[2021-12-07 18:42:03,718] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-07 18:42:03,718] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-07 18:42:03,718] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-07 18:42:03,719] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-07 18:42:03,719] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-07 18:42:03,719] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCLMMAFX3/merged [2021-12-07 18:42:05,286] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-07 18:42:05,286] multiqc [INFO ] This is MultiQC v1.9 [2021-12-07 18:42:05,286] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCLMMAFX3/merged [2021-12-07 18:42:05,287] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HCLMMAFX3/merged [2021-12-07 18:42:05,287] multiqc [INFO ] Template : default [2021-12-07 18:42:05,287] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-07 18:42:05,287] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HCLMMAFX3/merged [2021-12-07 18:42:05,287] 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 [2021-12-07 18:42:05,287] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12875240/tmpyayp4p8z [2021-12-07 18:42:05,387] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-07 18:42:05,390] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-07 18:42:05,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657in_flag_fastqc.html [2021-12-07 18:42:05,494] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657in_flag_fastqc.html [2021-12-07 18:42:05,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657spk-chp-Flag_fastqc.html [2021-12-07 18:42:05,535] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657spk-chp-Flag_fastqc.html [2021-12-07 18:42:05,595] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657in_flag_fastqc.html [2021-12-07 18:42:05,596] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657in_flag_fastqc.html [2021-12-07 18:42:05,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658chp_flag_fastqc.html [2021-12-07 18:42:05,637] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658chp_flag_fastqc.html [2021-12-07 18:42:05,677] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658chp_flag_fastqc.html [2021-12-07 18:42:05,679] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658chp_flag_fastqc.html [2021-12-07 18:42:05,748] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657chp_flag_fastqc.html [2021-12-07 18:42:05,750] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657chp_flag_fastqc.html [2021-12-07 18:42:05,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_undetermined_fastqc.html [2021-12-07 18:42:05,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_undetermined_fastqc.html [2021-12-07 18:42:05,851] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658spk-chp-Flag_fastqc.html [2021-12-07 18:42:05,853] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658spk-chp-Flag_fastqc.html [2021-12-07 18:42:05,892] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657chp_flag_fastqc.html [2021-12-07 18:42:05,894] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657chp_flag_fastqc.html [2021-12-07 18:42:05,933] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658spk-in-Flag_fastqc.html [2021-12-07 18:42:05,935] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658spk-in-Flag_fastqc.html [2021-12-07 18:42:05,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657spk-chp-Flag_fastqc.html [2021-12-07 18:42:05,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657spk-chp-Flag_fastqc.html [2021-12-07 18:42:06,037] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_undetermined_fastqc.html [2021-12-07 18:42:06,038] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_undetermined_fastqc.html [2021-12-07 18:42:06,077] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657spk-in-Flag_fastqc.html [2021-12-07 18:42:06,078] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11657spk-in-Flag_fastqc.html [2021-12-07 18:42:06,117] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658spk-in-Flag_fastqc.html [2021-12-07 18:42:06,118] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658spk-in-Flag_fastqc.html [2021-12-07 18:42:06,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658spk-chp-Flag_fastqc.html [2021-12-07 18:42:06,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658spk-chp-Flag_fastqc.html [2021-12-07 18:42:06,198] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657spk-in-Flag_fastqc.html [2021-12-07 18:42:06,199] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11657spk-in-Flag_fastqc.html [2021-12-07 18:42:06,238] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658in_flag_fastqc.html [2021-12-07 18:42:06,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n01_11658in_flag_fastqc.html [2021-12-07 18:42:06,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658in_flag_fastqc.html [2021-12-07 18:42:06,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCLMMAFX3_n02_11658in_flag_fastqc.html [2021-12-07 18:42:06,716] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-07 18:42:06,717] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-07 18:42:06,730] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-07 18:42:06,740] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-07 18:42:06,744] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2021-12-07 18:42:06,754] multiqc [DEBUG ] No samples found: conpair [2021-12-07 18:42:06,758] multiqc [DEBUG ] No samples found: peddy [2021-12-07 18:42:06,764] multiqc [DEBUG ] No samples found: somalier [2021-12-07 18:42:06,769] multiqc [DEBUG ] No samples found: methylQA [2021-12-07 18:42:06,800] multiqc [DEBUG ] No samples found: mosdepth [2021-12-07 18:42:06,811] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-07 18:42:06,821] multiqc [DEBUG ] No samples found: qualimap [2021-12-07 18:42:06,833] multiqc [DEBUG ] No samples found: preseq [2021-12-07 18:42:06,837] multiqc [DEBUG ] No samples found: quast [2021-12-07 18:42:06,841] multiqc [DEBUG ] No samples found: qorts [2021-12-07 18:42:06,855] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-07 18:42:06,866] multiqc [DEBUG ] No samples found: rockhopper [2021-12-07 18:42:06,877] multiqc [DEBUG ] No samples found: rsem [2021-12-07 18:42:06,938] multiqc [DEBUG ] No samples found: rseqc [2021-12-07 18:42:06,951] multiqc [DEBUG ] No samples found: busco [2021-12-07 18:42:06,961] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-07 18:42:06,964] multiqc [DEBUG ] No samples found: disambiguate [2021-12-07 18:42:06,977] multiqc [DEBUG ] No samples found: supernova [2021-12-07 18:42:07,027] multiqc [DEBUG ] No samples found: deeptools [2021-12-07 18:42:07,045] multiqc [DEBUG ] No samples found: sargasso [2021-12-07 18:42:07,064] multiqc [DEBUG ] No samples found: verifybamid [2021-12-07 18:42:07,073] multiqc [DEBUG ] No samples found: mirtrace [2021-12-07 18:42:07,086] multiqc [DEBUG ] No samples found: happy [2021-12-07 18:42:07,097] multiqc [DEBUG ] No samples found: mirtop [2021-12-07 18:42:07,116] multiqc [DEBUG ] No samples found: homer [2021-12-07 18:42:07,126] multiqc [DEBUG ] No samples found: macs2 [2021-12-07 18:42:07,131] multiqc [DEBUG ] No samples found: theta2 [2021-12-07 18:42:07,135] multiqc [DEBUG ] No samples found: snpeff [2021-12-07 18:42:07,155] multiqc [DEBUG ] No samples found: gatk [2021-12-07 18:42:07,166] multiqc [DEBUG ] No samples found: htseq [2021-12-07 18:42:07,189] multiqc [DEBUG ] No samples found: bcftools [2021-12-07 18:42:07,196] multiqc [DEBUG ] No samples found: featureCounts [2021-12-07 18:42:07,214] multiqc [DEBUG ] No samples found: fgbio [2021-12-07 18:42:07,251] multiqc [DEBUG ] No samples found: dragen [2021-12-07 18:42:07,256] multiqc [DEBUG ] No samples found: dedup [2021-12-07 18:42:07,263] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-07 18:42:07,311] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-07 18:42:07,320] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-07 18:42:07,322] multiqc [DEBUG ] No samples found: picard [2021-12-07 18:42:07,332] multiqc [DEBUG ] No samples found: prokka [2021-12-07 18:42:07,342] multiqc [DEBUG ] No samples found: samblaster [2021-12-07 18:42:07,349] multiqc [DEBUG ] No samples found: samtools [2021-12-07 18:42:07,360] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-07 18:42:07,371] multiqc [DEBUG ] No samples found: bamtools [2021-12-07 18:42:07,380] multiqc [DEBUG ] No samples found: jellyfish [2021-12-07 18:42:07,385] multiqc [DEBUG ] No samples found: vcftools [2021-12-07 18:42:07,395] multiqc [DEBUG ] No samples found: longranger [2021-12-07 18:42:07,401] multiqc [DEBUG ] No samples found: stacks [2021-12-07 18:42:07,404] multiqc [DEBUG ] No samples found: varscan2 [2021-12-07 18:42:07,474] multiqc [DEBUG ] No samples found: bbmap [2021-12-07 18:42:07,483] multiqc [DEBUG ] No samples found: bismark [2021-12-07 18:42:07,493] multiqc [DEBUG ] No samples found: biscuit [2021-12-07 18:42:07,497] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-07 18:42:07,506] multiqc [DEBUG ] No samples found: hicup [2021-12-07 18:42:07,518] multiqc [DEBUG ] No samples found: hicpro [2021-12-07 18:42:07,530] multiqc [DEBUG ] No samples found: salmon [2021-12-07 18:42:07,539] multiqc [DEBUG ] No samples found: kallisto [2021-12-07 18:42:07,550] multiqc [DEBUG ] No samples found: slamdunk [2021-12-07 18:42:07,553] multiqc [DEBUG ] No samples found: star [2021-12-07 18:42:07,563] multiqc [DEBUG ] No samples found: hisat2 [2021-12-07 18:42:07,574] multiqc [DEBUG ] No samples found: tophat [2021-12-07 18:42:07,592] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-07 18:42:07,596] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-07 18:42:07,607] multiqc [DEBUG ] No samples found: snpsplit [2021-12-07 18:42:07,623] multiqc [DEBUG ] No samples found: kat [2021-12-07 18:42:07,626] multiqc [DEBUG ] No samples found: leehom [2021-12-07 18:42:07,637] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-07 18:42:07,647] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-07 18:42:07,656] multiqc [DEBUG ] No samples found: cutadapt [2021-12-07 18:42:07,666] multiqc [DEBUG ] No samples found: flexbar [2021-12-07 18:42:07,683] multiqc [DEBUG ] No samples found: kaiju [2021-12-07 18:42:07,687] multiqc [DEBUG ] No samples found: kraken [2021-12-07 18:42:07,696] multiqc [DEBUG ] No samples found: malt [2021-12-07 18:42:07,702] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-07 18:42:07,705] multiqc [DEBUG ] No samples found: sickle [2021-12-07 18:42:07,715] multiqc [DEBUG ] No samples found: skewer [2021-12-07 18:42:07,719] multiqc [DEBUG ] No samples found: sortmerna [2021-12-07 18:42:07,722] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-07 18:42:07,741] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-07 18:42:07,745] multiqc [DEBUG ] No samples found: afterqc [2021-12-07 18:42:07,749] multiqc [DEBUG ] No samples found: fastp [2021-12-07 18:42:08,265] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2021-12-07 18:42:08,453] multiqc [DEBUG ] No samples found: pycoqc [2021-12-07 18:42:08,470] multiqc [DEBUG ] No samples found: minionqc [2021-12-07 18:42:08,487] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-07 18:42:08,498] multiqc [DEBUG ] No samples found: clusterflow [2021-12-07 18:42:08,518] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-07 18:42:08,530] multiqc [DEBUG ] No samples found: interop [2021-12-07 18:42:08,540] multiqc [DEBUG ] No samples found: ivar [2021-12-07 18:42:08,550] multiqc [DEBUG ] No samples found: flash [2021-12-07 18:42:08,560] multiqc [DEBUG ] No samples found: seqyclean [2021-12-07 18:42:08,560] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-07 18:42:08,560] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-07 18:42:08,560] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-07 18:42:08,560] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-07 18:42:08,582] multiqc [INFO ] Compressing plot data [2021-12-07 18:42:08,886] multiqc [INFO ] Report : multiqc_report.html [2021-12-07 18:42:08,886] multiqc [INFO ] Data : multiqc_data [2021-12-07 18:42:08,886] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12875240/tmpyayp4p8z/multiqc_data' to '/scratch/gencore/logs/html/HCLMMAFX3/merged/multiqc_data' [2021-12-07 18:42:09,004] multiqc [INFO ] MultiQC complete