[2023-01-18 22:14:41,219] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-01-18 22:14:41,220] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-01-18 22:14:41,220] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-01-18 22:14:41,222] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-01-18 22:14:41,222] 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}} [2023-01-18 22:14:41,222] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHLNCDMXY/merged [2023-01-18 22:14:41,752] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-01-18 22:14:41,752] multiqc [INFO ] This is MultiQC v1.9 [2023-01-18 22:14:41,752] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHLNCDMXY/merged [2023-01-18 22:14:41,752] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HHLNCDMXY/merged [2023-01-18 22:14:41,752] multiqc [INFO ] Template : default [2023-01-18 22:14:41,752] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-01-18 22:14:41,752] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HHLNCDMXY/merged [2023-01-18 22:14:41,752] 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 [2023-01-18 22:14:41,753] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-29281490/tmpb2dvvx60 [2023-01-18 22:14:41,898] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_F9_fastqc.html [2023-01-18 22:14:41,901] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2023-01-18 22:14:52,392] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n02_Dve_D12_fastqc.html [2023-01-18 22:14:52,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_C5_fastqc.html [2023-01-18 22:14:52,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_C5_fastqc.html [2023-01-18 22:14:52,494] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_C2_fastqc.html [2023-01-18 22:14:52,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_C2_fastqc.html [2023-01-18 22:14:52,552] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_B12_fastqc.html [2023-01-18 22:14:52,554] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_B12_fastqc.html [2023-01-18 22:14:52,615] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n02_Dve_C11_fastqc.html [2023-01-18 22:14:52,617] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n02_Dve_C11_fastqc.html [2023-01-18 22:14:52,659] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n02_Dve_B4_fastqc.html [2023-01-18 22:14:52,660] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n02_Dve_B4_fastqc.html [2023-01-18 22:14:52,721] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_E2_fastqc.html [2023-01-18 22:14:52,722] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n01_Dve_E2_fastqc.html [2023-01-18 22:14:52,777] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHLNCDMXY_n02_Dve_F7_fastqc.html [2023-01-18 22:14:52,779] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHLNCDMXY_n02_Dve_F7_fastqc.html [2023-01-18 22:14:53,179] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-01-18 22:14:53,181] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-01-18 22:14:53,191] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-01-18 22:14:53,201] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-01-18 22:14:53,244] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 94 samples (table) [2023-01-18 22:14:53,250] multiqc [DEBUG ] No samples found: conpair [2023-01-18 22:14:53,256] multiqc [DEBUG ] No samples found: peddy [2023-01-18 22:14:53,264] multiqc [DEBUG ] No samples found: somalier [2023-01-18 22:14:53,276] multiqc [DEBUG ] No samples found: methylQA [2023-01-18 22:14:53,288] multiqc [DEBUG ] No samples found: mosdepth [2023-01-18 22:14:53,293] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-01-18 22:14:53,298] multiqc [DEBUG ] No samples found: qualimap [2023-01-18 22:14:53,303] multiqc [DEBUG ] No samples found: preseq [2023-01-18 22:14:53,309] multiqc [DEBUG ] No samples found: quast [2023-01-18 22:14:53,315] multiqc [DEBUG ] No samples found: qorts [2023-01-18 22:14:53,320] multiqc [DEBUG ] No samples found: rna_seqc [2023-01-18 22:14:53,327] multiqc [DEBUG ] No samples found: rockhopper [2023-01-18 22:14:53,333] multiqc [DEBUG ] No samples found: rsem [2023-01-18 22:14:53,349] multiqc [DEBUG ] No samples found: rseqc [2023-01-18 22:14:53,354] multiqc [DEBUG ] No samples found: busco [2023-01-18 22:14:53,360] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-01-18 22:14:53,365] multiqc [DEBUG ] No samples found: disambiguate [2023-01-18 22:14:53,371] multiqc [DEBUG ] No samples found: supernova [2023-01-18 22:14:53,389] multiqc [DEBUG ] No samples found: deeptools [2023-01-18 22:14:53,395] multiqc [DEBUG ] No samples found: sargasso [2023-01-18 22:14:53,401] multiqc [DEBUG ] No samples found: verifybamid [2023-01-18 22:14:53,407] multiqc [DEBUG ] No samples found: mirtrace [2023-01-18 22:14:53,413] multiqc [DEBUG ] No samples found: happy [2023-01-18 22:14:53,418] multiqc [DEBUG ] No samples found: mirtop [2023-01-18 22:14:53,426] multiqc [DEBUG ] No samples found: homer [2023-01-18 22:14:53,431] multiqc [DEBUG ] No samples found: macs2 [2023-01-18 22:14:53,437] multiqc [DEBUG ] No samples found: theta2 [2023-01-18 22:14:53,442] multiqc [DEBUG ] No samples found: snpeff [2023-01-18 22:14:53,451] multiqc [DEBUG ] No samples found: gatk [2023-01-18 22:14:53,456] multiqc [DEBUG ] No samples found: htseq [2023-01-18 22:14:53,464] multiqc [DEBUG ] No samples found: bcftools [2023-01-18 22:14:53,469] multiqc [DEBUG ] No samples found: featureCounts [2023-01-18 22:14:53,477] multiqc [DEBUG ] No samples found: fgbio [2023-01-18 22:14:53,494] multiqc [DEBUG ] No samples found: dragen [2023-01-18 22:14:53,500] multiqc [DEBUG ] No samples found: dedup [2023-01-18 22:14:53,505] multiqc [DEBUG ] No samples found: damageprofiler [2023-01-18 22:14:53,536] multiqc [DEBUG ] No samples found: biobambam2 [2023-01-18 22:14:53,541] multiqc [DEBUG ] No samples found: mtnucratio [2023-01-18 22:14:53,543] multiqc [DEBUG ] No samples found: picard [2023-01-18 22:14:53,549] multiqc [DEBUG ] No samples found: prokka [2023-01-18 22:14:53,554] multiqc [DEBUG ] No samples found: samblaster [2023-01-18 22:14:53,568] multiqc [DEBUG ] No samples found: samtools [2023-01-18 22:14:53,574] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-01-18 22:14:53,580] multiqc [DEBUG ] No samples found: bamtools [2023-01-18 22:14:53,586] multiqc [DEBUG ] No samples found: jellyfish [2023-01-18 22:14:53,598] multiqc [DEBUG ] No samples found: vcftools [2023-01-18 22:14:53,603] multiqc [DEBUG ] No samples found: longranger [2023-01-18 22:14:53,609] multiqc [DEBUG ] No samples found: stacks [2023-01-18 22:14:53,615] multiqc [DEBUG ] No samples found: varscan2 [2023-01-18 22:14:53,632] multiqc [DEBUG ] No samples found: bbmap [2023-01-18 22:14:53,638] multiqc [DEBUG ] No samples found: bismark [2023-01-18 22:14:53,644] multiqc [DEBUG ] No samples found: biscuit [2023-01-18 22:14:53,650] multiqc [DEBUG ] No samples found: hicexplorer [2023-01-18 22:14:53,656] multiqc [DEBUG ] No samples found: hicup [2023-01-18 22:14:53,661] multiqc [DEBUG ] No samples found: hicpro [2023-01-18 22:14:53,666] multiqc [DEBUG ] No samples found: salmon [2023-01-18 22:14:53,672] multiqc [DEBUG ] No samples found: kallisto [2023-01-18 22:14:53,678] multiqc [DEBUG ] No samples found: slamdunk [2023-01-18 22:14:53,683] multiqc [DEBUG ] No samples found: star [2023-01-18 22:14:53,689] multiqc [DEBUG ] No samples found: hisat2 [2023-01-18 22:14:53,694] multiqc [DEBUG ] No samples found: tophat [2023-01-18 22:14:53,700] multiqc [DEBUG ] No samples found: bowtie2 [2023-01-18 22:14:53,705] multiqc [DEBUG ] No samples found: bowtie1 [2023-01-18 22:14:53,711] multiqc [DEBUG ] No samples found: snpsplit [2023-01-18 22:14:53,716] multiqc [DEBUG ] No samples found: kat [2023-01-18 22:14:53,721] multiqc [DEBUG ] No samples found: leehom [2023-01-18 22:14:53,727] multiqc [DEBUG ] No samples found: adapterRemoval [2023-01-18 22:14:53,732] multiqc [DEBUG ] No samples found: clipandmerge [2023-01-18 22:14:53,737] multiqc [DEBUG ] No samples found: cutadapt [2023-01-18 22:14:53,743] multiqc [DEBUG ] No samples found: flexbar [2023-01-18 22:14:53,748] multiqc [DEBUG ] No samples found: kaiju [2023-01-18 22:14:53,754] multiqc [DEBUG ] No samples found: kraken [2023-01-18 22:14:53,759] multiqc [DEBUG ] No samples found: malt [2023-01-18 22:14:53,765] multiqc [DEBUG ] No samples found: trimmomatic [2023-01-18 22:14:53,770] multiqc [DEBUG ] No samples found: sickle [2023-01-18 22:14:53,775] multiqc [DEBUG ] No samples found: skewer [2023-01-18 22:14:53,780] multiqc [DEBUG ] No samples found: sortmerna [2023-01-18 22:14:53,785] multiqc [DEBUG ] No samples found: biobloomtools [2023-01-18 22:14:53,791] multiqc [DEBUG ] No samples found: fastq_screen [2023-01-18 22:14:53,797] multiqc [DEBUG ] No samples found: afterqc [2023-01-18 22:14:53,803] multiqc [DEBUG ] No samples found: fastp [2023-01-18 22:15:19,552] multiqc.modules.fastqc.fastqc [INFO ] Found 188 reports [2023-01-18 22:15:35,909] multiqc [DEBUG ] No samples found: pycoqc [2023-01-18 22:15:35,914] multiqc [DEBUG ] No samples found: minionqc [2023-01-18 22:15:35,920] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-01-18 22:15:35,926] multiqc [DEBUG ] No samples found: clusterflow [2023-01-18 22:15:35,932] multiqc [DEBUG ] No samples found: bcl2fastq [2023-01-18 22:15:35,938] multiqc [DEBUG ] No samples found: interop [2023-01-18 22:15:35,943] multiqc [DEBUG ] No samples found: ivar [2023-01-18 22:15:35,949] multiqc [DEBUG ] No samples found: flash [2023-01-18 22:15:35,954] multiqc [DEBUG ] No samples found: seqyclean [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-01-18 22:15:35,955] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-01-18 22:15:36,171] multiqc [INFO ] Compressing plot data [2023-01-18 22:15:36,235] multiqc [INFO ] Report : multiqc_report.html [2023-01-18 22:15:36,235] multiqc [INFO ] Data : multiqc_data [2023-01-18 22:15:36,235] multiqc [DEBUG ] Moving data file from '/state/partition1/job-29281490/tmpb2dvvx60/multiqc_data' to '/scratch/gencore/logs/html/HHLNCDMXY/merged/multiqc_data' [2023-01-18 22:15:36,401] multiqc [INFO ] MultiQC complete