[2023-12-13 22:22:32,792] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-13 22:22:32,792] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-13 22:22:32,792] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-13 22:22:32,795] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-12-13 22:22:32,795] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-12-13 22:22:32,795] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJWLYBGXV/merged [2023-12-13 22:22:32,975] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-13 22:22:32,975] multiqc [INFO ] This is MultiQC v1.9 [2023-12-13 22:22:32,975] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJWLYBGXV/merged [2023-12-13 22:22:32,975] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJWLYBGXV/merged [2023-12-13 22:22:32,975] multiqc [INFO ] Template : default [2023-12-13 22:22:32,976] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-13 22:22:32,976] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJWLYBGXV/merged [2023-12-13 22:22:32,976] 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 [2023-12-13 22:22:32,976] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40829354/tmpzioo82_k [2023-12-13 22:22:33,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 22:22:33,093] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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[2023-12-13 22:22:33,994] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_YZ50_fastqc.html [2023-12-13 22:22:34,041] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_YZ49_fastqc.html [2023-12-13 22:22:34,043] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_YZ49_fastqc.html [2023-12-13 22:22:34,089] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO97_fastqc.html [2023-12-13 22:22:34,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO97_fastqc.html [2023-12-13 22:22:34,139] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO100_fastqc.html [2023-12-13 22:22:34,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO100_fastqc.html [2023-12-13 22:22:34,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO104_fastqc.html [2023-12-13 22:22:34,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO104_fastqc.html [2023-12-13 22:22:34,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO96_fastqc.html [2023-12-13 22:22:34,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO96_fastqc.html [2023-12-13 22:22:34,286] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_YZ53_fastqc.html [2023-12-13 22:22:34,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_YZ53_fastqc.html [2023-12-13 22:22:34,334] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO102_fastqc.html [2023-12-13 22:22:34,336] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO102_fastqc.html [2023-12-13 22:22:34,382] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO93_fastqc.html [2023-12-13 22:22:34,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO93_fastqc.html [2023-12-13 22:22:34,432] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO103_fastqc.html [2023-12-13 22:22:34,434] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO103_fastqc.html [2023-12-13 22:22:34,833] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 22:22:34,834] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 22:22:34,852] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-12-13 22:22:34,853] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-13 22:22:34,866] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2023-12-13 22:22:34,872] multiqc [DEBUG ] No samples found: conpair [2023-12-13 22:22:34,877] multiqc [DEBUG ] No samples found: peddy [2023-12-13 22:22:34,881] multiqc [DEBUG ] No samples found: somalier [2023-12-13 22:22:34,886] multiqc [DEBUG ] No samples found: methylQA [2023-12-13 22:22:34,893] multiqc [DEBUG ] No samples found: mosdepth [2023-12-13 22:22:34,898] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-13 22:22:34,901] multiqc [DEBUG ] No samples found: qualimap [2023-12-13 22:22:34,905] multiqc [DEBUG ] No samples found: preseq [2023-12-13 22:22:34,910] multiqc [DEBUG ] No samples found: quast [2023-12-13 22:22:34,914] multiqc [DEBUG ] No samples found: qorts [2023-12-13 22:22:34,919] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-13 22:22:34,924] multiqc [DEBUG ] No samples found: rockhopper [2023-12-13 22:22:34,928] multiqc [DEBUG ] No samples found: rsem [2023-12-13 22:22:34,938] multiqc [DEBUG ] No samples found: rseqc [2023-12-13 22:22:34,942] multiqc [DEBUG ] No samples found: busco [2023-12-13 22:22:34,947] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-13 22:22:34,951] multiqc [DEBUG ] No samples found: disambiguate [2023-12-13 22:22:34,956] multiqc [DEBUG ] No samples found: supernova [2023-12-13 22:22:34,968] multiqc [DEBUG ] No samples found: deeptools [2023-12-13 22:22:34,972] multiqc [DEBUG ] No samples found: sargasso [2023-12-13 22:22:34,977] multiqc [DEBUG ] No samples found: verifybamid [2023-12-13 22:22:34,981] multiqc [DEBUG ] No samples found: mirtrace [2023-12-13 22:22:34,986] multiqc [DEBUG ] No samples found: happy [2023-12-13 22:22:34,990] multiqc [DEBUG ] No samples found: mirtop [2023-12-13 22:22:34,996] multiqc [DEBUG ] No samples found: homer [2023-12-13 22:22:35,000] multiqc [DEBUG ] No samples found: macs2 [2023-12-13 22:22:35,004] multiqc [DEBUG ] No samples found: theta2 [2023-12-13 22:22:35,008] multiqc [DEBUG ] No samples found: snpeff [2023-12-13 22:22:35,014] multiqc [DEBUG ] No samples found: gatk [2023-12-13 22:22:35,019] multiqc [DEBUG ] No samples found: htseq [2023-12-13 22:22:35,024] multiqc [DEBUG ] No samples found: bcftools [2023-12-13 22:22:35,028] multiqc [DEBUG ] No samples found: featureCounts [2023-12-13 22:22:35,034] multiqc [DEBUG ] No samples found: fgbio [2023-12-13 22:22:35,045] multiqc [DEBUG ] No samples found: dragen [2023-12-13 22:22:35,050] multiqc [DEBUG ] No samples found: dedup [2023-12-13 22:22:35,054] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-13 22:22:35,074] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-13 22:22:35,078] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-13 22:22:35,081] multiqc [DEBUG ] No samples found: picard [2023-12-13 22:22:35,085] multiqc [DEBUG ] No samples found: prokka [2023-12-13 22:22:35,089] multiqc [DEBUG ] No samples found: samblaster [2023-12-13 22:22:35,096] multiqc [DEBUG ] No samples found: samtools [2023-12-13 22:22:35,101] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-13 22:22:35,105] multiqc [DEBUG ] No samples found: bamtools [2023-12-13 22:22:35,110] multiqc [DEBUG ] No samples found: jellyfish [2023-12-13 22:22:35,116] multiqc [DEBUG ] No samples found: vcftools [2023-12-13 22:22:35,139] multiqc [DEBUG ] No samples found: longranger [2023-12-13 22:22:35,147] multiqc [DEBUG ] No samples found: stacks [2023-12-13 22:22:35,151] multiqc [DEBUG ] No samples found: varscan2 [2023-12-13 22:22:35,223] multiqc [DEBUG ] No samples found: bbmap [2023-12-13 22:22:35,228] multiqc [DEBUG ] No samples found: bismark [2023-12-13 22:22:35,233] multiqc [DEBUG ] No samples found: biscuit [2023-12-13 22:22:35,241] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-13 22:22:35,245] multiqc [DEBUG ] No samples found: hicup [2023-12-13 22:22:35,250] multiqc [DEBUG ] No samples found: hicpro [2023-12-13 22:22:35,254] multiqc [DEBUG ] No samples found: salmon [2023-12-13 22:22:35,258] multiqc [DEBUG ] No samples found: kallisto [2023-12-13 22:22:35,262] multiqc [DEBUG ] No samples found: slamdunk [2023-12-13 22:22:35,267] multiqc [DEBUG ] No samples found: star [2023-12-13 22:22:35,271] multiqc [DEBUG ] No samples found: hisat2 [2023-12-13 22:22:35,276] multiqc [DEBUG ] No samples found: tophat [2023-12-13 22:22:35,280] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-13 22:22:35,284] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-13 22:22:35,288] multiqc [DEBUG ] No samples found: snpsplit [2023-12-13 22:22:35,293] multiqc [DEBUG ] No samples found: kat [2023-12-13 22:22:35,297] multiqc [DEBUG ] No samples found: leehom [2023-12-13 22:22:35,301] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-13 22:22:35,305] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-13 22:22:35,309] multiqc [DEBUG ] No samples found: cutadapt [2023-12-13 22:22:35,313] multiqc [DEBUG ] No samples found: flexbar [2023-12-13 22:22:35,318] multiqc [DEBUG ] No samples found: kaiju [2023-12-13 22:22:35,322] multiqc [DEBUG ] No samples found: kraken [2023-12-13 22:22:35,326] multiqc [DEBUG ] No samples found: malt [2023-12-13 22:22:35,331] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-13 22:22:35,335] multiqc [DEBUG ] No samples found: sickle [2023-12-13 22:22:35,339] multiqc [DEBUG ] No samples found: skewer [2023-12-13 22:22:35,343] multiqc [DEBUG ] No samples found: sortmerna [2023-12-13 22:22:35,347] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-13 22:22:35,352] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-13 22:22:35,356] multiqc [DEBUG ] No samples found: afterqc [2023-12-13 22:22:35,360] multiqc [DEBUG ] No samples found: fastp [2023-12-13 22:22:37,268] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2023-12-13 22:22:37,849] multiqc [DEBUG ] No samples found: pycoqc [2023-12-13 22:22:37,853] multiqc [DEBUG ] No samples found: minionqc [2023-12-13 22:22:37,858] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-13 22:22:37,863] multiqc [DEBUG ] No samples found: clusterflow [2023-12-13 22:22:37,868] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-13 22:22:37,872] multiqc [DEBUG ] No samples found: interop [2023-12-13 22:22:37,876] multiqc [DEBUG ] No samples found: ivar [2023-12-13 22:22:37,881] multiqc [DEBUG ] No samples found: flash [2023-12-13 22:22:37,885] multiqc [DEBUG ] No samples found: seqyclean [2023-12-13 22:22:37,885] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-13 22:22:37,885] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-13 22:22:37,885] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-13 22:22:37,885] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-12-13 22:22:37,885] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-12-13 22:22:37,885] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-12-13 22:22:37,885] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-13 22:22:37,886] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-13 22:22:37,917] multiqc [INFO ] Compressing plot data [2023-12-13 22:22:38,400] multiqc [INFO ] Report : multiqc_report.html [2023-12-13 22:22:38,400] multiqc [INFO ] Data : multiqc_data [2023-12-13 22:22:38,400] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40829354/tmpzioo82_k/multiqc_data' to '/scratch/gencore/logs/html/HJWLYBGXV/merged/multiqc_data' [2023-12-13 22:22:38,529] multiqc [INFO ] MultiQC complete