[2023-04-10 20:13:03,080] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-04-10 20:13:03,081] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-04-10 20:13:03,081] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-04-10 20:13:03,083] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-04-10 20:13:03,083] 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}} [2023-04-10 20:13:03,083] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK77KDMXY/merged [2023-04-10 20:13:03,446] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-04-10 20:13:03,446] multiqc [INFO ] This is MultiQC v1.9 [2023-04-10 20:13:03,446] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK77KDMXY/merged [2023-04-10 20:13:03,446] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HK77KDMXY/merged [2023-04-10 20:13:03,446] multiqc [INFO ] Template : default [2023-04-10 20:13:03,446] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-04-10 20:13:03,446] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HK77KDMXY/merged [2023-04-10 20:13:03,447] 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 [2023-04-10 20:13:03,447] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-31942013/tmpqbkmb2i4 [2023-04-10 20:13:03,566] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n02_NYULF_0789_a_fastqc.html [2023-04-10 20:13:03,569] multiqc [DEBUG ] File ignored by longranger/invocation because it 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exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0393_a_fastqc.html [2023-04-10 20:13:16,283] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n02_NYULF_0071_a_fastqc.html [2023-04-10 20:13:16,284] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK77KDMXY_n02_NYULF_0071_a_fastqc.html [2023-04-10 20:13:16,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n02_NYULF_0218_a_fastqc.html [2023-04-10 20:13:16,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK77KDMXY_n02_NYULF_0218_a_fastqc.html [2023-04-10 20:13:16,471] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0071_a_fastqc.html [2023-04-10 20:13:16,473] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0071_a_fastqc.html [2023-04-10 20:13:16,585] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0124_a_fastqc.html [2023-04-10 20:13:16,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0124_a_fastqc.html [2023-04-10 20:13:16,734] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0540_a_fastqc.html [2023-04-10 20:13:16,736] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0540_a_fastqc.html [2023-04-10 20:13:16,797] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0329_a_fastqc.html [2023-04-10 20:13:16,798] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK77KDMXY_n01_NYULF_0329_a_fastqc.html [2023-04-10 20:13:16,839] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK77KDMXY_n02_NYULF_0013_a_fastqc.html [2023-04-10 20:13:16,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK77KDMXY_n02_NYULF_0013_a_fastqc.html [2023-04-10 20:13:17,515] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-10 20:13:17,518] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-10 20:13:17,569] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 100 samples (table) [2023-04-10 20:13:17,571] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-04-10 20:13:17,580] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-04-10 20:13:17,585] multiqc [DEBUG ] No samples found: conpair [2023-04-10 20:13:17,592] multiqc [DEBUG ] No samples found: peddy [2023-04-10 20:13:17,600] multiqc [DEBUG ] No samples found: somalier [2023-04-10 20:13:17,605] multiqc [DEBUG ] No samples found: methylQA [2023-04-10 20:13:17,615] multiqc [DEBUG ] No samples found: mosdepth [2023-04-10 20:13:17,620] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-04-10 20:13:17,624] multiqc [DEBUG ] No samples found: qualimap [2023-04-10 20:13:17,630] multiqc [DEBUG ] No samples found: preseq [2023-04-10 20:13:17,635] multiqc [DEBUG ] No samples found: quast [2023-04-10 20:13:17,640] multiqc [DEBUG ] No samples found: qorts [2023-04-10 20:13:17,646] multiqc [DEBUG ] No samples found: rna_seqc [2023-04-10 20:13:17,653] multiqc [DEBUG ] No samples found: rockhopper [2023-04-10 20:13:17,658] multiqc [DEBUG ] No samples found: rsem [2023-04-10 20:13:17,672] multiqc [DEBUG ] No samples found: rseqc [2023-04-10 20:13:17,677] multiqc [DEBUG ] No samples found: busco [2023-04-10 20:13:17,683] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-04-10 20:13:17,688] multiqc [DEBUG ] No samples found: disambiguate [2023-04-10 20:13:17,695] multiqc [DEBUG ] No samples found: supernova [2023-04-10 20:13:17,709] multiqc [DEBUG ] No samples found: deeptools [2023-04-10 20:13:17,715] multiqc [DEBUG ] No samples found: sargasso [2023-04-10 20:13:17,721] multiqc [DEBUG ] No samples found: verifybamid [2023-04-10 20:13:17,729] multiqc [DEBUG ] No samples found: mirtrace [2023-04-10 20:13:17,735] multiqc [DEBUG ] No samples found: happy [2023-04-10 20:13:17,741] multiqc [DEBUG ] No samples found: mirtop [2023-04-10 20:13:17,749] multiqc [DEBUG ] No samples found: homer [2023-04-10 20:13:17,755] multiqc [DEBUG ] No samples found: macs2 [2023-04-10 20:13:17,760] multiqc [DEBUG ] No samples found: theta2 [2023-04-10 20:13:17,765] multiqc [DEBUG ] No samples found: snpeff [2023-04-10 20:13:17,776] multiqc [DEBUG ] No samples found: gatk [2023-04-10 20:13:17,783] multiqc [DEBUG ] No samples found: htseq [2023-04-10 20:13:17,789] multiqc [DEBUG ] No samples found: bcftools [2023-04-10 20:13:17,795] multiqc [DEBUG ] No samples found: featureCounts [2023-04-10 20:13:17,803] multiqc [DEBUG ] No samples found: fgbio [2023-04-10 20:13:17,818] multiqc [DEBUG ] No samples found: dragen [2023-04-10 20:13:17,825] multiqc [DEBUG ] No samples found: dedup [2023-04-10 20:13:17,831] multiqc [DEBUG ] No samples found: damageprofiler [2023-04-10 20:13:17,855] multiqc [DEBUG ] No samples found: biobambam2 [2023-04-10 20:13:17,861] multiqc [DEBUG ] No samples found: mtnucratio [2023-04-10 20:13:17,863] multiqc [DEBUG ] No samples found: picard [2023-04-10 20:13:17,868] multiqc [DEBUG ] No samples found: prokka [2023-04-10 20:13:17,873] multiqc [DEBUG ] No samples found: samblaster [2023-04-10 20:13:17,882] multiqc [DEBUG ] No samples found: samtools [2023-04-10 20:13:17,887] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-04-10 20:13:17,893] multiqc [DEBUG ] No samples found: bamtools [2023-04-10 20:13:17,898] multiqc [DEBUG ] No samples found: jellyfish [2023-04-10 20:13:17,906] multiqc [DEBUG ] No samples found: vcftools [2023-04-10 20:13:17,911] multiqc [DEBUG ] No samples found: longranger [2023-04-10 20:13:17,916] multiqc [DEBUG ] No samples found: stacks [2023-04-10 20:13:17,921] multiqc [DEBUG ] No samples found: varscan2 [2023-04-10 20:13:17,939] multiqc [DEBUG ] No samples found: bbmap [2023-04-10 20:13:17,944] multiqc [DEBUG ] No samples found: bismark [2023-04-10 20:13:17,950] multiqc [DEBUG ] No samples found: biscuit [2023-04-10 20:13:17,956] multiqc [DEBUG ] No samples found: hicexplorer [2023-04-10 20:13:17,961] multiqc [DEBUG ] No samples found: hicup [2023-04-10 20:13:17,967] multiqc [DEBUG ] No samples found: hicpro [2023-04-10 20:13:17,971] multiqc [DEBUG ] No samples found: salmon [2023-04-10 20:13:17,976] multiqc [DEBUG ] No samples found: kallisto [2023-04-10 20:13:17,981] multiqc [DEBUG ] No samples found: slamdunk [2023-04-10 20:13:17,986] multiqc [DEBUG ] No samples found: star [2023-04-10 20:13:17,991] multiqc [DEBUG ] No samples found: hisat2 [2023-04-10 20:13:17,997] multiqc [DEBUG ] No samples found: tophat [2023-04-10 20:13:18,002] multiqc [DEBUG ] No samples found: bowtie2 [2023-04-10 20:13:18,009] multiqc [DEBUG ] No samples found: bowtie1 [2023-04-10 20:13:18,015] multiqc [DEBUG ] No samples found: snpsplit [2023-04-10 20:13:18,020] multiqc [DEBUG ] No samples found: kat [2023-04-10 20:13:18,024] multiqc [DEBUG ] No samples found: leehom [2023-04-10 20:13:18,031] multiqc [DEBUG ] No samples found: adapterRemoval [2023-04-10 20:13:18,035] multiqc [DEBUG ] No samples found: clipandmerge [2023-04-10 20:13:18,041] multiqc [DEBUG ] No samples found: cutadapt [2023-04-10 20:13:18,045] multiqc [DEBUG ] No samples found: flexbar [2023-04-10 20:13:18,051] multiqc [DEBUG ] No samples found: kaiju [2023-04-10 20:13:18,056] multiqc [DEBUG ] No samples found: kraken [2023-04-10 20:13:18,061] multiqc [DEBUG ] No samples found: malt [2023-04-10 20:13:18,066] multiqc [DEBUG ] No samples found: trimmomatic [2023-04-10 20:13:18,071] multiqc [DEBUG ] No samples found: sickle [2023-04-10 20:13:18,078] multiqc [DEBUG ] No samples found: skewer [2023-04-10 20:13:18,084] multiqc [DEBUG ] No samples found: sortmerna [2023-04-10 20:13:18,092] multiqc [DEBUG ] No samples found: biobloomtools [2023-04-10 20:13:18,098] multiqc [DEBUG ] No samples found: fastq_screen [2023-04-10 20:13:18,103] multiqc [DEBUG ] No samples found: afterqc [2023-04-10 20:13:18,108] multiqc [DEBUG ] No samples found: fastp [2023-04-10 20:13:47,810] multiqc.modules.fastqc.fastqc [INFO ] Found 200 reports [2023-04-10 20:14:06,877] multiqc [DEBUG ] No samples found: pycoqc [2023-04-10 20:14:06,882] multiqc [DEBUG ] No samples found: minionqc [2023-04-10 20:14:06,887] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-04-10 20:14:06,891] multiqc [DEBUG ] No samples found: clusterflow [2023-04-10 20:14:06,896] multiqc [DEBUG ] No samples found: bcl2fastq [2023-04-10 20:14:06,901] multiqc [DEBUG ] No samples found: interop [2023-04-10 20:14:06,905] multiqc [DEBUG ] No samples found: ivar [2023-04-10 20:14:06,910] multiqc [DEBUG ] No samples found: flash [2023-04-10 20:14:06,914] multiqc [DEBUG ] No samples found: seqyclean [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-04-10 20:14:06,914] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-04-10 20:14:06,915] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-04-10 20:14:07,133] multiqc [INFO ] Compressing plot data [2023-04-10 20:14:07,199] multiqc [INFO ] Report : multiqc_report.html [2023-04-10 20:14:07,200] multiqc [INFO ] Data : multiqc_data [2023-04-10 20:14:07,200] multiqc [DEBUG ] Moving data file from '/state/partition1/job-31942013/tmpqbkmb2i4/multiqc_data' to '/scratch/gencore/logs/html/HK77KDMXY/merged/multiqc_data' [2023-04-10 20:14:07,333] multiqc [INFO ] MultiQC complete