[2023-06-02 22:18:05,254] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-06-02 22:18:05,255] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-06-02 22:18:05,255] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-02 22:18:05,257] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-06-02 22:18:05,257] 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}} [2023-06-02 22:18:05,257] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5NKTDRX3/merged [2023-06-02 22:18:05,429] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-06-02 22:18:05,430] multiqc [INFO ] This is MultiQC v1.9 [2023-06-02 22:18:05,430] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5NKTDRX3/merged [2023-06-02 22:18:05,430] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5NKTDRX3/merged [2023-06-02 22:18:05,430] multiqc [INFO ] Template : default [2023-06-02 22:18:05,430] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-06-02 22:18:05,430] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5NKTDRX3/merged [2023-06-02 22:18:05,430] 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 [2023-06-02 22:18:05,430] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-34162090/tmpy43ksh7t [2023-06-02 22:18:05,570] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_SS23_fastqc.html [2023-06-02 22:18:05,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3163_fastqc.html [2023-06-02 22:18:12,308] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3163_fastqc.html [2023-06-02 22:18:12,366] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3144_fastqc.html [2023-06-02 22:18:12,368] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3144_fastqc.html [2023-06-02 22:18:12,434] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3166_fastqc.html [2023-06-02 22:18:12,436] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3166_fastqc.html [2023-06-02 22:18:12,494] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n02_3178_fastqc.html [2023-06-02 22:18:12,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n02_3178_fastqc.html [2023-06-02 22:18:12,542] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n02_3129_fastqc.html [2023-06-02 22:18:12,544] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n02_3129_fastqc.html [2023-06-02 22:18:12,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3120_fastqc.html [2023-06-02 22:18:12,610] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3120_fastqc.html [2023-06-02 22:18:12,652] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_undetermined_fastqc.html [2023-06-02 22:18:12,654] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_undetermined_fastqc.html [2023-06-02 22:18:12,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3130_fastqc.html [2023-06-02 22:18:12,711] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3130_fastqc.html [2023-06-02 22:18:12,756] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3119_fastqc.html [2023-06-02 22:18:12,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3119_fastqc.html [2023-06-02 22:18:12,818] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3151_fastqc.html [2023-06-02 22:18:12,820] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKTDRX3_n01_3151_fastqc.html [2023-06-02 22:18:14,018] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-02 22:18:14,021] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-02 22:18:14,047] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-06-02 22:18:14,077] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 65 samples (table) [2023-06-02 22:18:14,079] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-06-02 22:18:14,084] multiqc [DEBUG ] No samples found: conpair [2023-06-02 22:18:14,089] multiqc [DEBUG ] No samples found: peddy [2023-06-02 22:18:14,106] multiqc [DEBUG ] No samples found: somalier [2023-06-02 22:18:14,118] multiqc [DEBUG ] No samples found: methylQA [2023-06-02 22:18:14,139] multiqc [DEBUG ] No samples found: mosdepth [2023-06-02 22:18:14,151] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-02 22:18:14,154] multiqc [DEBUG ] No samples found: qualimap [2023-06-02 22:18:14,160] multiqc [DEBUG ] No samples found: preseq [2023-06-02 22:18:14,165] multiqc [DEBUG ] No samples found: quast [2023-06-02 22:18:14,170] multiqc [DEBUG ] No samples found: qorts [2023-06-02 22:18:14,175] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-02 22:18:14,180] multiqc [DEBUG ] No samples found: rockhopper [2023-06-02 22:18:14,186] multiqc [DEBUG ] No samples found: rsem [2023-06-02 22:18:14,197] multiqc [DEBUG ] No samples found: rseqc [2023-06-02 22:18:14,202] multiqc [DEBUG ] No samples found: busco [2023-06-02 22:18:14,214] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-02 22:18:14,225] multiqc [DEBUG ] No samples found: disambiguate [2023-06-02 22:18:14,230] multiqc [DEBUG ] No samples found: supernova [2023-06-02 22:18:14,258] multiqc [DEBUG ] No samples found: deeptools [2023-06-02 22:18:14,263] multiqc [DEBUG ] No samples found: sargasso [2023-06-02 22:18:14,270] multiqc [DEBUG ] No samples found: verifybamid [2023-06-02 22:18:14,278] multiqc [DEBUG ] No samples found: mirtrace [2023-06-02 22:18:14,284] multiqc [DEBUG ] No samples found: happy [2023-06-02 22:18:14,296] multiqc [DEBUG ] No samples found: mirtop [2023-06-02 22:18:14,312] multiqc [DEBUG ] No samples found: homer [2023-06-02 22:18:14,325] multiqc [DEBUG ] No samples found: macs2 [2023-06-02 22:18:14,329] multiqc [DEBUG ] No samples found: theta2 [2023-06-02 22:18:14,334] multiqc [DEBUG ] No samples found: snpeff [2023-06-02 22:18:14,341] multiqc [DEBUG ] No samples found: gatk [2023-06-02 22:18:14,345] multiqc [DEBUG ] No samples found: htseq [2023-06-02 22:18:14,361] multiqc [DEBUG ] No samples found: bcftools [2023-06-02 22:18:14,366] multiqc [DEBUG ] No samples found: featureCounts [2023-06-02 22:18:14,390] multiqc [DEBUG ] No samples found: fgbio [2023-06-02 22:18:14,425] multiqc [DEBUG ] No samples found: dragen [2023-06-02 22:18:14,431] multiqc [DEBUG ] No samples found: dedup [2023-06-02 22:18:14,437] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-02 22:18:14,523] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-02 22:18:14,528] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-02 22:18:14,530] multiqc [DEBUG ] No samples found: picard [2023-06-02 22:18:14,535] multiqc [DEBUG ] No samples found: prokka [2023-06-02 22:18:14,539] multiqc [DEBUG ] No samples found: samblaster [2023-06-02 22:18:14,568] multiqc [DEBUG ] No samples found: samtools [2023-06-02 22:18:14,590] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-02 22:18:14,595] multiqc [DEBUG ] No samples found: bamtools [2023-06-02 22:18:14,600] multiqc [DEBUG ] No samples found: jellyfish [2023-06-02 22:18:14,638] multiqc [DEBUG ] No samples found: vcftools [2023-06-02 22:18:14,658] multiqc [DEBUG ] No samples found: longranger [2023-06-02 22:18:14,668] multiqc [DEBUG ] No samples found: stacks [2023-06-02 22:18:14,691] multiqc [DEBUG ] No samples found: varscan2 [2023-06-02 22:18:14,737] multiqc [DEBUG ] No samples found: bbmap [2023-06-02 22:18:14,760] multiqc [DEBUG ] No samples found: bismark [2023-06-02 22:18:14,772] multiqc [DEBUG ] No samples found: biscuit [2023-06-02 22:18:14,793] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-02 22:18:14,798] multiqc [DEBUG ] No samples found: hicup [2023-06-02 22:18:14,804] multiqc [DEBUG ] No samples found: hicpro [2023-06-02 22:18:14,809] multiqc [DEBUG ] No samples found: salmon [2023-06-02 22:18:14,816] multiqc [DEBUG ] No samples found: kallisto [2023-06-02 22:18:14,829] multiqc [DEBUG ] No samples found: slamdunk [2023-06-02 22:18:14,834] multiqc [DEBUG ] No samples found: star [2023-06-02 22:18:14,841] multiqc [DEBUG ] No samples found: hisat2 [2023-06-02 22:18:14,857] multiqc [DEBUG ] No samples found: tophat [2023-06-02 22:18:14,870] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-02 22:18:14,912] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-02 22:18:14,919] multiqc [DEBUG ] No samples found: snpsplit [2023-06-02 22:18:14,924] multiqc [DEBUG ] No samples found: kat [2023-06-02 22:18:14,928] multiqc [DEBUG ] No samples found: leehom [2023-06-02 22:18:14,933] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-02 22:18:14,938] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-02 22:18:14,943] multiqc [DEBUG ] No samples found: cutadapt [2023-06-02 22:18:14,948] multiqc [DEBUG ] No samples found: flexbar [2023-06-02 22:18:14,952] multiqc [DEBUG ] No samples found: kaiju [2023-06-02 22:18:14,958] multiqc [DEBUG ] No samples found: kraken [2023-06-02 22:18:14,970] multiqc [DEBUG ] No samples found: malt [2023-06-02 22:18:14,975] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-02 22:18:14,993] multiqc [DEBUG ] No samples found: sickle [2023-06-02 22:18:15,010] multiqc [DEBUG ] No samples found: skewer [2023-06-02 22:18:15,015] multiqc [DEBUG ] No samples found: sortmerna [2023-06-02 22:18:15,044] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-02 22:18:15,049] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-02 22:18:15,065] multiqc [DEBUG ] No samples found: afterqc [2023-06-02 22:18:15,078] multiqc [DEBUG ] No samples found: fastp [2023-06-02 22:18:20,379] multiqc.modules.fastqc.fastqc [INFO ] Found 130 reports [2023-06-02 22:18:34,389] multiqc [DEBUG ] No samples found: pycoqc [2023-06-02 22:18:34,394] multiqc [DEBUG ] No samples found: minionqc [2023-06-02 22:18:34,407] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-06-02 22:18:34,428] multiqc [DEBUG ] No samples found: clusterflow [2023-06-02 22:18:34,451] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-02 22:18:34,457] multiqc [DEBUG ] No samples found: interop [2023-06-02 22:18:34,464] multiqc [DEBUG ] No samples found: ivar [2023-06-02 22:18:34,469] multiqc [DEBUG ] No samples found: flash [2023-06-02 22:18:34,486] multiqc [DEBUG ] No samples found: seqyclean [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-06-02 22:18:34,486] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-06-02 22:18:34,487] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-06-02 22:18:34,487] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-06-02 22:18:34,487] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-06-02 22:18:34,487] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-06-02 22:18:34,487] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-06-02 22:18:34,487] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-06-02 22:18:34,487] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-06-02 22:18:34,635] multiqc [INFO ] Compressing plot data [2023-06-02 22:18:34,680] multiqc [INFO ] Report : multiqc_report.html [2023-06-02 22:18:34,680] multiqc [INFO ] Data : multiqc_data [2023-06-02 22:18:34,680] multiqc [DEBUG ] Moving data file from '/state/partition1/job-34162090/tmpy43ksh7t/multiqc_data' to '/scratch/gencore/logs/html/H5NKTDRX3/merged/multiqc_data' [2023-06-02 22:18:34,823] multiqc [INFO ] MultiQC complete