[2023-10-17 00:57:47,540] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-10-17 00:57:47,540] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-10-17 00:57:47,540] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-10-17 00:57:47,543] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-10-17 00:57:47,543] 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}} [2023-10-17 00:57:47,543] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMHCYDRX3/merged [2023-10-17 00:57:47,710] multiqc [WARNING] MultiQC Version v1.16 now available! [2023-10-17 00:57:47,710] multiqc [INFO ] This is MultiQC v1.9 [2023-10-17 00:57:47,710] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMHCYDRX3/merged [2023-10-17 00:57:47,710] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMHCYDRX3/merged [2023-10-17 00:57:47,710] multiqc [INFO ] Template : default [2023-10-17 00:57:47,710] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-10-17 00:57:47,711] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMHCYDRX3/merged [2023-10-17 00:57:47,711] 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 [2023-10-17 00:57:47,711] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-38941980/tmpd4kp8kyg [2023-10-17 00:57:47,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N2_fastqc.html [2023-10-17 00:57:47,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N2_fastqc.html [2023-10-17 00:57:47,922] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_undetermined_fastqc.html [2023-10-17 00:57:47,924] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_undetermined_fastqc.html [2023-10-17 00:57:47,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K1_fastqc.html [2023-10-17 00:57:47,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K1_fastqc.html [2023-10-17 00:57:48,033] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N2_fastqc.html [2023-10-17 00:57:48,035] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N2_fastqc.html [2023-10-17 00:57:48,084] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N1_fastqc.html [2023-10-17 00:57:48,086] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_N1_fastqc.html [2023-10-17 00:57:48,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K2_fastqc.html [2023-10-17 00:57:48,135] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_K2_fastqc.html [2023-10-17 00:57:48,191] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_undetermined_fastqc.html [2023-10-17 00:57:48,193] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_undetermined_fastqc.html [2023-10-17 00:57:48,240] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K1_fastqc.html [2023-10-17 00:57:48,242] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K1_fastqc.html [2023-10-17 00:57:48,288] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K2_fastqc.html [2023-10-17 00:57:48,290] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n02_K2_fastqc.html [2023-10-17 00:57:48,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N1_fastqc.html [2023-10-17 00:57:48,348] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMHCYDRX3_n01_N1_fastqc.html [2023-10-17 00:57:48,748] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 00:57:48,750] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 00:57:48,767] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-10-17 00:57:48,771] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2023-10-17 00:57:48,773] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-10-17 00:57:48,777] multiqc [DEBUG ] No samples found: conpair [2023-10-17 00:57:48,782] multiqc [DEBUG ] No samples found: peddy [2023-10-17 00:57:48,787] multiqc [DEBUG ] No samples found: somalier [2023-10-17 00:57:48,792] multiqc [DEBUG ] No samples found: methylQA [2023-10-17 00:57:48,801] multiqc [DEBUG ] No samples found: mosdepth [2023-10-17 00:57:48,805] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-10-17 00:57:48,809] multiqc [DEBUG ] No samples found: qualimap [2023-10-17 00:57:48,814] multiqc [DEBUG ] No samples found: preseq [2023-10-17 00:57:48,819] multiqc [DEBUG ] No samples found: quast [2023-10-17 00:57:48,824] multiqc [DEBUG ] No samples found: qorts [2023-10-17 00:57:48,828] multiqc [DEBUG ] No samples found: rna_seqc [2023-10-17 00:57:48,833] multiqc [DEBUG ] No samples found: rockhopper [2023-10-17 00:57:48,838] multiqc [DEBUG ] No samples found: rsem [2023-10-17 00:57:48,849] multiqc [DEBUG ] No samples found: rseqc [2023-10-17 00:57:48,854] multiqc [DEBUG ] No samples found: busco [2023-10-17 00:57:48,858] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-10-17 00:57:48,863] multiqc [DEBUG ] No samples found: disambiguate [2023-10-17 00:57:48,869] multiqc [DEBUG ] No samples found: supernova [2023-10-17 00:57:48,882] multiqc [DEBUG ] No samples found: deeptools [2023-10-17 00:57:48,887] multiqc [DEBUG ] No samples found: sargasso [2023-10-17 00:57:48,891] multiqc [DEBUG ] No samples found: verifybamid [2023-10-17 00:57:48,897] multiqc [DEBUG ] No samples found: mirtrace [2023-10-17 00:57:48,903] multiqc [DEBUG ] No samples found: happy [2023-10-17 00:57:48,907] multiqc [DEBUG ] No samples found: mirtop [2023-10-17 00:57:48,914] multiqc [DEBUG ] No samples found: homer [2023-10-17 00:57:48,919] multiqc [DEBUG ] No samples found: macs2 [2023-10-17 00:57:48,923] multiqc [DEBUG ] No samples found: theta2 [2023-10-17 00:57:48,928] multiqc [DEBUG ] No samples found: snpeff [2023-10-17 00:57:48,934] multiqc [DEBUG ] No samples found: gatk [2023-10-17 00:57:48,939] multiqc [DEBUG ] No samples found: htseq [2023-10-17 00:57:48,945] multiqc [DEBUG ] No samples found: bcftools [2023-10-17 00:57:48,950] multiqc [DEBUG ] No samples found: featureCounts [2023-10-17 00:57:48,957] multiqc [DEBUG ] No samples found: fgbio [2023-10-17 00:57:48,969] multiqc [DEBUG ] No samples found: dragen [2023-10-17 00:57:48,975] multiqc [DEBUG ] No samples found: dedup [2023-10-17 00:57:48,980] multiqc [DEBUG ] No samples found: damageprofiler [2023-10-17 00:57:49,002] multiqc [DEBUG ] No samples found: biobambam2 [2023-10-17 00:57:49,007] multiqc [DEBUG ] No samples found: mtnucratio [2023-10-17 00:57:49,010] multiqc [DEBUG ] No samples found: picard [2023-10-17 00:57:49,014] multiqc [DEBUG ] No samples found: prokka [2023-10-17 00:57:49,019] multiqc [DEBUG ] No samples found: samblaster [2023-10-17 00:57:49,027] multiqc [DEBUG ] No samples found: samtools [2023-10-17 00:57:49,033] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-10-17 00:57:49,039] multiqc [DEBUG ] No samples found: bamtools [2023-10-17 00:57:49,043] multiqc [DEBUG ] No samples found: jellyfish [2023-10-17 00:57:49,051] multiqc [DEBUG ] No samples found: vcftools [2023-10-17 00:57:49,056] multiqc [DEBUG ] No samples found: longranger [2023-10-17 00:57:49,061] multiqc [DEBUG ] No samples found: stacks [2023-10-17 00:57:49,066] multiqc [DEBUG ] No samples found: varscan2 [2023-10-17 00:57:49,079] multiqc [DEBUG ] No samples found: bbmap [2023-10-17 00:57:49,084] multiqc [DEBUG ] No samples found: bismark [2023-10-17 00:57:49,089] multiqc [DEBUG ] No samples found: biscuit [2023-10-17 00:57:49,094] multiqc [DEBUG ] No samples found: hicexplorer [2023-10-17 00:57:49,104] multiqc [DEBUG ] No samples found: hicup [2023-10-17 00:57:49,109] multiqc [DEBUG ] No samples found: hicpro [2023-10-17 00:57:49,115] multiqc [DEBUG ] No samples found: salmon [2023-10-17 00:57:49,119] multiqc [DEBUG ] No samples found: kallisto [2023-10-17 00:57:49,125] multiqc [DEBUG ] No samples found: slamdunk [2023-10-17 00:57:49,129] multiqc [DEBUG ] No samples found: star [2023-10-17 00:57:49,134] multiqc [DEBUG ] No samples found: hisat2 [2023-10-17 00:57:49,139] multiqc [DEBUG ] No samples found: tophat [2023-10-17 00:57:49,144] multiqc [DEBUG ] No samples found: bowtie2 [2023-10-17 00:57:49,148] multiqc [DEBUG ] No samples found: bowtie1 [2023-10-17 00:57:49,153] multiqc [DEBUG ] No samples found: snpsplit [2023-10-17 00:57:49,158] multiqc [DEBUG ] No samples found: kat [2023-10-17 00:57:49,162] multiqc [DEBUG ] No samples found: leehom [2023-10-17 00:57:49,167] multiqc [DEBUG ] No samples found: adapterRemoval [2023-10-17 00:57:49,172] multiqc [DEBUG ] No samples found: clipandmerge [2023-10-17 00:57:49,177] multiqc [DEBUG ] No samples found: cutadapt [2023-10-17 00:57:49,182] multiqc [DEBUG ] No samples found: flexbar [2023-10-17 00:57:49,186] multiqc [DEBUG ] No samples found: kaiju [2023-10-17 00:57:49,192] multiqc [DEBUG ] No samples found: kraken [2023-10-17 00:57:49,196] multiqc [DEBUG ] No samples found: malt [2023-10-17 00:57:49,200] multiqc [DEBUG ] No samples found: trimmomatic [2023-10-17 00:57:49,205] multiqc [DEBUG ] No samples found: sickle [2023-10-17 00:57:49,210] multiqc [DEBUG ] No samples found: skewer [2023-10-17 00:57:49,214] multiqc [DEBUG ] No samples found: sortmerna [2023-10-17 00:57:49,219] multiqc [DEBUG ] No samples found: biobloomtools [2023-10-17 00:57:49,224] multiqc [DEBUG ] No samples found: fastq_screen [2023-10-17 00:57:49,228] multiqc [DEBUG ] No samples found: afterqc [2023-10-17 00:57:49,233] multiqc [DEBUG ] No samples found: fastp [2023-10-17 00:57:49,789] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-10-17 00:57:49,953] multiqc [DEBUG ] No samples found: pycoqc [2023-10-17 00:57:49,958] multiqc [DEBUG ] No samples found: minionqc [2023-10-17 00:57:49,963] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-10-17 00:57:49,968] multiqc [DEBUG ] No samples found: clusterflow [2023-10-17 00:57:49,972] multiqc [DEBUG ] No samples found: bcl2fastq [2023-10-17 00:57:49,977] multiqc [DEBUG ] No samples found: interop [2023-10-17 00:57:49,982] multiqc [DEBUG ] No samples found: ivar [2023-10-17 00:57:49,987] multiqc [DEBUG ] No samples found: flash [2023-10-17 00:57:49,991] multiqc [DEBUG ] No samples found: seqyclean [2023-10-17 00:57:49,991] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-10-17 00:57:49,991] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-10-17 00:57:49,991] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-10-17 00:57:49,992] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-10-17 00:57:50,006] multiqc [INFO ] Compressing plot data [2023-10-17 00:57:50,177] multiqc [INFO ] Report : multiqc_report.html [2023-10-17 00:57:50,177] multiqc [INFO ] Data : multiqc_data [2023-10-17 00:57:50,177] multiqc [DEBUG ] Moving data file from '/state/partition1/job-38941980/tmpd4kp8kyg/multiqc_data' to '/scratch/gencore/logs/html/HMHCYDRX3/merged/multiqc_data' [2023-10-17 00:57:50,301] multiqc [INFO ] MultiQC complete