[2022-04-22 06:54:55,581] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-22 06:54:55,581] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-22 06:54:55,581] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-22 06:54:55,582] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-22 06:54:55,582] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-22 06:54:55,582] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKNNLAFX3/merged [2022-04-22 06:54:55,982] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-22 06:54:55,982] multiqc [INFO ] This is MultiQC v1.9 [2022-04-22 06:54:55,982] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKNNLAFX3/merged [2022-04-22 06:54:55,982] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKNNLAFX3/merged [2022-04-22 06:54:55,982] multiqc [INFO ] Template : default [2022-04-22 06:54:55,982] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-22 06:54:55,982] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKNNLAFX3/merged [2022-04-22 06:54:55,983] 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 [2022-04-22 06:54:55,983] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-18424804/tmpus8fwe1x [2022-04-22 06:54:56,088] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:56,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:56,091] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:56,091] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:56,091] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:56,091] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:56,091] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:56,130] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-22 06:54:57,946] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKNNLAFX3_n01_undetermined_fastqc.html [2022-04-22 06:54:57,948] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKNNLAFX3_n01_undetermined_fastqc.html [2022-04-22 06:54:57,987] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKNNLAFX3_n01_10x_Pura_r1_fastqc.html [2022-04-22 06:54:57,989] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKNNLAFX3_n01_10x_Pura_r1_fastqc.html [2022-04-22 06:54:58,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKNNLAFX3_n02_10x_Pura_r1_fastqc.html [2022-04-22 06:54:58,032] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKNNLAFX3_n02_10x_Pura_r1_fastqc.html [2022-04-22 06:54:58,073] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKNNLAFX3_n01_10x_Pura_r2_fastqc.html [2022-04-22 06:54:58,075] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKNNLAFX3_n01_10x_Pura_r2_fastqc.html [2022-04-22 06:54:58,115] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKNNLAFX3_n02_10x_Pura_r2_fastqc.html [2022-04-22 06:54:58,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKNNLAFX3_n02_10x_Pura_r2_fastqc.html [2022-04-22 06:54:58,159] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKNNLAFX3_n02_undetermined_fastqc.html [2022-04-22 06:54:58,161] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKNNLAFX3_n02_undetermined_fastqc.html [2022-04-22 06:54:58,490] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-22 06:54:58,492] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-22 06:54:58,499] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2022-04-22 06:54:58,509] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-22 06:54:58,511] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-22 06:54:58,515] multiqc [DEBUG ] No samples found: conpair [2022-04-22 06:54:58,520] multiqc [DEBUG ] No samples found: peddy [2022-04-22 06:54:58,525] multiqc [DEBUG ] No samples found: somalier [2022-04-22 06:54:58,529] multiqc [DEBUG ] No samples found: methylQA [2022-04-22 06:54:58,537] multiqc [DEBUG ] No samples found: mosdepth [2022-04-22 06:54:58,541] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-22 06:54:58,544] multiqc [DEBUG ] No samples found: qualimap [2022-04-22 06:54:58,549] multiqc [DEBUG ] No samples found: preseq [2022-04-22 06:54:58,553] multiqc [DEBUG ] No samples found: quast [2022-04-22 06:54:58,558] multiqc [DEBUG ] No samples found: qorts [2022-04-22 06:54:58,562] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-22 06:54:58,567] multiqc [DEBUG ] No samples found: rockhopper [2022-04-22 06:54:58,572] multiqc [DEBUG ] No samples found: rsem [2022-04-22 06:54:58,582] multiqc [DEBUG ] No samples found: rseqc [2022-04-22 06:54:58,586] multiqc [DEBUG ] No samples found: busco [2022-04-22 06:54:58,590] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-22 06:54:58,594] multiqc [DEBUG ] No samples found: disambiguate [2022-04-22 06:54:58,599] multiqc [DEBUG ] No samples found: supernova [2022-04-22 06:54:58,610] multiqc [DEBUG ] No samples found: deeptools [2022-04-22 06:54:58,614] multiqc [DEBUG ] No samples found: sargasso [2022-04-22 06:54:58,619] multiqc [DEBUG ] No samples found: verifybamid [2022-04-22 06:54:58,623] multiqc [DEBUG ] No samples found: mirtrace [2022-04-22 06:54:58,627] multiqc [DEBUG ] No samples found: happy [2022-04-22 06:54:58,632] multiqc [DEBUG ] No samples found: mirtop [2022-04-22 06:54:58,637] multiqc [DEBUG ] No samples found: homer [2022-04-22 06:54:58,642] multiqc [DEBUG ] No samples found: macs2 [2022-04-22 06:54:58,646] multiqc [DEBUG ] No samples found: theta2 [2022-04-22 06:54:58,651] multiqc [DEBUG ] No samples found: snpeff [2022-04-22 06:54:58,657] multiqc [DEBUG ] No samples found: gatk [2022-04-22 06:54:58,661] multiqc [DEBUG ] No samples found: htseq [2022-04-22 06:54:58,666] multiqc [DEBUG ] No samples found: bcftools [2022-04-22 06:54:58,670] multiqc [DEBUG ] No samples found: featureCounts [2022-04-22 06:54:58,676] multiqc [DEBUG ] No samples found: fgbio [2022-04-22 06:54:58,688] multiqc [DEBUG ] No samples found: dragen [2022-04-22 06:54:58,692] multiqc [DEBUG ] No samples found: dedup [2022-04-22 06:54:58,696] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-22 06:54:58,717] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-22 06:54:58,721] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-22 06:54:58,723] multiqc [DEBUG ] No samples found: picard [2022-04-22 06:54:58,727] multiqc [DEBUG ] No samples found: prokka [2022-04-22 06:54:58,731] multiqc [DEBUG ] No samples found: samblaster [2022-04-22 06:54:58,739] multiqc [DEBUG ] No samples found: samtools [2022-04-22 06:54:58,743] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-22 06:54:58,748] multiqc [DEBUG ] No samples found: bamtools [2022-04-22 06:54:58,753] multiqc [DEBUG ] No samples found: jellyfish [2022-04-22 06:54:58,760] multiqc [DEBUG ] No samples found: vcftools [2022-04-22 06:54:58,764] multiqc [DEBUG ] No samples found: longranger [2022-04-22 06:54:58,769] multiqc [DEBUG ] No samples found: stacks [2022-04-22 06:54:58,773] multiqc [DEBUG ] No samples found: varscan2 [2022-04-22 06:54:58,786] multiqc [DEBUG ] No samples found: bbmap [2022-04-22 06:54:58,790] multiqc [DEBUG ] No samples found: bismark [2022-04-22 06:54:58,795] multiqc [DEBUG ] No samples found: biscuit [2022-04-22 06:54:58,799] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-22 06:54:58,804] multiqc [DEBUG ] No samples found: hicup [2022-04-22 06:54:58,808] multiqc [DEBUG ] No samples found: hicpro [2022-04-22 06:54:58,812] multiqc [DEBUG ] No samples found: salmon [2022-04-22 06:54:58,816] multiqc [DEBUG ] No samples found: kallisto [2022-04-22 06:54:58,821] multiqc [DEBUG ] No samples found: slamdunk [2022-04-22 06:54:58,825] multiqc [DEBUG ] No samples found: star [2022-04-22 06:54:58,830] multiqc [DEBUG ] No samples found: hisat2 [2022-04-22 06:54:58,834] multiqc [DEBUG ] No samples found: tophat [2022-04-22 06:54:58,838] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-22 06:54:58,842] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-22 06:54:58,847] multiqc [DEBUG ] No samples found: snpsplit [2022-04-22 06:54:58,851] multiqc [DEBUG ] No samples found: kat [2022-04-22 06:54:58,855] multiqc [DEBUG ] No samples found: leehom [2022-04-22 06:54:58,860] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-22 06:54:58,864] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-22 06:54:58,868] multiqc [DEBUG ] No samples found: cutadapt [2022-04-22 06:54:58,872] multiqc [DEBUG ] No samples found: flexbar [2022-04-22 06:54:58,876] multiqc [DEBUG ] No samples found: kaiju [2022-04-22 06:54:58,881] multiqc [DEBUG ] No samples found: kraken [2022-04-22 06:54:58,885] multiqc [DEBUG ] No samples found: malt [2022-04-22 06:54:58,890] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-22 06:54:58,894] multiqc [DEBUG ] No samples found: sickle [2022-04-22 06:54:58,898] multiqc [DEBUG ] No samples found: skewer [2022-04-22 06:54:58,902] multiqc [DEBUG ] No samples found: sortmerna [2022-04-22 06:54:58,906] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-22 06:54:58,910] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-22 06:54:58,917] multiqc [DEBUG ] No samples found: afterqc [2022-04-22 06:54:58,921] multiqc [DEBUG ] No samples found: fastp [2022-04-22 06:54:59,124] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2022-04-22 06:54:59,191] multiqc [DEBUG ] No samples found: pycoqc [2022-04-22 06:54:59,196] multiqc [DEBUG ] No samples found: minionqc [2022-04-22 06:54:59,201] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-22 06:54:59,205] multiqc [DEBUG ] No samples found: clusterflow [2022-04-22 06:54:59,210] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-22 06:54:59,214] multiqc [DEBUG ] No samples found: interop [2022-04-22 06:54:59,219] multiqc [DEBUG ] No samples found: ivar [2022-04-22 06:54:59,223] multiqc [DEBUG ] No samples found: flash [2022-04-22 06:54:59,227] multiqc [DEBUG ] No samples found: seqyclean [2022-04-22 06:54:59,227] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-22 06:54:59,227] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-22 06:54:59,228] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-22 06:54:59,228] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-22 06:54:59,235] multiqc [INFO ] Compressing plot data [2022-04-22 06:54:59,345] multiqc [INFO ] Report : multiqc_report.html [2022-04-22 06:54:59,345] multiqc [INFO ] Data : multiqc_data [2022-04-22 06:54:59,345] multiqc [DEBUG ] Moving data file from '/state/partition1/job-18424804/tmpus8fwe1x/multiqc_data' to '/scratch/gencore/logs/html/HKNNLAFX3/merged/multiqc_data' [2022-04-22 06:54:59,462] multiqc [INFO ] MultiQC complete