[2023-10-10 19:38:37,574] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-10-10 19:38:37,574] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-10-10 19:38:37,575] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-10-10 19:38:37,577] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-10-10 19:38:37,577] 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}} [2023-10-10 19:38:37,577] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHGHDSX5/merged [2023-10-10 19:38:37,761] multiqc [WARNING] MultiQC Version v1.16 now available! [2023-10-10 19:38:37,761] multiqc [INFO ] This is MultiQC v1.9 [2023-10-10 19:38:37,761] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHGHDSX5/merged [2023-10-10 19:38:37,762] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTHGHDSX5/merged [2023-10-10 19:38:37,762] multiqc [INFO ] Template : default [2023-10-10 19:38:37,762] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-10-10 19:38:37,762] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTHGHDSX5/merged [2023-10-10 19:38:37,762] 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 [2023-10-10 19:38:37,762] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-38731982/tmpiu3xihhv [2023-10-10 19:38:38,110] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_02_b_fastqc.html [2023-10-10 19:38:38,112] multiqc [DEBUG ] File ignored by longranger/invocation because it 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because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_01_b_fastqc.html [2023-10-10 19:38:38,593] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_03_a_fastqc.html [2023-10-10 19:38:38,595] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_03_a_fastqc.html [2023-10-10 19:38:38,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_undetermined_fastqc.html [2023-10-10 19:38:38,688] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_undetermined_fastqc.html [2023-10-10 19:38:38,747] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_06_a_fastqc.html [2023-10-10 19:38:38,749] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_06_a_fastqc.html [2023-10-10 19:38:38,815] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_11_a_fastqc.html [2023-10-10 19:38:38,817] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_11_a_fastqc.html [2023-10-10 19:38:38,893] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_12_a_fastqc.html [2023-10-10 19:38:38,895] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_12_a_fastqc.html [2023-10-10 19:38:38,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_08_a_fastqc.html [2023-10-10 19:38:38,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_08_a_fastqc.html [2023-10-10 19:38:39,013] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_03_b_fastqc.html [2023-10-10 19:38:39,015] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_03_b_fastqc.html [2023-10-10 19:38:39,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_09_a_fastqc.html [2023-10-10 19:38:39,083] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_09_a_fastqc.html [2023-10-10 19:38:39,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_04_a_fastqc.html [2023-10-10 19:38:39,186] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHGHDSX5_n01_sr5965_2_04_a_fastqc.html [2023-10-10 19:38:40,299] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-10 19:38:40,335] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-10 19:38:40,386] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-10-10 19:38:40,387] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-10-10 19:38:40,395] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 16 samples (table) [2023-10-10 19:38:40,455] multiqc [DEBUG ] No samples found: conpair [2023-10-10 19:38:40,531] multiqc [DEBUG ] No samples found: peddy [2023-10-10 19:38:40,600] multiqc [DEBUG ] No samples found: somalier [2023-10-10 19:38:40,685] multiqc [DEBUG ] No samples found: methylQA [2023-10-10 19:38:40,852] multiqc [DEBUG ] No samples found: mosdepth [2023-10-10 19:38:40,918] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-10-10 19:38:40,946] multiqc [DEBUG ] No samples found: qualimap [2023-10-10 19:38:41,023] multiqc [DEBUG ] No samples found: preseq [2023-10-10 19:38:41,100] multiqc [DEBUG ] No samples found: quast [2023-10-10 19:38:41,178] multiqc [DEBUG ] No samples found: qorts [2023-10-10 19:38:41,255] multiqc [DEBUG ] No samples found: rna_seqc [2023-10-10 19:38:41,324] multiqc [DEBUG ] No samples found: rockhopper [2023-10-10 19:38:41,397] multiqc [DEBUG ] No samples found: rsem [2023-10-10 19:38:41,658] multiqc [DEBUG ] No samples found: rseqc [2023-10-10 19:38:41,723] multiqc [DEBUG ] No samples found: busco [2023-10-10 19:38:41,800] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-10-10 19:38:41,866] multiqc [DEBUG ] No samples found: disambiguate [2023-10-10 19:38:41,943] multiqc [DEBUG ] No samples found: supernova [2023-10-10 19:38:42,243] multiqc [DEBUG ] No samples found: deeptools [2023-10-10 19:38:42,320] multiqc [DEBUG ] No samples found: sargasso [2023-10-10 19:38:42,400] multiqc [DEBUG ] No samples found: verifybamid [2023-10-10 19:38:42,476] multiqc [DEBUG ] No samples found: mirtrace [2023-10-10 19:38:42,553] multiqc [DEBUG ] No samples found: happy [2023-10-10 19:38:42,630] multiqc [DEBUG ] No samples found: mirtop [2023-10-10 19:38:42,750] multiqc [DEBUG ] No samples found: homer [2023-10-10 19:38:42,827] multiqc [DEBUG ] No samples found: macs2 [2023-10-10 19:38:42,895] multiqc [DEBUG ] No samples found: theta2 [2023-10-10 19:38:42,952] multiqc [DEBUG ] No samples found: snpeff [2023-10-10 19:38:43,084] multiqc [DEBUG ] No samples found: gatk [2023-10-10 19:38:43,168] multiqc [DEBUG ] No samples found: htseq [2023-10-10 19:38:43,260] multiqc [DEBUG ] No samples found: bcftools [2023-10-10 19:38:43,337] multiqc [DEBUG ] No samples found: featureCounts [2023-10-10 19:38:43,456] multiqc [DEBUG ] No samples found: fgbio [2023-10-10 19:38:43,741] multiqc [DEBUG ] No samples found: dragen [2023-10-10 19:38:43,811] multiqc [DEBUG ] No samples found: dedup [2023-10-10 19:38:43,889] multiqc [DEBUG ] No samples found: damageprofiler [2023-10-10 19:38:44,481] multiqc [DEBUG ] No samples found: biobambam2 [2023-10-10 19:38:44,548] multiqc [DEBUG ] No samples found: mtnucratio [2023-10-10 19:38:44,550] multiqc [DEBUG ] No samples found: picard [2023-10-10 19:38:44,624] multiqc [DEBUG ] No samples found: prokka [2023-10-10 19:38:44,690] multiqc [DEBUG ] No samples found: samblaster [2023-10-10 19:38:44,872] multiqc [DEBUG ] No samples found: samtools [2023-10-10 19:38:44,953] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-10-10 19:38:45,036] multiqc [DEBUG ] No samples found: bamtools [2023-10-10 19:38:45,102] multiqc [DEBUG ] No samples found: jellyfish [2023-10-10 19:38:45,250] multiqc [DEBUG ] No samples found: vcftools [2023-10-10 19:38:45,327] multiqc [DEBUG ] No samples found: longranger [2023-10-10 19:38:45,403] multiqc [DEBUG ] No samples found: stacks [2023-10-10 19:38:45,481] multiqc [DEBUG ] No samples found: varscan2 [2023-10-10 19:38:45,824] multiqc [DEBUG ] No samples found: bbmap [2023-10-10 19:38:45,901] multiqc [DEBUG ] No samples found: bismark [2023-10-10 19:38:45,977] multiqc [DEBUG ] No samples found: biscuit [2023-10-10 19:38:46,035] multiqc [DEBUG ] No samples found: hicexplorer [2023-10-10 19:38:46,103] multiqc [DEBUG ] No samples found: hicup [2023-10-10 19:38:46,195] multiqc [DEBUG ] No samples found: hicpro [2023-10-10 19:38:46,254] multiqc [DEBUG ] No samples found: salmon [2023-10-10 19:38:46,326] multiqc [DEBUG ] No samples found: kallisto [2023-10-10 19:38:46,402] multiqc [DEBUG ] No samples found: slamdunk [2023-10-10 19:38:46,480] multiqc [DEBUG ] No samples found: star [2023-10-10 19:38:46,551] multiqc [DEBUG ] No samples found: hisat2 [2023-10-10 19:38:46,629] multiqc [DEBUG ] No samples found: tophat [2023-10-10 19:38:46,706] multiqc [DEBUG ] No samples found: bowtie2 [2023-10-10 19:38:46,776] multiqc [DEBUG ] No samples found: bowtie1 [2023-10-10 19:38:46,838] multiqc [DEBUG ] No samples found: snpsplit [2023-10-10 19:38:46,907] multiqc [DEBUG ] No samples found: kat [2023-10-10 19:38:46,962] multiqc [DEBUG ] No samples found: leehom [2023-10-10 19:38:47,040] multiqc [DEBUG ] No samples found: adapterRemoval [2023-10-10 19:38:47,106] multiqc [DEBUG ] No samples found: clipandmerge [2023-10-10 19:38:47,183] multiqc [DEBUG ] No samples found: cutadapt [2023-10-10 19:38:47,249] multiqc [DEBUG ] No samples found: flexbar [2023-10-10 19:38:47,322] multiqc [DEBUG ] No samples found: kaiju [2023-10-10 19:38:47,399] multiqc [DEBUG ] No samples found: kraken [2023-10-10 19:38:47,477] multiqc [DEBUG ] No samples found: malt [2023-10-10 19:38:47,547] multiqc [DEBUG ] No samples found: trimmomatic [2023-10-10 19:38:47,625] multiqc [DEBUG ] No samples found: sickle [2023-10-10 19:38:47,712] multiqc [DEBUG ] No samples found: skewer [2023-10-10 19:38:47,771] multiqc [DEBUG ] No samples found: sortmerna [2023-10-10 19:38:47,811] multiqc [DEBUG ] No samples found: biobloomtools [2023-10-10 19:38:47,876] multiqc [DEBUG ] No samples found: fastq_screen [2023-10-10 19:38:47,944] multiqc [DEBUG ] No samples found: afterqc [2023-10-10 19:38:48,020] multiqc [DEBUG ] No samples found: fastp [2023-10-10 19:38:50,239] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2023-10-10 19:38:50,491] multiqc [DEBUG ] No samples found: pycoqc [2023-10-10 19:38:50,560] multiqc [DEBUG ] No samples found: minionqc [2023-10-10 19:38:50,637] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-10-10 19:38:50,714] multiqc [DEBUG ] No samples found: clusterflow [2023-10-10 19:38:50,781] multiqc [DEBUG ] No samples found: bcl2fastq [2023-10-10 19:38:50,858] multiqc [DEBUG ] No samples found: interop [2023-10-10 19:38:50,935] multiqc [DEBUG ] No samples found: ivar [2023-10-10 19:38:51,012] multiqc [DEBUG ] No samples found: flash [2023-10-10 19:38:51,089] multiqc [DEBUG ] No samples found: seqyclean [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-10-10 19:38:51,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-10-10 19:38:51,090] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-10-10 19:38:51,090] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-10-10 19:38:51,090] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-10-10 19:38:51,090] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-10-10 19:38:51,090] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-10-10 19:38:51,109] multiqc [INFO ] Compressing plot data [2023-10-10 19:38:51,342] multiqc [INFO ] Report : multiqc_report.html [2023-10-10 19:38:51,342] multiqc [INFO ] Data : multiqc_data [2023-10-10 19:38:51,343] multiqc [DEBUG ] Moving data file from '/state/partition1/job-38731982/tmpiu3xihhv/multiqc_data' to '/scratch/gencore/logs/html/HTHGHDSX5/merged/multiqc_data' [2023-10-10 19:38:52,262] multiqc [INFO ] MultiQC complete