[2021-11-19 11:32:42,346] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-19 11:32:42,347] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-19 11:32:42,347] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-19 11:32:42,347] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-19 11:32:42,348] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-19 11:32:42,348] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLKNCDRXY/merged [2021-11-19 11:32:44,911] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-19 11:32:44,911] multiqc [INFO ] This is MultiQC v1.9 [2021-11-19 11:32:44,911] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLKNCDRXY/merged [2021-11-19 11:32:44,911] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLKNCDRXY/merged [2021-11-19 11:32:44,911] multiqc [INFO ] Template : default [2021-11-19 11:32:44,911] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-19 11:32:44,911] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLKNCDRXY/merged [2021-11-19 11:32:44,912] 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 [2021-11-19 11:32:44,912] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12151274/tmpnlow2k_d [2021-11-19 11:32:45,015] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK53_fastqc.html [2021-11-19 11:32:45,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK53_fastqc.html [2021-11-19 11:32:45,058] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:45,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:45,059] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:45,059] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:45,059] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:45,059] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:45,059] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:45,139] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-19 11:32:48,463] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK53_fastqc.html [2021-11-19 11:32:48,465] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK53_fastqc.html [2021-11-19 11:32:48,522] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK52_fastqc.html [2021-11-19 11:32:48,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK52_fastqc.html [2021-11-19 11:32:48,562] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK51_fastqc.html [2021-11-19 11:32:48,564] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK51_fastqc.html [2021-11-19 11:32:48,617] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK19_2_fastqc.html [2021-11-19 11:32:48,619] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK19_2_fastqc.html [2021-11-19 11:32:48,668] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n01_undetermined_fastqc.html [2021-11-19 11:32:48,670] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n01_undetermined_fastqc.html [2021-11-19 11:32:48,737] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK19_2_fastqc.html [2021-11-19 11:32:48,739] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK19_2_fastqc.html [2021-11-19 11:32:48,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK52_fastqc.html [2021-11-19 11:32:48,800] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n01_JK52_fastqc.html [2021-11-19 11:32:48,839] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK51_fastqc.html [2021-11-19 11:32:48,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n02_JK51_fastqc.html [2021-11-19 11:32:48,908] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLKNCDRXY_n02_undetermined_fastqc.html [2021-11-19 11:32:48,909] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLKNCDRXY_n02_undetermined_fastqc.html [2021-11-19 11:32:49,321] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-19 11:32:49,322] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-19 11:32:49,329] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-19 11:32:49,332] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2021-11-19 11:32:49,342] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-19 11:32:49,345] multiqc [DEBUG ] No samples found: conpair [2021-11-19 11:32:49,350] multiqc [DEBUG ] No samples found: peddy [2021-11-19 11:32:49,354] multiqc [DEBUG ] No samples found: somalier [2021-11-19 11:32:49,358] multiqc [DEBUG ] No samples found: methylQA [2021-11-19 11:32:49,365] multiqc [DEBUG ] No samples found: mosdepth [2021-11-19 11:32:49,369] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-19 11:32:49,372] multiqc [DEBUG ] No samples found: qualimap [2021-11-19 11:32:49,377] multiqc [DEBUG ] No samples found: preseq [2021-11-19 11:32:49,381] multiqc [DEBUG ] No samples found: quast [2021-11-19 11:32:49,385] multiqc [DEBUG ] No samples found: qorts [2021-11-19 11:32:49,389] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-19 11:32:49,394] multiqc [DEBUG ] No samples found: rockhopper [2021-11-19 11:32:49,398] multiqc [DEBUG ] No samples found: rsem [2021-11-19 11:32:49,406] multiqc [DEBUG ] No samples found: rseqc [2021-11-19 11:32:49,410] multiqc [DEBUG ] No samples found: busco [2021-11-19 11:32:49,414] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-19 11:32:49,418] multiqc [DEBUG ] No samples found: disambiguate [2021-11-19 11:32:49,425] multiqc [DEBUG ] No samples found: supernova [2021-11-19 11:32:49,436] multiqc [DEBUG ] No samples found: deeptools [2021-11-19 11:32:49,440] multiqc [DEBUG ] No samples found: sargasso [2021-11-19 11:32:49,444] multiqc [DEBUG ] No samples found: verifybamid [2021-11-19 11:32:49,449] multiqc [DEBUG ] No samples found: mirtrace [2021-11-19 11:32:49,453] multiqc [DEBUG ] No samples found: happy [2021-11-19 11:32:49,458] multiqc [DEBUG ] No samples found: mirtop [2021-11-19 11:32:49,463] multiqc [DEBUG ] No samples found: homer [2021-11-19 11:32:49,467] multiqc [DEBUG ] No samples found: macs2 [2021-11-19 11:32:49,471] multiqc [DEBUG ] No samples found: theta2 [2021-11-19 11:32:49,475] multiqc [DEBUG ] No samples found: snpeff [2021-11-19 11:32:49,481] multiqc [DEBUG ] No samples found: gatk [2021-11-19 11:32:49,484] multiqc [DEBUG ] No samples found: htseq [2021-11-19 11:32:49,489] multiqc [DEBUG ] No samples found: bcftools [2021-11-19 11:32:49,493] multiqc [DEBUG ] No samples found: featureCounts [2021-11-19 11:32:49,498] multiqc [DEBUG ] No samples found: fgbio [2021-11-19 11:32:49,509] multiqc [DEBUG ] No samples found: dragen [2021-11-19 11:32:49,513] multiqc [DEBUG ] No samples found: dedup [2021-11-19 11:32:49,517] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-19 11:32:49,537] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-19 11:32:49,541] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-19 11:32:49,543] multiqc [DEBUG ] No samples found: picard [2021-11-19 11:32:49,547] multiqc [DEBUG ] No samples found: prokka [2021-11-19 11:32:49,551] multiqc [DEBUG ] No samples found: samblaster [2021-11-19 11:32:49,558] multiqc [DEBUG ] No samples found: samtools [2021-11-19 11:32:49,563] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-19 11:32:49,567] multiqc [DEBUG ] No samples found: bamtools [2021-11-19 11:32:49,570] multiqc [DEBUG ] No samples found: jellyfish [2021-11-19 11:32:49,576] multiqc [DEBUG ] No samples found: vcftools [2021-11-19 11:32:49,580] multiqc [DEBUG ] No samples found: longranger [2021-11-19 11:32:49,585] multiqc [DEBUG ] No samples found: stacks [2021-11-19 11:32:49,589] multiqc [DEBUG ] No samples found: varscan2 [2021-11-19 11:32:49,600] multiqc [DEBUG ] No samples found: bbmap [2021-11-19 11:32:49,604] multiqc [DEBUG ] No samples found: bismark [2021-11-19 11:32:49,608] multiqc [DEBUG ] No samples found: biscuit [2021-11-19 11:32:49,612] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-19 11:32:49,617] multiqc [DEBUG ] No samples found: hicup [2021-11-19 11:32:49,621] multiqc [DEBUG ] No samples found: hicpro [2021-11-19 11:32:49,624] multiqc [DEBUG ] No samples found: salmon [2021-11-19 11:32:49,628] multiqc [DEBUG ] No samples found: kallisto [2021-11-19 11:32:49,633] multiqc [DEBUG ] No samples found: slamdunk [2021-11-19 11:32:49,637] multiqc [DEBUG ] No samples found: star [2021-11-19 11:32:49,641] multiqc [DEBUG ] No samples found: hisat2 [2021-11-19 11:32:49,645] multiqc [DEBUG ] No samples found: tophat [2021-11-19 11:32:49,649] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-19 11:32:49,653] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-19 11:32:49,657] multiqc [DEBUG ] No samples found: snpsplit [2021-11-19 11:32:49,661] multiqc [DEBUG ] No samples found: kat [2021-11-19 11:32:49,664] multiqc [DEBUG ] No samples found: leehom [2021-11-19 11:32:49,669] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-19 11:32:49,672] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-19 11:32:49,676] multiqc [DEBUG ] No samples found: cutadapt [2021-11-19 11:32:49,680] multiqc [DEBUG ] No samples found: flexbar [2021-11-19 11:32:49,684] multiqc [DEBUG ] No samples found: kaiju [2021-11-19 11:32:49,688] multiqc [DEBUG ] No samples found: kraken [2021-11-19 11:32:49,692] multiqc [DEBUG ] No samples found: malt [2021-11-19 11:32:49,697] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-19 11:32:49,701] multiqc [DEBUG ] No samples found: sickle [2021-11-19 11:32:49,705] multiqc [DEBUG ] No samples found: skewer [2021-11-19 11:32:49,708] multiqc [DEBUG ] No samples found: sortmerna [2021-11-19 11:32:49,712] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-19 11:32:49,716] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-19 11:32:49,720] multiqc [DEBUG ] No samples found: afterqc [2021-11-19 11:32:49,724] multiqc [DEBUG ] No samples found: fastp [2021-11-19 11:32:50,255] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-11-19 11:32:50,403] multiqc [DEBUG ] No samples found: pycoqc [2021-11-19 11:32:50,407] multiqc [DEBUG ] No samples found: minionqc [2021-11-19 11:32:50,437] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-19 11:32:50,441] multiqc [DEBUG ] No samples found: clusterflow [2021-11-19 11:32:50,445] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-19 11:32:50,449] multiqc [DEBUG ] No samples found: interop [2021-11-19 11:32:50,453] multiqc [DEBUG ] No samples found: ivar [2021-11-19 11:32:50,457] multiqc [DEBUG ] No samples found: flash [2021-11-19 11:32:50,461] multiqc [DEBUG ] No samples found: seqyclean [2021-11-19 11:32:50,461] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-19 11:32:50,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-19 11:32:50,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-19 11:32:50,462] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-19 11:32:50,474] multiqc [INFO ] Compressing plot data [2021-11-19 11:32:50,647] multiqc [INFO ] Report : multiqc_report.html [2021-11-19 11:32:50,647] multiqc [INFO ] Data : multiqc_data [2021-11-19 11:32:50,647] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12151274/tmpnlow2k_d/multiqc_data' to '/scratch/gencore/logs/html/HLKNCDRXY/merged/multiqc_data' [2021-11-19 11:32:50,771] multiqc [INFO ] MultiQC complete