[2022-03-01 19:50:18,881] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-01 19:50:18,881] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-01 19:50:18,881] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-01 19:50:18,882] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-01 19:50:18,882] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-01 19:50:18,882] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3725BGXL/merged [2022-03-01 19:50:19,443] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-01 19:50:19,443] multiqc [INFO ] This is MultiQC v1.9 [2022-03-01 19:50:19,443] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3725BGXL/merged [2022-03-01 19:50:19,443] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3725BGXL/merged [2022-03-01 19:50:19,443] multiqc [INFO ] Template : default [2022-03-01 19:50:19,443] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-01 19:50:19,443] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3725BGXL/merged [2022-03-01 19:50:19,444] 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 [2022-03-01 19:50:19,444] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15444283/tmpl45i777j [2022-03-01 19:50:19,544] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SNW-2_fastqc.html [2022-03-01 19:50:19,547] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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19:50:20,023] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NEW-1_fastqc.html [2022-03-01 19:50:20,025] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NEW-1_fastqc.html [2022-03-01 19:50:20,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SNN-3_fastqc.html [2022-03-01 19:50:20,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SNN-3_fastqc.html [2022-03-01 19:50:20,137] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NEN-3_fastqc.html [2022-03-01 19:50:20,139] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NEN-3_fastqc.html [2022-03-01 19:50:20,194] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SNN-2_fastqc.html [2022-03-01 19:50:20,196] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SNN-2_fastqc.html [2022-03-01 19:50:20,246] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NNW-3_fastqc.html [2022-03-01 19:50:20,248] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NNW-3_fastqc.html [2022-03-01 19:50:20,299] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NNW-1_fastqc.html [2022-03-01 19:50:20,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NNW-1_fastqc.html [2022-03-01 19:50:20,353] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SEN-3_fastqc.html [2022-03-01 19:50:20,355] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SEN-3_fastqc.html [2022-03-01 19:50:20,413] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NNN-3_fastqc.html [2022-03-01 19:50:20,415] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NNN-3_fastqc.html [2022-03-01 19:50:20,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SEW-3_fastqc.html [2022-03-01 19:50:20,469] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SEW-3_fastqc.html [2022-03-01 19:50:20,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NNN-2_fastqc.html [2022-03-01 19:50:20,528] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NNN-2_fastqc.html [2022-03-01 19:50:20,579] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SNW-1_fastqc.html [2022-03-01 19:50:20,581] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SNW-1_fastqc.html [2022-03-01 19:50:20,640] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SEW-1_fastqc.html [2022-03-01 19:50:20,642] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SEW-1_fastqc.html [2022-03-01 19:50:20,699] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NEW-2_fastqc.html [2022-03-01 19:50:20,701] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NEW-2_fastqc.html [2022-03-01 19:50:20,753] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SNW-3_fastqc.html [2022-03-01 19:50:20,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SNW-3_fastqc.html [2022-03-01 19:50:20,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NNW-2_fastqc.html [2022-03-01 19:50:20,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NNW-2_fastqc.html [2022-03-01 19:50:20,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_NEN-1_fastqc.html [2022-03-01 19:50:20,866] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_NEN-1_fastqc.html [2022-03-01 19:50:20,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SEW-2_fastqc.html [2022-03-01 19:50:20,921] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SEW-2_fastqc.html [2022-03-01 19:50:20,978] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3725BGXL_n01_SEN-1_fastqc.html [2022-03-01 19:50:20,980] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3725BGXL_n01_SEN-1_fastqc.html [2022-03-01 19:50:21,370] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-01 19:50:21,370] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-01 19:50:21,377] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-01 19:50:21,389] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 24 samples (table) [2022-03-01 19:50:21,400] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-01 19:50:21,403] multiqc [DEBUG ] No samples found: conpair [2022-03-01 19:50:21,407] multiqc [DEBUG ] No samples found: peddy [2022-03-01 19:50:21,410] multiqc [DEBUG ] No samples found: somalier [2022-03-01 19:50:21,413] multiqc [DEBUG ] No samples found: methylQA [2022-03-01 19:50:21,418] multiqc [DEBUG ] No samples found: mosdepth [2022-03-01 19:50:21,421] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-01 19:50:21,424] multiqc [DEBUG ] No samples found: qualimap [2022-03-01 19:50:21,427] multiqc [DEBUG ] No samples found: preseq [2022-03-01 19:50:21,430] multiqc [DEBUG ] No samples found: quast [2022-03-01 19:50:21,433] multiqc [DEBUG ] No samples found: qorts [2022-03-01 19:50:21,436] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-01 19:50:21,440] multiqc [DEBUG ] No samples found: rockhopper [2022-03-01 19:50:21,443] multiqc [DEBUG ] No samples found: rsem [2022-03-01 19:50:21,448] multiqc [DEBUG ] No samples found: rseqc [2022-03-01 19:50:21,451] multiqc [DEBUG ] No samples found: busco [2022-03-01 19:50:21,454] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-01 19:50:21,458] multiqc [DEBUG ] No samples found: disambiguate [2022-03-01 19:50:21,461] multiqc [DEBUG ] No samples found: supernova [2022-03-01 19:50:21,467] multiqc [DEBUG ] No samples found: deeptools [2022-03-01 19:50:21,470] multiqc [DEBUG ] No samples found: sargasso [2022-03-01 19:50:21,473] multiqc [DEBUG ] No samples found: verifybamid [2022-03-01 19:50:21,476] multiqc [DEBUG ] No samples found: mirtrace [2022-03-01 19:50:21,479] multiqc [DEBUG ] No samples found: happy [2022-03-01 19:50:21,482] multiqc [DEBUG ] No samples found: mirtop [2022-03-01 19:50:21,486] multiqc [DEBUG ] No samples found: homer [2022-03-01 19:50:21,489] multiqc [DEBUG ] No samples found: macs2 [2022-03-01 19:50:21,492] multiqc [DEBUG ] No samples found: theta2 [2022-03-01 19:50:21,495] multiqc [DEBUG ] No samples found: snpeff [2022-03-01 19:50:21,499] multiqc [DEBUG ] No samples found: gatk [2022-03-01 19:50:21,502] multiqc [DEBUG ] No samples found: htseq [2022-03-01 19:50:21,505] multiqc [DEBUG ] No samples found: bcftools [2022-03-01 19:50:21,508] multiqc [DEBUG ] No samples found: featureCounts [2022-03-01 19:50:21,512] multiqc [DEBUG ] No samples found: fgbio [2022-03-01 19:50:21,518] multiqc [DEBUG ] No samples found: dragen [2022-03-01 19:50:21,522] multiqc [DEBUG ] No samples found: dedup [2022-03-01 19:50:21,525] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-01 19:50:21,535] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-01 19:50:21,538] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-01 19:50:21,540] multiqc [DEBUG ] No samples found: picard [2022-03-01 19:50:21,547] multiqc [DEBUG ] No samples found: prokka [2022-03-01 19:50:21,551] multiqc [DEBUG ] No samples found: samblaster [2022-03-01 19:50:21,556] multiqc [DEBUG ] No samples found: samtools [2022-03-01 19:50:21,559] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-01 19:50:21,562] multiqc [DEBUG ] No samples found: bamtools [2022-03-01 19:50:21,565] multiqc [DEBUG ] No samples found: jellyfish [2022-03-01 19:50:21,570] multiqc [DEBUG ] No samples found: vcftools [2022-03-01 19:50:21,573] multiqc [DEBUG ] No samples found: longranger [2022-03-01 19:50:21,576] multiqc [DEBUG ] No samples found: stacks [2022-03-01 19:50:21,579] multiqc [DEBUG ] No samples found: varscan2 [2022-03-01 19:50:21,586] multiqc [DEBUG ] No samples found: bbmap [2022-03-01 19:50:21,589] multiqc [DEBUG ] No samples found: bismark [2022-03-01 19:50:21,593] multiqc [DEBUG ] No samples found: biscuit [2022-03-01 19:50:21,596] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-01 19:50:21,599] multiqc [DEBUG ] No samples found: hicup [2022-03-01 19:50:21,602] multiqc [DEBUG ] No samples found: hicpro [2022-03-01 19:50:21,605] multiqc [DEBUG ] No samples found: salmon [2022-03-01 19:50:21,608] multiqc [DEBUG ] No samples found: kallisto [2022-03-01 19:50:21,611] multiqc [DEBUG ] No samples found: slamdunk [2022-03-01 19:50:21,614] multiqc [DEBUG ] No samples found: star [2022-03-01 19:50:21,617] multiqc [DEBUG ] No samples found: hisat2 [2022-03-01 19:50:21,620] multiqc [DEBUG ] No samples found: tophat [2022-03-01 19:50:21,623] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-01 19:50:21,626] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-01 19:50:21,629] multiqc [DEBUG ] No samples found: snpsplit [2022-03-01 19:50:21,632] multiqc [DEBUG ] No samples found: kat [2022-03-01 19:50:21,636] multiqc [DEBUG ] No samples found: leehom [2022-03-01 19:50:21,639] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-01 19:50:21,643] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-01 19:50:21,646] multiqc [DEBUG ] No samples found: cutadapt [2022-03-01 19:50:21,649] multiqc [DEBUG ] No samples found: flexbar [2022-03-01 19:50:21,652] multiqc [DEBUG ] No samples found: kaiju [2022-03-01 19:50:21,655] multiqc [DEBUG ] No samples found: kraken [2022-03-01 19:50:21,658] multiqc [DEBUG ] No samples found: malt [2022-03-01 19:50:21,661] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-01 19:50:21,664] multiqc [DEBUG ] No samples found: sickle [2022-03-01 19:50:21,667] multiqc [DEBUG ] No samples found: skewer [2022-03-01 19:50:21,671] multiqc [DEBUG ] No samples found: sortmerna [2022-03-01 19:50:21,674] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-01 19:50:21,677] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-01 19:50:21,680] multiqc [DEBUG ] No samples found: afterqc [2022-03-01 19:50:21,683] multiqc [DEBUG ] No samples found: fastp [2022-03-01 19:50:23,332] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2022-03-01 19:50:23,869] multiqc [DEBUG ] No samples found: pycoqc [2022-03-01 19:50:23,872] multiqc [DEBUG ] No samples found: minionqc [2022-03-01 19:50:23,875] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-01 19:50:23,878] multiqc [DEBUG ] No samples found: clusterflow [2022-03-01 19:50:23,881] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-01 19:50:23,884] multiqc [DEBUG ] No samples found: interop [2022-03-01 19:50:23,887] multiqc [DEBUG ] No samples found: ivar [2022-03-01 19:50:23,890] multiqc [DEBUG ] No samples found: flash [2022-03-01 19:50:23,893] multiqc [DEBUG ] No samples found: seqyclean [2022-03-01 19:50:23,893] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-01 19:50:23,893] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-01 19:50:23,893] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-01 19:50:23,893] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-01 19:50:23,922] multiqc [INFO ] Compressing plot data [2022-03-01 19:50:24,374] multiqc [INFO ] Report : multiqc_report.html [2022-03-01 19:50:24,374] multiqc [INFO ] Data : multiqc_data [2022-03-01 19:50:24,374] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15444283/tmpl45i777j/multiqc_data' to '/scratch/gencore/logs/html/H3725BGXL/merged/multiqc_data' [2022-03-01 19:50:24,476] multiqc [INFO ] MultiQC complete