[2022-11-03 09:36:36,145] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-03 09:36:36,145] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-03 09:36:36,145] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-03 09:36:36,146] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-03 09:36:36,146] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-03 09:36:36,146] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVT2NAFX3/merged [2022-11-03 09:36:36,554] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-03 09:36:36,555] multiqc [INFO ] This is MultiQC v1.9 [2022-11-03 09:36:36,555] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVT2NAFX3/merged [2022-11-03 09:36:36,555] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVT2NAFX3/merged [2022-11-03 09:36:36,555] multiqc [INFO ] Template : default [2022-11-03 09:36:36,555] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-03 09:36:36,555] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVT2NAFX3/merged [2022-11-03 09:36:36,556] 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 [2022-11-03 09:36:36,557] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26610182/tmporh4xerc [2022-11-03 09:36:36,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n02_undetermined_fastqc.html [2022-11-03 09:36:36,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n02_undetermined_fastqc.html [2022-11-03 09:36:36,725] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n02_y_g2_fastqc.html [2022-11-03 09:36:36,726] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n02_y_g2_fastqc.html [2022-11-03 09:36:36,815] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,818] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,818] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,818] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,819] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,819] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,819] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:36,819] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-03 09:36:41,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n01_undetermined_fastqc.html [2022-11-03 09:36:41,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n01_undetermined_fastqc.html [2022-11-03 09:36:41,889] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n01_f_3-2_fastqc.html [2022-11-03 09:36:41,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n01_f_3-2_fastqc.html [2022-11-03 09:36:41,932] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n01_y_g2_fastqc.html [2022-11-03 09:36:41,933] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n01_y_g2_fastqc.html [2022-11-03 09:36:41,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n01_f_mtd_fastqc.html [2022-11-03 09:36:41,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n01_f_mtd_fastqc.html [2022-11-03 09:36:42,013] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n02_f_head_fastqc.html [2022-11-03 09:36:42,015] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n02_f_head_fastqc.html [2022-11-03 09:36:42,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n01_f_head_fastqc.html [2022-11-03 09:36:42,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n01_f_head_fastqc.html [2022-11-03 09:36:42,098] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n02_f_mtd_fastqc.html [2022-11-03 09:36:42,099] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n02_f_mtd_fastqc.html [2022-11-03 09:36:42,143] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n02_y_g1_fastqc.html [2022-11-03 09:36:42,144] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n02_y_g1_fastqc.html [2022-11-03 09:36:42,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n02_y_s_fastqc.html [2022-11-03 09:36:42,186] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n02_y_s_fastqc.html [2022-11-03 09:36:42,226] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n01_y_s_fastqc.html [2022-11-03 09:36:42,228] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n01_y_s_fastqc.html [2022-11-03 09:36:42,266] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n01_y_g1_fastqc.html [2022-11-03 09:36:42,267] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n01_y_g1_fastqc.html [2022-11-03 09:36:42,305] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVT2NAFX3_n02_f_3-2_fastqc.html [2022-11-03 09:36:42,307] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVT2NAFX3_n02_f_3-2_fastqc.html [2022-11-03 09:36:43,029] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-03 09:36:43,031] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-03 09:36:43,043] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2022-11-03 09:36:43,051] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-03 09:36:43,053] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-03 09:36:43,058] multiqc [DEBUG ] No samples found: conpair [2022-11-03 09:36:43,064] multiqc [DEBUG ] No samples found: peddy [2022-11-03 09:36:43,070] multiqc [DEBUG ] No samples found: somalier [2022-11-03 09:36:43,075] multiqc [DEBUG ] No samples found: methylQA [2022-11-03 09:36:43,085] multiqc [DEBUG ] No samples found: mosdepth [2022-11-03 09:36:43,091] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-03 09:36:43,094] multiqc [DEBUG ] No samples found: qualimap [2022-11-03 09:36:43,100] multiqc [DEBUG ] No samples found: preseq [2022-11-03 09:36:43,109] multiqc [DEBUG ] No samples found: quast [2022-11-03 09:36:43,116] multiqc [DEBUG ] No samples found: qorts [2022-11-03 09:36:43,122] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-03 09:36:43,127] multiqc [DEBUG ] No samples found: rockhopper [2022-11-03 09:36:43,132] multiqc [DEBUG ] No samples found: rsem [2022-11-03 09:36:43,146] multiqc [DEBUG ] No samples found: rseqc [2022-11-03 09:36:43,151] multiqc [DEBUG ] No samples found: busco [2022-11-03 09:36:43,161] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-03 09:36:43,167] multiqc [DEBUG ] No samples found: disambiguate [2022-11-03 09:36:43,174] multiqc [DEBUG ] No samples found: supernova [2022-11-03 09:36:43,190] multiqc [DEBUG ] No samples found: deeptools [2022-11-03 09:36:43,196] multiqc [DEBUG ] No samples found: sargasso [2022-11-03 09:36:43,202] multiqc [DEBUG ] No samples found: verifybamid [2022-11-03 09:36:43,207] multiqc [DEBUG ] No samples found: mirtrace [2022-11-03 09:36:43,213] multiqc [DEBUG ] No samples found: happy [2022-11-03 09:36:43,221] multiqc [DEBUG ] No samples found: mirtop [2022-11-03 09:36:43,229] multiqc [DEBUG ] No samples found: homer [2022-11-03 09:36:43,235] multiqc [DEBUG ] No samples found: macs2 [2022-11-03 09:36:43,240] multiqc [DEBUG ] No samples found: theta2 [2022-11-03 09:36:43,245] multiqc [DEBUG ] No samples found: snpeff [2022-11-03 09:36:43,253] multiqc [DEBUG ] No samples found: gatk [2022-11-03 09:36:43,258] multiqc [DEBUG ] No samples found: htseq [2022-11-03 09:36:43,264] multiqc [DEBUG ] No samples found: bcftools [2022-11-03 09:36:43,269] multiqc [DEBUG ] No samples found: featureCounts [2022-11-03 09:36:43,276] multiqc [DEBUG ] No samples found: fgbio [2022-11-03 09:36:43,291] multiqc [DEBUG ] No samples found: dragen [2022-11-03 09:36:43,297] multiqc [DEBUG ] No samples found: dedup [2022-11-03 09:36:43,302] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-03 09:36:43,335] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-03 09:36:43,341] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-03 09:36:43,344] multiqc [DEBUG ] No samples found: picard [2022-11-03 09:36:43,349] multiqc [DEBUG ] No samples found: prokka [2022-11-03 09:36:43,353] multiqc [DEBUG ] No samples found: samblaster [2022-11-03 09:36:43,363] multiqc [DEBUG ] No samples found: samtools [2022-11-03 09:36:43,368] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-03 09:36:43,374] multiqc [DEBUG ] No samples found: bamtools [2022-11-03 09:36:43,378] multiqc [DEBUG ] No samples found: jellyfish [2022-11-03 09:36:43,386] multiqc [DEBUG ] No samples found: vcftools [2022-11-03 09:36:43,391] multiqc [DEBUG ] No samples found: longranger [2022-11-03 09:36:43,396] multiqc [DEBUG ] No samples found: stacks [2022-11-03 09:36:43,402] multiqc [DEBUG ] No samples found: varscan2 [2022-11-03 09:36:43,418] multiqc [DEBUG ] No samples found: bbmap [2022-11-03 09:36:43,423] multiqc [DEBUG ] No samples found: bismark [2022-11-03 09:36:43,428] multiqc [DEBUG ] No samples found: biscuit [2022-11-03 09:36:43,434] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-03 09:36:43,439] multiqc [DEBUG ] No samples found: hicup [2022-11-03 09:36:43,445] multiqc [DEBUG ] No samples found: hicpro [2022-11-03 09:36:43,450] multiqc [DEBUG ] No samples found: salmon [2022-11-03 09:36:43,455] multiqc [DEBUG ] No samples found: kallisto [2022-11-03 09:36:43,461] multiqc [DEBUG ] No samples found: slamdunk [2022-11-03 09:36:43,466] multiqc [DEBUG ] No samples found: star [2022-11-03 09:36:43,471] multiqc [DEBUG ] No samples found: hisat2 [2022-11-03 09:36:43,476] multiqc [DEBUG ] No samples found: tophat [2022-11-03 09:36:43,481] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-03 09:36:43,486] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-03 09:36:43,491] multiqc [DEBUG ] No samples found: snpsplit [2022-11-03 09:36:43,495] multiqc [DEBUG ] No samples found: kat [2022-11-03 09:36:43,500] multiqc [DEBUG ] No samples found: leehom [2022-11-03 09:36:43,505] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-03 09:36:43,510] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-03 09:36:43,515] multiqc [DEBUG ] No samples found: cutadapt [2022-11-03 09:36:43,520] multiqc [DEBUG ] No samples found: flexbar [2022-11-03 09:36:43,525] multiqc [DEBUG ] No samples found: kaiju [2022-11-03 09:36:43,530] multiqc [DEBUG ] No samples found: kraken [2022-11-03 09:36:43,535] multiqc [DEBUG ] No samples found: malt [2022-11-03 09:36:43,540] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-03 09:36:43,545] multiqc [DEBUG ] No samples found: sickle [2022-11-03 09:36:43,551] multiqc [DEBUG ] No samples found: skewer [2022-11-03 09:36:43,556] multiqc [DEBUG ] No samples found: sortmerna [2022-11-03 09:36:43,561] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-03 09:36:43,566] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-03 09:36:43,577] multiqc [DEBUG ] No samples found: afterqc [2022-11-03 09:36:43,584] multiqc [DEBUG ] No samples found: fastp [2022-11-03 09:36:43,967] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2022-11-03 09:36:44,242] multiqc [DEBUG ] No samples found: pycoqc [2022-11-03 09:36:44,248] multiqc [DEBUG ] No samples found: minionqc [2022-11-03 09:36:44,254] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-03 09:36:44,259] multiqc [DEBUG ] No samples found: clusterflow [2022-11-03 09:36:44,264] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-03 09:36:44,271] multiqc [DEBUG ] No samples found: interop [2022-11-03 09:36:44,277] multiqc [DEBUG ] No samples found: ivar [2022-11-03 09:36:44,286] multiqc [DEBUG ] No samples found: flash [2022-11-03 09:36:44,292] multiqc [DEBUG ] No samples found: seqyclean [2022-11-03 09:36:44,292] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-03 09:36:44,292] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-03 09:36:44,292] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-03 09:36:44,292] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-03 09:36:44,308] multiqc [INFO ] Compressing plot data [2022-11-03 09:36:44,553] multiqc [INFO ] Report : multiqc_report.html [2022-11-03 09:36:44,554] multiqc [INFO ] Data : multiqc_data [2022-11-03 09:36:44,554] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26610182/tmporh4xerc/multiqc_data' to '/scratch/gencore/logs/html/HVT2NAFX3/merged/multiqc_data' [2022-11-03 09:36:44,687] multiqc [INFO ] MultiQC complete