[2023-11-16 13:14:02,460] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-11-16 13:14:02,460] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-11-16 13:14:02,460] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-11-16 13:14:02,463] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-11-16 13:14:02,463] 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}} [2023-11-16 13:14:02,463] 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-L9KNV/1 [2023-11-16 13:14:02,714] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-11-16 13:14:02,714] multiqc [INFO ] This is MultiQC v1.9 [2023-11-16 13:14:02,714] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-L9KNV/1 [2023-11-16 13:14:02,714] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-L9KNV/1 [2023-11-16 13:14:02,715] multiqc [INFO ] Template : default [2023-11-16 13:14:02,715] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-11-16 13:14:02,715] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-L9KNV/1 [2023-11-16 13:14:02,715] 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 [2023-11-16 13:14:02,715] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40194138/tmpymjv9qno [2023-11-16 13:14:02,845] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_612_fastqc.html [2023-11-16 13:14:02,848] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_612_fastqc.html [2023-11-16 13:14:02,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-16 13:14:02,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-16 13:14:02,899] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-16 13:14:02,899] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-16 13:14:02,899] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-16 13:14:02,899] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-16 13:14:02,899] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-16 13:14:03,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_16_fastqc.html [2023-11-16 13:14:03,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_16_fastqc.html [2023-11-16 13:14:03,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_16_fastqc.html [2023-11-16 13:14:03,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_16_fastqc.html [2023-11-16 13:14:03,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_51_fastqc.html [2023-11-16 13:14:03,620] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_51_fastqc.html [2023-11-16 13:14:03,664] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_26_fastqc.html [2023-11-16 13:14:03,666] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_26_fastqc.html [2023-11-16 13:14:03,710] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_813_fastqc.html [2023-11-16 13:14:03,712] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_813_fastqc.html [2023-11-16 13:14:03,757] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_813_fastqc.html [2023-11-16 13:14:03,759] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_813_fastqc.html [2023-11-16 13:14:03,803] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_26_fastqc.html [2023-11-16 13:14:03,805] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_26_fastqc.html [2023-11-16 13:14:03,849] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_51_fastqc.html [2023-11-16 13:14:03,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_51_fastqc.html [2023-11-16 13:14:03,896] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_undetermined_fastqc.html [2023-11-16 13:14:03,898] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n02_undetermined_fastqc.html [2023-11-16 13:14:03,944] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_undetermined_fastqc.html [2023-11-16 13:14:03,946] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_undetermined_fastqc.html [2023-11-16 13:14:03,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_612_fastqc.html [2023-11-16 13:14:03,992] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L9KNV_l01_n01_612_fastqc.html [2023-11-16 13:14:04,651] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-16 13:14:04,652] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-16 13:14:04,660] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-11-16 13:14:04,664] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 6 samples (table) [2023-11-16 13:14:04,674] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-11-16 13:14:04,679] multiqc [DEBUG ] No samples found: conpair [2023-11-16 13:14:04,684] multiqc [DEBUG ] No samples found: peddy [2023-11-16 13:14:04,689] multiqc [DEBUG ] No samples found: somalier [2023-11-16 13:14:04,694] multiqc [DEBUG ] No samples found: methylQA [2023-11-16 13:14:04,701] multiqc [DEBUG ] No samples found: mosdepth [2023-11-16 13:14:04,705] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-11-16 13:14:04,709] multiqc [DEBUG ] No samples found: qualimap [2023-11-16 13:14:04,714] multiqc [DEBUG ] No samples found: preseq [2023-11-16 13:14:04,718] multiqc [DEBUG ] No samples found: quast [2023-11-16 13:14:04,723] multiqc [DEBUG ] No samples found: qorts [2023-11-16 13:14:04,728] multiqc [DEBUG ] No samples found: rna_seqc [2023-11-16 13:14:04,732] multiqc [DEBUG ] No samples found: rockhopper [2023-11-16 13:14:04,737] multiqc [DEBUG ] No samples found: rsem [2023-11-16 13:14:04,747] multiqc [DEBUG ] No samples found: rseqc [2023-11-16 13:14:04,751] multiqc [DEBUG ] No samples found: busco [2023-11-16 13:14:04,756] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-11-16 13:14:04,761] multiqc [DEBUG ] No samples found: disambiguate [2023-11-16 13:14:04,766] multiqc [DEBUG ] No samples found: supernova [2023-11-16 13:14:04,778] multiqc [DEBUG ] No samples found: deeptools [2023-11-16 13:14:04,783] multiqc [DEBUG ] No samples found: sargasso [2023-11-16 13:14:04,788] multiqc [DEBUG ] No samples found: verifybamid [2023-11-16 13:14:04,793] multiqc [DEBUG ] No samples found: mirtrace [2023-11-16 13:14:04,798] multiqc [DEBUG ] No samples found: happy [2023-11-16 13:14:04,802] multiqc [DEBUG ] No samples found: mirtop [2023-11-16 13:14:04,808] multiqc [DEBUG ] No samples found: homer [2023-11-16 13:14:04,813] multiqc [DEBUG ] No samples found: macs2 [2023-11-16 13:14:04,818] multiqc [DEBUG ] No samples found: theta2 [2023-11-16 13:14:04,822] multiqc [DEBUG ] No samples found: snpeff [2023-11-16 13:14:04,829] multiqc [DEBUG ] No samples found: gatk [2023-11-16 13:14:04,833] multiqc [DEBUG ] No samples found: htseq [2023-11-16 13:14:04,839] multiqc [DEBUG ] No samples found: bcftools [2023-11-16 13:14:04,843] multiqc [DEBUG ] No samples found: featureCounts [2023-11-16 13:14:04,851] multiqc [DEBUG ] No samples found: fgbio [2023-11-16 13:14:04,863] multiqc [DEBUG ] No samples found: dragen [2023-11-16 13:14:04,868] multiqc [DEBUG ] No samples found: dedup [2023-11-16 13:14:04,872] multiqc [DEBUG ] No samples found: damageprofiler [2023-11-16 13:14:04,892] multiqc [DEBUG ] No samples found: biobambam2 [2023-11-16 13:14:04,898] multiqc [DEBUG ] No samples found: mtnucratio [2023-11-16 13:14:04,900] multiqc [DEBUG ] No samples found: picard [2023-11-16 13:14:04,905] multiqc [DEBUG ] No samples found: prokka [2023-11-16 13:14:04,915] multiqc [DEBUG ] No samples found: samblaster [2023-11-16 13:14:04,923] multiqc [DEBUG ] No samples found: samtools [2023-11-16 13:14:04,927] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-11-16 13:14:04,933] multiqc [DEBUG ] No samples found: bamtools [2023-11-16 13:14:04,937] multiqc [DEBUG ] No samples found: jellyfish [2023-11-16 13:14:04,944] multiqc [DEBUG ] No samples found: vcftools [2023-11-16 13:14:04,949] multiqc [DEBUG ] No samples found: longranger [2023-11-16 13:14:04,954] multiqc [DEBUG ] No samples found: stacks [2023-11-16 13:14:04,958] multiqc [DEBUG ] No samples found: varscan2 [2023-11-16 13:14:04,972] multiqc [DEBUG ] No samples found: bbmap [2023-11-16 13:14:04,977] multiqc [DEBUG ] No samples found: bismark [2023-11-16 13:14:04,982] multiqc [DEBUG ] No samples found: biscuit [2023-11-16 13:14:04,987] multiqc [DEBUG ] No samples found: hicexplorer [2023-11-16 13:14:04,992] multiqc [DEBUG ] No samples found: hicup [2023-11-16 13:14:04,997] multiqc [DEBUG ] No samples found: hicpro [2023-11-16 13:14:05,002] multiqc [DEBUG ] No samples found: salmon [2023-11-16 13:14:05,007] multiqc [DEBUG ] No samples found: kallisto [2023-11-16 13:14:05,012] multiqc [DEBUG ] No samples found: slamdunk [2023-11-16 13:14:05,016] multiqc [DEBUG ] No samples found: star [2023-11-16 13:14:05,021] multiqc [DEBUG ] No samples found: hisat2 [2023-11-16 13:14:05,026] multiqc [DEBUG ] No samples found: tophat [2023-11-16 13:14:05,030] multiqc [DEBUG ] No samples found: bowtie2 [2023-11-16 13:14:05,035] multiqc [DEBUG ] No samples found: bowtie1 [2023-11-16 13:14:05,040] multiqc [DEBUG ] No samples found: snpsplit [2023-11-16 13:14:05,044] multiqc [DEBUG ] No samples found: kat [2023-11-16 13:14:05,049] multiqc [DEBUG ] No samples found: leehom [2023-11-16 13:14:05,053] multiqc [DEBUG ] No samples found: adapterRemoval [2023-11-16 13:14:05,058] multiqc [DEBUG ] No samples found: clipandmerge [2023-11-16 13:14:05,062] multiqc [DEBUG ] No samples found: cutadapt [2023-11-16 13:14:05,067] multiqc [DEBUG ] No samples found: flexbar [2023-11-16 13:14:05,072] multiqc [DEBUG ] No samples found: kaiju [2023-11-16 13:14:05,076] multiqc [DEBUG ] No samples found: kraken [2023-11-16 13:14:05,081] multiqc [DEBUG ] No samples found: malt [2023-11-16 13:14:05,086] multiqc [DEBUG ] No samples found: trimmomatic [2023-11-16 13:14:05,090] multiqc [DEBUG ] No samples found: sickle [2023-11-16 13:14:05,095] multiqc [DEBUG ] No samples found: skewer [2023-11-16 13:14:05,099] multiqc [DEBUG ] No samples found: sortmerna [2023-11-16 13:14:05,104] multiqc [DEBUG ] No samples found: biobloomtools [2023-11-16 13:14:05,108] multiqc [DEBUG ] No samples found: fastq_screen [2023-11-16 13:14:05,113] multiqc [DEBUG ] No samples found: afterqc [2023-11-16 13:14:05,117] multiqc [DEBUG ] No samples found: fastp [2023-11-16 13:14:05,192] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2023-11-16 13:14:05,308] multiqc [DEBUG ] No samples found: pycoqc [2023-11-16 13:14:05,313] multiqc [DEBUG ] No samples found: minionqc [2023-11-16 13:14:05,318] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-11-16 13:14:05,323] multiqc [DEBUG ] No samples found: clusterflow [2023-11-16 13:14:05,327] multiqc [DEBUG ] No samples found: bcl2fastq [2023-11-16 13:14:05,332] multiqc [DEBUG ] No samples found: interop [2023-11-16 13:14:05,337] multiqc [DEBUG ] No samples found: ivar [2023-11-16 13:14:05,342] multiqc [DEBUG ] No samples found: flash [2023-11-16 13:14:05,347] multiqc [DEBUG ] No samples found: seqyclean [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-11-16 13:14:05,347] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-11-16 13:14:05,348] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-11-16 13:14:05,363] multiqc [INFO ] Compressing plot data [2023-11-16 13:14:05,570] multiqc [INFO ] Report : multiqc_report.html [2023-11-16 13:14:05,570] multiqc [INFO ] Data : multiqc_data [2023-11-16 13:14:05,570] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40194138/tmpymjv9qno/multiqc_data' to '/scratch/gencore/logs/html/000000000-L9KNV/1/multiqc_data' [2023-11-16 13:14:05,694] multiqc [INFO ] MultiQC complete