[2022-06-09 08:06:07,396] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-06-09 08:06:07,396] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-06-09 08:06:07,396] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-06-09 08:06:07,397] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-06-09 08:06:07,397] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-06-09 08:06:07,398] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVWHCBGXL/merged [2022-06-09 08:06:07,801] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-06-09 08:06:07,801] multiqc [INFO ] This is MultiQC v1.9 [2022-06-09 08:06:07,801] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVWHCBGXL/merged [2022-06-09 08:06:07,801] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVWHCBGXL/merged [2022-06-09 08:06:07,801] multiqc [INFO ] Template : default [2022-06-09 08:06:07,801] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-06-09 08:06:07,801] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVWHCBGXL/merged [2022-06-09 08:06:07,801] 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 [2022-06-09 08:06:07,802] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20677857/tmp0si4_n8h [2022-06-09 08:06:07,913] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVWHCBGXL_n01_AZUCENA-1__fastqc.html [2022-06-09 08:06:07,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVWHCBGXL_n01_AZUCENA-1__fastqc.html [2022-06-09 08:06:07,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVWHCBGXL_n01_IR64-2__fastqc.html [2022-06-09 08:06:07,960] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVWHCBGXL_n01_IR64-2__fastqc.html [2022-06-09 08:06:07,998] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:08,000] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:08,000] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:08,000] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:08,000] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:08,000] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:08,000] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:08,066] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-09 08:06:11,019] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVWHCBGXL_n02_undetermined_fastqc.html [2022-06-09 08:06:11,021] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVWHCBGXL_n02_undetermined_fastqc.html [2022-06-09 08:06:11,062] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVWHCBGXL_n01_undetermined_fastqc.html [2022-06-09 08:06:11,064] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVWHCBGXL_n01_undetermined_fastqc.html [2022-06-09 08:06:11,103] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVWHCBGXL_n02_IR64-2__fastqc.html [2022-06-09 08:06:11,105] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVWHCBGXL_n02_IR64-2__fastqc.html [2022-06-09 08:06:11,146] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVWHCBGXL_n02_AZUCENA-1__fastqc.html [2022-06-09 08:06:11,147] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVWHCBGXL_n02_AZUCENA-1__fastqc.html [2022-06-09 08:06:11,528] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-09 08:06:11,529] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-09 08:06:11,538] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2022-06-09 08:06:11,539] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-06-09 08:06:11,549] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-06-09 08:06:11,554] multiqc [DEBUG ] No samples found: conpair [2022-06-09 08:06:11,559] multiqc [DEBUG ] No samples found: peddy [2022-06-09 08:06:11,566] multiqc [DEBUG ] No samples found: somalier [2022-06-09 08:06:11,571] multiqc [DEBUG ] No samples found: methylQA [2022-06-09 08:06:11,581] multiqc [DEBUG ] No samples found: mosdepth [2022-06-09 08:06:11,585] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-06-09 08:06:11,588] multiqc [DEBUG ] No samples found: qualimap [2022-06-09 08:06:11,594] multiqc [DEBUG ] No samples found: preseq [2022-06-09 08:06:11,599] multiqc [DEBUG ] No samples found: quast [2022-06-09 08:06:11,604] multiqc [DEBUG ] No samples found: qorts [2022-06-09 08:06:11,610] multiqc [DEBUG ] No samples found: rna_seqc [2022-06-09 08:06:11,615] multiqc [DEBUG ] No samples found: rockhopper [2022-06-09 08:06:11,620] multiqc [DEBUG ] No samples found: rsem [2022-06-09 08:06:11,632] multiqc [DEBUG ] No samples found: rseqc [2022-06-09 08:06:11,637] multiqc [DEBUG ] No samples found: busco [2022-06-09 08:06:11,642] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-06-09 08:06:11,648] multiqc [DEBUG ] No samples found: disambiguate [2022-06-09 08:06:11,653] multiqc [DEBUG ] No samples found: supernova [2022-06-09 08:06:11,667] multiqc [DEBUG ] No samples found: deeptools [2022-06-09 08:06:11,672] multiqc [DEBUG ] No samples found: sargasso [2022-06-09 08:06:11,678] multiqc [DEBUG ] No samples found: verifybamid [2022-06-09 08:06:11,683] multiqc [DEBUG ] No samples found: mirtrace [2022-06-09 08:06:11,688] multiqc [DEBUG ] No samples found: happy [2022-06-09 08:06:11,693] multiqc [DEBUG ] No samples found: mirtop [2022-06-09 08:06:11,701] multiqc [DEBUG ] No samples found: homer [2022-06-09 08:06:11,706] multiqc [DEBUG ] No samples found: macs2 [2022-06-09 08:06:11,711] multiqc [DEBUG ] No samples found: theta2 [2022-06-09 08:06:11,716] multiqc [DEBUG ] No samples found: snpeff [2022-06-09 08:06:11,724] multiqc [DEBUG ] No samples found: gatk [2022-06-09 08:06:11,729] multiqc [DEBUG ] No samples found: htseq [2022-06-09 08:06:11,735] multiqc [DEBUG ] No samples found: bcftools [2022-06-09 08:06:11,740] multiqc [DEBUG ] No samples found: featureCounts [2022-06-09 08:06:11,747] multiqc [DEBUG ] No samples found: fgbio [2022-06-09 08:06:11,761] multiqc [DEBUG ] No samples found: dragen [2022-06-09 08:06:11,766] multiqc [DEBUG ] No samples found: dedup [2022-06-09 08:06:11,771] multiqc [DEBUG ] No samples found: damageprofiler [2022-06-09 08:06:11,797] multiqc [DEBUG ] No samples found: biobambam2 [2022-06-09 08:06:11,801] multiqc [DEBUG ] No samples found: mtnucratio [2022-06-09 08:06:11,803] multiqc [DEBUG ] No samples found: picard [2022-06-09 08:06:11,808] multiqc [DEBUG ] No samples found: prokka [2022-06-09 08:06:11,813] multiqc [DEBUG ] No samples found: samblaster [2022-06-09 08:06:11,822] multiqc [DEBUG ] No samples found: samtools [2022-06-09 08:06:11,827] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-06-09 08:06:11,833] multiqc [DEBUG ] No samples found: bamtools [2022-06-09 08:06:11,837] multiqc [DEBUG ] No samples found: jellyfish [2022-06-09 08:06:11,845] multiqc [DEBUG ] No samples found: vcftools [2022-06-09 08:06:11,851] multiqc [DEBUG ] No samples found: longranger [2022-06-09 08:06:11,856] multiqc [DEBUG ] No samples found: stacks [2022-06-09 08:06:11,862] multiqc [DEBUG ] No samples found: varscan2 [2022-06-09 08:06:11,875] multiqc [DEBUG ] No samples found: bbmap [2022-06-09 08:06:11,880] multiqc [DEBUG ] No samples found: bismark [2022-06-09 08:06:11,886] multiqc [DEBUG ] No samples found: biscuit [2022-06-09 08:06:11,891] multiqc [DEBUG ] No samples found: hicexplorer [2022-06-09 08:06:11,897] multiqc [DEBUG ] No samples found: hicup [2022-06-09 08:06:11,902] multiqc [DEBUG ] No samples found: hicpro [2022-06-09 08:06:11,906] multiqc [DEBUG ] No samples found: salmon [2022-06-09 08:06:11,911] multiqc [DEBUG ] No samples found: kallisto [2022-06-09 08:06:11,917] multiqc [DEBUG ] No samples found: slamdunk [2022-06-09 08:06:11,922] multiqc [DEBUG ] No samples found: star [2022-06-09 08:06:11,926] multiqc [DEBUG ] No samples found: hisat2 [2022-06-09 08:06:11,931] multiqc [DEBUG ] No samples found: tophat [2022-06-09 08:06:11,936] multiqc [DEBUG ] No samples found: bowtie2 [2022-06-09 08:06:11,941] multiqc [DEBUG ] No samples found: bowtie1 [2022-06-09 08:06:11,946] multiqc [DEBUG ] No samples found: snpsplit [2022-06-09 08:06:11,951] multiqc [DEBUG ] No samples found: kat [2022-06-09 08:06:11,956] multiqc [DEBUG ] No samples found: leehom [2022-06-09 08:06:11,961] multiqc [DEBUG ] No samples found: adapterRemoval [2022-06-09 08:06:11,966] multiqc [DEBUG ] No samples found: clipandmerge [2022-06-09 08:06:11,971] multiqc [DEBUG ] No samples found: cutadapt [2022-06-09 08:06:11,976] multiqc [DEBUG ] No samples found: flexbar [2022-06-09 08:06:11,981] multiqc [DEBUG ] No samples found: kaiju [2022-06-09 08:06:11,986] multiqc [DEBUG ] No samples found: kraken [2022-06-09 08:06:11,991] multiqc [DEBUG ] No samples found: malt [2022-06-09 08:06:11,996] multiqc [DEBUG ] No samples found: trimmomatic [2022-06-09 08:06:12,001] multiqc [DEBUG ] No samples found: sickle [2022-06-09 08:06:12,009] multiqc [DEBUG ] No samples found: skewer [2022-06-09 08:06:12,014] multiqc [DEBUG ] No samples found: sortmerna [2022-06-09 08:06:12,018] multiqc [DEBUG ] No samples found: biobloomtools [2022-06-09 08:06:12,023] multiqc [DEBUG ] No samples found: fastq_screen [2022-06-09 08:06:12,029] multiqc [DEBUG ] No samples found: afterqc [2022-06-09 08:06:12,034] multiqc [DEBUG ] No samples found: fastp [2022-06-09 08:06:12,405] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2022-06-09 08:06:12,476] multiqc [DEBUG ] No samples found: pycoqc [2022-06-09 08:06:12,481] multiqc [DEBUG ] No samples found: minionqc [2022-06-09 08:06:12,486] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-06-09 08:06:12,491] multiqc [DEBUG ] No samples found: clusterflow [2022-06-09 08:06:12,497] multiqc [DEBUG ] No samples found: bcl2fastq [2022-06-09 08:06:12,502] multiqc [DEBUG ] No samples found: interop [2022-06-09 08:06:12,507] multiqc [DEBUG ] No samples found: ivar [2022-06-09 08:06:12,511] multiqc [DEBUG ] No samples found: flash [2022-06-09 08:06:12,516] multiqc [DEBUG ] No samples found: seqyclean [2022-06-09 08:06:12,516] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-06-09 08:06:12,516] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-06-09 08:06:12,516] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-06-09 08:06:12,516] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-06-09 08:06:12,524] multiqc [INFO ] Compressing plot data [2022-06-09 08:06:12,638] multiqc [INFO ] Report : multiqc_report.html [2022-06-09 08:06:12,638] multiqc [INFO ] Data : multiqc_data [2022-06-09 08:06:12,638] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20677857/tmp0si4_n8h/multiqc_data' to '/scratch/gencore/logs/html/HVWHCBGXL/merged/multiqc_data' [2022-06-09 08:06:12,766] multiqc [INFO ] MultiQC complete