[2022-04-22 07:38:18,215] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-22 07:38:18,215] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-22 07:38:18,216] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-22 07:38:18,216] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-22 07:38:18,217] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-22 07:38:18,217] 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-K5J99/1 [2022-04-22 07:38:18,615] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-22 07:38:18,615] multiqc [INFO ] This is MultiQC v1.9 [2022-04-22 07:38:18,615] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-K5J99/1 [2022-04-22 07:38:18,615] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-K5J99/1 [2022-04-22 07:38:18,615] multiqc [INFO ] Template : default [2022-04-22 07:38:18,615] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-22 07:38:18,615] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-K5J99/1 [2022-04-22 07:38:18,615] 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 [2022-04-22 07:38:18,615] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-18425107/tmp1vi8rsij [2022-04-22 07:38:18,731] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:18,734] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:18,734] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:18,734] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:18,734] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:18,734] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:18,734] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:18,756] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 07:38:19,660] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_undetermined_fastqc.html [2022-04-22 07:38:19,662] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_undetermined_fastqc.html [2022-04-22 07:38:19,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_AS_60_fastqc.html [2022-04-22 07:38:19,711] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_AS_60_fastqc.html [2022-04-22 07:38:19,773] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_RY_300_fastqc.html [2022-04-22 07:38:19,775] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_RY_300_fastqc.html [2022-04-22 07:38:19,840] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14SpLowlib_fastqc.html [2022-04-22 07:38:19,842] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14SpLowlib_fastqc.html [2022-04-22 07:38:19,896] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14SpMediumlib_fastqc.html [2022-04-22 07:38:19,898] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14SpMediumlib_fastqc.html [2022-04-22 07:38:19,950] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTF_PGC03lib_fastqc.html [2022-04-22 07:38:19,952] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTF_PGC03lib_fastqc.html [2022-04-22 07:38:20,049] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14SpHighlib_fastqc.html [2022-04-22 07:38:20,051] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14SpHighlib_fastqc.html [2022-04-22 07:38:20,104] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14lib_fastqc.html [2022-04-22 07:38:20,106] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K5J99_l01_n01_hTFPCC14lib_fastqc.html [2022-04-22 07:38:20,590] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-22 07:38:20,591] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-22 07:38:20,599] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-22 07:38:20,609] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-22 07:38:20,613] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 8 samples (table) [2022-04-22 07:38:20,618] multiqc [DEBUG ] No samples found: conpair [2022-04-22 07:38:20,622] multiqc [DEBUG ] No samples found: peddy [2022-04-22 07:38:20,627] multiqc [DEBUG ] No samples found: somalier [2022-04-22 07:38:20,632] multiqc [DEBUG ] No samples found: methylQA [2022-04-22 07:38:20,640] multiqc [DEBUG ] No samples found: mosdepth [2022-04-22 07:38:20,644] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-22 07:38:20,648] multiqc [DEBUG ] No samples found: qualimap [2022-04-22 07:38:20,652] multiqc [DEBUG ] No samples found: preseq [2022-04-22 07:38:20,658] multiqc [DEBUG ] No samples found: quast [2022-04-22 07:38:20,663] multiqc [DEBUG ] No samples found: qorts [2022-04-22 07:38:20,667] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-22 07:38:20,672] multiqc [DEBUG ] No samples found: rockhopper [2022-04-22 07:38:20,677] multiqc [DEBUG ] No samples found: rsem [2022-04-22 07:38:20,688] multiqc [DEBUG ] No samples found: rseqc [2022-04-22 07:38:20,692] multiqc [DEBUG ] No samples found: busco [2022-04-22 07:38:20,696] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-22 07:38:20,700] multiqc [DEBUG ] No samples found: disambiguate [2022-04-22 07:38:20,705] multiqc [DEBUG ] No samples found: supernova [2022-04-22 07:38:20,717] multiqc [DEBUG ] No samples found: deeptools [2022-04-22 07:38:20,721] multiqc [DEBUG ] No samples found: sargasso [2022-04-22 07:38:20,726] multiqc [DEBUG ] No samples found: verifybamid [2022-04-22 07:38:20,730] multiqc [DEBUG ] No samples found: mirtrace [2022-04-22 07:38:20,734] multiqc [DEBUG ] No samples found: happy [2022-04-22 07:38:20,739] multiqc [DEBUG ] No samples found: mirtop [2022-04-22 07:38:20,745] multiqc [DEBUG ] No samples found: homer [2022-04-22 07:38:20,749] multiqc [DEBUG ] No samples found: macs2 [2022-04-22 07:38:20,754] multiqc [DEBUG ] No samples found: theta2 [2022-04-22 07:38:20,759] multiqc [DEBUG ] No samples found: snpeff [2022-04-22 07:38:20,765] multiqc [DEBUG ] No samples found: gatk [2022-04-22 07:38:20,770] multiqc [DEBUG ] No samples found: htseq [2022-04-22 07:38:20,775] multiqc [DEBUG ] No samples found: bcftools [2022-04-22 07:38:20,779] multiqc [DEBUG ] No samples found: featureCounts [2022-04-22 07:38:20,785] multiqc [DEBUG ] No samples found: fgbio [2022-04-22 07:38:20,798] multiqc [DEBUG ] No samples found: dragen [2022-04-22 07:38:20,802] multiqc [DEBUG ] No samples found: dedup [2022-04-22 07:38:20,806] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-22 07:38:20,828] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-22 07:38:20,832] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-22 07:38:20,834] multiqc [DEBUG ] No samples found: picard [2022-04-22 07:38:20,839] multiqc [DEBUG ] No samples found: prokka [2022-04-22 07:38:20,843] multiqc [DEBUG ] No samples found: samblaster [2022-04-22 07:38:20,851] multiqc [DEBUG ] No samples found: samtools [2022-04-22 07:38:20,855] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-22 07:38:20,860] multiqc [DEBUG ] No samples found: bamtools [2022-04-22 07:38:20,864] multiqc [DEBUG ] No samples found: jellyfish [2022-04-22 07:38:20,874] multiqc [DEBUG ] No samples found: vcftools [2022-04-22 07:38:20,878] multiqc [DEBUG ] No samples found: longranger [2022-04-22 07:38:20,883] multiqc [DEBUG ] No samples found: stacks [2022-04-22 07:38:20,887] multiqc [DEBUG ] No samples found: varscan2 [2022-04-22 07:38:20,901] multiqc [DEBUG ] No samples found: bbmap [2022-04-22 07:38:20,906] multiqc [DEBUG ] No samples found: bismark [2022-04-22 07:38:20,910] multiqc [DEBUG ] No samples found: biscuit [2022-04-22 07:38:20,915] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-22 07:38:20,919] multiqc [DEBUG ] No samples found: hicup [2022-04-22 07:38:20,924] multiqc [DEBUG ] No samples found: hicpro [2022-04-22 07:38:20,928] multiqc [DEBUG ] No samples found: salmon [2022-04-22 07:38:20,932] multiqc [DEBUG ] No samples found: kallisto [2022-04-22 07:38:20,937] multiqc [DEBUG ] No samples found: slamdunk [2022-04-22 07:38:20,942] multiqc [DEBUG ] No samples found: star [2022-04-22 07:38:20,946] multiqc [DEBUG ] No samples found: hisat2 [2022-04-22 07:38:20,951] multiqc [DEBUG ] No samples found: tophat [2022-04-22 07:38:20,955] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-22 07:38:20,959] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-22 07:38:20,964] multiqc [DEBUG ] No samples found: snpsplit [2022-04-22 07:38:20,968] multiqc [DEBUG ] No samples found: kat [2022-04-22 07:38:20,972] multiqc [DEBUG ] No samples found: leehom [2022-04-22 07:38:20,977] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-22 07:38:20,982] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-22 07:38:20,986] multiqc [DEBUG ] No samples found: cutadapt [2022-04-22 07:38:20,990] multiqc [DEBUG ] No samples found: flexbar [2022-04-22 07:38:20,995] multiqc [DEBUG ] No samples found: kaiju [2022-04-22 07:38:21,001] multiqc [DEBUG ] No samples found: kraken [2022-04-22 07:38:21,005] multiqc [DEBUG ] No samples found: malt [2022-04-22 07:38:21,010] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-22 07:38:21,014] multiqc [DEBUG ] No samples found: sickle [2022-04-22 07:38:21,018] multiqc [DEBUG ] No samples found: skewer [2022-04-22 07:38:21,022] multiqc [DEBUG ] No samples found: sortmerna [2022-04-22 07:38:21,027] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-22 07:38:21,031] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-22 07:38:21,036] multiqc [DEBUG ] No samples found: afterqc [2022-04-22 07:38:21,041] multiqc [DEBUG ] No samples found: fastp [2022-04-22 07:38:21,103] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-04-22 07:38:21,186] multiqc [DEBUG ] No samples found: pycoqc [2022-04-22 07:38:21,191] multiqc [DEBUG ] No samples found: minionqc [2022-04-22 07:38:21,195] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-22 07:38:21,200] multiqc [DEBUG ] No samples found: clusterflow [2022-04-22 07:38:21,204] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-22 07:38:21,210] multiqc [DEBUG ] No samples found: interop [2022-04-22 07:38:21,214] multiqc [DEBUG ] No samples found: ivar [2022-04-22 07:38:21,219] multiqc [DEBUG ] No samples found: flash [2022-04-22 07:38:21,223] multiqc [DEBUG ] No samples found: seqyclean [2022-04-22 07:38:21,223] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-04-22 07:38:21,223] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-04-22 07:38:21,223] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-22 07:38:21,223] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-04-22 07:38:21,223] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-22 07:38:21,233] multiqc [INFO ] Compressing plot data [2022-04-22 07:38:21,346] multiqc [INFO ] Report : multiqc_report.html [2022-04-22 07:38:21,346] multiqc [INFO ] Data : multiqc_data [2022-04-22 07:38:21,346] multiqc [DEBUG ] Moving data file from '/state/partition1/job-18425107/tmp1vi8rsij/multiqc_data' to '/scratch/gencore/logs/html/000000000-K5J99/1/multiqc_data' [2022-04-22 07:38:21,502] multiqc [INFO ] MultiQC complete