[2022-07-26 06:12:44,186] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-26 06:12:44,186] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-26 06:12:44,187] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-26 06:12:44,187] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-26 06:12:44,187] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-26 06:12:44,188] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HG7LFBGXM/merged [2022-07-26 06:12:44,786] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-26 06:12:44,786] multiqc [INFO ] This is MultiQC v1.9 [2022-07-26 06:12:44,787] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HG7LFBGXM/merged [2022-07-26 06:12:44,787] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HG7LFBGXM/merged [2022-07-26 06:12:44,787] multiqc [INFO ] Template : default [2022-07-26 06:12:44,787] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-26 06:12:44,787] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HG7LFBGXM/merged [2022-07-26 06:12:44,787] 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 [2022-07-26 06:12:44,787] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22805652/tmp7iu2xuot [2022-07-26 06:12:44,904] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R21_fastqc.html [2022-07-26 06:12:44,907] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R21_fastqc.html [2022-07-26 06:12:44,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-26 06:12:44,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-26 06:12:44,976] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-26 06:12:44,976] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-26 06:12:44,976] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-26 06:12:44,976] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-26 06:12:44,976] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-26 06:12:45,989] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01_undetermined_fastqc.html [2022-07-26 06:12:45,991] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01_undetermined_fastqc.html [2022-07-26 06:12:46,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R24_fastqc.html [2022-07-26 06:12:46,052] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R24_fastqc.html [2022-07-26 06:12:46,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R18_fastqc.html [2022-07-26 06:12:46,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R18_fastqc.html [2022-07-26 06:12:46,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R15_fastqc.html [2022-07-26 06:12:46,186] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R15_fastqc.html [2022-07-26 06:12:46,253] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R19_fastqc.html [2022-07-26 06:12:46,255] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R19_fastqc.html [2022-07-26 06:12:46,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R16_fastqc.html [2022-07-26 06:12:46,323] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R16_fastqc.html [2022-07-26 06:12:46,389] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R20_fastqc.html [2022-07-26 06:12:46,391] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R20_fastqc.html [2022-07-26 06:12:46,456] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R22_fastqc.html [2022-07-26 06:12:46,458] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R22_fastqc.html [2022-07-26 06:12:46,521] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R23_fastqc.html [2022-07-26 06:12:46,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R23_fastqc.html [2022-07-26 06:12:46,585] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R13_fastqc.html [2022-07-26 06:12:46,587] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R13_fastqc.html [2022-07-26 06:12:46,657] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R17_fastqc.html [2022-07-26 06:12:46,658] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R17_fastqc.html [2022-07-26 06:12:46,726] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R14_fastqc.html [2022-07-26 06:12:46,728] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG7LFBGXM_n01__R14_fastqc.html [2022-07-26 06:12:47,090] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-26 06:12:47,092] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-26 06:12:47,100] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-26 06:12:47,109] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-26 06:12:47,116] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 13 samples (table) [2022-07-26 06:12:47,120] multiqc [DEBUG ] No samples found: conpair [2022-07-26 06:12:47,126] multiqc [DEBUG ] No samples found: peddy [2022-07-26 06:12:47,132] multiqc [DEBUG ] No samples found: somalier [2022-07-26 06:12:47,137] multiqc [DEBUG ] No samples found: methylQA [2022-07-26 06:12:47,146] multiqc [DEBUG ] No samples found: mosdepth [2022-07-26 06:12:47,151] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-26 06:12:47,154] multiqc [DEBUG ] No samples found: qualimap [2022-07-26 06:12:47,159] multiqc [DEBUG ] No samples found: preseq [2022-07-26 06:12:47,164] multiqc [DEBUG ] No samples found: quast [2022-07-26 06:12:47,169] multiqc [DEBUG ] No samples found: qorts [2022-07-26 06:12:47,174] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-26 06:12:47,179] multiqc [DEBUG ] No samples found: rockhopper [2022-07-26 06:12:47,184] multiqc [DEBUG ] No samples found: rsem [2022-07-26 06:12:47,195] multiqc [DEBUG ] No samples found: rseqc [2022-07-26 06:12:47,199] multiqc [DEBUG ] No samples found: busco [2022-07-26 06:12:47,204] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-26 06:12:47,208] multiqc [DEBUG ] No samples found: disambiguate [2022-07-26 06:12:47,213] multiqc [DEBUG ] No samples found: supernova [2022-07-26 06:12:47,228] multiqc [DEBUG ] No samples found: deeptools [2022-07-26 06:12:47,233] multiqc [DEBUG ] No samples found: sargasso [2022-07-26 06:12:47,238] multiqc [DEBUG ] No samples found: verifybamid [2022-07-26 06:12:47,243] multiqc [DEBUG ] No samples found: mirtrace [2022-07-26 06:12:47,248] multiqc [DEBUG ] No samples found: happy [2022-07-26 06:12:47,253] multiqc [DEBUG ] No samples found: mirtop [2022-07-26 06:12:47,259] multiqc [DEBUG ] No samples found: homer [2022-07-26 06:12:47,264] multiqc [DEBUG ] No samples found: macs2 [2022-07-26 06:12:47,269] multiqc [DEBUG ] No samples found: theta2 [2022-07-26 06:12:47,273] multiqc [DEBUG ] No samples found: snpeff [2022-07-26 06:12:47,280] multiqc [DEBUG ] No samples found: gatk [2022-07-26 06:12:47,285] multiqc [DEBUG ] No samples found: htseq [2022-07-26 06:12:47,290] multiqc [DEBUG ] No samples found: bcftools [2022-07-26 06:12:47,297] multiqc [DEBUG ] No samples found: featureCounts [2022-07-26 06:12:47,303] multiqc [DEBUG ] No samples found: fgbio [2022-07-26 06:12:47,316] multiqc [DEBUG ] No samples found: dragen [2022-07-26 06:12:47,321] multiqc [DEBUG ] No samples found: dedup [2022-07-26 06:12:47,326] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-26 06:12:47,349] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-26 06:12:47,353] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-26 06:12:47,356] multiqc [DEBUG ] No samples found: picard [2022-07-26 06:12:47,362] multiqc [DEBUG ] No samples found: prokka [2022-07-26 06:12:47,367] multiqc [DEBUG ] No samples found: samblaster [2022-07-26 06:12:47,380] multiqc [DEBUG ] No samples found: samtools [2022-07-26 06:12:47,385] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-26 06:12:47,390] multiqc [DEBUG ] No samples found: bamtools [2022-07-26 06:12:47,395] multiqc [DEBUG ] No samples found: jellyfish [2022-07-26 06:12:47,402] multiqc [DEBUG ] No samples found: vcftools [2022-07-26 06:12:47,407] multiqc [DEBUG ] No samples found: longranger [2022-07-26 06:12:47,412] multiqc [DEBUG ] No samples found: stacks [2022-07-26 06:12:47,417] multiqc [DEBUG ] No samples found: varscan2 [2022-07-26 06:12:47,432] multiqc [DEBUG ] No samples found: bbmap [2022-07-26 06:12:47,437] multiqc [DEBUG ] No samples found: bismark [2022-07-26 06:12:47,443] multiqc [DEBUG ] No samples found: biscuit [2022-07-26 06:12:47,448] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-26 06:12:47,453] multiqc [DEBUG ] No samples found: hicup [2022-07-26 06:12:47,457] multiqc [DEBUG ] No samples found: hicpro [2022-07-26 06:12:47,462] multiqc [DEBUG ] No samples found: salmon [2022-07-26 06:12:47,467] multiqc [DEBUG ] No samples found: kallisto [2022-07-26 06:12:47,472] multiqc [DEBUG ] No samples found: slamdunk [2022-07-26 06:12:47,476] multiqc [DEBUG ] No samples found: star [2022-07-26 06:12:47,482] multiqc [DEBUG ] No samples found: hisat2 [2022-07-26 06:12:47,486] multiqc [DEBUG ] No samples found: tophat [2022-07-26 06:12:47,491] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-26 06:12:47,495] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-26 06:12:47,500] multiqc [DEBUG ] No samples found: snpsplit [2022-07-26 06:12:47,504] multiqc [DEBUG ] No samples found: kat [2022-07-26 06:12:47,508] multiqc [DEBUG ] No samples found: leehom [2022-07-26 06:12:47,513] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-26 06:12:47,517] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-26 06:12:47,522] multiqc [DEBUG ] No samples found: cutadapt [2022-07-26 06:12:47,526] multiqc [DEBUG ] No samples found: flexbar [2022-07-26 06:12:47,531] multiqc [DEBUG ] No samples found: kaiju [2022-07-26 06:12:47,536] multiqc [DEBUG ] No samples found: kraken [2022-07-26 06:12:47,541] multiqc [DEBUG ] No samples found: malt [2022-07-26 06:12:47,545] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-26 06:12:47,550] multiqc [DEBUG ] No samples found: sickle [2022-07-26 06:12:47,556] multiqc [DEBUG ] No samples found: skewer [2022-07-26 06:12:47,560] multiqc [DEBUG ] No samples found: sortmerna [2022-07-26 06:12:47,565] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-26 06:12:47,570] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-26 06:12:47,574] multiqc [DEBUG ] No samples found: afterqc [2022-07-26 06:12:47,579] multiqc [DEBUG ] No samples found: fastp [2022-07-26 06:12:49,026] multiqc.modules.fastqc.fastqc [INFO ] Found 13 reports [2022-07-26 06:12:49,341] multiqc [DEBUG ] No samples found: pycoqc [2022-07-26 06:12:49,346] multiqc [DEBUG ] No samples found: minionqc [2022-07-26 06:12:49,351] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-26 06:12:49,359] multiqc [DEBUG ] No samples found: clusterflow [2022-07-26 06:12:49,367] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-26 06:12:49,376] multiqc [DEBUG ] No samples found: interop [2022-07-26 06:12:49,382] multiqc [DEBUG ] No samples found: ivar [2022-07-26 06:12:49,391] multiqc [DEBUG ] No samples found: flash [2022-07-26 06:12:49,397] multiqc [DEBUG ] No samples found: seqyclean [2022-07-26 06:12:49,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-26 06:12:49,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-26 06:12:49,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-26 06:12:49,397] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-26 06:12:49,413] multiqc [INFO ] Compressing plot data [2022-07-26 06:12:49,638] multiqc [INFO ] Report : multiqc_report.html [2022-07-26 06:12:49,638] multiqc [INFO ] Data : multiqc_data [2022-07-26 06:12:49,638] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22805652/tmp7iu2xuot/multiqc_data' to '/scratch/gencore/logs/html/HG7LFBGXM/merged/multiqc_data' [2022-07-26 06:12:49,842] multiqc [INFO ] MultiQC complete