[2021-06-30 14:15:45,218] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-30 14:15:45,219] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-30 14:15:45,219] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-30 14:15:45,219] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-30 14:15:45,220] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-30 14:15:45,220] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGMJJDRXY/merged [2021-06-30 14:15:46,578] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-30 14:15:46,578] multiqc [INFO ] This is MultiQC v1.9 [2021-06-30 14:15:46,578] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGMJJDRXY/merged [2021-06-30 14:15:46,578] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGMJJDRXY/merged [2021-06-30 14:15:46,578] multiqc [INFO ] Template : default [2021-06-30 14:15:46,578] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-30 14:15:46,579] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGMJJDRXY/merged [2021-06-30 14:15:46,579] 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 [2021-06-30 14:15:46,579] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8219577/tmp67lqpgnn [2021-06-30 14:15:46,697] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJJDRXY_3_fastqc.html [2021-06-30 14:15:46,700] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJJDRXY_3_fastqc.html [2021-06-30 14:15:46,767] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJJDRXY_1_fastqc.html [2021-06-30 14:15:46,769] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJJDRXY_1_fastqc.html [2021-06-30 14:15:46,807] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJJDRXY_4_fastqc.html [2021-06-30 14:15:46,808] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJJDRXY_4_fastqc.html [2021-06-30 14:15:46,860] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJJDRXY_2_fastqc.html [2021-06-30 14:15:46,861] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJJDRXY_2_fastqc.html [2021-06-30 14:15:47,537] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-30 14:15:47,538] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-30 14:15:47,542] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2021-06-30 14:15:47,544] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-30 14:15:47,550] multiqc [DEBUG ] No samples found: conpair [2021-06-30 14:15:47,555] multiqc [DEBUG ] No samples found: peddy [2021-06-30 14:15:47,560] multiqc [DEBUG ] No samples found: somalier [2021-06-30 14:15:47,565] multiqc [DEBUG ] No samples found: methylQA [2021-06-30 14:15:47,574] multiqc [DEBUG ] No samples found: mosdepth [2021-06-30 14:15:47,578] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-30 14:15:47,582] multiqc [DEBUG ] No samples found: qualimap [2021-06-30 14:15:47,586] multiqc [DEBUG ] No samples found: preseq [2021-06-30 14:15:47,591] multiqc [DEBUG ] No samples found: quast [2021-06-30 14:15:47,596] multiqc [DEBUG ] No samples found: qorts [2021-06-30 14:15:47,601] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-30 14:15:47,606] multiqc [DEBUG ] No samples found: rockhopper [2021-06-30 14:15:47,611] multiqc [DEBUG ] No samples found: rsem [2021-06-30 14:15:47,622] multiqc [DEBUG ] No samples found: rseqc [2021-06-30 14:15:47,626] multiqc [DEBUG ] No samples found: busco [2021-06-30 14:15:47,632] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-30 14:15:47,637] multiqc [DEBUG ] No samples found: disambiguate [2021-06-30 14:15:47,642] multiqc [DEBUG ] No samples found: supernova [2021-06-30 14:15:47,656] multiqc [DEBUG ] No samples found: deeptools [2021-06-30 14:15:47,661] multiqc [DEBUG ] No samples found: sargasso [2021-06-30 14:15:47,666] multiqc [DEBUG ] No samples found: verifybamid [2021-06-30 14:15:47,671] multiqc [DEBUG ] No samples found: mirtrace [2021-06-30 14:15:47,676] multiqc [DEBUG ] No samples found: happy [2021-06-30 14:15:47,681] multiqc [DEBUG ] No samples found: mirtop [2021-06-30 14:15:47,688] multiqc [DEBUG ] No samples found: homer [2021-06-30 14:15:47,693] multiqc [DEBUG ] No samples found: macs2 [2021-06-30 14:15:47,698] multiqc [DEBUG ] No samples found: theta2 [2021-06-30 14:15:47,703] multiqc [DEBUG ] No samples found: snpeff [2021-06-30 14:15:47,710] multiqc [DEBUG ] No samples found: gatk [2021-06-30 14:15:47,715] multiqc [DEBUG ] No samples found: htseq [2021-06-30 14:15:47,721] multiqc [DEBUG ] No samples found: bcftools [2021-06-30 14:15:47,726] multiqc [DEBUG ] No samples found: featureCounts [2021-06-30 14:15:47,732] multiqc [DEBUG ] No samples found: fgbio [2021-06-30 14:15:47,746] multiqc [DEBUG ] No samples found: dragen [2021-06-30 14:15:47,751] multiqc [DEBUG ] No samples found: dedup [2021-06-30 14:15:47,755] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-30 14:15:47,779] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-30 14:15:47,784] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-30 14:15:47,786] multiqc [DEBUG ] No samples found: picard [2021-06-30 14:15:47,791] multiqc [DEBUG ] No samples found: prokka [2021-06-30 14:15:47,795] multiqc [DEBUG ] No samples found: samblaster [2021-06-30 14:15:47,804] multiqc [DEBUG ] No samples found: samtools [2021-06-30 14:15:47,808] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-30 14:15:47,814] multiqc [DEBUG ] No samples found: bamtools [2021-06-30 14:15:47,818] multiqc [DEBUG ] No samples found: jellyfish [2021-06-30 14:15:47,826] multiqc [DEBUG ] No samples found: vcftools [2021-06-30 14:15:47,830] multiqc [DEBUG ] No samples found: longranger [2021-06-30 14:15:47,835] multiqc [DEBUG ] No samples found: stacks [2021-06-30 14:15:47,840] multiqc [DEBUG ] No samples found: varscan2 [2021-06-30 14:15:47,855] multiqc [DEBUG ] No samples found: bbmap [2021-06-30 14:15:47,859] multiqc [DEBUG ] No samples found: bismark [2021-06-30 14:15:47,864] multiqc [DEBUG ] No samples found: biscuit [2021-06-30 14:15:47,870] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-30 14:15:47,875] multiqc [DEBUG ] No samples found: hicup [2021-06-30 14:15:47,879] multiqc [DEBUG ] No samples found: hicpro [2021-06-30 14:15:47,884] multiqc [DEBUG ] No samples found: salmon [2021-06-30 14:15:47,889] multiqc [DEBUG ] No samples found: kallisto [2021-06-30 14:15:47,893] multiqc [DEBUG ] No samples found: slamdunk [2021-06-30 14:15:47,899] multiqc [DEBUG ] No samples found: star [2021-06-30 14:15:47,903] multiqc [DEBUG ] No samples found: hisat2 [2021-06-30 14:15:47,908] multiqc [DEBUG ] No samples found: tophat [2021-06-30 14:15:47,913] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-30 14:15:47,918] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-30 14:15:47,923] multiqc [DEBUG ] No samples found: snpsplit [2021-06-30 14:15:47,928] multiqc [DEBUG ] No samples found: kat [2021-06-30 14:15:47,932] multiqc [DEBUG ] No samples found: leehom [2021-06-30 14:15:47,937] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-30 14:15:47,942] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-30 14:15:47,946] multiqc [DEBUG ] No samples found: cutadapt [2021-06-30 14:15:47,951] multiqc [DEBUG ] No samples found: flexbar [2021-06-30 14:15:47,956] multiqc [DEBUG ] No samples found: kaiju [2021-06-30 14:15:47,960] multiqc [DEBUG ] No samples found: kraken [2021-06-30 14:15:47,965] multiqc [DEBUG ] No samples found: malt [2021-06-30 14:15:47,969] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-30 14:15:47,974] multiqc [DEBUG ] No samples found: sickle [2021-06-30 14:15:47,979] multiqc [DEBUG ] No samples found: skewer [2021-06-30 14:15:47,983] multiqc [DEBUG ] No samples found: sortmerna [2021-06-30 14:15:47,987] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-30 14:15:47,992] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-30 14:15:47,997] multiqc [DEBUG ] No samples found: afterqc [2021-06-30 14:15:48,001] multiqc [DEBUG ] No samples found: fastp [2021-06-30 14:15:48,259] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2021-06-30 14:15:48,305] multiqc [DEBUG ] No samples found: pycoqc [2021-06-30 14:15:48,309] multiqc [DEBUG ] No samples found: minionqc [2021-06-30 14:15:48,314] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-30 14:15:48,319] multiqc [DEBUG ] No samples found: clusterflow [2021-06-30 14:15:48,324] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-30 14:15:48,329] multiqc [DEBUG ] No samples found: interop [2021-06-30 14:15:48,334] multiqc [DEBUG ] No samples found: ivar [2021-06-30 14:15:48,338] multiqc [DEBUG ] No samples found: flash [2021-06-30 14:15:48,343] multiqc [DEBUG ] No samples found: seqyclean [2021-06-30 14:15:48,343] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-06-30 14:15:48,343] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-06-30 14:15:48,343] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-30 14:15:48,349] multiqc [INFO ] Compressing plot data [2021-06-30 14:15:48,413] multiqc [INFO ] Report : multiqc_report.html [2021-06-30 14:15:48,413] multiqc [INFO ] Data : multiqc_data [2021-06-30 14:15:48,413] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8219577/tmp67lqpgnn/multiqc_data' to '/scratch/gencore/logs/html/HGMJJDRXY/merged/multiqc_data' [2021-06-30 14:15:49,325] multiqc [INFO ] MultiQC complete