[2023-04-04 06:00:58,084] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-04-04 06:00:58,085] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-04-04 06:00:58,085] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-04-04 06:00:58,087] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-04-04 06:00:58,087] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-04-04 06:00:58,087] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVMH3DRX2/merged [2023-04-04 06:00:58,500] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-04-04 06:00:58,500] multiqc [INFO ] This is MultiQC v1.9 [2023-04-04 06:00:58,500] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVMH3DRX2/merged [2023-04-04 06:00:58,500] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVMH3DRX2/merged [2023-04-04 06:00:58,500] multiqc [INFO ] Template : default [2023-04-04 06:00:58,500] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-04-04 06:00:58,500] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVMH3DRX2/merged [2023-04-04 06:00:58,500] 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 [2023-04-04 06:00:58,500] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-31567599/tmprpzk_mrd [2023-04-04 06:00:58,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayFour2_fastqc.html [2023-04-04 06:00:58,611] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayFour2_fastqc.html [2023-04-04 06:00:58,652] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-04 06:00:58,654] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-04 06:00:58,654] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-04 06:00:58,654] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-04 06:00:58,654] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-04 06:00:58,654] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-04 06:00:58,654] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-04 06:00:59,392] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayZero1_fastqc.html [2023-04-04 06:00:59,394] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayZero1_fastqc.html [2023-04-04 06:00:59,450] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayFour2_fastqc.html [2023-04-04 06:00:59,451] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayFour2_fastqc.html [2023-04-04 06:00:59,500] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n02_undetermined_fastqc.html [2023-04-04 06:00:59,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n02_undetermined_fastqc.html [2023-04-04 06:00:59,568] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayZero1_fastqc.html [2023-04-04 06:00:59,569] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayZero1_fastqc.html [2023-04-04 06:00:59,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayFour1_fastqc.html [2023-04-04 06:00:59,619] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayFour1_fastqc.html [2023-04-04 06:00:59,659] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayZero2_fastqc.html [2023-04-04 06:00:59,661] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayZero2_fastqc.html [2023-04-04 06:00:59,710] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayFour1_fastqc.html [2023-04-04 06:00:59,712] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n02_DayFour1_fastqc.html [2023-04-04 06:00:59,761] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n01_undetermined_fastqc.html [2023-04-04 06:00:59,763] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n01_undetermined_fastqc.html [2023-04-04 06:00:59,802] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayZero2_fastqc.html [2023-04-04 06:00:59,804] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVMH3DRX2_n01_DayZero2_fastqc.html [2023-04-04 06:01:00,336] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-04 06:01:00,338] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-04 06:01:00,345] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-04-04 06:01:00,348] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2023-04-04 06:01:00,358] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-04-04 06:01:00,363] multiqc [DEBUG ] No samples found: conpair [2023-04-04 06:01:00,368] multiqc [DEBUG ] No samples found: peddy [2023-04-04 06:01:00,373] multiqc [DEBUG ] No samples found: somalier [2023-04-04 06:01:00,379] multiqc [DEBUG ] No samples found: methylQA [2023-04-04 06:01:00,388] multiqc [DEBUG ] No samples found: mosdepth [2023-04-04 06:01:00,392] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-04-04 06:01:00,395] multiqc [DEBUG ] No samples found: qualimap [2023-04-04 06:01:00,401] multiqc [DEBUG ] No samples found: preseq [2023-04-04 06:01:00,406] multiqc [DEBUG ] No samples found: quast [2023-04-04 06:01:00,411] multiqc [DEBUG ] No samples found: qorts [2023-04-04 06:01:00,416] multiqc [DEBUG ] No samples found: rna_seqc [2023-04-04 06:01:00,421] multiqc [DEBUG ] No samples found: rockhopper [2023-04-04 06:01:00,426] multiqc [DEBUG ] No samples found: rsem [2023-04-04 06:01:00,436] multiqc [DEBUG ] No samples found: rseqc [2023-04-04 06:01:00,441] multiqc [DEBUG ] No samples found: busco [2023-04-04 06:01:00,446] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-04-04 06:01:00,450] multiqc [DEBUG ] No samples found: disambiguate [2023-04-04 06:01:00,456] multiqc [DEBUG ] No samples found: supernova [2023-04-04 06:01:00,468] multiqc [DEBUG ] No samples found: deeptools [2023-04-04 06:01:00,473] multiqc [DEBUG ] No samples found: sargasso [2023-04-04 06:01:00,480] multiqc [DEBUG ] No samples found: verifybamid [2023-04-04 06:01:00,485] multiqc [DEBUG ] No samples found: mirtrace [2023-04-04 06:01:00,490] multiqc [DEBUG ] No samples found: happy [2023-04-04 06:01:00,496] multiqc [DEBUG ] No samples found: mirtop [2023-04-04 06:01:00,503] multiqc [DEBUG ] No samples found: homer [2023-04-04 06:01:00,508] multiqc [DEBUG ] No samples found: macs2 [2023-04-04 06:01:00,512] multiqc [DEBUG ] No samples found: theta2 [2023-04-04 06:01:00,517] multiqc [DEBUG ] No samples found: snpeff [2023-04-04 06:01:00,524] multiqc [DEBUG ] No samples found: gatk [2023-04-04 06:01:00,529] multiqc [DEBUG ] No samples found: htseq [2023-04-04 06:01:00,535] multiqc [DEBUG ] No samples found: bcftools [2023-04-04 06:01:00,540] multiqc [DEBUG ] No samples found: featureCounts [2023-04-04 06:01:00,550] multiqc [DEBUG ] No samples found: fgbio [2023-04-04 06:01:00,564] multiqc [DEBUG ] No samples found: dragen [2023-04-04 06:01:00,568] multiqc [DEBUG ] No samples found: dedup [2023-04-04 06:01:00,573] multiqc [DEBUG ] No samples found: damageprofiler [2023-04-04 06:01:00,596] multiqc [DEBUG ] No samples found: biobambam2 [2023-04-04 06:01:00,601] multiqc [DEBUG ] No samples found: mtnucratio [2023-04-04 06:01:00,603] multiqc [DEBUG ] No samples found: picard [2023-04-04 06:01:00,608] multiqc [DEBUG ] No samples found: prokka [2023-04-04 06:01:00,612] multiqc [DEBUG ] No samples found: samblaster [2023-04-04 06:01:00,620] multiqc [DEBUG ] No samples found: samtools [2023-04-04 06:01:00,625] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-04-04 06:01:00,630] multiqc [DEBUG ] No samples found: bamtools [2023-04-04 06:01:00,635] multiqc [DEBUG ] No samples found: jellyfish [2023-04-04 06:01:00,642] multiqc [DEBUG ] No samples found: vcftools [2023-04-04 06:01:00,647] multiqc [DEBUG ] No samples found: longranger [2023-04-04 06:01:00,652] multiqc [DEBUG ] No samples found: stacks [2023-04-04 06:01:00,657] multiqc [DEBUG ] No samples found: varscan2 [2023-04-04 06:01:00,670] multiqc [DEBUG ] No samples found: bbmap [2023-04-04 06:01:00,675] multiqc [DEBUG ] No samples found: bismark [2023-04-04 06:01:00,683] multiqc [DEBUG ] No samples found: biscuit [2023-04-04 06:01:00,688] multiqc [DEBUG ] No samples found: hicexplorer [2023-04-04 06:01:00,698] multiqc [DEBUG ] No samples found: hicup [2023-04-04 06:01:00,707] multiqc [DEBUG ] No samples found: hicpro [2023-04-04 06:01:00,715] multiqc [DEBUG ] No samples found: salmon [2023-04-04 06:01:00,721] multiqc [DEBUG ] No samples found: kallisto [2023-04-04 06:01:00,726] multiqc [DEBUG ] No samples found: slamdunk [2023-04-04 06:01:00,731] multiqc [DEBUG ] No samples found: star [2023-04-04 06:01:00,737] multiqc [DEBUG ] No samples found: hisat2 [2023-04-04 06:01:00,742] multiqc [DEBUG ] No samples found: tophat [2023-04-04 06:01:00,746] multiqc [DEBUG ] No samples found: bowtie2 [2023-04-04 06:01:00,751] multiqc [DEBUG ] No samples found: bowtie1 [2023-04-04 06:01:00,756] multiqc [DEBUG ] No samples found: snpsplit [2023-04-04 06:01:00,761] multiqc [DEBUG ] No samples found: kat [2023-04-04 06:01:00,765] multiqc [DEBUG ] No samples found: leehom [2023-04-04 06:01:00,770] multiqc [DEBUG ] No samples found: adapterRemoval [2023-04-04 06:01:00,775] multiqc [DEBUG ] No samples found: clipandmerge [2023-04-04 06:01:00,779] multiqc [DEBUG ] No samples found: cutadapt [2023-04-04 06:01:00,784] multiqc [DEBUG ] No samples found: flexbar [2023-04-04 06:01:00,789] multiqc [DEBUG ] No samples found: kaiju [2023-04-04 06:01:00,794] multiqc [DEBUG ] No samples found: kraken [2023-04-04 06:01:00,799] multiqc [DEBUG ] No samples found: malt [2023-04-04 06:01:00,804] multiqc [DEBUG ] No samples found: trimmomatic [2023-04-04 06:01:00,808] multiqc [DEBUG ] No samples found: sickle [2023-04-04 06:01:00,814] multiqc [DEBUG ] No samples found: skewer [2023-04-04 06:01:00,818] multiqc [DEBUG ] No samples found: sortmerna [2023-04-04 06:01:00,822] multiqc [DEBUG ] No samples found: biobloomtools [2023-04-04 06:01:00,827] multiqc [DEBUG ] No samples found: fastq_screen [2023-04-04 06:01:00,832] multiqc [DEBUG ] No samples found: afterqc [2023-04-04 06:01:00,837] multiqc [DEBUG ] No samples found: fastp [2023-04-04 06:01:01,125] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-04-04 06:01:01,216] multiqc [DEBUG ] No samples found: pycoqc [2023-04-04 06:01:01,221] multiqc [DEBUG ] No samples found: minionqc [2023-04-04 06:01:01,226] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-04-04 06:01:01,230] multiqc [DEBUG ] No samples found: clusterflow [2023-04-04 06:01:01,236] multiqc [DEBUG ] No samples found: bcl2fastq [2023-04-04 06:01:01,241] multiqc [DEBUG ] No samples found: interop [2023-04-04 06:01:01,246] multiqc [DEBUG ] No samples found: ivar [2023-04-04 06:01:01,250] multiqc [DEBUG ] No samples found: flash [2023-04-04 06:01:01,281] multiqc [DEBUG ] No samples found: seqyclean [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-04-04 06:01:01,281] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-04-04 06:01:01,282] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-04-04 06:01:01,294] multiqc [INFO ] Compressing plot data [2023-04-04 06:01:01,463] multiqc [INFO ] Report : multiqc_report.html [2023-04-04 06:01:01,463] multiqc [INFO ] Data : multiqc_data [2023-04-04 06:01:01,463] multiqc [DEBUG ] Moving data file from '/state/partition1/job-31567599/tmprpzk_mrd/multiqc_data' to '/scratch/gencore/logs/html/HVMH3DRX2/merged/multiqc_data' [2023-04-04 06:01:01,590] multiqc [INFO ] MultiQC complete