[2022-07-01 11:41:44,235] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-01 11:41:44,235] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-01 11:41:44,235] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-01 11:41:44,236] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-01 11:41:44,236] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-01 11:41:44,236] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFFVHBGXM/merged [2022-07-01 11:41:44,800] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-01 11:41:44,800] multiqc [INFO ] This is MultiQC v1.9 [2022-07-01 11:41:44,800] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFFVHBGXM/merged [2022-07-01 11:41:44,800] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFFVHBGXM/merged [2022-07-01 11:41:44,800] multiqc [INFO ] Template : default [2022-07-01 11:41:44,800] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-01 11:41:44,800] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFFVHBGXM/merged [2022-07-01 11:41:44,801] 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 [2022-07-01 11:41:44,801] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-21765014/tmp0vsu7djz [2022-07-01 11:41:44,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVHBGXM_3_fastqc.html [2022-07-01 11:41:44,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVHBGXM_3_fastqc.html [2022-07-01 11:41:45,001] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVHBGXM_4_fastqc.html [2022-07-01 11:41:45,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVHBGXM_4_fastqc.html [2022-07-01 11:41:45,076] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVHBGXM_1_fastqc.html [2022-07-01 11:41:45,078] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVHBGXM_1_fastqc.html [2022-07-01 11:41:45,126] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVHBGXM_2_fastqc.html [2022-07-01 11:41:45,128] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVHBGXM_2_fastqc.html [2022-07-01 11:41:45,475] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-01 11:41:45,478] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-01 11:41:45,483] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-07-01 11:41:45,486] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-01 11:41:45,491] multiqc [DEBUG ] No samples found: conpair [2022-07-01 11:41:45,498] multiqc [DEBUG ] No samples found: peddy [2022-07-01 11:41:45,504] multiqc [DEBUG ] No samples found: somalier [2022-07-01 11:41:45,511] multiqc [DEBUG ] No samples found: methylQA [2022-07-01 11:41:45,523] multiqc [DEBUG ] No samples found: mosdepth [2022-07-01 11:41:45,529] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-01 11:41:45,534] multiqc [DEBUG ] No samples found: qualimap [2022-07-01 11:41:45,539] multiqc [DEBUG ] No samples found: preseq [2022-07-01 11:41:45,547] multiqc [DEBUG ] No samples found: quast [2022-07-01 11:41:45,552] multiqc [DEBUG ] No samples found: qorts [2022-07-01 11:41:45,557] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-01 11:41:45,562] multiqc [DEBUG ] No samples found: rockhopper [2022-07-01 11:41:45,568] multiqc [DEBUG ] No samples found: rsem [2022-07-01 11:41:45,583] multiqc [DEBUG ] No samples found: rseqc [2022-07-01 11:41:45,588] multiqc [DEBUG ] No samples found: busco [2022-07-01 11:41:45,595] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-01 11:41:45,603] multiqc [DEBUG ] No samples found: disambiguate [2022-07-01 11:41:45,607] multiqc [DEBUG ] No samples found: supernova [2022-07-01 11:41:45,625] multiqc [DEBUG ] No samples found: deeptools [2022-07-01 11:41:45,629] multiqc [DEBUG ] No samples found: sargasso [2022-07-01 11:41:45,635] multiqc [DEBUG ] No samples found: verifybamid [2022-07-01 11:41:45,642] multiqc [DEBUG ] No samples found: mirtrace [2022-07-01 11:41:45,648] multiqc [DEBUG ] No samples found: happy [2022-07-01 11:41:45,652] multiqc [DEBUG ] No samples found: mirtop [2022-07-01 11:41:45,661] multiqc [DEBUG ] No samples found: homer [2022-07-01 11:41:45,666] multiqc [DEBUG ] No samples found: macs2 [2022-07-01 11:41:45,670] multiqc [DEBUG ] No samples found: theta2 [2022-07-01 11:41:45,675] multiqc [DEBUG ] No samples found: snpeff [2022-07-01 11:41:45,684] multiqc [DEBUG ] No samples found: gatk [2022-07-01 11:41:45,692] multiqc [DEBUG ] No samples found: htseq [2022-07-01 11:41:45,699] multiqc [DEBUG ] No samples found: bcftools [2022-07-01 11:41:45,703] multiqc [DEBUG ] No samples found: featureCounts [2022-07-01 11:41:45,713] multiqc [DEBUG ] No samples found: fgbio [2022-07-01 11:41:45,730] multiqc [DEBUG ] No samples found: dragen [2022-07-01 11:41:45,735] multiqc [DEBUG ] No samples found: dedup [2022-07-01 11:41:45,741] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-01 11:41:45,768] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-01 11:41:45,773] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-01 11:41:45,776] multiqc [DEBUG ] No samples found: picard [2022-07-01 11:41:45,780] multiqc [DEBUG ] No samples found: prokka [2022-07-01 11:41:45,785] multiqc [DEBUG ] No samples found: samblaster [2022-07-01 11:41:45,799] multiqc [DEBUG ] No samples found: samtools [2022-07-01 11:41:45,805] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-01 11:41:45,812] multiqc [DEBUG ] No samples found: bamtools [2022-07-01 11:41:45,816] multiqc [DEBUG ] No samples found: jellyfish [2022-07-01 11:41:45,827] multiqc [DEBUG ] No samples found: vcftools [2022-07-01 11:41:45,832] multiqc [DEBUG ] No samples found: longranger [2022-07-01 11:41:45,840] multiqc [DEBUG ] No samples found: stacks [2022-07-01 11:41:45,845] multiqc [DEBUG ] No samples found: varscan2 [2022-07-01 11:41:45,865] multiqc [DEBUG ] No samples found: bbmap [2022-07-01 11:41:45,869] multiqc [DEBUG ] No samples found: bismark [2022-07-01 11:41:45,875] multiqc [DEBUG ] No samples found: biscuit [2022-07-01 11:41:45,880] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-01 11:41:45,885] multiqc [DEBUG ] No samples found: hicup [2022-07-01 11:41:45,890] multiqc [DEBUG ] No samples found: hicpro [2022-07-01 11:41:45,895] multiqc [DEBUG ] No samples found: salmon [2022-07-01 11:41:45,903] multiqc [DEBUG ] No samples found: kallisto [2022-07-01 11:41:45,909] multiqc [DEBUG ] No samples found: slamdunk [2022-07-01 11:41:45,915] multiqc [DEBUG ] No samples found: star [2022-07-01 11:41:45,919] multiqc [DEBUG ] No samples found: hisat2 [2022-07-01 11:41:45,926] multiqc [DEBUG ] No samples found: tophat [2022-07-01 11:41:45,932] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-01 11:41:45,936] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-01 11:41:45,942] multiqc [DEBUG ] No samples found: snpsplit [2022-07-01 11:41:45,950] multiqc [DEBUG ] No samples found: kat [2022-07-01 11:41:45,956] multiqc [DEBUG ] No samples found: leehom [2022-07-01 11:41:45,964] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-01 11:41:45,968] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-01 11:41:45,973] multiqc [DEBUG ] No samples found: cutadapt [2022-07-01 11:41:45,977] multiqc [DEBUG ] No samples found: flexbar [2022-07-01 11:41:45,981] multiqc [DEBUG ] No samples found: kaiju [2022-07-01 11:41:45,987] multiqc [DEBUG ] No samples found: kraken [2022-07-01 11:41:45,992] multiqc [DEBUG ] No samples found: malt [2022-07-01 11:41:45,997] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-01 11:41:46,001] multiqc [DEBUG ] No samples found: sickle [2022-07-01 11:41:46,005] multiqc [DEBUG ] No samples found: skewer [2022-07-01 11:41:46,012] multiqc [DEBUG ] No samples found: sortmerna [2022-07-01 11:41:46,018] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-01 11:41:46,023] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-01 11:41:46,027] multiqc [DEBUG ] No samples found: afterqc [2022-07-01 11:41:46,034] multiqc [DEBUG ] No samples found: fastp [2022-07-01 11:41:46,298] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-07-01 11:41:46,345] multiqc [DEBUG ] No samples found: pycoqc [2022-07-01 11:41:46,349] multiqc [DEBUG ] No samples found: minionqc [2022-07-01 11:41:46,355] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-01 11:41:46,360] multiqc [DEBUG ] No samples found: clusterflow [2022-07-01 11:41:46,366] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-01 11:41:46,370] multiqc [DEBUG ] No samples found: interop [2022-07-01 11:41:46,376] multiqc [DEBUG ] No samples found: ivar [2022-07-01 11:41:46,380] multiqc [DEBUG ] No samples found: flash [2022-07-01 11:41:46,386] multiqc [DEBUG ] No samples found: seqyclean [2022-07-01 11:41:46,386] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-07-01 11:41:46,386] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-01 11:41:46,386] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-01 11:41:46,391] multiqc [INFO ] Compressing plot data [2022-07-01 11:41:46,458] multiqc [INFO ] Report : multiqc_report.html [2022-07-01 11:41:46,458] multiqc [INFO ] Data : multiqc_data [2022-07-01 11:41:46,458] multiqc [DEBUG ] Moving data file from '/state/partition1/job-21765014/tmp0vsu7djz/multiqc_data' to '/scratch/gencore/logs/html/HFFVHBGXM/merged/multiqc_data' [2022-07-01 11:41:46,588] multiqc [INFO ] MultiQC complete