[2022-10-29 11:01:30,701] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-29 11:01:30,701] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-29 11:01:30,701] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-29 11:01:30,702] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-29 11:01:30,702] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-29 11:01:30,702] 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-GB7NH/1 [2022-10-29 11:01:31,189] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-29 11:01:31,189] multiqc [INFO ] This is MultiQC v1.9 [2022-10-29 11:01:31,190] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-GB7NH/1 [2022-10-29 11:01:31,190] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-GB7NH/1 [2022-10-29 11:01:31,190] multiqc [INFO ] Template : default [2022-10-29 11:01:31,190] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-29 11:01:31,190] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-GB7NH/1 [2022-10-29 11:01:31,190] 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 [2022-10-29 11:01:31,190] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26419080/tmpwnpo15_u [2022-10-29 11:01:31,326] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GB7NH_l01_n01_undetermined_fastqc.html [2022-10-29 11:01:31,328] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GB7NH_l01_n01_undetermined_fastqc.html [2022-10-29 11:01:31,349] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GB7NH_l01_n01_LH_221025_fastqc.html [2022-10-29 11:01:31,351] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GB7NH_l01_n01_LH_221025_fastqc.html [2022-10-29 11:01:31,722] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-29 11:01:31,726] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-29 11:01:31,734] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-10-29 11:01:31,736] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 2 samples (table) [2022-10-29 11:01:31,737] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-29 11:01:31,744] multiqc [DEBUG ] No samples found: conpair [2022-10-29 11:01:31,753] multiqc [DEBUG ] No samples found: peddy [2022-10-29 11:01:31,762] multiqc [DEBUG ] No samples found: somalier [2022-10-29 11:01:31,771] multiqc [DEBUG ] No samples found: methylQA [2022-10-29 11:01:31,786] multiqc [DEBUG ] No samples found: mosdepth [2022-10-29 11:01:31,792] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-29 11:01:31,800] multiqc [DEBUG ] No samples found: qualimap [2022-10-29 11:01:31,807] multiqc [DEBUG ] No samples found: preseq [2022-10-29 11:01:31,813] multiqc [DEBUG ] No samples found: quast [2022-10-29 11:01:31,822] multiqc [DEBUG ] No samples found: qorts [2022-10-29 11:01:31,829] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-29 11:01:31,838] multiqc [DEBUG ] No samples found: rockhopper [2022-10-29 11:01:31,847] multiqc [DEBUG ] No samples found: rsem [2022-10-29 11:01:31,865] multiqc [DEBUG ] No samples found: rseqc [2022-10-29 11:01:31,870] multiqc [DEBUG ] No samples found: busco [2022-10-29 11:01:31,879] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-29 11:01:31,885] multiqc [DEBUG ] No samples found: disambiguate [2022-10-29 11:01:31,893] multiqc [DEBUG ] No samples found: supernova [2022-10-29 11:01:31,920] multiqc [DEBUG ] No samples found: deeptools [2022-10-29 11:01:31,930] multiqc [DEBUG ] No samples found: sargasso [2022-10-29 11:01:31,938] multiqc [DEBUG ] No samples found: verifybamid [2022-10-29 11:01:31,946] multiqc [DEBUG ] No samples found: mirtrace [2022-10-29 11:01:31,955] multiqc [DEBUG ] No samples found: happy [2022-10-29 11:01:31,963] multiqc [DEBUG ] No samples found: mirtop [2022-10-29 11:01:31,974] multiqc [DEBUG ] No samples found: homer [2022-10-29 11:01:31,983] multiqc [DEBUG ] No samples found: macs2 [2022-10-29 11:01:31,987] multiqc [DEBUG ] No samples found: theta2 [2022-10-29 11:01:31,996] multiqc [DEBUG ] No samples found: snpeff [2022-10-29 11:01:32,008] multiqc [DEBUG ] No samples found: gatk [2022-10-29 11:01:32,015] multiqc [DEBUG ] No samples found: htseq [2022-10-29 11:01:32,026] multiqc [DEBUG ] No samples found: bcftools [2022-10-29 11:01:32,034] multiqc [DEBUG ] No samples found: featureCounts [2022-10-29 11:01:32,048] multiqc [DEBUG ] No samples found: fgbio [2022-10-29 11:01:32,070] multiqc [DEBUG ] No samples found: dragen [2022-10-29 11:01:32,077] multiqc [DEBUG ] No samples found: dedup [2022-10-29 11:01:32,086] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-29 11:01:32,135] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-29 11:01:32,142] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-29 11:01:32,145] multiqc [DEBUG ] No samples found: picard [2022-10-29 11:01:32,152] multiqc [DEBUG ] No samples found: prokka [2022-10-29 11:01:32,157] multiqc [DEBUG ] No samples found: samblaster [2022-10-29 11:01:32,173] multiqc [DEBUG ] No samples found: samtools [2022-10-29 11:01:32,182] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-29 11:01:32,189] multiqc [DEBUG ] No samples found: bamtools [2022-10-29 11:01:32,195] multiqc [DEBUG ] No samples found: jellyfish [2022-10-29 11:01:32,206] multiqc [DEBUG ] No samples found: vcftools [2022-10-29 11:01:32,212] multiqc [DEBUG ] No samples found: longranger [2022-10-29 11:01:32,221] multiqc [DEBUG ] No samples found: stacks [2022-10-29 11:01:32,228] multiqc [DEBUG ] No samples found: varscan2 [2022-10-29 11:01:32,257] multiqc [DEBUG ] No samples found: bbmap [2022-10-29 11:01:32,267] multiqc [DEBUG ] No samples found: bismark [2022-10-29 11:01:32,274] multiqc [DEBUG ] No samples found: biscuit [2022-10-29 11:01:32,280] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-29 11:01:32,289] multiqc [DEBUG ] No samples found: hicup [2022-10-29 11:01:32,296] multiqc [DEBUG ] No samples found: hicpro [2022-10-29 11:01:32,304] multiqc [DEBUG ] No samples found: salmon [2022-10-29 11:01:32,312] multiqc [DEBUG ] No samples found: kallisto [2022-10-29 11:01:32,322] multiqc [DEBUG ] No samples found: slamdunk [2022-10-29 11:01:32,330] multiqc [DEBUG ] No samples found: star [2022-10-29 11:01:32,338] multiqc [DEBUG ] No samples found: hisat2 [2022-10-29 11:01:32,346] multiqc [DEBUG ] No samples found: tophat [2022-10-29 11:01:32,351] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-29 11:01:32,359] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-29 11:01:32,367] multiqc [DEBUG ] No samples found: snpsplit [2022-10-29 11:01:32,374] multiqc [DEBUG ] No samples found: kat [2022-10-29 11:01:32,380] multiqc [DEBUG ] No samples found: leehom [2022-10-29 11:01:32,389] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-29 11:01:32,396] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-29 11:01:32,404] multiqc [DEBUG ] No samples found: cutadapt [2022-10-29 11:01:32,411] multiqc [DEBUG ] No samples found: flexbar [2022-10-29 11:01:32,421] multiqc [DEBUG ] No samples found: kaiju [2022-10-29 11:01:32,427] multiqc [DEBUG ] No samples found: kraken [2022-10-29 11:01:32,435] multiqc [DEBUG ] No samples found: malt [2022-10-29 11:01:32,440] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-29 11:01:32,448] multiqc [DEBUG ] No samples found: sickle [2022-10-29 11:01:32,457] multiqc [DEBUG ] No samples found: skewer [2022-10-29 11:01:32,463] multiqc [DEBUG ] No samples found: sortmerna [2022-10-29 11:01:32,470] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-29 11:01:32,478] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-29 11:01:32,487] multiqc [DEBUG ] No samples found: afterqc [2022-10-29 11:01:32,495] multiqc [DEBUG ] No samples found: fastp [2022-10-29 11:01:32,509] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2022-10-29 11:01:32,509] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-GB7NH_l01_n01_undetermined' [2022-10-29 11:01:32,566] multiqc [DEBUG ] No samples found: pycoqc [2022-10-29 11:01:32,573] multiqc [DEBUG ] No samples found: minionqc [2022-10-29 11:01:32,581] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-29 11:01:32,589] multiqc [DEBUG ] No samples found: clusterflow [2022-10-29 11:01:32,598] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-29 11:01:32,606] multiqc [DEBUG ] No samples found: interop [2022-10-29 11:01:32,611] multiqc [DEBUG ] No samples found: ivar [2022-10-29 11:01:32,619] multiqc [DEBUG ] No samples found: flash [2022-10-29 11:01:32,626] multiqc [DEBUG ] No samples found: seqyclean [2022-10-29 11:01:32,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-10-29 11:01:32,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-10-29 11:01:32,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-10-29 11:01:32,626] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-29 11:01:32,629] multiqc [INFO ] Compressing plot data [2022-10-29 11:01:32,670] multiqc [INFO ] Report : multiqc_report.html [2022-10-29 11:01:32,670] multiqc [INFO ] Data : multiqc_data [2022-10-29 11:01:32,670] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26419080/tmpwnpo15_u/multiqc_data' to '/scratch/gencore/logs/html/000000000-GB7NH/1/multiqc_data' [2022-10-29 11:01:58,013] multiqc [INFO ] MultiQC complete