[2021-11-18 06:44:11,423] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-18 06:44:11,423] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-18 06:44:11,423] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-18 06:44:11,424] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-18 06:44:11,424] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-18 06:44:11,425] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7FVWAFX3/merged [2021-11-18 06:44:12,790] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-18 06:44:12,791] multiqc [INFO ] This is MultiQC v1.9 [2021-11-18 06:44:12,791] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7FVWAFX3/merged [2021-11-18 06:44:12,791] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7FVWAFX3/merged [2021-11-18 06:44:12,791] multiqc [INFO ] Template : default [2021-11-18 06:44:12,791] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-18 06:44:12,791] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7FVWAFX3/merged [2021-11-18 06:44:12,791] 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 [2021-11-18 06:44:12,791] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12051827/tmpcdsaus7p [2021-11-18 06:44:12,899] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n01_undetermined_fastqc.html [2021-11-18 06:44:12,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n01_undetermined_fastqc.html [2021-11-18 06:44:12,944] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 06:44:12,946] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 06:44:13,037] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n02_11617_in_fastqc.html [2021-11-18 06:44:13,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n02_11617_in_fastqc.html [2021-11-18 06:44:13,077] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n02_undetermined_fastqc.html [2021-11-18 06:44:13,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n02_undetermined_fastqc.html [2021-11-18 06:44:13,136] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n02_11617_chp_fastqc.html [2021-11-18 06:44:13,137] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n02_11617_chp_fastqc.html [2021-11-18 06:44:13,176] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n01_7797_chp_fastqc.html [2021-11-18 06:44:13,178] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n01_7797_chp_fastqc.html [2021-11-18 06:44:13,217] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n01_7797_in_fastqc.html [2021-11-18 06:44:13,218] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n01_7797_in_fastqc.html [2021-11-18 06:44:13,257] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n02_5184_chp_fastqc.html [2021-11-18 06:44:13,258] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n02_5184_chp_fastqc.html [2021-11-18 06:44:13,298] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n01_11617_in_fastqc.html [2021-11-18 06:44:13,299] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n01_11617_in_fastqc.html [2021-11-18 06:44:13,340] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n01_5184_in_fastqc.html [2021-11-18 06:44:13,342] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n01_5184_in_fastqc.html [2021-11-18 06:44:13,397] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n01_11617_chp_fastqc.html [2021-11-18 06:44:13,399] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n01_11617_chp_fastqc.html [2021-11-18 06:44:13,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n02_7797_in_fastqc.html [2021-11-18 06:44:13,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n02_7797_in_fastqc.html [2021-11-18 06:44:13,484] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n02_7797_chp_fastqc.html [2021-11-18 06:44:13,486] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n02_7797_chp_fastqc.html [2021-11-18 06:44:13,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n01_5184_chp_fastqc.html [2021-11-18 06:44:13,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n01_5184_chp_fastqc.html [2021-11-18 06:44:13,566] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7FVWAFX3_n02_5184_in_fastqc.html [2021-11-18 06:44:13,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7FVWAFX3_n02_5184_in_fastqc.html [2021-11-18 06:44:13,910] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 06:44:13,912] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 06:44:13,923] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-18 06:44:13,927] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2021-11-18 06:44:13,937] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-18 06:44:13,944] multiqc [DEBUG ] No samples found: conpair [2021-11-18 06:44:13,950] multiqc [DEBUG ] No samples found: peddy [2021-11-18 06:44:13,958] multiqc [DEBUG ] No samples found: somalier [2021-11-18 06:44:13,966] multiqc [DEBUG ] No samples found: methylQA [2021-11-18 06:44:13,980] multiqc [DEBUG ] No samples found: mosdepth [2021-11-18 06:44:13,985] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-18 06:44:13,989] multiqc [DEBUG ] No samples found: qualimap [2021-11-18 06:44:13,996] multiqc [DEBUG ] No samples found: preseq [2021-11-18 06:44:14,002] multiqc [DEBUG ] No samples found: quast [2021-11-18 06:44:14,008] multiqc [DEBUG ] No samples found: qorts [2021-11-18 06:44:14,014] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-18 06:44:14,022] multiqc [DEBUG ] No samples found: rockhopper [2021-11-18 06:44:14,028] multiqc [DEBUG ] No samples found: rsem [2021-11-18 06:44:14,070] multiqc [DEBUG ] No samples found: rseqc [2021-11-18 06:44:14,079] multiqc [DEBUG ] No samples found: busco [2021-11-18 06:44:14,085] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-18 06:44:14,092] multiqc [DEBUG ] No samples found: disambiguate [2021-11-18 06:44:14,099] multiqc [DEBUG ] No samples found: supernova [2021-11-18 06:44:14,124] multiqc [DEBUG ] No samples found: deeptools [2021-11-18 06:44:14,130] multiqc [DEBUG ] No samples found: sargasso [2021-11-18 06:44:14,136] multiqc [DEBUG ] No samples found: verifybamid [2021-11-18 06:44:14,144] multiqc [DEBUG ] No samples found: mirtrace [2021-11-18 06:44:14,151] multiqc [DEBUG ] No samples found: happy [2021-11-18 06:44:14,157] multiqc [DEBUG ] No samples found: mirtop [2021-11-18 06:44:14,165] multiqc [DEBUG ] No samples found: homer [2021-11-18 06:44:14,171] multiqc [DEBUG ] No samples found: macs2 [2021-11-18 06:44:14,178] multiqc [DEBUG ] No samples found: theta2 [2021-11-18 06:44:14,184] multiqc [DEBUG ] No samples found: snpeff [2021-11-18 06:44:14,197] multiqc [DEBUG ] No samples found: gatk [2021-11-18 06:44:14,203] multiqc [DEBUG ] No samples found: htseq [2021-11-18 06:44:14,210] multiqc [DEBUG ] No samples found: bcftools [2021-11-18 06:44:14,214] multiqc [DEBUG ] No samples found: featureCounts [2021-11-18 06:44:14,222] multiqc [DEBUG ] No samples found: fgbio [2021-11-18 06:44:14,249] multiqc [DEBUG ] No samples found: dragen [2021-11-18 06:44:14,257] multiqc [DEBUG ] No samples found: dedup [2021-11-18 06:44:14,264] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-18 06:44:14,293] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-18 06:44:14,300] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-18 06:44:14,302] multiqc [DEBUG ] No samples found: picard [2021-11-18 06:44:14,308] multiqc [DEBUG ] No samples found: prokka [2021-11-18 06:44:14,315] multiqc [DEBUG ] No samples found: samblaster [2021-11-18 06:44:14,326] multiqc [DEBUG ] No samples found: samtools [2021-11-18 06:44:14,333] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-18 06:44:14,339] multiqc [DEBUG ] No samples found: bamtools [2021-11-18 06:44:14,345] multiqc [DEBUG ] No samples found: jellyfish [2021-11-18 06:44:14,355] multiqc [DEBUG ] No samples found: vcftools [2021-11-18 06:44:14,362] multiqc [DEBUG ] No samples found: longranger [2021-11-18 06:44:14,370] multiqc [DEBUG ] No samples found: stacks [2021-11-18 06:44:14,376] multiqc [DEBUG ] No samples found: varscan2 [2021-11-18 06:44:14,402] multiqc [DEBUG ] No samples found: bbmap [2021-11-18 06:44:14,408] multiqc [DEBUG ] No samples found: bismark [2021-11-18 06:44:14,414] multiqc [DEBUG ] No samples found: biscuit [2021-11-18 06:44:14,421] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-18 06:44:14,427] multiqc [DEBUG ] No samples found: hicup [2021-11-18 06:44:14,435] multiqc [DEBUG ] No samples found: hicpro [2021-11-18 06:44:14,442] multiqc [DEBUG ] No samples found: salmon [2021-11-18 06:44:14,448] multiqc [DEBUG ] No samples found: kallisto [2021-11-18 06:44:14,454] multiqc [DEBUG ] No samples found: slamdunk [2021-11-18 06:44:14,459] multiqc [DEBUG ] No samples found: star [2021-11-18 06:44:14,466] multiqc [DEBUG ] No samples found: hisat2 [2021-11-18 06:44:14,473] multiqc [DEBUG ] No samples found: tophat [2021-11-18 06:44:14,479] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-18 06:44:14,486] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-18 06:44:14,491] multiqc [DEBUG ] No samples found: snpsplit [2021-11-18 06:44:14,499] multiqc [DEBUG ] No samples found: kat [2021-11-18 06:44:14,505] multiqc [DEBUG ] No samples found: leehom [2021-11-18 06:44:14,511] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-18 06:44:14,518] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-18 06:44:14,525] multiqc [DEBUG ] No samples found: cutadapt [2021-11-18 06:44:14,531] multiqc [DEBUG ] No samples found: flexbar [2021-11-18 06:44:14,541] multiqc [DEBUG ] No samples found: kaiju [2021-11-18 06:44:14,548] multiqc [DEBUG ] No samples found: kraken [2021-11-18 06:44:14,555] multiqc [DEBUG ] No samples found: malt [2021-11-18 06:44:14,562] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-18 06:44:14,569] multiqc [DEBUG ] No samples found: sickle [2021-11-18 06:44:14,576] multiqc [DEBUG ] No samples found: skewer [2021-11-18 06:44:14,583] multiqc [DEBUG ] No samples found: sortmerna [2021-11-18 06:44:14,591] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-18 06:44:14,598] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-18 06:44:14,604] multiqc [DEBUG ] No samples found: afterqc [2021-11-18 06:44:14,609] multiqc [DEBUG ] No samples found: fastp [2021-11-18 06:44:15,171] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2021-11-18 06:44:15,331] multiqc [DEBUG ] No samples found: pycoqc [2021-11-18 06:44:15,337] multiqc [DEBUG ] No samples found: minionqc [2021-11-18 06:44:15,343] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-18 06:44:15,349] multiqc [DEBUG ] No samples found: clusterflow [2021-11-18 06:44:15,355] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-18 06:44:15,361] multiqc [DEBUG ] No samples found: interop [2021-11-18 06:44:15,367] multiqc [DEBUG ] No samples found: ivar [2021-11-18 06:44:15,373] multiqc [DEBUG ] No samples found: flash [2021-11-18 06:44:15,379] multiqc [DEBUG ] No samples found: seqyclean [2021-11-18 06:44:15,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-18 06:44:15,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-18 06:44:15,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-18 06:44:15,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-18 06:44:15,396] multiqc [INFO ] Compressing plot data [2021-11-18 06:44:15,642] multiqc [INFO ] Report : multiqc_report.html [2021-11-18 06:44:15,642] multiqc [INFO ] Data : multiqc_data [2021-11-18 06:44:15,642] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12051827/tmpcdsaus7p/multiqc_data' to '/scratch/gencore/logs/html/H7FVWAFX3/merged/multiqc_data' [2021-11-18 06:44:15,763] multiqc [INFO ] MultiQC complete