[2022-10-28 16:01:15,561] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-28 16:01:15,561] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-28 16:01:15,561] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-28 16:01:15,562] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-28 16:01:15,562] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-28 16:01:15,563] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLGK3BGXM/merged [2022-10-28 16:01:15,962] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-28 16:01:15,963] multiqc [INFO ] This is MultiQC v1.9 [2022-10-28 16:01:15,963] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLGK3BGXM/merged [2022-10-28 16:01:15,963] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLGK3BGXM/merged [2022-10-28 16:01:15,963] multiqc [INFO ] Template : default [2022-10-28 16:01:15,963] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-28 16:01:15,963] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLGK3BGXM/merged [2022-10-28 16:01:15,963] 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 [2022-10-28 16:01:15,963] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26399158/tmp21_zky_8 [2022-10-28 16:01:16,097] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_WT_22_26_B_fastqc.html [2022-10-28 16:01:16,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_WT_22_26_B_fastqc.html [2022-10-28 16:01:16,142] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-10-28 16:01:16,144] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-10-28 16:01:16,290] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_WT_22_26_B_fastqc.html [2022-10-28 16:01:16,292] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_WT_22_26_B_fastqc.html [2022-10-28 16:01:16,333] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_26_B_fastqc.html [2022-10-28 16:01:16,335] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_26_B_fastqc.html [2022-10-28 16:01:16,379] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_24_B_fastqc.html [2022-10-28 16:01:16,381] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_24_B_fastqc.html [2022-10-28 16:01:16,425] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_28_B_fastqc.html [2022-10-28 16:01:16,426] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_28_B_fastqc.html [2022-10-28 16:01:16,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_22_B_fastqc.html [2022-10-28 16:01:16,471] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_22_B_fastqc.html [2022-10-28 16:01:16,514] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_28_B_fastqc.html [2022-10-28 16:01:16,516] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_dmd-3_28_B_fastqc.html [2022-10-28 16:01:16,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_undetermined_fastqc.html [2022-10-28 16:01:16,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_undetermined_fastqc.html [2022-10-28 16:01:16,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_WT_28_B_fastqc.html [2022-10-28 16:01:16,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_WT_28_B_fastqc.html [2022-10-28 16:01:16,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_WT_24_25_B_fastqc.html [2022-10-28 16:01:16,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_WT_24_25_B_fastqc.html [2022-10-28 16:01:16,692] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_22_B_fastqc.html [2022-10-28 16:01:16,694] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_22_B_fastqc.html [2022-10-28 16:01:16,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_WT_24_25_B_fastqc.html [2022-10-28 16:01:16,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_WT_24_25_B_fastqc.html [2022-10-28 16:01:16,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_24_B_fastqc.html [2022-10-28 16:01:16,781] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_24_B_fastqc.html [2022-10-28 16:01:16,824] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_26_B_fastqc.html [2022-10-28 16:01:16,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n01_dmd-3_26_B_fastqc.html [2022-10-28 16:01:16,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_undetermined_fastqc.html [2022-10-28 16:01:16,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_undetermined_fastqc.html [2022-10-28 16:01:16,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGK3BGXM_n02_WT_28_B_fastqc.html [2022-10-28 16:01:16,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGK3BGXM_n02_WT_28_B_fastqc.html [2022-10-28 16:01:17,296] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-28 16:01:17,298] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-28 16:01:17,308] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2022-10-28 16:01:17,318] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-10-28 16:01:17,319] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-28 16:01:17,340] multiqc [DEBUG ] No samples found: conpair [2022-10-28 16:01:17,349] multiqc [DEBUG ] No samples found: peddy [2022-10-28 16:01:17,357] multiqc [DEBUG ] No samples found: somalier [2022-10-28 16:01:17,365] multiqc [DEBUG ] No samples found: methylQA [2022-10-28 16:01:17,377] multiqc [DEBUG ] No samples found: mosdepth [2022-10-28 16:01:17,382] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-28 16:01:17,386] multiqc [DEBUG ] No samples found: qualimap [2022-10-28 16:01:17,391] multiqc [DEBUG ] No samples found: preseq [2022-10-28 16:01:17,397] multiqc [DEBUG ] No samples found: quast [2022-10-28 16:01:17,403] multiqc [DEBUG ] No samples found: qorts [2022-10-28 16:01:17,410] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-28 16:01:17,418] multiqc [DEBUG ] No samples found: rockhopper [2022-10-28 16:01:17,424] multiqc [DEBUG ] No samples found: rsem [2022-10-28 16:01:17,439] multiqc [DEBUG ] No samples found: rseqc [2022-10-28 16:01:17,444] multiqc [DEBUG ] No samples found: busco [2022-10-28 16:01:17,450] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-28 16:01:17,455] multiqc [DEBUG ] No samples found: disambiguate [2022-10-28 16:01:17,460] multiqc [DEBUG ] No samples found: supernova [2022-10-28 16:01:17,480] multiqc [DEBUG ] No samples found: deeptools [2022-10-28 16:01:17,487] multiqc [DEBUG ] No samples found: sargasso [2022-10-28 16:01:17,493] multiqc [DEBUG ] No samples found: verifybamid [2022-10-28 16:01:17,499] multiqc [DEBUG ] No samples found: mirtrace [2022-10-28 16:01:17,505] multiqc [DEBUG ] No samples found: happy [2022-10-28 16:01:17,511] multiqc [DEBUG ] No samples found: mirtop [2022-10-28 16:01:17,520] multiqc [DEBUG ] No samples found: homer [2022-10-28 16:01:17,526] multiqc [DEBUG ] No samples found: macs2 [2022-10-28 16:01:17,531] multiqc [DEBUG ] No samples found: theta2 [2022-10-28 16:01:17,536] multiqc [DEBUG ] No samples found: snpeff [2022-10-28 16:01:17,545] multiqc [DEBUG ] No samples found: gatk [2022-10-28 16:01:17,550] multiqc [DEBUG ] No samples found: htseq [2022-10-28 16:01:17,557] multiqc [DEBUG ] No samples found: bcftools [2022-10-28 16:01:17,563] multiqc [DEBUG ] No samples found: featureCounts [2022-10-28 16:01:17,571] multiqc [DEBUG ] No samples found: fgbio [2022-10-28 16:01:17,589] multiqc [DEBUG ] No samples found: dragen [2022-10-28 16:01:17,595] multiqc [DEBUG ] No samples found: dedup [2022-10-28 16:01:17,601] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-28 16:01:17,637] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-28 16:01:17,642] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-28 16:01:17,644] multiqc [DEBUG ] No samples found: picard [2022-10-28 16:01:17,650] multiqc [DEBUG ] No samples found: prokka [2022-10-28 16:01:17,655] multiqc [DEBUG ] No samples found: samblaster [2022-10-28 16:01:17,669] multiqc [DEBUG ] No samples found: samtools [2022-10-28 16:01:17,675] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-28 16:01:17,681] multiqc [DEBUG ] No samples found: bamtools [2022-10-28 16:01:17,686] multiqc [DEBUG ] No samples found: jellyfish [2022-10-28 16:01:17,699] multiqc [DEBUG ] No samples found: vcftools [2022-10-28 16:01:17,709] multiqc [DEBUG ] No samples found: longranger [2022-10-28 16:01:17,720] multiqc [DEBUG ] No samples found: stacks [2022-10-28 16:01:17,730] multiqc [DEBUG ] No samples found: varscan2 [2022-10-28 16:01:17,770] multiqc [DEBUG ] No samples found: bbmap [2022-10-28 16:01:17,782] multiqc [DEBUG ] No samples found: bismark [2022-10-28 16:01:17,792] multiqc [DEBUG ] No samples found: biscuit [2022-10-28 16:01:17,801] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-28 16:01:17,809] multiqc [DEBUG ] No samples found: hicup [2022-10-28 16:01:17,816] multiqc [DEBUG ] No samples found: hicpro [2022-10-28 16:01:17,821] multiqc [DEBUG ] No samples found: salmon [2022-10-28 16:01:17,827] multiqc [DEBUG ] No samples found: kallisto [2022-10-28 16:01:17,833] multiqc [DEBUG ] No samples found: slamdunk [2022-10-28 16:01:17,840] multiqc [DEBUG ] No samples found: star [2022-10-28 16:01:17,848] multiqc [DEBUG ] No samples found: hisat2 [2022-10-28 16:01:17,854] multiqc [DEBUG ] No samples found: tophat [2022-10-28 16:01:17,859] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-28 16:01:17,865] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-28 16:01:17,871] multiqc [DEBUG ] No samples found: snpsplit [2022-10-28 16:01:17,876] multiqc [DEBUG ] No samples found: kat [2022-10-28 16:01:17,881] multiqc [DEBUG ] No samples found: leehom [2022-10-28 16:01:17,889] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-28 16:01:17,894] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-28 16:01:17,900] multiqc [DEBUG ] No samples found: cutadapt [2022-10-28 16:01:17,905] multiqc [DEBUG ] No samples found: flexbar [2022-10-28 16:01:17,911] multiqc [DEBUG ] No samples found: kaiju [2022-10-28 16:01:17,917] multiqc [DEBUG ] No samples found: kraken [2022-10-28 16:01:17,923] multiqc [DEBUG ] No samples found: malt [2022-10-28 16:01:17,929] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-28 16:01:17,936] multiqc [DEBUG ] No samples found: sickle [2022-10-28 16:01:17,942] multiqc [DEBUG ] No samples found: skewer [2022-10-28 16:01:17,947] multiqc [DEBUG ] No samples found: sortmerna [2022-10-28 16:01:17,952] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-28 16:01:17,958] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-28 16:01:17,964] multiqc [DEBUG ] No samples found: afterqc [2022-10-28 16:01:17,971] multiqc [DEBUG ] No samples found: fastp [2022-10-28 16:01:18,529] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2022-10-28 16:01:18,602] multiqc [DEBUG ] No samples found: pycoqc [2022-10-28 16:01:18,609] multiqc [DEBUG ] No samples found: minionqc [2022-10-28 16:01:18,653] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-28 16:01:18,660] multiqc [DEBUG ] No samples found: clusterflow [2022-10-28 16:01:18,668] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-28 16:01:18,674] multiqc [DEBUG ] No samples found: interop [2022-10-28 16:01:18,680] multiqc [DEBUG ] No samples found: ivar [2022-10-28 16:01:18,686] multiqc [DEBUG ] No samples found: flash [2022-10-28 16:01:18,692] multiqc [DEBUG ] No samples found: seqyclean [2022-10-28 16:01:18,692] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-10-28 16:01:18,692] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-10-28 16:01:18,692] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-10-28 16:01:18,692] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-28 16:01:18,713] multiqc [INFO ] Compressing plot data [2022-10-28 16:01:18,950] multiqc [INFO ] Report : multiqc_report.html [2022-10-28 16:01:18,950] multiqc [INFO ] Data : multiqc_data [2022-10-28 16:01:18,950] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26399158/tmp21_zky_8/multiqc_data' to '/scratch/gencore/logs/html/HLGK3BGXM/merged/multiqc_data' [2022-10-28 16:01:19,092] multiqc [INFO ] MultiQC complete