-07 02:28:21,011] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_AtTGA5_Md-B_s_fastqc.html [2021-07-07 02:28:21,012] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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pattern filesize limit: HGTNGBGXJ_n01_VvHYH_ampPN94-B_s1_fastqc.html [2021-07-07 02:28:21,182] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_MdPS98_Md-B_s2_fastqc.html [2021-07-07 02:28:21,183] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_MdPS98_Md-B_s2_fastqc.html [2021-07-07 02:28:21,225] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvFemaleYABBY3_3351.27-B_s2_fastqc.html [2021-07-07 02:28:21,227] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvFemaleYABBY3_3351.27-B_s2_fastqc.html [2021-07-07 02:28:21,270] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_Halo_ampPN94-B_s_fastqc.html [2021-07-07 02:28:21,272] multiqc [DEBUG ] File ignored by 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[DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvMYB175_PN94-B_s2_fastqc.html [2021-07-07 02:28:21,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_undetermined_fastqc.html [2021-07-07 02:28:21,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_undetermined_fastqc.html [2021-07-07 02:28:21,484] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_AtXBAT33_Col-B_s_fastqc.html [2021-07-07 02:28:21,486] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_AtXBAT33_Col-B_s_fastqc.html [2021-07-07 02:28:21,528] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_Halo_Col-B_training_s_fastqc.html [2021-07-07 02:28:21,530] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_Halo_Col-B_training_s_fastqc.html [2021-07-07 02:28:21,569] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvFemaleYABBY3_3351.27-B_s1_fastqc.html [2021-07-07 02:28:21,571] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvFemaleYABBY3_3351.27-B_s1_fastqc.html [2021-07-07 02:28:21,613] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvMYBPA1_PN94-B_s2_fastqc.html [2021-07-07 02:28:21,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvMYBPA1_PN94-B_s2_fastqc.html [2021-07-07 02:28:21,657] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_ps-bZIP1..ph-bZIP11_Col..s-B..h-B_s_fastqc.html [2021-07-07 02:28:21,659] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_ps-bZIP1..ph-bZIP11_Col..s-B..h-B_s_fastqc.html [2021-07-07 02:28:21,706] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvHYH_ampPN94-B_s2_fastqc.html [2021-07-07 02:28:21,707] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_VvHYH_ampPN94-B_s2_fastqc.html [2021-07-07 02:28:21,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_MdPS90_Md-B_s1_fastqc.html [2021-07-07 02:28:21,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGTNGBGXJ_n01_MdPS90_Md-B_s1_fastqc.html [2021-07-07 02:28:22,306] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-07 02:28:22,307] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-07 02:28:22,315] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-07-07 02:28:22,332] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 37 samples (table) [2021-07-07 02:28:22,342] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-07-07 02:28:22,346] multiqc [DEBUG ] No samples found: conpair [2021-07-07 02:28:22,352] multiqc [DEBUG ] No samples found: peddy [2021-07-07 02:28:22,358] multiqc [DEBUG ] No samples found: somalier [2021-07-07 02:28:22,362] multiqc [DEBUG ] No samples found: methylQA [2021-07-07 02:28:22,371] multiqc [DEBUG ] No samples found: mosdepth [2021-07-07 02:28:22,375] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-07-07 02:28:22,380] multiqc [DEBUG ] No samples found: qualimap [2021-07-07 02:28:22,384] multiqc [DEBUG ] No samples found: preseq [2021-07-07 02:28:22,388] multiqc [DEBUG ] No samples found: quast [2021-07-07 02:28:22,392] multiqc [DEBUG ] No samples found: qorts [2021-07-07 02:28:22,396] multiqc [DEBUG ] No samples found: rna_seqc [2021-07-07 02:28:22,404] multiqc [DEBUG ] No samples found: rockhopper [2021-07-07 02:28:22,408] multiqc [DEBUG ] No samples found: rsem [2021-07-07 02:28:22,424] multiqc [DEBUG ] No samples found: rseqc [2021-07-07 02:28:22,428] multiqc [DEBUG ] No samples found: busco [2021-07-07 02:28:22,434] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-07-07 02:28:22,439] multiqc [DEBUG ] No samples found: disambiguate [2021-07-07 02:28:22,444] multiqc [DEBUG ] No samples found: supernova [2021-07-07 02:28:22,458] multiqc [DEBUG ] No samples found: deeptools [2021-07-07 02:28:22,462] multiqc [DEBUG ] No samples found: sargasso [2021-07-07 02:28:22,466] multiqc [DEBUG ] No samples found: verifybamid [2021-07-07 02:28:22,470] multiqc [DEBUG ] No samples found: mirtrace [2021-07-07 02:28:22,474] multiqc [DEBUG ] No samples found: happy [2021-07-07 02:28:22,478] multiqc [DEBUG ] No samples found: mirtop [2021-07-07 02:28:22,486] multiqc [DEBUG ] No samples found: homer [2021-07-07 02:28:22,490] multiqc [DEBUG ] No samples found: macs2 [2021-07-07 02:28:22,495] multiqc [DEBUG ] No samples found: theta2 [2021-07-07 02:28:22,500] multiqc [DEBUG ] No samples found: snpeff [2021-07-07 02:28:22,509] multiqc [DEBUG ] No samples found: gatk [2021-07-07 02:28:22,516] multiqc [DEBUG ] No samples found: htseq [2021-07-07 02:28:22,522] multiqc [DEBUG ] No samples found: bcftools [2021-07-07 02:28:22,526] multiqc [DEBUG ] No samples found: featureCounts [2021-07-07 02:28:22,533] multiqc [DEBUG ] No samples found: fgbio [2021-07-07 02:28:22,548] multiqc [DEBUG ] No samples found: dragen [2021-07-07 02:28:22,552] multiqc [DEBUG ] No samples found: dedup [2021-07-07 02:28:22,557] multiqc [DEBUG ] No samples found: damageprofiler [2021-07-07 02:28:22,583] multiqc [DEBUG ] No samples found: biobambam2 [2021-07-07 02:28:22,588] multiqc [DEBUG ] No samples found: mtnucratio [2021-07-07 02:28:22,590] multiqc [DEBUG ] No samples found: picard [2021-07-07 02:28:22,595] multiqc [DEBUG ] No samples found: prokka [2021-07-07 02:28:22,600] multiqc [DEBUG ] No samples found: samblaster [2021-07-07 02:28:22,611] multiqc [DEBUG ] No samples found: samtools [2021-07-07 02:28:22,615] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-07-07 02:28:22,620] multiqc [DEBUG ] No samples found: bamtools [2021-07-07 02:28:22,624] multiqc [DEBUG ] No samples found: jellyfish [2021-07-07 02:28:22,633] multiqc [DEBUG ] No samples found: vcftools [2021-07-07 02:28:22,639] multiqc [DEBUG ] No samples found: longranger [2021-07-07 02:28:22,645] multiqc [DEBUG ] No samples found: stacks [2021-07-07 02:28:22,649] multiqc [DEBUG ] No samples found: varscan2 [2021-07-07 02:28:22,663] multiqc [DEBUG ] No samples found: bbmap [2021-07-07 02:28:22,668] multiqc [DEBUG ] No samples found: bismark [2021-07-07 02:28:22,672] multiqc [DEBUG ] No samples found: biscuit [2021-07-07 02:28:22,678] multiqc [DEBUG ] No samples found: hicexplorer [2021-07-07 02:28:22,682] multiqc [DEBUG ] No samples found: hicup [2021-07-07 02:28:22,686] multiqc [DEBUG ] No samples found: hicpro [2021-07-07 02:28:22,691] multiqc [DEBUG ] No samples found: salmon [2021-07-07 02:28:22,695] multiqc [DEBUG ] No samples found: kallisto [2021-07-07 02:28:22,700] multiqc [DEBUG ] No samples found: slamdunk [2021-07-07 02:28:22,706] multiqc [DEBUG ] No samples found: star [2021-07-07 02:28:22,710] multiqc [DEBUG ] No samples found: hisat2 [2021-07-07 02:28:22,714] multiqc [DEBUG ] No samples found: tophat [2021-07-07 02:28:22,720] multiqc [DEBUG ] No samples found: bowtie2 [2021-07-07 02:28:22,727] multiqc [DEBUG ] No samples found: bowtie1 [2021-07-07 02:28:22,732] multiqc [DEBUG ] No samples found: snpsplit [2021-07-07 02:28:22,738] multiqc [DEBUG ] No samples found: kat [2021-07-07 02:28:22,742] multiqc [DEBUG ] No samples found: leehom [2021-07-07 02:28:22,748] multiqc [DEBUG ] No samples found: adapterRemoval [2021-07-07 02:28:22,752] multiqc [DEBUG ] No samples found: clipandmerge [2021-07-07 02:28:22,756] multiqc [DEBUG ] No samples found: cutadapt [2021-07-07 02:28:22,760] multiqc [DEBUG ] No samples found: flexbar [2021-07-07 02:28:22,767] multiqc [DEBUG ] No samples found: kaiju [2021-07-07 02:28:22,771] multiqc [DEBUG ] No samples found: kraken [2021-07-07 02:28:22,775] multiqc [DEBUG ] No samples found: malt [2021-07-07 02:28:22,779] multiqc [DEBUG ] No samples found: trimmomatic [2021-07-07 02:28:22,783] multiqc [DEBUG ] No samples found: sickle [2021-07-07 02:28:22,787] multiqc [DEBUG ] No samples found: skewer [2021-07-07 02:28:22,792] multiqc [DEBUG ] No samples found: sortmerna [2021-07-07 02:28:22,797] multiqc [DEBUG ] No samples found: biobloomtools [2021-07-07 02:28:22,801] multiqc [DEBUG ] No samples found: fastq_screen [2021-07-07 02:28:22,805] multiqc [DEBUG ] No samples found: afterqc [2021-07-07 02:28:22,810] multiqc [DEBUG ] No samples found: fastp [2021-07-07 02:28:25,319] multiqc.modules.fastqc.fastqc [INFO ] Found 37 reports [2021-07-07 02:28:26,071] multiqc [DEBUG ] No samples found: pycoqc [2021-07-07 02:28:26,076] multiqc [DEBUG ] No samples found: minionqc [2021-07-07 02:28:26,081] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-07-07 02:28:26,087] multiqc [DEBUG ] No samples found: clusterflow [2021-07-07 02:28:26,092] multiqc [DEBUG ] No samples found: bcl2fastq [2021-07-07 02:28:26,097] multiqc [DEBUG ] No samples found: interop [2021-07-07 02:28:26,103] multiqc [DEBUG ] No samples found: ivar [2021-07-07 02:28:26,108] multiqc [DEBUG ] No samples found: flash [2021-07-07 02:28:26,118] multiqc [DEBUG ] No samples found: seqyclean [2021-07-07 02:28:26,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-07-07 02:28:26,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-07-07 02:28:26,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-07-07 02:28:26,118] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-07-07 02:28:26,164] multiqc [INFO ] Compressing plot data [2021-07-07 02:28:26,807] multiqc [INFO ] Report : multiqc_report.html [2021-07-07 02:28:26,807] multiqc [INFO ] Data : multiqc_data [2021-07-07 02:28:26,807] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8429305/tmpej366e6p/multiqc_data' to '/scratch/gencore/logs/html/HGTNGBGXJ/merged/multiqc_data' [2021-07-07 02:28:26,941] multiqc [INFO ] MultiQC complete