[2022-02-18 09:00:24,043] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-02-18 09:00:24,043] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-02-18 09:00:24,043] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-18 09:00:24,043] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-02-18 09:00:24,044] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-02-18 09:00:24,044] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHMFFAFX3/merged [2022-02-18 09:00:24,455] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-02-18 09:00:24,455] multiqc [INFO ] This is MultiQC v1.9 [2022-02-18 09:00:24,455] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHMFFAFX3/merged [2022-02-18 09:00:24,455] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HHMFFAFX3/merged [2022-02-18 09:00:24,455] multiqc [INFO ] Template : default [2022-02-18 09:00:24,455] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-02-18 09:00:24,455] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HHMFFAFX3/merged [2022-02-18 09:00:24,455] 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 [2022-02-18 09:00:24,455] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15019539/tmp9oppd2jc [2022-02-18 09:00:24,543] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,546] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,546] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,546] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,546] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,546] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,546] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:24,546] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-18 09:00:28,614] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep3_new_fastqc.html [2022-02-18 09:00:28,616] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep3_new_fastqc.html [2022-02-18 09:00:28,660] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n01_undetermined_fastqc.html [2022-02-18 09:00:28,661] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n01_undetermined_fastqc.html [2022-02-18 09:00:28,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH4_rep1_new_fastqc.html [2022-02-18 09:00:28,706] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH4_rep1_new_fastqc.html [2022-02-18 09:00:28,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep2_reseq_fastqc.html [2022-02-18 09:00:28,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep2_reseq_fastqc.html [2022-02-18 09:00:28,794] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep3_new_fastqc.html [2022-02-18 09:00:28,796] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep3_new_fastqc.html [2022-02-18 09:00:28,840] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH4.5_rep2_new_fastqc.html [2022-02-18 09:00:28,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH4.5_rep2_new_fastqc.html [2022-02-18 09:00:28,884] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep3_reseq_fastqc.html [2022-02-18 09:00:28,886] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep3_reseq_fastqc.html [2022-02-18 09:00:28,930] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH4_rep1_new_fastqc.html [2022-02-18 09:00:28,932] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH4_rep1_new_fastqc.html [2022-02-18 09:00:28,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n02_undetermined_fastqc.html [2022-02-18 09:00:28,977] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n02_undetermined_fastqc.html [2022-02-18 09:00:29,019] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep3_reseq_fastqc.html [2022-02-18 09:00:29,021] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep3_reseq_fastqc.html [2022-02-18 09:00:29,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep2_reseq_fastqc.html [2022-02-18 09:00:29,066] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep2_reseq_fastqc.html [2022-02-18 09:00:29,112] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep1_reseq_fastqc.html [2022-02-18 09:00:29,114] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n02_Tvag_CHAR29_pH6.2_rep1_reseq_fastqc.html [2022-02-18 09:00:29,159] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH4.5_rep2_new_fastqc.html [2022-02-18 09:00:29,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH4.5_rep2_new_fastqc.html [2022-02-18 09:00:29,204] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep1_reseq_fastqc.html [2022-02-18 09:00:29,206] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMFFAFX3_n01_Tvag_CHAR29_pH6.2_rep1_reseq_fastqc.html [2022-02-18 09:00:29,503] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-18 09:00:29,504] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-18 09:00:29,510] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-02-18 09:00:29,514] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2022-02-18 09:00:29,524] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-02-18 09:00:29,527] multiqc [DEBUG ] No samples found: conpair [2022-02-18 09:00:29,530] multiqc [DEBUG ] No samples found: peddy [2022-02-18 09:00:29,533] multiqc [DEBUG ] No samples found: somalier [2022-02-18 09:00:29,536] multiqc [DEBUG ] No samples found: methylQA [2022-02-18 09:00:29,540] multiqc [DEBUG ] No samples found: mosdepth [2022-02-18 09:00:29,543] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-18 09:00:29,546] multiqc [DEBUG ] No samples found: qualimap [2022-02-18 09:00:29,549] multiqc [DEBUG ] No samples found: preseq [2022-02-18 09:00:29,552] multiqc [DEBUG ] No samples found: quast [2022-02-18 09:00:29,555] multiqc [DEBUG ] No samples found: qorts [2022-02-18 09:00:29,558] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-18 09:00:29,561] multiqc [DEBUG ] No samples found: rockhopper [2022-02-18 09:00:29,564] multiqc [DEBUG ] No samples found: rsem [2022-02-18 09:00:29,569] multiqc [DEBUG ] No samples found: rseqc [2022-02-18 09:00:29,572] multiqc [DEBUG ] No samples found: busco [2022-02-18 09:00:29,575] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-18 09:00:29,578] multiqc [DEBUG ] No samples found: disambiguate [2022-02-18 09:00:29,581] multiqc [DEBUG ] No samples found: supernova [2022-02-18 09:00:29,587] multiqc [DEBUG ] No samples found: deeptools [2022-02-18 09:00:29,590] multiqc [DEBUG ] No samples found: sargasso [2022-02-18 09:00:29,593] multiqc [DEBUG ] No samples found: verifybamid [2022-02-18 09:00:29,595] multiqc [DEBUG ] No samples found: mirtrace [2022-02-18 09:00:29,599] multiqc [DEBUG ] No samples found: happy [2022-02-18 09:00:29,601] multiqc [DEBUG ] No samples found: mirtop [2022-02-18 09:00:29,605] multiqc [DEBUG ] No samples found: homer [2022-02-18 09:00:29,608] multiqc [DEBUG ] No samples found: macs2 [2022-02-18 09:00:29,611] multiqc [DEBUG ] No samples found: theta2 [2022-02-18 09:00:29,614] multiqc [DEBUG ] No samples found: snpeff [2022-02-18 09:00:29,618] multiqc [DEBUG ] No samples found: gatk [2022-02-18 09:00:29,620] multiqc [DEBUG ] No samples found: htseq [2022-02-18 09:00:29,624] multiqc [DEBUG ] No samples found: bcftools [2022-02-18 09:00:29,627] multiqc [DEBUG ] No samples found: featureCounts [2022-02-18 09:00:29,630] multiqc [DEBUG ] No samples found: fgbio [2022-02-18 09:00:29,636] multiqc [DEBUG ] No samples found: dragen [2022-02-18 09:00:29,639] multiqc [DEBUG ] No samples found: dedup [2022-02-18 09:00:29,642] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-18 09:00:29,651] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-18 09:00:29,654] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-18 09:00:29,656] multiqc [DEBUG ] No samples found: picard [2022-02-18 09:00:29,659] multiqc [DEBUG ] No samples found: prokka [2022-02-18 09:00:29,662] multiqc [DEBUG ] No samples found: samblaster [2022-02-18 09:00:29,666] multiqc [DEBUG ] No samples found: samtools [2022-02-18 09:00:29,669] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-18 09:00:29,673] multiqc [DEBUG ] No samples found: bamtools [2022-02-18 09:00:29,676] multiqc [DEBUG ] No samples found: jellyfish [2022-02-18 09:00:29,680] multiqc [DEBUG ] No samples found: vcftools [2022-02-18 09:00:29,683] multiqc [DEBUG ] No samples found: longranger [2022-02-18 09:00:29,686] multiqc [DEBUG ] No samples found: stacks [2022-02-18 09:00:29,689] multiqc [DEBUG ] No samples found: varscan2 [2022-02-18 09:00:29,695] multiqc [DEBUG ] No samples found: bbmap [2022-02-18 09:00:29,698] multiqc [DEBUG ] No samples found: bismark [2022-02-18 09:00:29,701] multiqc [DEBUG ] No samples found: biscuit [2022-02-18 09:00:29,704] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-18 09:00:29,707] multiqc [DEBUG ] No samples found: hicup [2022-02-18 09:00:29,710] multiqc [DEBUG ] No samples found: hicpro [2022-02-18 09:00:29,713] multiqc [DEBUG ] No samples found: salmon [2022-02-18 09:00:29,716] multiqc [DEBUG ] No samples found: kallisto [2022-02-18 09:00:29,719] multiqc [DEBUG ] No samples found: slamdunk [2022-02-18 09:00:29,722] multiqc [DEBUG ] No samples found: star [2022-02-18 09:00:29,725] multiqc [DEBUG ] No samples found: hisat2 [2022-02-18 09:00:29,728] multiqc [DEBUG ] No samples found: tophat [2022-02-18 09:00:29,732] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-18 09:00:29,735] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-18 09:00:29,738] multiqc [DEBUG ] No samples found: snpsplit [2022-02-18 09:00:29,741] multiqc [DEBUG ] No samples found: kat [2022-02-18 09:00:29,744] multiqc [DEBUG ] No samples found: leehom [2022-02-18 09:00:29,747] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-18 09:00:29,750] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-18 09:00:29,753] multiqc [DEBUG ] No samples found: cutadapt [2022-02-18 09:00:29,756] multiqc [DEBUG ] No samples found: flexbar [2022-02-18 09:00:29,758] multiqc [DEBUG ] No samples found: kaiju [2022-02-18 09:00:29,761] multiqc [DEBUG ] No samples found: kraken [2022-02-18 09:00:29,764] multiqc [DEBUG ] No samples found: malt [2022-02-18 09:00:29,767] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-18 09:00:29,770] multiqc [DEBUG ] No samples found: sickle [2022-02-18 09:00:29,773] multiqc [DEBUG ] No samples found: skewer [2022-02-18 09:00:29,776] multiqc [DEBUG ] No samples found: sortmerna [2022-02-18 09:00:29,779] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-18 09:00:29,782] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-18 09:00:29,785] multiqc [DEBUG ] No samples found: afterqc [2022-02-18 09:00:29,788] multiqc [DEBUG ] No samples found: fastp [2022-02-18 09:00:30,271] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2022-02-18 09:00:30,574] multiqc [DEBUG ] No samples found: pycoqc [2022-02-18 09:00:30,577] multiqc [DEBUG ] No samples found: minionqc [2022-02-18 09:00:30,580] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-02-18 09:00:30,583] multiqc [DEBUG ] No samples found: clusterflow [2022-02-18 09:00:30,586] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-18 09:00:30,589] multiqc [DEBUG ] No samples found: interop [2022-02-18 09:00:30,592] multiqc [DEBUG ] No samples found: ivar [2022-02-18 09:00:30,595] multiqc [DEBUG ] No samples found: flash [2022-02-18 09:00:30,598] multiqc [DEBUG ] No samples found: seqyclean [2022-02-18 09:00:30,598] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-02-18 09:00:30,598] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-02-18 09:00:30,598] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-02-18 09:00:30,598] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-02-18 09:00:30,615] multiqc [INFO ] Compressing plot data [2022-02-18 09:00:30,910] multiqc [INFO ] Report : multiqc_report.html [2022-02-18 09:00:30,910] multiqc [INFO ] Data : multiqc_data [2022-02-18 09:00:30,910] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15019539/tmp9oppd2jc/multiqc_data' to '/scratch/gencore/logs/html/HHMFFAFX3/merged/multiqc_data' [2022-02-18 09:00:31,005] multiqc [INFO ] MultiQC complete