[2022-10-20 12:12:25,608] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-20 12:12:25,608] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-20 12:12:25,608] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-20 12:12:25,609] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-20 12:12:25,609] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-20 12:12:25,609] 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-G98TK/1 [2022-10-20 12:12:26,169] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-20 12:12:26,169] multiqc [INFO ] This is MultiQC v1.9 [2022-10-20 12:12:26,169] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-G98TK/1 [2022-10-20 12:12:26,169] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-G98TK/1 [2022-10-20 12:12:26,170] multiqc [INFO ] Template : default [2022-10-20 12:12:26,170] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-20 12:12:26,170] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-G98TK/1 [2022-10-20 12:12:26,170] 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 [2022-10-20 12:12:26,170] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26092275/tmpuxvaty3p [2022-10-20 12:12:26,303] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G98TK_l01.3_fastqc.html [2022-10-20 12:12:26,305] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G98TK_l01.3_fastqc.html [2022-10-20 12:12:26,347] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G98TK_l01.1_fastqc.html [2022-10-20 12:12:26,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G98TK_l01.1_fastqc.html [2022-10-20 12:12:26,349] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: 000000000-G98TK_l01.1_fastqc.html [2022-10-20 12:12:26,349] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 000000000-G98TK_l01.1_fastqc.html [2022-10-20 12:12:26,349] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 000000000-G98TK_l01.1_fastqc.html [2022-10-20 12:12:26,349] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 000000000-G98TK_l01.1_fastqc.html [2022-10-20 12:12:26,349] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 000000000-G98TK_l01.1_fastqc.html [2022-10-20 12:12:26,417] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G98TK_l01.2_fastqc.html [2022-10-20 12:12:26,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G98TK_l01.2_fastqc.html [2022-10-20 12:12:26,777] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-20 12:12:26,779] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-20 12:12:26,784] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-10-20 12:12:26,786] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-20 12:12:26,792] multiqc [DEBUG ] No samples found: conpair [2022-10-20 12:12:26,798] multiqc [DEBUG ] No samples found: peddy [2022-10-20 12:12:26,804] multiqc [DEBUG ] No samples found: somalier [2022-10-20 12:12:26,809] multiqc [DEBUG ] No samples found: methylQA [2022-10-20 12:12:26,819] multiqc [DEBUG ] No samples found: mosdepth [2022-10-20 12:12:26,824] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-20 12:12:26,828] multiqc [DEBUG ] No samples found: qualimap [2022-10-20 12:12:26,833] multiqc [DEBUG ] No samples found: preseq [2022-10-20 12:12:26,839] multiqc [DEBUG ] No samples found: quast [2022-10-20 12:12:26,845] multiqc [DEBUG ] No samples found: qorts [2022-10-20 12:12:26,851] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-20 12:12:26,857] multiqc [DEBUG ] No samples found: rockhopper [2022-10-20 12:12:26,863] multiqc [DEBUG ] No samples found: rsem [2022-10-20 12:12:26,876] multiqc [DEBUG ] No samples found: rseqc [2022-10-20 12:12:26,881] multiqc [DEBUG ] No samples found: busco [2022-10-20 12:12:26,887] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-20 12:12:26,892] multiqc [DEBUG ] No samples found: disambiguate [2022-10-20 12:12:26,898] multiqc [DEBUG ] No samples found: supernova [2022-10-20 12:12:26,911] multiqc [DEBUG ] No samples found: deeptools [2022-10-20 12:12:26,917] multiqc [DEBUG ] No samples found: sargasso [2022-10-20 12:12:26,922] multiqc [DEBUG ] No samples found: verifybamid [2022-10-20 12:12:26,929] multiqc [DEBUG ] No samples found: mirtrace [2022-10-20 12:12:26,935] multiqc [DEBUG ] No samples found: happy [2022-10-20 12:12:26,940] multiqc [DEBUG ] No samples found: mirtop [2022-10-20 12:12:26,947] multiqc [DEBUG ] No samples found: homer [2022-10-20 12:12:26,952] multiqc [DEBUG ] No samples found: macs2 [2022-10-20 12:12:26,957] multiqc [DEBUG ] No samples found: theta2 [2022-10-20 12:12:26,963] multiqc [DEBUG ] No samples found: snpeff [2022-10-20 12:12:26,971] multiqc [DEBUG ] No samples found: gatk [2022-10-20 12:12:26,977] multiqc [DEBUG ] No samples found: htseq [2022-10-20 12:12:26,983] multiqc [DEBUG ] No samples found: bcftools [2022-10-20 12:12:26,992] multiqc [DEBUG ] No samples found: featureCounts [2022-10-20 12:12:26,998] multiqc [DEBUG ] No samples found: fgbio [2022-10-20 12:12:27,014] multiqc [DEBUG ] No samples found: dragen [2022-10-20 12:12:27,019] multiqc [DEBUG ] No samples found: dedup [2022-10-20 12:12:27,025] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-20 12:12:27,051] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-20 12:12:27,056] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-20 12:12:27,059] multiqc [DEBUG ] No samples found: picard [2022-10-20 12:12:27,065] multiqc [DEBUG ] No samples found: prokka [2022-10-20 12:12:27,070] multiqc [DEBUG ] No samples found: samblaster [2022-10-20 12:12:27,080] multiqc [DEBUG ] No samples found: samtools [2022-10-20 12:12:27,085] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-20 12:12:27,091] multiqc [DEBUG ] No samples found: bamtools [2022-10-20 12:12:27,096] multiqc [DEBUG ] No samples found: jellyfish [2022-10-20 12:12:27,105] multiqc [DEBUG ] No samples found: vcftools [2022-10-20 12:12:27,110] multiqc [DEBUG ] No samples found: longranger [2022-10-20 12:12:27,116] multiqc [DEBUG ] No samples found: stacks [2022-10-20 12:12:27,121] multiqc [DEBUG ] No samples found: varscan2 [2022-10-20 12:12:27,138] multiqc [DEBUG ] No samples found: bbmap [2022-10-20 12:12:27,144] multiqc [DEBUG ] No samples found: bismark [2022-10-20 12:12:27,149] multiqc [DEBUG ] No samples found: biscuit [2022-10-20 12:12:27,156] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-20 12:12:27,161] multiqc [DEBUG ] No samples found: hicup [2022-10-20 12:12:27,167] multiqc [DEBUG ] No samples found: hicpro [2022-10-20 12:12:27,173] multiqc [DEBUG ] No samples found: salmon [2022-10-20 12:12:27,178] multiqc [DEBUG ] No samples found: kallisto [2022-10-20 12:12:27,184] multiqc [DEBUG ] No samples found: slamdunk [2022-10-20 12:12:27,189] multiqc [DEBUG ] No samples found: star [2022-10-20 12:12:27,194] multiqc [DEBUG ] No samples found: hisat2 [2022-10-20 12:12:27,200] multiqc [DEBUG ] No samples found: tophat [2022-10-20 12:12:27,205] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-20 12:12:27,210] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-20 12:12:27,215] multiqc [DEBUG ] No samples found: snpsplit [2022-10-20 12:12:27,220] multiqc [DEBUG ] No samples found: kat [2022-10-20 12:12:27,225] multiqc [DEBUG ] No samples found: leehom [2022-10-20 12:12:27,231] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-20 12:12:27,236] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-20 12:12:27,241] multiqc [DEBUG ] No samples found: cutadapt [2022-10-20 12:12:27,246] multiqc [DEBUG ] No samples found: flexbar [2022-10-20 12:12:27,252] multiqc [DEBUG ] No samples found: kaiju [2022-10-20 12:12:27,257] multiqc [DEBUG ] No samples found: kraken [2022-10-20 12:12:27,262] multiqc [DEBUG ] No samples found: malt [2022-10-20 12:12:27,268] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-20 12:12:27,273] multiqc [DEBUG ] No samples found: sickle [2022-10-20 12:12:27,278] multiqc [DEBUG ] No samples found: skewer [2022-10-20 12:12:27,283] multiqc [DEBUG ] No samples found: sortmerna [2022-10-20 12:12:27,288] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-20 12:12:27,294] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-20 12:12:27,299] multiqc [DEBUG ] No samples found: afterqc [2022-10-20 12:12:27,305] multiqc [DEBUG ] No samples found: fastp [2022-10-20 12:12:27,320] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2022-10-20 12:12:27,378] multiqc [DEBUG ] No samples found: pycoqc [2022-10-20 12:12:27,383] multiqc [DEBUG ] No samples found: minionqc [2022-10-20 12:12:27,388] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-20 12:12:27,393] multiqc [DEBUG ] No samples found: clusterflow [2022-10-20 12:12:27,399] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-20 12:12:27,404] multiqc [DEBUG ] No samples found: interop [2022-10-20 12:12:27,410] multiqc [DEBUG ] No samples found: ivar [2022-10-20 12:12:27,415] multiqc [DEBUG ] No samples found: flash [2022-10-20 12:12:27,421] multiqc [DEBUG ] No samples found: seqyclean [2022-10-20 12:12:27,421] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-10-20 12:12:27,421] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-10-20 12:12:27,421] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-20 12:12:27,426] multiqc [INFO ] Compressing plot data [2022-10-20 12:12:27,483] multiqc [INFO ] Report : multiqc_report.html [2022-10-20 12:12:27,483] multiqc [INFO ] Data : multiqc_data [2022-10-20 12:12:27,483] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26092275/tmpuxvaty3p/multiqc_data' to '/scratch/gencore/logs/html/000000000-G98TK/1/multiqc_data' [2022-10-20 12:12:27,786] multiqc [INFO ] MultiQC complete