[2021-08-03 07:09:05,378] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-03 07:09:05,378] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-03 07:09:05,378] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-03 07:09:05,379] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-03 07:09:05,379] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-03 07:09:05,379] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JR6YD/1 [2021-08-03 07:09:06,735] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-03 07:09:06,735] multiqc [INFO ] This is MultiQC v1.9 [2021-08-03 07:09:06,735] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JR6YD/1 [2021-08-03 07:09:06,735] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-JR6YD/1 [2021-08-03 07:09:06,735] multiqc [INFO ] Template : default [2021-08-03 07:09:06,735] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-03 07:09:06,735] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-JR6YD/1 [2021-08-03 07:09:06,735] 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 [2021-08-03 07:09:06,736] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9133103/tmpilgiz1hh [2021-08-03 07:09:06,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_2354.2.ld_fastqc.html [2021-08-03 07:09:06,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_2354.2.ld_fastqc.html [2021-08-03 07:09:06,903] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-03 07:09:06,905] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-03 07:09:07,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_undetermined_fastqc.html [2021-08-03 07:09:07,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_undetermined_fastqc.html [2021-08-03 07:09:07,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_2355.2.ld_fastqc.html [2021-08-03 07:09:07,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_2355.2.ld_fastqc.html [2021-08-03 07:09:07,197] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_93.ld_fastqc.html [2021-08-03 07:09:07,198] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_93.ld_fastqc.html [2021-08-03 07:09:07,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_2367.ld_fastqc.html [2021-08-03 07:09:07,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_2367.ld_fastqc.html [2021-08-03 07:09:07,278] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_2354.2.ld_fastqc.html [2021-08-03 07:09:07,280] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_2354.2.ld_fastqc.html [2021-08-03 07:09:07,320] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_93.ld_fastqc.html [2021-08-03 07:09:07,321] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_93.ld_fastqc.html [2021-08-03 07:09:07,361] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_2367.ld_fastqc.html [2021-08-03 07:09:07,363] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_2367.ld_fastqc.html [2021-08-03 07:09:07,402] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_undetermined_fastqc.html [2021-08-03 07:09:07,404] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n01_undetermined_fastqc.html [2021-08-03 07:09:07,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_2355.2.ld_fastqc.html [2021-08-03 07:09:07,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JR6YD_l01_n02_2355.2.ld_fastqc.html [2021-08-03 07:09:08,066] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-03 07:09:08,067] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-03 07:09:08,075] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-03 07:09:08,078] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 5 samples (table) [2021-08-03 07:09:08,087] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-03 07:09:08,092] multiqc [DEBUG ] No samples found: conpair [2021-08-03 07:09:08,096] multiqc [DEBUG ] No samples found: peddy [2021-08-03 07:09:08,101] multiqc [DEBUG ] No samples found: somalier [2021-08-03 07:09:08,106] multiqc [DEBUG ] No samples found: methylQA [2021-08-03 07:09:08,113] multiqc [DEBUG ] No samples found: mosdepth [2021-08-03 07:09:08,117] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-03 07:09:08,121] multiqc [DEBUG ] No samples found: qualimap [2021-08-03 07:09:08,126] multiqc [DEBUG ] No samples found: preseq [2021-08-03 07:09:08,130] multiqc [DEBUG ] No samples found: quast [2021-08-03 07:09:08,135] multiqc [DEBUG ] No samples found: qorts [2021-08-03 07:09:08,140] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-03 07:09:08,144] multiqc [DEBUG ] No samples found: rockhopper [2021-08-03 07:09:08,149] multiqc [DEBUG ] No samples found: rsem [2021-08-03 07:09:08,159] multiqc [DEBUG ] No samples found: rseqc [2021-08-03 07:09:08,163] multiqc [DEBUG ] No samples found: busco [2021-08-03 07:09:08,168] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-03 07:09:08,172] multiqc [DEBUG ] No samples found: disambiguate [2021-08-03 07:09:08,176] multiqc [DEBUG ] No samples found: supernova [2021-08-03 07:09:08,188] multiqc [DEBUG ] No samples found: deeptools [2021-08-03 07:09:08,193] multiqc [DEBUG ] No samples found: sargasso [2021-08-03 07:09:08,197] multiqc [DEBUG ] No samples found: verifybamid [2021-08-03 07:09:08,202] multiqc [DEBUG ] No samples found: mirtrace [2021-08-03 07:09:08,206] multiqc [DEBUG ] No samples found: happy [2021-08-03 07:09:08,211] multiqc [DEBUG ] No samples found: mirtop [2021-08-03 07:09:08,217] multiqc [DEBUG ] No samples found: homer [2021-08-03 07:09:08,222] multiqc [DEBUG ] No samples found: macs2 [2021-08-03 07:09:08,226] multiqc [DEBUG ] No samples found: theta2 [2021-08-03 07:09:08,230] multiqc [DEBUG ] No samples found: snpeff [2021-08-03 07:09:08,237] multiqc [DEBUG ] No samples found: gatk [2021-08-03 07:09:08,241] multiqc [DEBUG ] No samples found: htseq [2021-08-03 07:09:08,246] multiqc [DEBUG ] No samples found: bcftools [2021-08-03 07:09:08,251] multiqc [DEBUG ] No samples found: featureCounts [2021-08-03 07:09:08,257] multiqc [DEBUG ] No samples found: fgbio [2021-08-03 07:09:08,269] multiqc [DEBUG ] No samples found: dragen [2021-08-03 07:09:08,273] multiqc [DEBUG ] No samples found: dedup [2021-08-03 07:09:08,278] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-03 07:09:08,299] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-03 07:09:08,303] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-03 07:09:08,305] multiqc [DEBUG ] No samples found: picard [2021-08-03 07:09:08,310] multiqc [DEBUG ] No samples found: prokka [2021-08-03 07:09:08,314] multiqc [DEBUG ] No samples found: samblaster [2021-08-03 07:09:08,323] multiqc [DEBUG ] No samples found: samtools [2021-08-03 07:09:08,328] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-03 07:09:08,333] multiqc [DEBUG ] No samples found: bamtools [2021-08-03 07:09:08,337] multiqc [DEBUG ] No samples found: jellyfish [2021-08-03 07:09:08,344] multiqc [DEBUG ] No samples found: vcftools [2021-08-03 07:09:08,349] multiqc [DEBUG ] No samples found: longranger [2021-08-03 07:09:08,353] multiqc [DEBUG ] No samples found: stacks [2021-08-03 07:09:08,358] multiqc [DEBUG ] No samples found: varscan2 [2021-08-03 07:09:08,371] multiqc [DEBUG ] No samples found: bbmap [2021-08-03 07:09:08,376] multiqc [DEBUG ] No samples found: bismark [2021-08-03 07:09:08,382] multiqc [DEBUG ] No samples found: biscuit [2021-08-03 07:09:08,387] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-03 07:09:08,391] multiqc [DEBUG ] No samples found: hicup [2021-08-03 07:09:08,396] multiqc [DEBUG ] No samples found: hicpro [2021-08-03 07:09:08,400] multiqc [DEBUG ] No samples found: salmon [2021-08-03 07:09:08,405] multiqc [DEBUG ] No samples found: kallisto [2021-08-03 07:09:08,410] multiqc [DEBUG ] No samples found: slamdunk [2021-08-03 07:09:08,415] multiqc [DEBUG ] No samples found: star [2021-08-03 07:09:08,420] multiqc [DEBUG ] No samples found: hisat2 [2021-08-03 07:09:08,424] multiqc [DEBUG ] No samples found: tophat [2021-08-03 07:09:08,429] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-03 07:09:08,433] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-03 07:09:08,438] multiqc [DEBUG ] No samples found: snpsplit [2021-08-03 07:09:08,442] multiqc [DEBUG ] No samples found: kat [2021-08-03 07:09:08,447] multiqc [DEBUG ] No samples found: leehom [2021-08-03 07:09:08,451] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-03 07:09:08,455] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-03 07:09:08,460] multiqc [DEBUG ] No samples found: cutadapt [2021-08-03 07:09:08,464] multiqc [DEBUG ] No samples found: flexbar [2021-08-03 07:09:08,469] multiqc [DEBUG ] No samples found: kaiju [2021-08-03 07:09:08,474] multiqc [DEBUG ] No samples found: kraken [2021-08-03 07:09:08,478] multiqc [DEBUG ] No samples found: malt [2021-08-03 07:09:08,483] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-03 07:09:08,487] multiqc [DEBUG ] No samples found: sickle [2021-08-03 07:09:08,492] multiqc [DEBUG ] No samples found: skewer [2021-08-03 07:09:08,496] multiqc [DEBUG ] No samples found: sortmerna [2021-08-03 07:09:08,500] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-03 07:09:08,505] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-03 07:09:08,509] multiqc [DEBUG ] No samples found: afterqc [2021-08-03 07:09:08,514] multiqc [DEBUG ] No samples found: fastp [2021-08-03 07:09:08,597] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-08-03 07:09:08,812] multiqc [DEBUG ] No samples found: pycoqc [2021-08-03 07:09:08,817] multiqc [DEBUG ] No samples found: minionqc [2021-08-03 07:09:08,822] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-03 07:09:08,826] multiqc [DEBUG ] No samples found: clusterflow [2021-08-03 07:09:08,831] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-03 07:09:08,836] multiqc [DEBUG ] No samples found: interop [2021-08-03 07:09:08,841] multiqc [DEBUG ] No samples found: ivar [2021-08-03 07:09:08,845] multiqc [DEBUG ] No samples found: flash [2021-08-03 07:09:08,850] multiqc [DEBUG ] No samples found: seqyclean [2021-08-03 07:09:08,850] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-08-03 07:09:08,850] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-08-03 07:09:08,850] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-08-03 07:09:08,850] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-03 07:09:08,850] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-03 07:09:08,862] multiqc [INFO ] Compressing plot data [2021-08-03 07:09:09,045] multiqc [INFO ] Report : multiqc_report.html [2021-08-03 07:09:09,045] multiqc [INFO ] Data : multiqc_data [2021-08-03 07:09:09,045] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9133103/tmpilgiz1hh/multiqc_data' to '/scratch/gencore/logs/html/000000000-JR6YD/1/multiqc_data' [2021-08-03 07:09:09,172] multiqc [INFO ] MultiQC complete