[2023-05-14 23:43:07,745] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-14 23:43:07,745] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-14 23:43:07,745] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-14 23:43:07,748] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-14 23:43:07,748] 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 23:43:07,748] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/4 [2023-05-14 23:43:07,939] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-14 23:43:07,939] multiqc [INFO ] This is MultiQC v1.9 [2023-05-14 23:43:07,939] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H52YHDSX7/4 [2023-05-14 23:43:07,939] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H52YHDSX7/4 [2023-05-14 23:43:07,939] multiqc [INFO ] Template : default [2023-05-14 23:43:07,939] 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 23:43:07,939] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H52YHDSX7/4 [2023-05-14 23:43:07,940] 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 23:43:07,940] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33331815/tmpk8c5h8fw [2023-05-14 23:43:08,062] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n02_7R_1-6_fastqc.html [2023-05-14 23:43:08,065] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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H52YHDSX7_l04_n02_2R_1-7_fastqc.html [2023-05-14 23:43:21,933] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_2R-1-17-re_fastqc.html [2023-05-14 23:43:21,935] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_2R-1-17-re_fastqc.html [2023-05-14 23:43:22,006] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n02_8G_1-5_fastqc.html [2023-05-14 23:43:22,008] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n02_8G_1-5_fastqc.html [2023-05-14 23:43:22,068] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_5R_1-7_fastqc.html [2023-05-14 23:43:22,070] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_5R_1-7_fastqc.html [2023-05-14 23:43:22,404] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 23:43:22,404] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-14 23:43:22,455] multiqc.modules.custom_content.custom_content [INFO ] demux_report-4: Found 98 samples (table) [2023-05-14 23:43:22,465] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-14 23:43:22,466] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-14 23:43:22,469] multiqc [DEBUG ] No samples found: conpair [2023-05-14 23:43:22,472] multiqc [DEBUG ] No samples found: peddy [2023-05-14 23:43:22,475] multiqc [DEBUG ] No samples found: somalier [2023-05-14 23:43:22,478] multiqc [DEBUG ] No samples found: methylQA [2023-05-14 23:43:22,482] multiqc [DEBUG ] No samples found: mosdepth [2023-05-14 23:43:22,485] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-14 23:43:22,487] multiqc [DEBUG ] No samples found: qualimap [2023-05-14 23:43:22,490] multiqc [DEBUG ] No samples found: preseq [2023-05-14 23:43:22,493] multiqc [DEBUG ] No samples found: quast [2023-05-14 23:43:22,496] multiqc [DEBUG ] No samples found: qorts [2023-05-14 23:43:22,499] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-14 23:43:22,502] multiqc [DEBUG ] No samples found: rockhopper [2023-05-14 23:43:22,504] multiqc [DEBUG ] No samples found: rsem [2023-05-14 23:43:22,509] multiqc [DEBUG ] No samples found: rseqc [2023-05-14 23:43:22,512] multiqc [DEBUG ] No samples found: busco [2023-05-14 23:43:22,515] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-14 23:43:22,518] multiqc [DEBUG ] No samples found: disambiguate [2023-05-14 23:43:22,520] multiqc [DEBUG ] No samples found: supernova [2023-05-14 23:43:22,526] multiqc [DEBUG ] No samples found: deeptools [2023-05-14 23:43:22,529] multiqc [DEBUG ] No samples found: sargasso [2023-05-14 23:43:22,532] multiqc [DEBUG ] No samples found: verifybamid [2023-05-14 23:43:22,534] multiqc [DEBUG ] No samples found: mirtrace [2023-05-14 23:43:22,537] multiqc [DEBUG ] No samples found: happy [2023-05-14 23:43:22,540] multiqc [DEBUG ] No samples found: mirtop [2023-05-14 23:43:22,543] multiqc [DEBUG ] No samples found: homer [2023-05-14 23:43:22,546] multiqc [DEBUG ] No samples found: macs2 [2023-05-14 23:43:22,549] multiqc [DEBUG ] No samples found: theta2 [2023-05-14 23:43:22,552] multiqc [DEBUG ] No samples found: snpeff [2023-05-14 23:43:22,555] multiqc [DEBUG ] No samples found: gatk [2023-05-14 23:43:22,558] multiqc [DEBUG ] No samples found: htseq [2023-05-14 23:43:22,561] multiqc [DEBUG ] No samples found: bcftools [2023-05-14 23:43:22,564] multiqc [DEBUG ] No samples found: featureCounts [2023-05-14 23:43:22,567] multiqc [DEBUG ] No samples found: fgbio [2023-05-14 23:43:22,572] multiqc [DEBUG ] No samples found: dragen [2023-05-14 23:43:22,575] multiqc [DEBUG ] No samples found: dedup [2023-05-14 23:43:22,578] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-14 23:43:22,586] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-14 23:43:22,589] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-14 23:43:22,591] multiqc [DEBUG ] No samples found: picard [2023-05-14 23:43:22,594] multiqc [DEBUG ] No samples found: prokka [2023-05-14 23:43:22,597] multiqc [DEBUG ] No samples found: samblaster [2023-05-14 23:43:22,601] multiqc [DEBUG ] No samples found: samtools [2023-05-14 23:43:22,604] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-14 23:43:22,606] multiqc [DEBUG ] No samples found: bamtools [2023-05-14 23:43:22,609] multiqc [DEBUG ] No samples found: jellyfish [2023-05-14 23:43:22,613] multiqc [DEBUG ] No samples found: vcftools [2023-05-14 23:43:22,616] multiqc [DEBUG ] No samples found: longranger [2023-05-14 23:43:22,618] multiqc [DEBUG ] No samples found: stacks [2023-05-14 23:43:22,621] multiqc [DEBUG ] No samples found: varscan2 [2023-05-14 23:43:22,627] multiqc [DEBUG ] No samples found: bbmap [2023-05-14 23:43:22,630] multiqc [DEBUG ] No samples found: bismark [2023-05-14 23:43:22,633] multiqc [DEBUG ] No samples found: biscuit [2023-05-14 23:43:22,636] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-14 23:43:22,638] multiqc [DEBUG ] No samples found: hicup [2023-05-14 23:43:22,641] multiqc [DEBUG ] No samples found: hicpro [2023-05-14 23:43:22,644] multiqc [DEBUG ] No samples found: salmon [2023-05-14 23:43:22,647] multiqc [DEBUG ] No samples found: kallisto [2023-05-14 23:43:22,650] multiqc [DEBUG ] No samples found: slamdunk [2023-05-14 23:43:22,653] multiqc [DEBUG ] No samples found: star [2023-05-14 23:43:22,656] multiqc [DEBUG ] No samples found: hisat2 [2023-05-14 23:43:22,658] multiqc [DEBUG ] No samples found: tophat [2023-05-14 23:43:22,661] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-14 23:43:22,664] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-14 23:43:22,667] multiqc [DEBUG ] No samples found: snpsplit [2023-05-14 23:43:22,669] multiqc [DEBUG ] No samples found: kat [2023-05-14 23:43:22,672] multiqc [DEBUG ] No samples found: leehom [2023-05-14 23:43:22,675] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-14 23:43:22,678] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-14 23:43:22,680] multiqc [DEBUG ] No samples found: cutadapt [2023-05-14 23:43:22,683] multiqc [DEBUG ] No samples found: flexbar [2023-05-14 23:43:22,686] multiqc [DEBUG ] No samples found: kaiju [2023-05-14 23:43:22,689] multiqc [DEBUG ] No samples found: kraken [2023-05-14 23:43:22,691] multiqc [DEBUG ] No samples found: malt [2023-05-14 23:43:22,694] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-14 23:43:22,697] multiqc [DEBUG ] No samples found: sickle [2023-05-14 23:43:22,700] multiqc [DEBUG ] No samples found: skewer [2023-05-14 23:43:22,703] multiqc [DEBUG ] No samples found: sortmerna [2023-05-14 23:43:22,705] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-14 23:43:22,708] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-14 23:43:22,711] multiqc [DEBUG ] No samples found: afterqc [2023-05-14 23:43:22,714] multiqc [DEBUG ] No samples found: fastp [2023-05-14 23:44:06,592] multiqc.modules.fastqc.fastqc [INFO ] Found 196 reports [2023-05-14 23:44:29,162] multiqc [DEBUG ] No samples found: pycoqc [2023-05-14 23:44:29,165] multiqc [DEBUG ] No samples found: minionqc [2023-05-14 23:44:29,168] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-14 23:44:29,171] multiqc [DEBUG ] No samples found: clusterflow [2023-05-14 23:44:29,174] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-14 23:44:29,177] multiqc [DEBUG ] No samples found: interop [2023-05-14 23:44:29,180] multiqc [DEBUG ] No samples found: ivar [2023-05-14 23:44:29,182] multiqc [DEBUG ] No samples found: flash [2023-05-14 23:44:29,185] multiqc [DEBUG ] No samples found: seqyclean [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 23:44:29,185] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 4 Demultiplexing Report'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 4 Demultiplexing Report'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 4 Demultiplexing Report'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 4 Demultiplexing Report'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 4 Demultiplexing Report'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 4 Demultiplexing Report'. [2023-05-14 23:44:29,186] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 4 Demultiplexing Report'. [2023-05-14 23:44:29,408] multiqc [INFO ] Compressing plot data [2023-05-14 23:44:29,478] multiqc [INFO ] Report : multiqc_report.html [2023-05-14 23:44:29,479] multiqc [INFO ] Data : multiqc_data [2023-05-14 23:44:29,479] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33331815/tmpk8c5h8fw/multiqc_data' to '/scratch/gencore/logs/html/H52YHDSX7/4/multiqc_data' [2023-05-14 23:44:29,587] multiqc [INFO ] MultiQC complete