[2022-05-28 22:05:17,433] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-28 22:05:17,433] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-28 22:05:17,433] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-28 22:05:17,434] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-28 22:05:17,434] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-28 22:05:17,434] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTCW5BGXL/merged [2022-05-28 22:05:18,072] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-28 22:05:18,072] multiqc [INFO ] This is MultiQC v1.9 [2022-05-28 22:05:18,072] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTCW5BGXL/merged [2022-05-28 22:05:18,072] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTCW5BGXL/merged [2022-05-28 22:05:18,072] multiqc [INFO ] Template : default [2022-05-28 22:05:18,072] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-28 22:05:18,072] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTCW5BGXL/merged [2022-05-28 22:05:18,072] 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 [2022-05-28 22:05:18,072] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20248480/tmpsbv6heww [2022-05-28 22:05:18,163] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n01_AZUCENA-2__fastqc.html [2022-05-28 22:05:18,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n01_AZUCENA-2__fastqc.html [2022-05-28 22:05:18,207] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:18,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:18,208] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:18,208] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:18,208] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:18,208] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:18,208] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:18,292] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-28 22:05:21,960] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n02_AZUCENA-1__fastqc.html [2022-05-28 22:05:21,962] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n02_AZUCENA-1__fastqc.html [2022-05-28 22:05:22,002] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n02_undetermined_fastqc.html [2022-05-28 22:05:22,004] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n02_undetermined_fastqc.html [2022-05-28 22:05:22,043] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n01_undetermined_fastqc.html [2022-05-28 22:05:22,044] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n01_undetermined_fastqc.html [2022-05-28 22:05:22,084] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n02_IR64-2__fastqc.html [2022-05-28 22:05:22,086] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n02_IR64-2__fastqc.html [2022-05-28 22:05:22,126] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n01_IR64-2__fastqc.html [2022-05-28 22:05:22,128] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n01_IR64-2__fastqc.html [2022-05-28 22:05:22,168] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n01_AZUCENA-1__fastqc.html [2022-05-28 22:05:22,170] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n01_AZUCENA-1__fastqc.html [2022-05-28 22:05:22,209] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCW5BGXL_n02_AZUCENA-2__fastqc.html [2022-05-28 22:05:22,211] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCW5BGXL_n02_AZUCENA-2__fastqc.html [2022-05-28 22:05:22,535] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-28 22:05:22,536] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-28 22:05:22,542] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-28 22:05:22,552] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-28 22:05:22,554] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 4 samples (table) [2022-05-28 22:05:22,557] multiqc [DEBUG ] No samples found: conpair [2022-05-28 22:05:22,560] multiqc [DEBUG ] No samples found: peddy [2022-05-28 22:05:22,564] multiqc [DEBUG ] No samples found: somalier [2022-05-28 22:05:22,567] multiqc [DEBUG ] No samples found: methylQA [2022-05-28 22:05:22,571] multiqc [DEBUG ] No samples found: mosdepth [2022-05-28 22:05:22,574] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-28 22:05:22,576] multiqc [DEBUG ] No samples found: qualimap [2022-05-28 22:05:22,579] multiqc [DEBUG ] No samples found: preseq [2022-05-28 22:05:22,583] multiqc [DEBUG ] No samples found: quast [2022-05-28 22:05:22,586] multiqc [DEBUG ] No samples found: qorts [2022-05-28 22:05:22,589] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-28 22:05:22,592] multiqc [DEBUG ] No samples found: rockhopper [2022-05-28 22:05:22,595] multiqc [DEBUG ] No samples found: rsem [2022-05-28 22:05:22,600] multiqc [DEBUG ] No samples found: rseqc [2022-05-28 22:05:22,603] multiqc [DEBUG ] No samples found: busco [2022-05-28 22:05:22,606] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-28 22:05:22,609] multiqc [DEBUG ] No samples found: disambiguate [2022-05-28 22:05:22,612] multiqc [DEBUG ] No samples found: supernova [2022-05-28 22:05:22,618] multiqc [DEBUG ] No samples found: deeptools [2022-05-28 22:05:22,621] multiqc [DEBUG ] No samples found: sargasso [2022-05-28 22:05:22,624] multiqc [DEBUG ] No samples found: verifybamid [2022-05-28 22:05:22,627] multiqc [DEBUG ] No samples found: mirtrace [2022-05-28 22:05:22,630] multiqc [DEBUG ] No samples found: happy [2022-05-28 22:05:22,633] multiqc [DEBUG ] No samples found: mirtop [2022-05-28 22:05:22,637] multiqc [DEBUG ] No samples found: homer [2022-05-28 22:05:22,640] multiqc [DEBUG ] No samples found: macs2 [2022-05-28 22:05:22,643] multiqc [DEBUG ] No samples found: theta2 [2022-05-28 22:05:22,646] multiqc [DEBUG ] No samples found: snpeff [2022-05-28 22:05:22,650] multiqc [DEBUG ] No samples found: gatk [2022-05-28 22:05:22,653] multiqc [DEBUG ] No samples found: htseq [2022-05-28 22:05:22,656] multiqc [DEBUG ] No samples found: bcftools [2022-05-28 22:05:22,659] multiqc [DEBUG ] No samples found: featureCounts [2022-05-28 22:05:22,662] multiqc [DEBUG ] No samples found: fgbio [2022-05-28 22:05:22,669] multiqc [DEBUG ] No samples found: dragen [2022-05-28 22:05:22,672] multiqc [DEBUG ] No samples found: dedup [2022-05-28 22:05:22,675] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-28 22:05:22,684] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-28 22:05:22,687] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-28 22:05:22,689] multiqc [DEBUG ] No samples found: picard [2022-05-28 22:05:22,692] multiqc [DEBUG ] No samples found: prokka [2022-05-28 22:05:22,695] multiqc [DEBUG ] No samples found: samblaster [2022-05-28 22:05:22,700] multiqc [DEBUG ] No samples found: samtools [2022-05-28 22:05:22,703] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-28 22:05:22,706] multiqc [DEBUG ] No samples found: bamtools [2022-05-28 22:05:22,709] multiqc [DEBUG ] No samples found: jellyfish [2022-05-28 22:05:22,713] multiqc [DEBUG ] No samples found: vcftools [2022-05-28 22:05:22,716] multiqc [DEBUG ] No samples found: longranger [2022-05-28 22:05:22,719] multiqc [DEBUG ] No samples found: stacks [2022-05-28 22:05:22,722] multiqc [DEBUG ] No samples found: varscan2 [2022-05-28 22:05:22,728] multiqc [DEBUG ] No samples found: bbmap [2022-05-28 22:05:22,732] multiqc [DEBUG ] No samples found: bismark [2022-05-28 22:05:22,735] multiqc [DEBUG ] No samples found: biscuit [2022-05-28 22:05:22,738] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-28 22:05:22,741] multiqc [DEBUG ] No samples found: hicup [2022-05-28 22:05:22,744] multiqc [DEBUG ] No samples found: hicpro [2022-05-28 22:05:22,747] multiqc [DEBUG ] No samples found: salmon [2022-05-28 22:05:22,750] multiqc [DEBUG ] No samples found: kallisto [2022-05-28 22:05:22,753] multiqc [DEBUG ] No samples found: slamdunk [2022-05-28 22:05:22,756] multiqc [DEBUG ] No samples found: star [2022-05-28 22:05:22,759] multiqc [DEBUG ] No samples found: hisat2 [2022-05-28 22:05:22,762] multiqc [DEBUG ] No samples found: tophat [2022-05-28 22:05:22,765] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-28 22:05:22,768] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-28 22:05:22,771] multiqc [DEBUG ] No samples found: snpsplit [2022-05-28 22:05:22,774] multiqc [DEBUG ] No samples found: kat [2022-05-28 22:05:22,777] multiqc [DEBUG ] No samples found: leehom [2022-05-28 22:05:22,780] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-28 22:05:22,783] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-28 22:05:22,786] multiqc [DEBUG ] No samples found: cutadapt [2022-05-28 22:05:22,789] multiqc [DEBUG ] No samples found: flexbar [2022-05-28 22:05:22,792] multiqc [DEBUG ] No samples found: kaiju [2022-05-28 22:05:22,795] multiqc [DEBUG ] No samples found: kraken [2022-05-28 22:05:22,798] multiqc [DEBUG ] No samples found: malt [2022-05-28 22:05:22,801] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-28 22:05:22,804] multiqc [DEBUG ] No samples found: sickle [2022-05-28 22:05:22,807] multiqc [DEBUG ] No samples found: skewer [2022-05-28 22:05:22,810] multiqc [DEBUG ] No samples found: sortmerna [2022-05-28 22:05:22,813] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-28 22:05:22,816] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-28 22:05:22,819] multiqc [DEBUG ] No samples found: afterqc [2022-05-28 22:05:22,822] multiqc [DEBUG ] No samples found: fastp [2022-05-28 22:05:23,305] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-05-28 22:05:23,388] multiqc [DEBUG ] No samples found: pycoqc [2022-05-28 22:05:23,391] multiqc [DEBUG ] No samples found: minionqc [2022-05-28 22:05:23,394] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-28 22:05:23,397] multiqc [DEBUG ] No samples found: clusterflow [2022-05-28 22:05:23,400] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-28 22:05:23,403] multiqc [DEBUG ] No samples found: interop [2022-05-28 22:05:23,407] multiqc [DEBUG ] No samples found: ivar [2022-05-28 22:05:23,410] multiqc [DEBUG ] No samples found: flash [2022-05-28 22:05:23,412] multiqc [DEBUG ] No samples found: seqyclean [2022-05-28 22:05:23,413] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-05-28 22:05:23,413] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-05-28 22:05:23,413] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-28 22:05:23,413] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-28 22:05:23,423] multiqc [INFO ] Compressing plot data [2022-05-28 22:05:23,567] multiqc [INFO ] Report : multiqc_report.html [2022-05-28 22:05:23,567] multiqc [INFO ] Data : multiqc_data [2022-05-28 22:05:23,567] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20248480/tmpsbv6heww/multiqc_data' to '/scratch/gencore/logs/html/HTCW5BGXL/merged/multiqc_data' [2022-05-28 22:05:23,665] multiqc [INFO ] MultiQC complete