[2022-07-29 05:21:05,550] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-29 05:21:05,550] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-29 05:21:05,550] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-29 05:21:05,551] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-29 05:21:05,551] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-29 05:21:05,551] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFWYFDRX2/2 [2022-07-29 05:21:05,949] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-29 05:21:05,949] multiqc [INFO ] This is MultiQC v1.9 [2022-07-29 05:21:05,949] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFWYFDRX2/2 [2022-07-29 05:21:05,949] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFWYFDRX2/2 [2022-07-29 05:21:05,949] multiqc [INFO ] Template : default [2022-07-29 05:21:05,949] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-29 05:21:05,949] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFWYFDRX2/2 [2022-07-29 05:21:05,949] 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 [2022-07-29 05:21:05,949] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22959527/tmpeulsd_67 [2022-07-29 05:21:06,042] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,044] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,044] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,044] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,044] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,044] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,045] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,045] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:06,045] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 05:21:09,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_N1_4DNAseq_fastqc.html [2022-07-29 05:21:09,866] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_N1_4DNAseq_fastqc.html [2022-07-29 05:21:09,906] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_N1_1DNAseq_fastqc.html [2022-07-29 05:21:09,908] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_N1_1DNAseq_fastqc.html [2022-07-29 05:21:09,947] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_undetermined_fastqc.html [2022-07-29 05:21:09,949] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_undetermined_fastqc.html [2022-07-29 05:21:09,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_N1_1DNAseq_fastqc.html [2022-07-29 05:21:09,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_N1_1DNAseq_fastqc.html [2022-07-29 05:21:10,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_N1_2DNAseq_fastqc.html [2022-07-29 05:21:10,031] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_N1_2DNAseq_fastqc.html [2022-07-29 05:21:10,071] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_N1_2DNAseq_fastqc.html [2022-07-29 05:21:10,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_N1_2DNAseq_fastqc.html [2022-07-29 05:21:10,112] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_undetermined_fastqc.html [2022-07-29 05:21:10,114] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n01_undetermined_fastqc.html [2022-07-29 05:21:10,154] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_N1_4DNAseq_fastqc.html [2022-07-29 05:21:10,156] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l02_n02_N1_4DNAseq_fastqc.html [2022-07-29 05:21:10,462] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-29 05:21:10,463] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-29 05:21:10,471] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 4 samples (table) [2022-07-29 05:21:10,481] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-29 05:21:10,482] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-29 05:21:10,486] multiqc [DEBUG ] No samples found: conpair [2022-07-29 05:21:10,489] multiqc [DEBUG ] No samples found: peddy [2022-07-29 05:21:10,492] multiqc [DEBUG ] No samples found: somalier [2022-07-29 05:21:10,495] multiqc [DEBUG ] No samples found: methylQA [2022-07-29 05:21:10,500] multiqc [DEBUG ] No samples found: mosdepth [2022-07-29 05:21:10,503] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-29 05:21:10,505] multiqc [DEBUG ] No samples found: qualimap [2022-07-29 05:21:10,508] multiqc [DEBUG ] No samples found: preseq [2022-07-29 05:21:10,511] multiqc [DEBUG ] No samples found: quast [2022-07-29 05:21:10,515] multiqc [DEBUG ] No samples found: qorts [2022-07-29 05:21:10,518] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-29 05:21:10,521] multiqc [DEBUG ] No samples found: rockhopper [2022-07-29 05:21:10,524] multiqc [DEBUG ] No samples found: rsem [2022-07-29 05:21:10,530] multiqc [DEBUG ] No samples found: rseqc [2022-07-29 05:21:10,533] multiqc [DEBUG ] No samples found: busco [2022-07-29 05:21:10,536] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-29 05:21:10,539] multiqc [DEBUG ] No samples found: disambiguate [2022-07-29 05:21:10,542] multiqc [DEBUG ] No samples found: supernova [2022-07-29 05:21:10,548] multiqc [DEBUG ] No samples found: deeptools [2022-07-29 05:21:10,551] multiqc [DEBUG ] No samples found: sargasso [2022-07-29 05:21:10,554] multiqc [DEBUG ] No samples found: verifybamid [2022-07-29 05:21:10,557] multiqc [DEBUG ] No samples found: mirtrace [2022-07-29 05:21:10,560] multiqc [DEBUG ] No samples found: happy [2022-07-29 05:21:10,563] multiqc [DEBUG ] No samples found: mirtop [2022-07-29 05:21:10,567] multiqc [DEBUG ] No samples found: homer [2022-07-29 05:21:10,570] multiqc [DEBUG ] No samples found: macs2 [2022-07-29 05:21:10,573] multiqc [DEBUG ] No samples found: theta2 [2022-07-29 05:21:10,576] multiqc [DEBUG ] No samples found: snpeff [2022-07-29 05:21:10,580] multiqc [DEBUG ] No samples found: gatk [2022-07-29 05:21:10,583] multiqc [DEBUG ] No samples found: htseq [2022-07-29 05:21:10,586] multiqc [DEBUG ] No samples found: bcftools [2022-07-29 05:21:10,589] multiqc [DEBUG ] No samples found: featureCounts [2022-07-29 05:21:10,593] multiqc [DEBUG ] No samples found: fgbio [2022-07-29 05:21:10,599] multiqc [DEBUG ] No samples found: dragen [2022-07-29 05:21:10,602] multiqc [DEBUG ] No samples found: dedup [2022-07-29 05:21:10,605] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-29 05:21:10,614] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-29 05:21:10,617] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-29 05:21:10,619] multiqc [DEBUG ] No samples found: picard [2022-07-29 05:21:10,622] multiqc [DEBUG ] No samples found: prokka [2022-07-29 05:21:10,625] multiqc [DEBUG ] No samples found: samblaster [2022-07-29 05:21:10,630] multiqc [DEBUG ] No samples found: samtools [2022-07-29 05:21:10,633] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-29 05:21:10,636] multiqc [DEBUG ] No samples found: bamtools [2022-07-29 05:21:10,639] multiqc [DEBUG ] No samples found: jellyfish [2022-07-29 05:21:10,643] multiqc [DEBUG ] No samples found: vcftools [2022-07-29 05:21:10,646] multiqc [DEBUG ] No samples found: longranger [2022-07-29 05:21:10,649] multiqc [DEBUG ] No samples found: stacks [2022-07-29 05:21:10,652] multiqc [DEBUG ] No samples found: varscan2 [2022-07-29 05:21:10,658] multiqc [DEBUG ] No samples found: bbmap [2022-07-29 05:21:10,661] multiqc [DEBUG ] No samples found: bismark [2022-07-29 05:21:10,665] multiqc [DEBUG ] No samples found: biscuit [2022-07-29 05:21:10,668] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-29 05:21:10,671] multiqc [DEBUG ] No samples found: hicup [2022-07-29 05:21:10,674] multiqc [DEBUG ] No samples found: hicpro [2022-07-29 05:21:10,677] multiqc [DEBUG ] No samples found: salmon [2022-07-29 05:21:10,680] multiqc [DEBUG ] No samples found: kallisto [2022-07-29 05:21:10,683] multiqc [DEBUG ] No samples found: slamdunk [2022-07-29 05:21:10,686] multiqc [DEBUG ] No samples found: star [2022-07-29 05:21:10,689] multiqc [DEBUG ] No samples found: hisat2 [2022-07-29 05:21:10,692] multiqc [DEBUG ] No samples found: tophat [2022-07-29 05:21:10,695] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-29 05:21:10,698] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-29 05:21:10,701] multiqc [DEBUG ] No samples found: snpsplit [2022-07-29 05:21:10,704] multiqc [DEBUG ] No samples found: kat [2022-07-29 05:21:10,707] multiqc [DEBUG ] No samples found: leehom [2022-07-29 05:21:10,710] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-29 05:21:10,713] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-29 05:21:10,716] multiqc [DEBUG ] No samples found: cutadapt [2022-07-29 05:21:10,719] multiqc [DEBUG ] No samples found: flexbar [2022-07-29 05:21:10,722] multiqc [DEBUG ] No samples found: kaiju [2022-07-29 05:21:10,725] multiqc [DEBUG ] No samples found: kraken [2022-07-29 05:21:10,728] multiqc [DEBUG ] No samples found: malt [2022-07-29 05:21:10,731] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-29 05:21:10,734] multiqc [DEBUG ] No samples found: sickle [2022-07-29 05:21:10,737] multiqc [DEBUG ] No samples found: skewer [2022-07-29 05:21:10,740] multiqc [DEBUG ] No samples found: sortmerna [2022-07-29 05:21:10,743] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-29 05:21:10,746] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-29 05:21:10,749] multiqc [DEBUG ] No samples found: afterqc [2022-07-29 05:21:10,752] multiqc [DEBUG ] No samples found: fastp [2022-07-29 05:21:10,938] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-07-29 05:21:11,044] multiqc [DEBUG ] No samples found: pycoqc [2022-07-29 05:21:11,047] multiqc [DEBUG ] No samples found: minionqc [2022-07-29 05:21:11,050] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-29 05:21:11,053] multiqc [DEBUG ] No samples found: clusterflow [2022-07-29 05:21:11,056] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-29 05:21:11,059] multiqc [DEBUG ] No samples found: interop [2022-07-29 05:21:11,062] multiqc [DEBUG ] No samples found: ivar [2022-07-29 05:21:11,065] multiqc [DEBUG ] No samples found: flash [2022-07-29 05:21:11,068] multiqc [DEBUG ] No samples found: seqyclean [2022-07-29 05:21:11,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-07-29 05:21:11,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2022-07-29 05:21:11,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-29 05:21:11,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-07-29 05:21:11,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-29 05:21:11,078] multiqc [INFO ] Compressing plot data [2022-07-29 05:21:11,228] multiqc [INFO ] Report : multiqc_report.html [2022-07-29 05:21:11,229] multiqc [INFO ] Data : multiqc_data [2022-07-29 05:21:11,229] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22959527/tmpeulsd_67/multiqc_data' to '/scratch/gencore/logs/html/HFWYFDRX2/2/multiqc_data' [2022-07-29 05:21:11,328] multiqc [INFO ] MultiQC complete