[2022-11-28 17:05:45,558] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-28 17:05:45,558] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-28 17:05:45,558] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-28 17:05:45,559] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-28 17:05:45,559] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-28 17:05:45,559] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNGC3DRX2/2 [2022-11-28 17:05:46,000] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-28 17:05:46,000] multiqc [INFO ] This is MultiQC v1.9 [2022-11-28 17:05:46,000] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNGC3DRX2/2 [2022-11-28 17:05:46,000] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNGC3DRX2/2 [2022-11-28 17:05:46,000] multiqc [INFO ] Template : default [2022-11-28 17:05:46,000] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-28 17:05:46,000] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNGC3DRX2/2 [2022-11-28 17:05:46,000] 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 [2022-11-28 17:05:46,000] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27440387/tmp4uhcvkww [2022-11-28 17:05:46,091] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T14_F3_b_fastqc.html [2022-11-28 17:05:46,094] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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rseqc/bam_stat because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_B3_b_fastqc.html [2022-11-28 17:05:47,382] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_B3_b_fastqc.html [2022-11-28 17:05:47,382] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_B3_b_fastqc.html [2022-11-28 17:05:47,382] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_B3_b_fastqc.html [2022-11-28 17:05:47,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_D3_b_fastqc.html [2022-11-28 17:05:47,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_D3_b_fastqc.html [2022-11-28 17:05:47,449] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_D3_b_fastqc.html [2022-11-28 17:05:47,449] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_D3_b_fastqc.html [2022-11-28 17:05:47,449] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_D3_b_fastqc.html [2022-11-28 17:05:47,449] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_D3_b_fastqc.html [2022-11-28 17:05:47,449] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T14_D3_b_fastqc.html [2022-11-28 17:05:47,514] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T12_A10_b_fastqc.html [2022-11-28 17:05:47,515] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T12_A10_b_fastqc.html [2022-11-28 17:05:47,585] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T12_F9_b_fastqc.html [2022-11-28 17:05:47,587] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T12_F9_b_fastqc.html [2022-11-28 17:05:47,587] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T12_F9_b_fastqc.html [2022-11-28 17:05:47,587] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T12_F9_b_fastqc.html [2022-11-28 17:05:47,587] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T12_F9_b_fastqc.html [2022-11-28 17:05:47,587] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T12_F9_b_fastqc.html [2022-11-28 17:05:47,587] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T12_F9_b_fastqc.html [2022-11-28 17:05:47,653] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T12_C10_b_fastqc.html [2022-11-28 17:05:47,655] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T12_C10_b_fastqc.html [2022-11-28 17:05:47,724] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T14_D3_b_fastqc.html [2022-11-28 17:05:47,725] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n01_T14_D3_b_fastqc.html [2022-11-28 17:05:47,795] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T12_B9_b_fastqc.html [2022-11-28 17:05:47,797] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l02_n02_T12_B9_b_fastqc.html [2022-11-28 17:05:48,114] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-28 17:05:48,115] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-28 17:05:48,126] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 13 samples (table) [2022-11-28 17:05:48,128] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-28 17:05:48,138] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-28 17:05:48,141] multiqc [DEBUG ] No samples found: conpair [2022-11-28 17:05:48,144] multiqc [DEBUG ] No samples found: peddy [2022-11-28 17:05:48,147] multiqc [DEBUG ] No samples found: somalier [2022-11-28 17:05:48,150] multiqc [DEBUG ] No samples found: methylQA [2022-11-28 17:05:48,154] multiqc [DEBUG ] No samples found: mosdepth [2022-11-28 17:05:48,157] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-28 17:05:48,159] multiqc [DEBUG ] No samples found: qualimap [2022-11-28 17:05:48,162] multiqc [DEBUG ] No samples found: preseq [2022-11-28 17:05:48,165] multiqc [DEBUG ] No samples found: quast [2022-11-28 17:05:48,168] multiqc [DEBUG ] No samples found: qorts [2022-11-28 17:05:48,171] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-28 17:05:48,174] multiqc [DEBUG ] No samples found: rockhopper [2022-11-28 17:05:48,177] multiqc [DEBUG ] No samples found: rsem [2022-11-28 17:05:48,183] multiqc [DEBUG ] No samples found: rseqc [2022-11-28 17:05:48,186] multiqc [DEBUG ] No samples found: busco [2022-11-28 17:05:48,189] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-28 17:05:48,192] multiqc [DEBUG ] No samples found: disambiguate [2022-11-28 17:05:48,195] multiqc [DEBUG ] No samples found: supernova [2022-11-28 17:05:48,200] multiqc [DEBUG ] No samples found: deeptools [2022-11-28 17:05:48,203] multiqc [DEBUG ] No samples found: sargasso [2022-11-28 17:05:48,206] multiqc [DEBUG ] No samples found: verifybamid [2022-11-28 17:05:48,209] multiqc [DEBUG ] No samples found: mirtrace [2022-11-28 17:05:48,212] multiqc [DEBUG ] No samples found: happy [2022-11-28 17:05:48,215] multiqc [DEBUG ] No samples found: mirtop [2022-11-28 17:05:48,219] multiqc [DEBUG ] No samples found: homer [2022-11-28 17:05:48,222] multiqc [DEBUG ] No samples found: macs2 [2022-11-28 17:05:48,224] multiqc [DEBUG ] No samples found: theta2 [2022-11-28 17:05:48,227] multiqc [DEBUG ] No samples found: snpeff [2022-11-28 17:05:48,231] multiqc [DEBUG ] No samples found: gatk [2022-11-28 17:05:48,234] multiqc [DEBUG ] No samples found: htseq [2022-11-28 17:05:48,237] multiqc [DEBUG ] No samples found: bcftools [2022-11-28 17:05:48,240] multiqc [DEBUG ] No samples found: featureCounts [2022-11-28 17:05:48,244] multiqc [DEBUG ] No samples found: fgbio [2022-11-28 17:05:48,250] multiqc [DEBUG ] No samples found: dragen [2022-11-28 17:05:48,253] multiqc [DEBUG ] No samples found: dedup [2022-11-28 17:05:48,256] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-28 17:05:48,265] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-28 17:05:48,268] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-28 17:05:48,270] multiqc [DEBUG ] No samples found: picard [2022-11-28 17:05:48,273] multiqc [DEBUG ] No samples found: prokka [2022-11-28 17:05:48,276] multiqc [DEBUG ] No samples found: samblaster [2022-11-28 17:05:48,280] multiqc [DEBUG ] No samples found: samtools [2022-11-28 17:05:48,283] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-28 17:05:48,286] multiqc [DEBUG ] No samples found: bamtools [2022-11-28 17:05:48,289] multiqc [DEBUG ] No samples found: jellyfish [2022-11-28 17:05:48,293] multiqc [DEBUG ] No samples found: vcftools [2022-11-28 17:05:48,296] multiqc [DEBUG ] No samples found: longranger [2022-11-28 17:05:48,299] multiqc [DEBUG ] No samples found: stacks [2022-11-28 17:05:48,302] multiqc [DEBUG ] No samples found: varscan2 [2022-11-28 17:05:48,308] multiqc [DEBUG ] No samples found: bbmap [2022-11-28 17:05:48,311] multiqc [DEBUG ] No samples found: bismark [2022-11-28 17:05:48,314] multiqc [DEBUG ] No samples found: biscuit [2022-11-28 17:05:48,317] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-28 17:05:48,320] multiqc [DEBUG ] No samples found: hicup [2022-11-28 17:05:48,323] multiqc [DEBUG ] No samples found: hicpro [2022-11-28 17:05:48,326] multiqc [DEBUG ] No samples found: salmon [2022-11-28 17:05:48,329] multiqc [DEBUG ] No samples found: kallisto [2022-11-28 17:05:48,332] multiqc [DEBUG ] No samples found: slamdunk [2022-11-28 17:05:48,335] multiqc [DEBUG ] No samples found: star [2022-11-28 17:05:48,338] multiqc [DEBUG ] No samples found: hisat2 [2022-11-28 17:05:48,341] multiqc [DEBUG ] No samples found: tophat [2022-11-28 17:05:48,344] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-28 17:05:48,347] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-28 17:05:48,350] multiqc [DEBUG ] No samples found: snpsplit [2022-11-28 17:05:48,352] multiqc [DEBUG ] No samples found: kat [2022-11-28 17:05:48,355] multiqc [DEBUG ] No samples found: leehom [2022-11-28 17:05:48,358] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-28 17:05:48,361] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-28 17:05:48,364] multiqc [DEBUG ] No samples found: cutadapt [2022-11-28 17:05:48,367] multiqc [DEBUG ] No samples found: flexbar [2022-11-28 17:05:48,370] multiqc [DEBUG ] No samples found: kaiju [2022-11-28 17:05:48,373] multiqc [DEBUG ] No samples found: kraken [2022-11-28 17:05:48,376] multiqc [DEBUG ] No samples found: malt [2022-11-28 17:05:48,379] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-28 17:05:48,382] multiqc [DEBUG ] No samples found: sickle [2022-11-28 17:05:48,385] multiqc [DEBUG ] No samples found: skewer [2022-11-28 17:05:48,388] multiqc [DEBUG ] No samples found: sortmerna [2022-11-28 17:05:48,390] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-28 17:05:48,393] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-28 17:05:48,396] multiqc [DEBUG ] No samples found: afterqc [2022-11-28 17:05:48,399] multiqc [DEBUG ] No samples found: fastp [2022-11-28 17:05:49,258] multiqc.modules.fastqc.fastqc [INFO ] Found 26 reports [2022-11-28 17:05:49,622] multiqc [DEBUG ] No samples found: pycoqc [2022-11-28 17:05:49,625] multiqc [DEBUG ] No samples found: minionqc [2022-11-28 17:05:49,628] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-28 17:05:49,631] multiqc [DEBUG ] No samples found: clusterflow [2022-11-28 17:05:49,634] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-28 17:05:49,637] multiqc [DEBUG ] No samples found: interop [2022-11-28 17:05:49,640] multiqc [DEBUG ] No samples found: ivar [2022-11-28 17:05:49,643] multiqc [DEBUG ] No samples found: flash [2022-11-28 17:05:49,646] multiqc [DEBUG ] No samples found: seqyclean [2022-11-28 17:05:49,646] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-28 17:05:49,646] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2022-11-28 17:05:49,646] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-11-28 17:05:49,646] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-28 17:05:49,646] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-28 17:05:49,677] multiqc [INFO ] Compressing plot data [2022-11-28 17:05:50,094] multiqc [INFO ] Report : multiqc_report.html [2022-11-28 17:05:50,094] multiqc [INFO ] Data : multiqc_data [2022-11-28 17:05:50,094] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27440387/tmp4uhcvkww/multiqc_data' to '/scratch/gencore/logs/html/HNGC3DRX2/2/multiqc_data' [2022-11-28 17:06:30,158] multiqc [INFO ] MultiQC complete