[2023-04-06 17:25:08,044] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-04-06 17:25:08,044] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-04-06 17:25:08,044] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-04-06 17:25:08,046] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-04-06 17:25:08,046] 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}} [2023-04-06 17:25:08,046] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFVVWAFX5/merged [2023-04-06 17:25:08,301] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-04-06 17:25:08,301] multiqc [INFO ] This is MultiQC v1.9 [2023-04-06 17:25:08,301] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFVVWAFX5/merged [2023-04-06 17:25:08,301] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFVVWAFX5/merged [2023-04-06 17:25:08,301] multiqc [INFO ] Template : default [2023-04-06 17:25:08,301] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-04-06 17:25:08,302] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFVVWAFX5/merged [2023-04-06 17:25:08,302] 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 [2023-04-06 17:25:08,302] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-31690695/tmpt993kss3 [2023-04-06 17:25:08,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n02_2861_T3_Rep1_ChIP_fastqc.html [2023-04-06 17:25:08,407] multiqc [DEBUG ] File ignored by longranger/invocation because it 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filesize limit: HFVVWAFX5_n01_7797_T3_Rep1_ChIP_fastqc.html [2023-04-06 17:25:09,580] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n01_2861_T3_Rep2_ChIP_fastqc.html [2023-04-06 17:25:09,582] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFVVWAFX5_n01_2861_T3_Rep2_ChIP_fastqc.html [2023-04-06 17:25:09,622] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n01_9113_T3_Input_fastqc.html [2023-04-06 17:25:09,624] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFVVWAFX5_n01_9113_T3_Input_fastqc.html [2023-04-06 17:25:09,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n01_9113_T3_ChIP_fastqc.html [2023-04-06 17:25:09,664] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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longranger/invocation because it exceeded search pattern filesize limit: HFVVWAFX5_n01_7799_midlog_Rep1_Input_fastqc.html [2023-04-06 17:25:09,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n01_7797_T3_Rep2_ChIP_fastqc.html [2023-04-06 17:25:09,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFVVWAFX5_n01_7797_T3_Rep2_ChIP_fastqc.html [2023-04-06 17:25:09,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n02_2861_T3_Rep1_Input_fastqc.html [2023-04-06 17:25:09,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFVVWAFX5_n02_2861_T3_Rep1_Input_fastqc.html [2023-04-06 17:25:09,913] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n02_7797_T3_Rep1_Input_fastqc.html [2023-04-06 17:25:09,915] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFVVWAFX5_n02_7797_T3_Rep1_Input_fastqc.html [2023-04-06 17:25:09,954] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFVVWAFX5_n02_7797_T3_Rep2_Input_fastqc.html [2023-04-06 17:25:09,956] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFVVWAFX5_n02_7797_T3_Rep2_Input_fastqc.html [2023-04-06 17:25:10,419] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-06 17:25:10,420] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-06 17:25:10,436] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-04-06 17:25:10,437] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-04-06 17:25:10,446] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 18 samples (table) [2023-04-06 17:25:10,450] multiqc [DEBUG ] No samples found: conpair [2023-04-06 17:25:10,454] multiqc [DEBUG ] No samples found: peddy [2023-04-06 17:25:10,458] multiqc [DEBUG ] No samples found: somalier [2023-04-06 17:25:10,462] multiqc [DEBUG ] No samples found: methylQA [2023-04-06 17:25:10,468] multiqc [DEBUG ] No samples found: mosdepth [2023-04-06 17:25:10,472] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-04-06 17:25:10,475] multiqc [DEBUG ] No samples found: qualimap [2023-04-06 17:25:10,479] multiqc [DEBUG ] No samples found: preseq [2023-04-06 17:25:10,483] multiqc [DEBUG ] No samples found: quast [2023-04-06 17:25:10,487] multiqc [DEBUG ] No samples found: qorts [2023-04-06 17:25:10,491] multiqc [DEBUG ] No samples found: rna_seqc [2023-04-06 17:25:10,495] multiqc [DEBUG ] No samples found: rockhopper [2023-04-06 17:25:10,499] multiqc [DEBUG ] No samples found: rsem [2023-04-06 17:25:10,507] multiqc [DEBUG ] No samples found: rseqc [2023-04-06 17:25:10,511] multiqc [DEBUG ] No samples found: busco [2023-04-06 17:25:10,515] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-04-06 17:25:10,519] multiqc [DEBUG ] No samples found: disambiguate [2023-04-06 17:25:10,523] multiqc [DEBUG ] No samples found: supernova [2023-04-06 17:25:10,533] multiqc [DEBUG ] No samples found: deeptools [2023-04-06 17:25:10,537] multiqc [DEBUG ] No samples found: sargasso [2023-04-06 17:25:10,541] multiqc [DEBUG ] No samples found: verifybamid [2023-04-06 17:25:10,544] multiqc [DEBUG ] No samples found: mirtrace [2023-04-06 17:25:10,548] multiqc [DEBUG ] No samples found: happy [2023-04-06 17:25:10,552] multiqc [DEBUG ] No samples found: mirtop [2023-04-06 17:25:10,558] multiqc [DEBUG ] No samples found: homer [2023-04-06 17:25:10,562] multiqc [DEBUG ] No samples found: macs2 [2023-04-06 17:25:10,565] multiqc [DEBUG ] No samples found: theta2 [2023-04-06 17:25:10,569] multiqc [DEBUG ] No samples found: snpeff [2023-04-06 17:25:10,575] multiqc [DEBUG ] No samples found: gatk [2023-04-06 17:25:10,579] multiqc [DEBUG ] No samples found: htseq [2023-04-06 17:25:10,583] multiqc [DEBUG ] No samples found: bcftools [2023-04-06 17:25:10,587] multiqc [DEBUG ] No samples found: featureCounts [2023-04-06 17:25:10,592] multiqc [DEBUG ] No samples found: fgbio [2023-04-06 17:25:10,602] multiqc [DEBUG ] No samples found: dragen [2023-04-06 17:25:10,606] multiqc [DEBUG ] No samples found: dedup [2023-04-06 17:25:10,610] multiqc [DEBUG ] No samples found: damageprofiler [2023-04-06 17:25:10,627] multiqc [DEBUG ] No samples found: biobambam2 [2023-04-06 17:25:10,631] multiqc [DEBUG ] No samples found: mtnucratio [2023-04-06 17:25:10,633] multiqc [DEBUG ] No samples found: picard [2023-04-06 17:25:10,637] multiqc [DEBUG ] No samples found: prokka [2023-04-06 17:25:10,641] multiqc [DEBUG ] No samples found: samblaster [2023-04-06 17:25:10,648] multiqc [DEBUG ] No samples found: samtools [2023-04-06 17:25:10,652] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-04-06 17:25:10,656] multiqc [DEBUG ] No samples found: bamtools [2023-04-06 17:25:10,660] multiqc [DEBUG ] No samples found: jellyfish [2023-04-06 17:25:10,666] multiqc [DEBUG ] No samples found: vcftools [2023-04-06 17:25:10,670] multiqc [DEBUG ] No samples found: longranger [2023-04-06 17:25:10,674] multiqc [DEBUG ] No samples found: stacks [2023-04-06 17:25:10,677] multiqc [DEBUG ] No samples found: varscan2 [2023-04-06 17:25:10,688] multiqc [DEBUG ] No samples found: bbmap [2023-04-06 17:25:10,692] multiqc [DEBUG ] No samples found: bismark [2023-04-06 17:25:10,696] multiqc [DEBUG ] No samples found: biscuit [2023-04-06 17:25:10,700] multiqc [DEBUG ] No samples found: hicexplorer [2023-04-06 17:25:10,704] multiqc [DEBUG ] No samples found: hicup [2023-04-06 17:25:10,708] multiqc [DEBUG ] No samples found: hicpro [2023-04-06 17:25:10,712] multiqc [DEBUG ] No samples found: salmon [2023-04-06 17:25:10,716] multiqc [DEBUG ] No samples found: kallisto [2023-04-06 17:25:10,720] multiqc [DEBUG ] No samples found: slamdunk [2023-04-06 17:25:10,723] multiqc [DEBUG ] No samples found: star [2023-04-06 17:25:10,727] multiqc [DEBUG ] No samples found: hisat2 [2023-04-06 17:25:10,731] multiqc [DEBUG ] No samples found: tophat [2023-04-06 17:25:10,735] multiqc [DEBUG ] No samples found: bowtie2 [2023-04-06 17:25:10,739] multiqc [DEBUG ] No samples found: bowtie1 [2023-04-06 17:25:10,743] multiqc [DEBUG ] No samples found: snpsplit [2023-04-06 17:25:10,747] multiqc [DEBUG ] No samples found: kat [2023-04-06 17:25:10,750] multiqc [DEBUG ] No samples found: leehom [2023-04-06 17:25:10,754] multiqc [DEBUG ] No samples found: adapterRemoval [2023-04-06 17:25:10,758] multiqc [DEBUG ] No samples found: clipandmerge [2023-04-06 17:25:10,762] multiqc [DEBUG ] No samples found: cutadapt [2023-04-06 17:25:10,766] multiqc [DEBUG ] No samples found: flexbar [2023-04-06 17:25:10,770] multiqc [DEBUG ] No samples found: kaiju [2023-04-06 17:25:10,773] multiqc [DEBUG ] No samples found: kraken [2023-04-06 17:25:10,777] multiqc [DEBUG ] No samples found: malt [2023-04-06 17:25:10,781] multiqc [DEBUG ] No samples found: trimmomatic [2023-04-06 17:25:10,785] multiqc [DEBUG ] No samples found: sickle [2023-04-06 17:25:10,789] multiqc [DEBUG ] No samples found: skewer [2023-04-06 17:25:10,793] multiqc [DEBUG ] No samples found: sortmerna [2023-04-06 17:25:10,796] multiqc [DEBUG ] No samples found: biobloomtools [2023-04-06 17:25:10,800] multiqc [DEBUG ] No samples found: fastq_screen [2023-04-06 17:25:10,805] multiqc [DEBUG ] No samples found: afterqc [2023-04-06 17:25:10,809] multiqc [DEBUG ] No samples found: fastp [2023-04-06 17:25:11,574] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2023-04-06 17:25:11,867] multiqc [DEBUG ] No samples found: pycoqc [2023-04-06 17:25:11,871] multiqc [DEBUG ] No samples found: minionqc [2023-04-06 17:25:11,875] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-04-06 17:25:11,879] multiqc [DEBUG ] No samples found: clusterflow [2023-04-06 17:25:11,883] multiqc [DEBUG ] No samples found: bcl2fastq [2023-04-06 17:25:11,887] multiqc [DEBUG ] No samples found: interop [2023-04-06 17:25:11,891] multiqc [DEBUG ] No samples found: ivar [2023-04-06 17:25:11,895] multiqc [DEBUG ] No samples found: flash [2023-04-06 17:25:11,899] multiqc [DEBUG ] No samples found: seqyclean [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-04-06 17:25:11,899] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-04-06 17:25:11,900] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-04-06 17:25:11,942] multiqc [INFO ] Compressing plot data [2023-04-06 17:25:12,522] multiqc [INFO ] Report : multiqc_report.html [2023-04-06 17:25:12,522] multiqc [INFO ] Data : multiqc_data [2023-04-06 17:25:12,522] multiqc [DEBUG ] Moving data file from '/state/partition1/job-31690695/tmpt993kss3/multiqc_data' to '/scratch/gencore/logs/html/HFVVWAFX5/merged/multiqc_data' [2023-04-06 17:25:12,634] multiqc [INFO ] MultiQC complete