[2021-10-02 10:06:54,835] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-02 10:06:54,835] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-02 10:06:54,835] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-02 10:06:54,836] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-02 10:06:54,836] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-02 10:06:54,836] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-G9BKV/1 [2021-10-02 10:06:56,578] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-02 10:06:56,578] multiqc [INFO ] This is MultiQC v1.9 [2021-10-02 10:06:56,578] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-G9BKV/1 [2021-10-02 10:06:56,578] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-G9BKV/1 [2021-10-02 10:06:56,578] multiqc [INFO ] Template : default [2021-10-02 10:06:56,578] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-02 10:06:56,578] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-G9BKV/1 [2021-10-02 10:06:56,578] 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 [2021-10-02 10:06:56,578] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10506517/tmpas7gxnni [2021-10-02 10:06:56,688] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_undetermined_fastqc.html [2021-10-02 10:06:56,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_undetermined_fastqc.html [2021-10-02 10:06:56,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-2_fastqc.html [2021-10-02 10:06:56,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-2_fastqc.html [2021-10-02 10:06:56,792] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-02 10:06:56,793] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-02 10:06:56,793] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-02 10:06:56,793] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-02 10:06:56,793] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-02 10:06:56,793] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-02 10:06:56,793] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-02 10:06:57,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-6_fastqc.html [2021-10-02 10:06:57,630] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-6_fastqc.html [2021-10-02 10:06:57,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-4_fastqc.html [2021-10-02 10:06:57,689] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-4_fastqc.html [2021-10-02 10:06:57,752] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-1_fastqc.html [2021-10-02 10:06:57,754] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-1_fastqc.html [2021-10-02 10:06:57,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-3_fastqc.html [2021-10-02 10:06:57,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-3_fastqc.html [2021-10-02 10:06:57,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-1_fastqc.html [2021-10-02 10:06:57,868] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-1_fastqc.html [2021-10-02 10:06:57,932] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_undetermined_fastqc.html [2021-10-02 10:06:57,933] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_undetermined_fastqc.html [2021-10-02 10:06:57,976] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-2_fastqc.html [2021-10-02 10:06:57,978] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-2_fastqc.html [2021-10-02 10:06:58,041] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-7_fastqc.html [2021-10-02 10:06:58,043] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-7_fastqc.html [2021-10-02 10:06:58,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-5_fastqc.html [2021-10-02 10:06:58,095] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-5_fastqc.html [2021-10-02 10:06:58,161] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-6_fastqc.html [2021-10-02 10:06:58,163] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-6_fastqc.html [2021-10-02 10:06:58,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-3_fastqc.html [2021-10-02 10:06:58,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-3_fastqc.html [2021-10-02 10:06:58,285] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-4_fastqc.html [2021-10-02 10:06:58,287] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-4_fastqc.html [2021-10-02 10:06:58,342] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-7_fastqc.html [2021-10-02 10:06:58,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n02_WGS20-7_fastqc.html [2021-10-02 10:06:58,400] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-5_fastqc.html [2021-10-02 10:06:58,401] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G9BKV_l01_n01_WGS20-5_fastqc.html [2021-10-02 10:06:58,871] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-02 10:06:58,873] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-02 10:06:58,883] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 8 samples (table) [2021-10-02 10:06:58,893] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-02 10:06:58,894] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-02 10:06:58,899] multiqc [DEBUG ] No samples found: conpair [2021-10-02 10:06:58,905] multiqc [DEBUG ] No samples found: peddy [2021-10-02 10:06:58,911] multiqc [DEBUG ] No samples found: somalier [2021-10-02 10:06:58,916] multiqc [DEBUG ] No samples found: methylQA [2021-10-02 10:06:58,926] multiqc [DEBUG ] No samples found: mosdepth [2021-10-02 10:06:58,931] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-02 10:06:58,935] multiqc [DEBUG ] No samples found: qualimap [2021-10-02 10:06:58,940] multiqc [DEBUG ] No samples found: preseq [2021-10-02 10:06:58,946] multiqc [DEBUG ] No samples found: quast [2021-10-02 10:06:58,951] multiqc [DEBUG ] No samples found: qorts [2021-10-02 10:06:58,962] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-02 10:06:58,967] multiqc [DEBUG ] No samples found: rockhopper [2021-10-02 10:06:58,972] multiqc [DEBUG ] No samples found: rsem [2021-10-02 10:06:58,984] multiqc [DEBUG ] No samples found: rseqc [2021-10-02 10:06:58,989] multiqc [DEBUG ] No samples found: busco [2021-10-02 10:06:58,995] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-02 10:06:59,006] multiqc [DEBUG ] No samples found: disambiguate [2021-10-02 10:06:59,012] multiqc [DEBUG ] No samples found: supernova [2021-10-02 10:06:59,026] multiqc [DEBUG ] No samples found: deeptools [2021-10-02 10:06:59,032] multiqc [DEBUG ] No samples found: sargasso [2021-10-02 10:06:59,037] multiqc [DEBUG ] No samples found: verifybamid [2021-10-02 10:06:59,043] multiqc [DEBUG ] No samples found: mirtrace [2021-10-02 10:06:59,048] multiqc [DEBUG ] No samples found: happy [2021-10-02 10:06:59,054] multiqc [DEBUG ] No samples found: mirtop [2021-10-02 10:06:59,061] multiqc [DEBUG ] No samples found: homer [2021-10-02 10:06:59,066] multiqc [DEBUG ] No samples found: macs2 [2021-10-02 10:06:59,071] multiqc [DEBUG ] No samples found: theta2 [2021-10-02 10:06:59,076] multiqc [DEBUG ] No samples found: snpeff [2021-10-02 10:06:59,084] multiqc [DEBUG ] No samples found: gatk [2021-10-02 10:06:59,089] multiqc [DEBUG ] No samples found: htseq [2021-10-02 10:06:59,096] multiqc [DEBUG ] No samples found: bcftools [2021-10-02 10:06:59,101] multiqc [DEBUG ] No samples found: featureCounts [2021-10-02 10:06:59,108] multiqc [DEBUG ] No samples found: fgbio [2021-10-02 10:06:59,128] multiqc [DEBUG ] No samples found: dragen [2021-10-02 10:06:59,133] multiqc [DEBUG ] No samples found: dedup [2021-10-02 10:06:59,138] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-02 10:06:59,165] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-02 10:06:59,171] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-02 10:06:59,173] multiqc [DEBUG ] No samples found: picard [2021-10-02 10:06:59,186] multiqc [DEBUG ] No samples found: prokka [2021-10-02 10:06:59,191] multiqc [DEBUG ] No samples found: samblaster [2021-10-02 10:06:59,200] multiqc [DEBUG ] No samples found: samtools [2021-10-02 10:06:59,208] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-02 10:06:59,218] multiqc [DEBUG ] No samples found: bamtools [2021-10-02 10:06:59,225] multiqc [DEBUG ] No samples found: jellyfish [2021-10-02 10:06:59,236] multiqc [DEBUG ] No samples found: vcftools [2021-10-02 10:06:59,243] multiqc [DEBUG ] No samples found: longranger [2021-10-02 10:06:59,251] multiqc [DEBUG ] No samples found: stacks [2021-10-02 10:06:59,259] multiqc [DEBUG ] No samples found: varscan2 [2021-10-02 10:06:59,275] multiqc [DEBUG ] No samples found: bbmap [2021-10-02 10:06:59,280] multiqc [DEBUG ] No samples found: bismark [2021-10-02 10:06:59,286] multiqc [DEBUG ] No samples found: biscuit [2021-10-02 10:06:59,291] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-02 10:06:59,297] multiqc [DEBUG ] No samples found: hicup [2021-10-02 10:06:59,302] multiqc [DEBUG ] No samples found: hicpro [2021-10-02 10:06:59,307] multiqc [DEBUG ] No samples found: salmon [2021-10-02 10:06:59,315] multiqc [DEBUG ] No samples found: kallisto [2021-10-02 10:06:59,323] multiqc [DEBUG ] No samples found: slamdunk [2021-10-02 10:06:59,331] multiqc [DEBUG ] No samples found: star [2021-10-02 10:06:59,339] multiqc [DEBUG ] No samples found: hisat2 [2021-10-02 10:06:59,347] multiqc [DEBUG ] No samples found: tophat [2021-10-02 10:06:59,355] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-02 10:06:59,363] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-02 10:06:59,371] multiqc [DEBUG ] No samples found: snpsplit [2021-10-02 10:06:59,377] multiqc [DEBUG ] No samples found: kat [2021-10-02 10:06:59,385] multiqc [DEBUG ] No samples found: leehom [2021-10-02 10:06:59,392] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-02 10:06:59,399] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-02 10:06:59,407] multiqc [DEBUG ] No samples found: cutadapt [2021-10-02 10:06:59,414] multiqc [DEBUG ] No samples found: flexbar [2021-10-02 10:06:59,422] multiqc [DEBUG ] No samples found: kaiju [2021-10-02 10:06:59,430] multiqc [DEBUG ] No samples found: kraken [2021-10-02 10:06:59,437] multiqc [DEBUG ] No samples found: malt [2021-10-02 10:06:59,442] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-02 10:06:59,447] multiqc [DEBUG ] No samples found: sickle [2021-10-02 10:06:59,452] multiqc [DEBUG ] No samples found: skewer [2021-10-02 10:06:59,457] multiqc [DEBUG ] No samples found: sortmerna [2021-10-02 10:06:59,462] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-02 10:06:59,467] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-02 10:06:59,473] multiqc [DEBUG ] No samples found: afterqc [2021-10-02 10:06:59,478] multiqc [DEBUG ] No samples found: fastp [2021-10-02 10:06:59,536] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2021-10-02 10:06:59,732] multiqc [DEBUG ] No samples found: pycoqc [2021-10-02 10:06:59,737] multiqc [DEBUG ] No samples found: minionqc [2021-10-02 10:06:59,742] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-02 10:06:59,747] multiqc [DEBUG ] No samples found: clusterflow [2021-10-02 10:06:59,751] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-02 10:06:59,757] multiqc [DEBUG ] No samples found: interop [2021-10-02 10:06:59,762] multiqc [DEBUG ] No samples found: ivar [2021-10-02 10:06:59,767] multiqc [DEBUG ] No samples found: flash [2021-10-02 10:06:59,772] multiqc [DEBUG ] No samples found: seqyclean [2021-10-02 10:06:59,772] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-10-02 10:06:59,772] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-10-02 10:06:59,772] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-02 10:06:59,772] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-10-02 10:06:59,772] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-02 10:06:59,792] multiqc [INFO ] Compressing plot data [2021-10-02 10:07:00,051] multiqc [INFO ] Report : multiqc_report.html [2021-10-02 10:07:00,051] multiqc [INFO ] Data : multiqc_data [2021-10-02 10:07:00,051] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10506517/tmpas7gxnni/multiqc_data' to '/scratch/gencore/logs/html/000000000-G9BKV/1/multiqc_data' [2021-10-02 10:07:00,183] multiqc [INFO ] MultiQC complete