[2022-12-22 09:09:12,287] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-12-22 09:09:12,287] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-12-22 09:09:12,287] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-12-22 09:09:12,288] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-12-22 09:09:12,288] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-12-22 09:09:12,288] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7JYTBGXN/merged [2022-12-22 09:09:12,797] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-12-22 09:09:12,797] multiqc [INFO ] This is MultiQC v1.9 [2022-12-22 09:09:12,797] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7JYTBGXN/merged [2022-12-22 09:09:12,797] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7JYTBGXN/merged [2022-12-22 09:09:12,797] multiqc [INFO ] Template : default [2022-12-22 09:09:12,797] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-12-22 09:09:12,797] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7JYTBGXN/merged [2022-12-22 09:09:12,798] 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 [2022-12-22 09:09:12,798] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-28540844/tmp_xfnaw6z [2022-12-22 09:09:12,931] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY150_fastqc.html [2022-12-22 09:09:12,934] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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09:09:31,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY124_fastqc.html [2022-12-22 09:09:31,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY124_fastqc.html [2022-12-22 09:09:31,163] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY140_fastqc.html [2022-12-22 09:09:31,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY140_fastqc.html [2022-12-22 09:09:31,221] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY212_fastqc.html [2022-12-22 09:09:31,222] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY212_fastqc.html [2022-12-22 09:09:31,273] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY167_fastqc.html [2022-12-22 09:09:31,275] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY167_fastqc.html [2022-12-22 09:09:31,317] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY240_fastqc.html [2022-12-22 09:09:31,318] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY240_fastqc.html [2022-12-22 09:09:31,361] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY239_fastqc.html [2022-12-22 09:09:31,362] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY239_fastqc.html [2022-12-22 09:09:31,424] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY170_fastqc.html [2022-12-22 09:09:31,426] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY170_fastqc.html [2022-12-22 09:09:31,487] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY266_fastqc.html [2022-12-22 09:09:31,489] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY266_fastqc.html [2022-12-22 09:09:31,545] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY131_fastqc.html [2022-12-22 09:09:31,547] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7JYTBGXN_n01_YY131_fastqc.html [2022-12-22 09:09:31,918] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-22 09:09:31,920] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-22 09:09:31,937] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-12-22 09:09:31,939] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-12-22 09:09:32,021] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 183 samples (table) [2022-12-22 09:09:32,027] multiqc [DEBUG ] No samples found: conpair [2022-12-22 09:09:32,034] multiqc [DEBUG ] No samples found: peddy [2022-12-22 09:09:32,040] multiqc [DEBUG ] No samples found: somalier [2022-12-22 09:09:32,046] multiqc [DEBUG ] No samples found: methylQA [2022-12-22 09:09:32,055] multiqc [DEBUG ] No samples found: mosdepth [2022-12-22 09:09:32,060] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-12-22 09:09:32,064] multiqc [DEBUG ] No samples found: qualimap [2022-12-22 09:09:32,070] multiqc [DEBUG ] No samples found: preseq [2022-12-22 09:09:32,076] multiqc [DEBUG ] No samples found: quast [2022-12-22 09:09:32,082] multiqc [DEBUG ] No samples found: qorts [2022-12-22 09:09:32,087] multiqc [DEBUG ] No samples found: rna_seqc [2022-12-22 09:09:32,092] multiqc [DEBUG ] No samples found: rockhopper [2022-12-22 09:09:32,098] multiqc [DEBUG ] No samples found: rsem [2022-12-22 09:09:32,110] multiqc [DEBUG ] No samples found: rseqc [2022-12-22 09:09:32,115] multiqc [DEBUG ] No samples found: busco [2022-12-22 09:09:32,121] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-12-22 09:09:32,126] multiqc [DEBUG ] No samples found: disambiguate [2022-12-22 09:09:32,132] multiqc [DEBUG ] No samples found: supernova [2022-12-22 09:09:32,148] multiqc [DEBUG ] No samples found: deeptools [2022-12-22 09:09:32,154] multiqc [DEBUG ] No samples found: sargasso [2022-12-22 09:09:32,160] multiqc [DEBUG ] No samples found: verifybamid [2022-12-22 09:09:32,166] multiqc [DEBUG ] No samples found: mirtrace [2022-12-22 09:09:32,171] multiqc [DEBUG ] No samples found: happy [2022-12-22 09:09:32,179] multiqc [DEBUG ] No samples found: mirtop [2022-12-22 09:09:32,187] multiqc [DEBUG ] No samples found: homer [2022-12-22 09:09:32,192] multiqc [DEBUG ] No samples found: macs2 [2022-12-22 09:09:32,198] multiqc [DEBUG ] No samples found: theta2 [2022-12-22 09:09:32,204] multiqc [DEBUG ] No samples found: snpeff [2022-12-22 09:09:32,213] multiqc [DEBUG ] No samples found: gatk [2022-12-22 09:09:32,219] multiqc [DEBUG ] No samples found: htseq [2022-12-22 09:09:32,225] multiqc [DEBUG ] No samples found: bcftools [2022-12-22 09:09:32,231] multiqc [DEBUG ] No samples found: featureCounts [2022-12-22 09:09:32,239] multiqc [DEBUG ] No samples found: fgbio [2022-12-22 09:09:32,254] multiqc [DEBUG ] No samples found: dragen [2022-12-22 09:09:32,260] multiqc [DEBUG ] No samples found: dedup [2022-12-22 09:09:32,266] multiqc [DEBUG ] No samples found: damageprofiler [2022-12-22 09:09:32,294] multiqc [DEBUG ] No samples found: biobambam2 [2022-12-22 09:09:32,300] multiqc [DEBUG ] No samples found: mtnucratio [2022-12-22 09:09:32,302] multiqc [DEBUG ] No samples found: picard [2022-12-22 09:09:32,308] multiqc [DEBUG ] No samples found: prokka [2022-12-22 09:09:32,313] multiqc [DEBUG ] No samples found: samblaster [2022-12-22 09:09:32,323] multiqc [DEBUG ] No samples found: samtools [2022-12-22 09:09:32,328] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-12-22 09:09:32,335] multiqc [DEBUG ] No samples found: bamtools [2022-12-22 09:09:32,340] multiqc [DEBUG ] No samples found: jellyfish [2022-12-22 09:09:32,349] multiqc [DEBUG ] No samples found: vcftools [2022-12-22 09:09:32,354] multiqc [DEBUG ] No samples found: longranger [2022-12-22 09:09:32,360] multiqc [DEBUG ] No samples found: stacks [2022-12-22 09:09:32,366] multiqc [DEBUG ] No samples found: varscan2 [2022-12-22 09:09:32,381] multiqc [DEBUG ] No samples found: bbmap [2022-12-22 09:09:32,387] multiqc [DEBUG ] No samples found: bismark [2022-12-22 09:09:32,393] multiqc [DEBUG ] No samples found: biscuit [2022-12-22 09:09:32,399] multiqc [DEBUG ] No samples found: hicexplorer [2022-12-22 09:09:32,404] multiqc [DEBUG ] No samples found: hicup [2022-12-22 09:09:32,410] multiqc [DEBUG ] No samples found: hicpro [2022-12-22 09:09:32,415] multiqc [DEBUG ] No samples found: salmon [2022-12-22 09:09:32,421] multiqc [DEBUG ] No samples found: kallisto [2022-12-22 09:09:32,427] multiqc [DEBUG ] No samples found: slamdunk [2022-12-22 09:09:32,432] multiqc [DEBUG ] No samples found: star [2022-12-22 09:09:32,437] multiqc [DEBUG ] No samples found: hisat2 [2022-12-22 09:09:32,443] multiqc [DEBUG ] No samples found: tophat [2022-12-22 09:09:32,448] multiqc [DEBUG ] No samples found: bowtie2 [2022-12-22 09:09:32,453] multiqc [DEBUG ] No samples found: bowtie1 [2022-12-22 09:09:32,459] multiqc [DEBUG ] No samples found: snpsplit [2022-12-22 09:09:32,464] multiqc [DEBUG ] No samples found: kat [2022-12-22 09:09:32,468] multiqc [DEBUG ] No samples found: leehom [2022-12-22 09:09:32,474] multiqc [DEBUG ] No samples found: adapterRemoval [2022-12-22 09:09:32,479] multiqc [DEBUG ] No samples found: clipandmerge [2022-12-22 09:09:32,484] multiqc [DEBUG ] No samples found: cutadapt [2022-12-22 09:09:32,490] multiqc [DEBUG ] No samples found: flexbar [2022-12-22 09:09:32,495] multiqc [DEBUG ] No samples found: kaiju [2022-12-22 09:09:32,501] multiqc [DEBUG ] No samples found: kraken [2022-12-22 09:09:32,507] multiqc [DEBUG ] No samples found: malt [2022-12-22 09:09:32,512] multiqc [DEBUG ] No samples found: trimmomatic [2022-12-22 09:09:32,517] multiqc [DEBUG ] No samples found: sickle [2022-12-22 09:09:32,523] multiqc [DEBUG ] No samples found: skewer [2022-12-22 09:09:32,529] multiqc [DEBUG ] No samples found: sortmerna [2022-12-22 09:09:32,534] multiqc [DEBUG ] No samples found: biobloomtools [2022-12-22 09:09:32,539] multiqc [DEBUG ] No samples found: fastq_screen [2022-12-22 09:09:32,545] multiqc [DEBUG ] No samples found: afterqc [2022-12-22 09:09:32,552] multiqc [DEBUG ] No samples found: fastp [2022-12-22 09:10:05,502] multiqc.modules.fastqc.fastqc [INFO ] Found 366 reports [2022-12-22 09:10:39,583] multiqc [DEBUG ] No samples found: pycoqc [2022-12-22 09:10:39,589] multiqc [DEBUG ] No samples found: minionqc [2022-12-22 09:10:39,596] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-12-22 09:10:39,602] multiqc [DEBUG ] No samples found: clusterflow [2022-12-22 09:10:39,607] multiqc [DEBUG ] No samples found: bcl2fastq [2022-12-22 09:10:39,613] multiqc [DEBUG ] No samples found: interop [2022-12-22 09:10:39,618] multiqc [DEBUG ] No samples found: ivar [2022-12-22 09:10:39,623] multiqc [DEBUG ] No samples found: flash [2022-12-22 09:10:39,628] multiqc [DEBUG ] No samples found: seqyclean [2022-12-22 09:10:39,628] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-12-22 09:10:39,628] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-12-22 09:10:39,629] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-12-22 09:10:39,629] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-12-22 09:10:40,043] multiqc [INFO ] Compressing plot data [2022-12-22 09:10:40,394] multiqc [INFO ] Report : multiqc_report.html [2022-12-22 09:10:40,394] multiqc [INFO ] Data : multiqc_data [2022-12-22 09:10:40,394] multiqc [DEBUG ] Moving data file from '/state/partition1/job-28540844/tmp_xfnaw6z/multiqc_data' to '/scratch/gencore/logs/html/H7JYTBGXN/merged/multiqc_data' [2022-12-22 09:10:40,548] multiqc [INFO ] MultiQC complete