[2022-06-14 07:09:35,396] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-06-14 07:09:35,396] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-06-14 07:09:35,396] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-06-14 07:09:35,397] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-06-14 07:09:35,397] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-06-14 07:09:35,398] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3NGLBGXM/merged [2022-06-14 07:09:36,140] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-06-14 07:09:36,140] multiqc [INFO ] This is MultiQC v1.9 [2022-06-14 07:09:36,140] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3NGLBGXM/merged [2022-06-14 07:09:36,140] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3NGLBGXM/merged [2022-06-14 07:09:36,140] multiqc [INFO ] Template : default [2022-06-14 07:09:36,140] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-06-14 07:09:36,140] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3NGLBGXM/merged [2022-06-14 07:09:36,141] 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 [2022-06-14 07:09:36,141] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20844467/tmplpqs24gy [2022-06-14 07:09:36,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-14 07:09:36,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-14 07:09:36,485] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n02_HTO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,487] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n02_HTO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,547] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n01_GDO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,549] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n01_GDO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,632] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n01_HTO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,634] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n01_HTO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n02_cDNA_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,677] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n02_cDNA_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n01_undetermined_fastqc.html [2022-06-14 07:09:36,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n01_undetermined_fastqc.html [2022-06-14 07:09:36,778] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n02_undetermined_fastqc.html [2022-06-14 07:09:36,780] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n02_undetermined_fastqc.html [2022-06-14 07:09:36,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n02_GDO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,827] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n02_GDO_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,894] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3NGLBGXM_n01_cDNA_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:36,896] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3NGLBGXM_n01_cDNA_A1_PS_ASV1_fastqc.html [2022-06-14 07:09:37,407] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-14 07:09:37,408] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-14 07:09:37,417] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 4 samples (table) [2022-06-14 07:09:37,419] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-06-14 07:09:37,428] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-06-14 07:09:37,433] multiqc [DEBUG ] No samples found: conpair [2022-06-14 07:09:37,438] multiqc [DEBUG ] No samples found: peddy [2022-06-14 07:09:37,443] multiqc [DEBUG ] No samples found: somalier [2022-06-14 07:09:37,448] multiqc [DEBUG ] No samples found: methylQA [2022-06-14 07:09:37,457] multiqc [DEBUG ] No samples found: mosdepth [2022-06-14 07:09:37,461] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-06-14 07:09:37,465] multiqc [DEBUG ] No samples found: qualimap [2022-06-14 07:09:37,470] multiqc [DEBUG ] No samples found: preseq [2022-06-14 07:09:37,474] multiqc [DEBUG ] No samples found: quast [2022-06-14 07:09:37,479] multiqc [DEBUG ] No samples found: qorts [2022-06-14 07:09:37,484] multiqc [DEBUG ] No samples found: rna_seqc [2022-06-14 07:09:37,489] multiqc [DEBUG ] No samples found: rockhopper [2022-06-14 07:09:37,493] multiqc [DEBUG ] No samples found: rsem [2022-06-14 07:09:37,505] multiqc [DEBUG ] No samples found: rseqc [2022-06-14 07:09:37,510] multiqc [DEBUG ] No samples found: busco [2022-06-14 07:09:37,515] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-06-14 07:09:37,519] multiqc [DEBUG ] No samples found: disambiguate [2022-06-14 07:09:37,524] multiqc [DEBUG ] No samples found: supernova [2022-06-14 07:09:37,537] multiqc [DEBUG ] No samples found: deeptools [2022-06-14 07:09:37,541] multiqc [DEBUG ] No samples found: sargasso [2022-06-14 07:09:37,546] multiqc [DEBUG ] No samples found: verifybamid [2022-06-14 07:09:37,551] multiqc [DEBUG ] No samples found: mirtrace [2022-06-14 07:09:37,556] multiqc [DEBUG ] No samples found: happy [2022-06-14 07:09:37,560] multiqc [DEBUG ] No samples found: mirtop [2022-06-14 07:09:37,567] multiqc [DEBUG ] No samples found: homer [2022-06-14 07:09:37,572] multiqc [DEBUG ] No samples found: macs2 [2022-06-14 07:09:37,576] multiqc [DEBUG ] No samples found: theta2 [2022-06-14 07:09:37,581] multiqc [DEBUG ] No samples found: snpeff [2022-06-14 07:09:37,588] multiqc [DEBUG ] No samples found: gatk [2022-06-14 07:09:37,593] multiqc [DEBUG ] No samples found: htseq [2022-06-14 07:09:37,598] multiqc [DEBUG ] No samples found: bcftools [2022-06-14 07:09:37,603] multiqc [DEBUG ] No samples found: featureCounts [2022-06-14 07:09:37,609] multiqc [DEBUG ] No samples found: fgbio [2022-06-14 07:09:37,622] multiqc [DEBUG ] No samples found: dragen [2022-06-14 07:09:37,627] multiqc [DEBUG ] No samples found: dedup [2022-06-14 07:09:37,632] multiqc [DEBUG ] No samples found: damageprofiler [2022-06-14 07:09:37,655] multiqc [DEBUG ] No samples found: biobambam2 [2022-06-14 07:09:37,660] multiqc [DEBUG ] No samples found: mtnucratio [2022-06-14 07:09:37,663] multiqc [DEBUG ] No samples found: picard [2022-06-14 07:09:37,668] multiqc [DEBUG ] No samples found: prokka [2022-06-14 07:09:37,672] multiqc [DEBUG ] No samples found: samblaster [2022-06-14 07:09:37,681] multiqc [DEBUG ] No samples found: samtools [2022-06-14 07:09:37,685] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-06-14 07:09:37,691] multiqc [DEBUG ] No samples found: bamtools [2022-06-14 07:09:37,695] multiqc [DEBUG ] No samples found: jellyfish [2022-06-14 07:09:37,702] multiqc [DEBUG ] No samples found: vcftools [2022-06-14 07:09:37,708] multiqc [DEBUG ] No samples found: longranger [2022-06-14 07:09:37,712] multiqc [DEBUG ] No samples found: stacks [2022-06-14 07:09:37,717] multiqc [DEBUG ] No samples found: varscan2 [2022-06-14 07:09:37,731] multiqc [DEBUG ] No samples found: bbmap [2022-06-14 07:09:37,736] multiqc [DEBUG ] No samples found: bismark [2022-06-14 07:09:37,741] multiqc [DEBUG ] No samples found: biscuit [2022-06-14 07:09:37,746] multiqc [DEBUG ] No samples found: hicexplorer [2022-06-14 07:09:37,751] multiqc [DEBUG ] No samples found: hicup [2022-06-14 07:09:37,756] multiqc [DEBUG ] No samples found: hicpro [2022-06-14 07:09:37,760] multiqc [DEBUG ] No samples found: salmon [2022-06-14 07:09:37,764] multiqc [DEBUG ] No samples found: kallisto [2022-06-14 07:09:37,769] multiqc [DEBUG ] No samples found: slamdunk [2022-06-14 07:09:37,774] multiqc [DEBUG ] No samples found: star [2022-06-14 07:09:37,779] multiqc [DEBUG ] No samples found: hisat2 [2022-06-14 07:09:37,783] multiqc [DEBUG ] No samples found: tophat [2022-06-14 07:09:37,788] multiqc [DEBUG ] No samples found: bowtie2 [2022-06-14 07:09:37,793] multiqc [DEBUG ] No samples found: bowtie1 [2022-06-14 07:09:37,798] multiqc [DEBUG ] No samples found: snpsplit [2022-06-14 07:09:37,802] multiqc [DEBUG ] No samples found: kat [2022-06-14 07:09:37,806] multiqc [DEBUG ] No samples found: leehom [2022-06-14 07:09:37,811] multiqc [DEBUG ] No samples found: adapterRemoval [2022-06-14 07:09:37,816] multiqc [DEBUG ] No samples found: clipandmerge [2022-06-14 07:09:37,820] multiqc [DEBUG ] No samples found: cutadapt [2022-06-14 07:09:37,824] multiqc [DEBUG ] No samples found: flexbar [2022-06-14 07:09:37,829] multiqc [DEBUG ] No samples found: kaiju [2022-06-14 07:09:37,834] multiqc [DEBUG ] No samples found: kraken [2022-06-14 07:09:37,839] multiqc [DEBUG ] No samples found: malt [2022-06-14 07:09:37,843] multiqc [DEBUG ] No samples found: trimmomatic [2022-06-14 07:09:37,848] multiqc [DEBUG ] No samples found: sickle [2022-06-14 07:09:37,853] multiqc [DEBUG ] No samples found: skewer [2022-06-14 07:09:37,857] multiqc [DEBUG ] No samples found: sortmerna [2022-06-14 07:09:37,862] multiqc [DEBUG ] No samples found: biobloomtools [2022-06-14 07:09:37,867] multiqc [DEBUG ] No samples found: fastq_screen [2022-06-14 07:09:37,872] multiqc [DEBUG ] No samples found: afterqc [2022-06-14 07:09:37,877] multiqc [DEBUG ] No samples found: fastp [2022-06-14 07:09:38,357] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-06-14 07:09:38,438] multiqc [DEBUG ] No samples found: pycoqc [2022-06-14 07:09:38,443] multiqc [DEBUG ] No samples found: minionqc [2022-06-14 07:09:38,447] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-06-14 07:09:38,452] multiqc [DEBUG ] No samples found: clusterflow [2022-06-14 07:09:38,457] multiqc [DEBUG ] No samples found: bcl2fastq [2022-06-14 07:09:38,462] multiqc [DEBUG ] No samples found: interop [2022-06-14 07:09:38,466] multiqc [DEBUG ] No samples found: ivar [2022-06-14 07:09:38,471] multiqc [DEBUG ] No samples found: flash [2022-06-14 07:09:38,476] multiqc [DEBUG ] No samples found: seqyclean [2022-06-14 07:09:38,476] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-06-14 07:09:38,476] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-06-14 07:09:38,476] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-06-14 07:09:38,476] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-06-14 07:09:38,486] multiqc [INFO ] Compressing plot data [2022-06-14 07:09:38,628] multiqc [INFO ] Report : multiqc_report.html [2022-06-14 07:09:38,629] multiqc [INFO ] Data : multiqc_data [2022-06-14 07:09:38,629] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20844467/tmplpqs24gy/multiqc_data' to '/scratch/gencore/logs/html/H3NGLBGXM/merged/multiqc_data' [2022-06-14 07:09:38,796] multiqc [INFO ] MultiQC complete