[2023-05-14 19:01:09,080] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-14 19:01:09,080] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-14 19:01:09,080] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-14 19:01:09,082] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-14 19:01:09,082] 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}} [2023-05-14 19:01:09,082] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/2 [2023-05-14 19:01:10,450] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-14 19:01:10,451] multiqc [INFO ] This is MultiQC v1.9 [2023-05-14 19:01:10,451] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/2 [2023-05-14 19:01:10,451] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H52YHDSX7/2 [2023-05-14 19:01:10,451] multiqc [INFO ] Template : default [2023-05-14 19:01:10,451] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-14 19:01:10,451] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H52YHDSX7/2 [2023-05-14 19:01:10,451] 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 [2023-05-14 19:01:10,451] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33331815/tmpzg_d7e9_ [2023-05-14 19:01:10,569] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_2R_1-12_fastqc.html [2023-05-14 19:01:10,572] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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H52YHDSX7_l02_n01_10R_1-12_fastqc.html [2023-05-14 19:01:23,499] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_12G_1-12_fastqc.html [2023-05-14 19:01:23,501] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_12G_1-12_fastqc.html [2023-05-14 19:01:23,563] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_13G_1-12_fastqc.html [2023-05-14 19:01:23,565] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n01_13G_1-12_fastqc.html [2023-05-14 19:01:23,627] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_8R_1-15_fastqc.html [2023-05-14 19:01:23,629] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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limit: H52YHDSX7_l02_n02_3G_1-18_fastqc.html [2023-05-14 19:01:23,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-8_fastqc.html [2023-05-14 19:01:23,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-8_fastqc.html [2023-05-14 19:01:23,989] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-14_fastqc.html [2023-05-14 19:01:23,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_15G_1-14_fastqc.html [2023-05-14 19:01:24,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_14G_1-8_fastqc.html [2023-05-14 19:01:24,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l02_n02_14G_1-8_fastqc.html [2023-05-14 19:01:24,515] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 19:01:24,516] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 19:01:24,523] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-14 19:01:24,567] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 98 samples (table) [2023-05-14 19:01:24,577] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-14 19:01:24,580] multiqc [DEBUG ] No samples found: conpair [2023-05-14 19:01:24,582] multiqc [DEBUG ] No samples found: peddy [2023-05-14 19:01:24,585] multiqc [DEBUG ] No samples found: somalier [2023-05-14 19:01:24,588] multiqc [DEBUG ] No samples found: methylQA [2023-05-14 19:01:24,592] multiqc [DEBUG ] No samples found: mosdepth [2023-05-14 19:01:24,594] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-14 19:01:24,597] multiqc [DEBUG ] No samples found: qualimap [2023-05-14 19:01:24,599] multiqc [DEBUG ] No samples found: preseq [2023-05-14 19:01:24,602] multiqc [DEBUG ] No samples found: quast [2023-05-14 19:01:24,605] multiqc [DEBUG ] No samples found: qorts [2023-05-14 19:01:24,608] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-14 19:01:24,610] multiqc [DEBUG ] No samples found: rockhopper [2023-05-14 19:01:24,613] multiqc [DEBUG ] No samples found: rsem [2023-05-14 19:01:24,618] multiqc [DEBUG ] No samples found: rseqc [2023-05-14 19:01:24,620] multiqc [DEBUG ] No samples found: busco [2023-05-14 19:01:24,623] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-14 19:01:24,626] multiqc [DEBUG ] No samples found: disambiguate [2023-05-14 19:01:24,629] multiqc [DEBUG ] No samples found: supernova [2023-05-14 19:01:24,633] multiqc [DEBUG ] No samples found: deeptools [2023-05-14 19:01:24,636] multiqc [DEBUG ] No samples found: sargasso [2023-05-14 19:01:24,639] multiqc [DEBUG ] No samples found: verifybamid [2023-05-14 19:01:24,642] multiqc [DEBUG ] No samples found: mirtrace [2023-05-14 19:01:24,644] multiqc [DEBUG ] No samples found: happy [2023-05-14 19:01:24,647] multiqc [DEBUG ] No samples found: mirtop [2023-05-14 19:01:24,650] multiqc [DEBUG ] No samples found: homer [2023-05-14 19:01:24,653] multiqc [DEBUG ] No samples found: macs2 [2023-05-14 19:01:24,655] multiqc [DEBUG ] No samples found: theta2 [2023-05-14 19:01:24,658] multiqc [DEBUG ] No samples found: snpeff [2023-05-14 19:01:24,661] multiqc [DEBUG ] No samples found: gatk [2023-05-14 19:01:24,664] multiqc [DEBUG ] No samples found: htseq [2023-05-14 19:01:24,667] multiqc [DEBUG ] No samples found: bcftools [2023-05-14 19:01:24,670] multiqc [DEBUG ] No samples found: featureCounts [2023-05-14 19:01:24,673] multiqc [DEBUG ] No samples found: fgbio [2023-05-14 19:01:24,678] multiqc [DEBUG ] No samples found: dragen [2023-05-14 19:01:24,680] multiqc [DEBUG ] No samples found: dedup [2023-05-14 19:01:24,683] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-14 19:01:24,691] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-14 19:01:24,693] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-14 19:01:24,695] multiqc [DEBUG ] No samples found: picard [2023-05-14 19:01:24,698] multiqc [DEBUG ] No samples found: prokka [2023-05-14 19:01:24,701] multiqc [DEBUG ] No samples found: samblaster [2023-05-14 19:01:24,704] multiqc [DEBUG ] No samples found: samtools [2023-05-14 19:01:24,707] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-14 19:01:24,710] multiqc [DEBUG ] No samples found: bamtools [2023-05-14 19:01:24,712] multiqc [DEBUG ] No samples found: jellyfish [2023-05-14 19:01:24,716] multiqc [DEBUG ] No samples found: vcftools [2023-05-14 19:01:24,718] multiqc [DEBUG ] No samples found: longranger [2023-05-14 19:01:24,721] multiqc [DEBUG ] No samples found: stacks [2023-05-14 19:01:24,724] multiqc [DEBUG ] No samples found: varscan2 [2023-05-14 19:01:24,729] multiqc [DEBUG ] No samples found: bbmap [2023-05-14 19:01:24,732] multiqc [DEBUG ] No samples found: bismark [2023-05-14 19:01:24,735] multiqc [DEBUG ] No samples found: biscuit [2023-05-14 19:01:24,737] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-14 19:01:24,740] multiqc [DEBUG ] No samples found: hicup [2023-05-14 19:01:24,743] multiqc [DEBUG ] No samples found: hicpro [2023-05-14 19:01:24,745] multiqc [DEBUG ] No samples found: salmon [2023-05-14 19:01:24,748] multiqc [DEBUG ] No samples found: kallisto [2023-05-14 19:01:24,751] multiqc [DEBUG ] No samples found: slamdunk [2023-05-14 19:01:24,753] multiqc [DEBUG ] No samples found: star [2023-05-14 19:01:24,756] multiqc [DEBUG ] No samples found: hisat2 [2023-05-14 19:01:24,759] multiqc [DEBUG ] No samples found: tophat [2023-05-14 19:01:24,762] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-14 19:01:24,764] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-14 19:01:24,767] multiqc [DEBUG ] No samples found: snpsplit [2023-05-14 19:01:24,770] multiqc [DEBUG ] No samples found: kat [2023-05-14 19:01:24,772] multiqc [DEBUG ] No samples found: leehom [2023-05-14 19:01:24,775] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-14 19:01:24,778] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-14 19:01:24,780] multiqc [DEBUG ] No samples found: cutadapt [2023-05-14 19:01:24,783] multiqc [DEBUG ] No samples found: flexbar [2023-05-14 19:01:24,786] multiqc [DEBUG ] No samples found: kaiju [2023-05-14 19:01:24,788] multiqc [DEBUG ] No samples found: kraken [2023-05-14 19:01:24,791] multiqc [DEBUG ] No samples found: malt [2023-05-14 19:01:24,794] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-14 19:01:24,796] multiqc [DEBUG ] No samples found: sickle [2023-05-14 19:01:24,799] multiqc [DEBUG ] No samples found: skewer [2023-05-14 19:01:24,802] multiqc [DEBUG ] No samples found: sortmerna [2023-05-14 19:01:24,804] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-14 19:01:24,807] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-14 19:01:24,810] multiqc [DEBUG ] No samples found: afterqc [2023-05-14 19:01:24,812] multiqc [DEBUG ] No samples found: fastp [2023-05-14 19:02:10,058] multiqc.modules.fastqc.fastqc [INFO ] Found 196 reports [2023-05-14 19:02:31,771] multiqc [DEBUG ] No samples found: pycoqc [2023-05-14 19:02:31,774] multiqc [DEBUG ] No samples found: minionqc [2023-05-14 19:02:31,777] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-14 19:02:31,780] multiqc [DEBUG ] No samples found: clusterflow [2023-05-14 19:02:31,783] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-14 19:02:31,785] multiqc [DEBUG ] No samples found: interop [2023-05-14 19:02:31,788] multiqc [DEBUG ] No samples found: ivar [2023-05-14 19:02:31,791] multiqc [DEBUG ] No samples found: flash [2023-05-14 19:02:31,793] multiqc [DEBUG ] No samples found: seqyclean [2023-05-14 19:02:31,793] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-14 19:02:31,793] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 2 Demultiplexing Report'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 2 Demultiplexing Report'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 2 Demultiplexing Report'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 2 Demultiplexing Report'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 2 Demultiplexing Report'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 2 Demultiplexing Report'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-14 19:02:31,794] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-14 19:02:32,014] multiqc [INFO ] Compressing plot data [2023-05-14 19:02:32,082] multiqc [INFO ] Report : multiqc_report.html [2023-05-14 19:02:32,083] multiqc [INFO ] Data : multiqc_data [2023-05-14 19:02:32,083] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33331815/tmpzg_d7e9_/multiqc_data' to '/scratch/gencore/logs/html/H52YHDSX7/2/multiqc_data' [2023-05-14 19:02:32,188] multiqc [INFO ] MultiQC complete