[2023-03-25 08:27:56,348] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-03-25 08:27:56,348] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-03-25 08:27:56,348] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-03-25 08:27:56,350] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-03-25 08:27:56,350] 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}} [2023-03-25 08:27:56,350] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-DKV2Y/1 [2023-03-25 08:27:57,250] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-03-25 08:27:57,250] multiqc [INFO ] This is MultiQC v1.9 [2023-03-25 08:27:57,250] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-DKV2Y/1 [2023-03-25 08:27:57,251] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-DKV2Y/1 [2023-03-25 08:27:57,251] multiqc [INFO ] Template : default [2023-03-25 08:27:57,251] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-03-25 08:27:57,251] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-DKV2Y/1 [2023-03-25 08:27:57,251] 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 [2023-03-25 08:27:57,251] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-31308311/tmp8sj4d42x [2023-03-25 08:27:57,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_C12_DVE_fastqc.html [2023-03-25 08:27:57,346] multiqc [DEBUG ] File ignored by longranger/invocation because it 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longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_C01_CHI_fastqc.html [2023-03-25 08:28:20,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_A01_ATH_fastqc.html [2023-03-25 08:28:20,264] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_A01_ATH_fastqc.html [2023-03-25 08:28:20,305] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_B01_ATH_fastqc.html [2023-03-25 08:28:20,307] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_B01_ATH_fastqc.html [2023-03-25 08:28:20,347] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_G06_ATH_fastqc.html [2023-03-25 08:28:20,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_G06_ATH_fastqc.html [2023-03-25 08:28:20,389] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_H08_CHI_fastqc.html [2023-03-25 08:28:20,391] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_H08_CHI_fastqc.html [2023-03-25 08:28:20,431] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_C01_ATH_fastqc.html [2023-03-25 08:28:20,433] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_C01_ATH_fastqc.html [2023-03-25 08:28:20,474] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_G06_CHI_fastqc.html [2023-03-25 08:28:20,475] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_G06_CHI_fastqc.html [2023-03-25 08:28:20,516] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_G06_DVE_fastqc.html [2023-03-25 08:28:20,518] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_G06_DVE_fastqc.html [2023-03-25 08:28:20,559] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_E03_CHI_fastqc.html [2023-03-25 08:28:20,560] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n02_E03_CHI_fastqc.html [2023-03-25 08:28:20,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_F06_ATH_fastqc.html [2023-03-25 08:28:20,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DKV2Y_l01_n01_F06_ATH_fastqc.html [2023-03-25 08:28:20,891] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-25 08:28:20,892] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-25 08:28:20,900] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-03-25 08:28:20,910] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-03-25 08:28:21,028] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 263 samples (table) [2023-03-25 08:28:21,031] multiqc [DEBUG ] No samples found: conpair [2023-03-25 08:28:21,034] multiqc [DEBUG ] No samples found: peddy [2023-03-25 08:28:21,037] multiqc [DEBUG ] No samples found: somalier [2023-03-25 08:28:21,040] multiqc [DEBUG ] No samples found: methylQA [2023-03-25 08:28:21,043] multiqc [DEBUG ] No samples found: mosdepth [2023-03-25 08:28:21,046] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-03-25 08:28:21,048] multiqc [DEBUG ] No samples found: qualimap [2023-03-25 08:28:21,051] multiqc [DEBUG ] No samples found: preseq [2023-03-25 08:28:21,054] multiqc [DEBUG ] No samples found: quast [2023-03-25 08:28:21,057] multiqc [DEBUG ] No samples found: qorts [2023-03-25 08:28:21,059] multiqc [DEBUG ] No samples found: rna_seqc [2023-03-25 08:28:21,062] multiqc [DEBUG ] No samples found: rockhopper [2023-03-25 08:28:21,065] multiqc [DEBUG ] No samples found: rsem [2023-03-25 08:28:21,069] multiqc [DEBUG ] No samples found: rseqc [2023-03-25 08:28:21,072] multiqc [DEBUG ] No samples found: busco [2023-03-25 08:28:21,075] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-03-25 08:28:21,077] multiqc [DEBUG ] No samples found: disambiguate [2023-03-25 08:28:21,080] multiqc [DEBUG ] No samples found: supernova [2023-03-25 08:28:21,085] multiqc [DEBUG ] No samples found: deeptools [2023-03-25 08:28:21,088] multiqc [DEBUG ] No samples found: sargasso [2023-03-25 08:28:21,090] multiqc [DEBUG ] No samples found: verifybamid [2023-03-25 08:28:21,093] multiqc [DEBUG ] No samples found: mirtrace [2023-03-25 08:28:21,096] multiqc [DEBUG ] No samples found: happy [2023-03-25 08:28:21,098] multiqc [DEBUG ] No samples found: mirtop [2023-03-25 08:28:21,102] multiqc [DEBUG ] No samples found: homer [2023-03-25 08:28:21,104] multiqc [DEBUG ] No samples found: macs2 [2023-03-25 08:28:21,107] multiqc [DEBUG ] No samples found: theta2 [2023-03-25 08:28:21,110] multiqc [DEBUG ] No samples found: snpeff [2023-03-25 08:28:21,113] multiqc [DEBUG ] No samples found: gatk [2023-03-25 08:28:21,116] multiqc [DEBUG ] No samples found: htseq [2023-03-25 08:28:21,118] multiqc [DEBUG ] No samples found: bcftools [2023-03-25 08:28:21,121] multiqc [DEBUG ] No samples found: featureCounts [2023-03-25 08:28:21,124] multiqc [DEBUG ] No samples found: fgbio [2023-03-25 08:28:21,129] multiqc [DEBUG ] No samples found: dragen [2023-03-25 08:28:21,132] multiqc [DEBUG ] No samples found: dedup [2023-03-25 08:28:21,135] multiqc [DEBUG ] No samples found: damageprofiler [2023-03-25 08:28:21,142] multiqc [DEBUG ] No samples found: biobambam2 [2023-03-25 08:28:21,145] multiqc [DEBUG ] No samples found: mtnucratio [2023-03-25 08:28:21,147] multiqc [DEBUG ] No samples found: picard [2023-03-25 08:28:21,150] multiqc [DEBUG ] No samples found: prokka [2023-03-25 08:28:21,152] multiqc [DEBUG ] No samples found: samblaster [2023-03-25 08:28:21,156] multiqc [DEBUG ] No samples found: samtools [2023-03-25 08:28:21,159] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-03-25 08:28:21,161] multiqc [DEBUG ] No samples found: bamtools [2023-03-25 08:28:21,164] multiqc [DEBUG ] No samples found: jellyfish [2023-03-25 08:28:21,168] multiqc [DEBUG ] No samples found: vcftools [2023-03-25 08:28:21,170] multiqc [DEBUG ] No samples found: longranger [2023-03-25 08:28:21,173] multiqc [DEBUG ] No samples found: stacks [2023-03-25 08:28:21,176] multiqc [DEBUG ] No samples found: varscan2 [2023-03-25 08:28:21,181] multiqc [DEBUG ] No samples found: bbmap [2023-03-25 08:28:21,183] multiqc [DEBUG ] No samples found: bismark [2023-03-25 08:28:21,186] multiqc [DEBUG ] No samples found: biscuit [2023-03-25 08:28:21,189] multiqc [DEBUG ] No samples found: hicexplorer [2023-03-25 08:28:21,192] multiqc [DEBUG ] No samples found: hicup [2023-03-25 08:28:21,194] multiqc [DEBUG ] No samples found: hicpro [2023-03-25 08:28:21,197] multiqc [DEBUG ] No samples found: salmon [2023-03-25 08:28:21,200] multiqc [DEBUG ] No samples found: kallisto [2023-03-25 08:28:21,203] multiqc [DEBUG ] No samples found: slamdunk [2023-03-25 08:28:21,205] multiqc [DEBUG ] No samples found: star [2023-03-25 08:28:21,208] multiqc [DEBUG ] No samples found: hisat2 [2023-03-25 08:28:21,211] multiqc [DEBUG ] No samples found: tophat [2023-03-25 08:28:21,213] multiqc [DEBUG ] No samples found: bowtie2 [2023-03-25 08:28:21,216] multiqc [DEBUG ] No samples found: bowtie1 [2023-03-25 08:28:21,219] multiqc [DEBUG ] No samples found: snpsplit [2023-03-25 08:28:21,221] multiqc [DEBUG ] No samples found: kat [2023-03-25 08:28:21,224] multiqc [DEBUG ] No samples found: leehom [2023-03-25 08:28:21,226] multiqc [DEBUG ] No samples found: adapterRemoval [2023-03-25 08:28:21,229] multiqc [DEBUG ] No samples found: clipandmerge [2023-03-25 08:28:21,232] multiqc [DEBUG ] No samples found: cutadapt [2023-03-25 08:28:21,235] multiqc [DEBUG ] No samples found: flexbar [2023-03-25 08:28:21,237] multiqc [DEBUG ] No samples found: kaiju [2023-03-25 08:28:21,240] multiqc [DEBUG ] No samples found: kraken [2023-03-25 08:28:21,242] multiqc [DEBUG ] No samples found: malt [2023-03-25 08:28:21,245] multiqc [DEBUG ] No samples found: trimmomatic [2023-03-25 08:28:21,248] multiqc [DEBUG ] No samples found: sickle [2023-03-25 08:28:21,250] multiqc [DEBUG ] No samples found: skewer [2023-03-25 08:28:21,253] multiqc [DEBUG ] No samples found: sortmerna [2023-03-25 08:28:21,256] multiqc [DEBUG ] No samples found: biobloomtools [2023-03-25 08:28:21,258] multiqc [DEBUG ] No samples found: fastq_screen [2023-03-25 08:28:21,261] multiqc [DEBUG ] No samples found: afterqc [2023-03-25 08:28:21,264] multiqc [DEBUG ] No samples found: fastp [2023-03-25 08:28:22,350] multiqc.modules.fastqc.fastqc [INFO ] Found 526 reports [2023-03-25 08:28:59,045] multiqc [DEBUG ] No samples found: pycoqc [2023-03-25 08:28:59,048] multiqc [DEBUG ] No samples found: minionqc [2023-03-25 08:28:59,051] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-03-25 08:28:59,054] multiqc [DEBUG ] No samples found: clusterflow [2023-03-25 08:28:59,057] multiqc [DEBUG ] No samples found: bcl2fastq [2023-03-25 08:28:59,059] multiqc [DEBUG ] No samples found: interop [2023-03-25 08:28:59,062] multiqc [DEBUG ] No samples found: ivar [2023-03-25 08:28:59,065] multiqc [DEBUG ] No samples found: flash [2023-03-25 08:28:59,068] multiqc [DEBUG ] No samples found: seqyclean [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-03-25 08:28:59,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-03-25 08:28:59,069] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-03-25 08:28:59,069] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-03-25 08:28:59,069] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-03-25 08:28:59,072] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 526 samples [2023-03-25 08:28:59,075] multiqc [INFO ] Compressing plot data [2023-03-25 08:28:59,353] multiqc [INFO ] Report : multiqc_report.html [2023-03-25 08:28:59,353] multiqc [INFO ] Data : multiqc_data [2023-03-25 08:28:59,353] multiqc [DEBUG ] Moving data file from '/state/partition1/job-31308311/tmp8sj4d42x/multiqc_data' to '/scratch/gencore/logs/html/000000000-DKV2Y/1/multiqc_data' [2023-03-25 08:28:59,461] multiqc [INFO ] MultiQC complete