[2024-01-18 21:17:08,080] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-18 21:17:08,080] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-18 21:17:08,080] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-18 21:17:08,082] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2024-01-18 21:17:08,082] 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}} [2024-01-18 21:17:08,082] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2L2LDSXC/3 [2024-01-18 21:17:08,244] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-18 21:17:08,244] multiqc [INFO ] This is MultiQC v1.9 [2024-01-18 21:17:08,244] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2L2LDSXC/3 [2024-01-18 21:17:08,244] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H2L2LDSXC/3 [2024-01-18 21:17:08,244] multiqc [INFO ] Template : default [2024-01-18 21:17:08,244] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-18 21:17:08,244] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H2L2LDSXC/3 [2024-01-18 21:17:08,244] 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 [2024-01-18 21:17:08,244] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-41889910/tmpauwteea0 [2024-01-18 21:17:08,348] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n02_undetermined_fastqc.html [2024-01-18 21:17:08,351] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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search pattern filesize limit: H2L2LDSXC_l03_n02_B_QG3359_fastqc.html [2024-01-18 21:17:21,789] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n02_A_QG3348_fastqc.html [2024-01-18 21:17:21,791] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n02_A_QG3348_fastqc.html [2024-01-18 21:17:21,921] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n01_B_QG3359_fastqc.html [2024-01-18 21:17:21,923] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n01_B_QG3359_fastqc.html [2024-01-18 21:17:22,026] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n02_A_QG3334_fastqc.html [2024-01-18 21:17:22,027] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n02_A_QG3334_fastqc.html [2024-01-18 21:17:22,085] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n01_B_QG3376_fastqc.html [2024-01-18 21:17:22,087] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n01_B_QG3376_fastqc.html [2024-01-18 21:17:22,142] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n02_B_QG3308_fastqc.html [2024-01-18 21:17:22,144] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l03_n02_B_QG3308_fastqc.html [2024-01-18 21:17:22,443] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-18 21:17:22,444] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-18 21:17:22,451] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-18 21:17:22,461] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-18 21:17:22,504] multiqc.modules.custom_content.custom_content [INFO ] demux_report-3: Found 96 samples (table) [2024-01-18 21:17:22,507] multiqc [DEBUG ] No samples found: conpair [2024-01-18 21:17:22,510] multiqc [DEBUG ] No samples found: peddy [2024-01-18 21:17:22,513] multiqc [DEBUG ] No samples found: somalier [2024-01-18 21:17:22,516] multiqc [DEBUG ] No samples found: methylQA [2024-01-18 21:17:22,519] multiqc [DEBUG ] No samples found: mosdepth [2024-01-18 21:17:22,522] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-18 21:17:22,524] multiqc [DEBUG ] No samples found: qualimap [2024-01-18 21:17:22,527] multiqc [DEBUG ] No samples found: preseq [2024-01-18 21:17:22,530] multiqc [DEBUG ] No samples found: quast [2024-01-18 21:17:22,532] multiqc [DEBUG ] No samples found: qorts [2024-01-18 21:17:22,535] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-18 21:17:22,538] multiqc [DEBUG ] No samples found: rockhopper [2024-01-18 21:17:22,541] multiqc [DEBUG ] No samples found: rsem [2024-01-18 21:17:22,545] multiqc [DEBUG ] No samples found: rseqc [2024-01-18 21:17:22,548] multiqc [DEBUG ] No samples found: busco [2024-01-18 21:17:22,550] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-18 21:17:22,553] multiqc [DEBUG ] No samples found: disambiguate [2024-01-18 21:17:22,556] multiqc [DEBUG ] No samples found: supernova [2024-01-18 21:17:22,561] multiqc [DEBUG ] No samples found: deeptools [2024-01-18 21:17:22,563] multiqc [DEBUG ] No samples found: sargasso [2024-01-18 21:17:22,566] multiqc [DEBUG ] No samples found: verifybamid [2024-01-18 21:17:22,569] multiqc [DEBUG ] No samples found: mirtrace [2024-01-18 21:17:22,571] multiqc [DEBUG ] No samples found: happy [2024-01-18 21:17:22,574] multiqc [DEBUG ] No samples found: mirtop [2024-01-18 21:17:22,577] multiqc [DEBUG ] No samples found: homer [2024-01-18 21:17:22,580] multiqc [DEBUG ] No samples found: macs2 [2024-01-18 21:17:22,583] multiqc [DEBUG ] No samples found: theta2 [2024-01-18 21:17:22,585] multiqc [DEBUG ] No samples found: snpeff [2024-01-18 21:17:22,589] multiqc [DEBUG ] No samples found: gatk [2024-01-18 21:17:22,591] multiqc [DEBUG ] No samples found: htseq [2024-01-18 21:17:22,594] multiqc [DEBUG ] No samples found: bcftools [2024-01-18 21:17:22,597] multiqc [DEBUG ] No samples found: featureCounts [2024-01-18 21:17:22,600] multiqc [DEBUG ] No samples found: fgbio [2024-01-18 21:17:22,605] multiqc [DEBUG ] No samples found: dragen [2024-01-18 21:17:22,608] multiqc [DEBUG ] No samples found: dedup [2024-01-18 21:17:22,611] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-18 21:17:22,618] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-18 21:17:22,621] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-18 21:17:22,623] multiqc [DEBUG ] No samples found: picard [2024-01-18 21:17:22,625] multiqc [DEBUG ] No samples found: prokka [2024-01-18 21:17:22,628] multiqc [DEBUG ] No samples found: samblaster [2024-01-18 21:17:22,632] multiqc [DEBUG ] No samples found: samtools [2024-01-18 21:17:22,634] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-18 21:17:22,637] multiqc [DEBUG ] No samples found: bamtools [2024-01-18 21:17:22,640] multiqc [DEBUG ] No samples found: jellyfish [2024-01-18 21:17:22,643] multiqc [DEBUG ] No samples found: vcftools [2024-01-18 21:17:22,646] multiqc [DEBUG ] No samples found: longranger [2024-01-18 21:17:22,649] multiqc [DEBUG ] No samples found: stacks [2024-01-18 21:17:22,652] multiqc [DEBUG ] No samples found: varscan2 [2024-01-18 21:17:22,657] multiqc [DEBUG ] No samples found: bbmap [2024-01-18 21:17:22,659] multiqc [DEBUG ] No samples found: bismark [2024-01-18 21:17:22,662] multiqc [DEBUG ] No samples found: biscuit [2024-01-18 21:17:22,665] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-18 21:17:22,668] multiqc [DEBUG ] No samples found: hicup [2024-01-18 21:17:22,670] multiqc [DEBUG ] No samples found: hicpro [2024-01-18 21:17:22,673] multiqc [DEBUG ] No samples found: salmon [2024-01-18 21:17:22,676] multiqc [DEBUG ] No samples found: kallisto [2024-01-18 21:17:22,679] multiqc [DEBUG ] No samples found: slamdunk [2024-01-18 21:17:22,681] multiqc [DEBUG ] No samples found: star [2024-01-18 21:17:22,684] multiqc [DEBUG ] No samples found: hisat2 [2024-01-18 21:17:22,687] multiqc [DEBUG ] No samples found: tophat [2024-01-18 21:17:22,689] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-18 21:17:22,692] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-18 21:17:22,695] multiqc [DEBUG ] No samples found: snpsplit [2024-01-18 21:17:22,697] multiqc [DEBUG ] No samples found: kat [2024-01-18 21:17:22,700] multiqc [DEBUG ] No samples found: leehom [2024-01-18 21:17:22,703] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-18 21:17:22,706] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-18 21:17:22,708] multiqc [DEBUG ] No samples found: cutadapt [2024-01-18 21:17:22,711] multiqc [DEBUG ] No samples found: flexbar [2024-01-18 21:17:22,714] multiqc [DEBUG ] No samples found: kaiju [2024-01-18 21:17:22,716] multiqc [DEBUG ] No samples found: kraken [2024-01-18 21:17:22,719] multiqc [DEBUG ] No samples found: malt [2024-01-18 21:17:22,722] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-18 21:17:22,724] multiqc [DEBUG ] No samples found: sickle [2024-01-18 21:17:22,727] multiqc [DEBUG ] No samples found: skewer [2024-01-18 21:17:22,730] multiqc [DEBUG ] No samples found: sortmerna [2024-01-18 21:17:22,732] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-18 21:17:22,735] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-18 21:17:22,738] multiqc [DEBUG ] No samples found: afterqc [2024-01-18 21:17:22,741] multiqc [DEBUG ] No samples found: fastp [2024-01-18 21:17:55,116] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2024-01-18 21:18:10,806] multiqc [DEBUG ] No samples found: pycoqc [2024-01-18 21:18:10,809] multiqc [DEBUG ] No samples found: minionqc [2024-01-18 21:18:10,812] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-18 21:18:10,815] multiqc [DEBUG ] No samples found: clusterflow [2024-01-18 21:18:10,817] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-18 21:18:10,820] multiqc [DEBUG ] No samples found: interop [2024-01-18 21:18:10,823] multiqc [DEBUG ] No samples found: ivar [2024-01-18 21:18:10,826] multiqc [DEBUG ] No samples found: flash [2024-01-18 21:18:10,828] multiqc [DEBUG ] No samples found: seqyclean [2024-01-18 21:18:10,828] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-18 21:18:10,828] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-01-18 21:18:10,828] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-18 21:18:10,828] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-18 21:18:10,828] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 21:18:10,828] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 3 Demultiplexing Report'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 3 Demultiplexing Report'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 3 Demultiplexing Report'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 3 Demultiplexing Report'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 3 Demultiplexing Report'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 3 Demultiplexing Report'. [2024-01-18 21:18:10,829] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 3 Demultiplexing Report'. [2024-01-18 21:18:11,047] multiqc [INFO ] Compressing plot data [2024-01-18 21:18:11,113] multiqc [INFO ] Report : multiqc_report.html [2024-01-18 21:18:11,113] multiqc [INFO ] Data : multiqc_data [2024-01-18 21:18:11,113] multiqc [DEBUG ] Moving data file from '/state/partition1/job-41889910/tmpauwteea0/multiqc_data' to '/scratch/gencore/logs/html/H2L2LDSXC/3/multiqc_data' [2024-01-18 21:29:31,691] multiqc [INFO ] MultiQC complete