[2024-03-14 04:39:53,888] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-03-14 04:39:53,888] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-03-14 04:39:53,889] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-03-14 04:39:53,891] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-03-14 04:39:53,891] 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}} [2024-03-14 04:39:53,891] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-14 04:39:54,258] multiqc [WARNING] MultiQC Version v1.21 now available! [2024-03-14 04:39:54,259] multiqc [INFO ] This is MultiQC v1.9 [2024-03-14 04:39:54,259] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-14 04:39:54,259] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/e5/082816ed8286413532f49e56026108/1 [2024-03-14 04:39:54,259] multiqc [INFO ] Template : default [2024-03-14 04:39:54,259] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-03-14 04:39:54,259] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/e5/082816ed8286413532f49e56026108/1 [2024-03-14 04:39:54,259] 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 [2024-03-14 04:39:54,259] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-44067593/tmpi00fjgmo [2024-03-14 04:39:54,380] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_31_fastqc.html [2024-03-14 04:39:54,390] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_31_fastqc.html [2024-03-14 04:39:54,506] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_32_fastqc.html [2024-03-14 04:39:54,522] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_32_fastqc.html [2024-03-14 04:39:54,602] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_33_fastqc.html [2024-03-14 04:39:54,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_33_fastqc.html [2024-03-14 04:39:54,695] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_34_fastqc.html [2024-03-14 04:39:54,703] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_BS_CR_34_fastqc.html [2024-03-14 04:39:54,793] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_undetermined_fastqc.html [2024-03-14 04:39:54,807] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n01_undetermined_fastqc.html [2024-03-14 04:39:54,899] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_31_fastqc.html [2024-03-14 04:39:54,911] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_31_fastqc.html [2024-03-14 04:39:54,998] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_32_fastqc.html [2024-03-14 04:39:55,013] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_32_fastqc.html [2024-03-14 04:39:55,128] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_33_fastqc.html [2024-03-14 04:39:55,156] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_33_fastqc.html [2024-03-14 04:39:55,254] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_34_fastqc.html [2024-03-14 04:39:55,262] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_BS_CR_34_fastqc.html [2024-03-14 04:39:55,335] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_undetermined_fastqc.html [2024-03-14 04:39:55,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LHBCL_l01_n02_undetermined_fastqc.html [2024-03-14 04:39:55,423] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:55,433] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:55,433] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:55,433] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:55,433] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:55,433] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:55,433] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:55,464] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-14 04:39:57,063] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-14 04:39:57,064] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-14 04:39:57,078] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2024-03-14 04:39:57,079] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-03-14 04:39:57,089] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-03-14 04:39:57,094] multiqc [DEBUG ] No samples found: conpair [2024-03-14 04:39:57,099] multiqc [DEBUG ] No samples found: peddy [2024-03-14 04:39:57,104] multiqc [DEBUG ] No samples found: somalier [2024-03-14 04:39:57,108] multiqc [DEBUG ] No samples found: methylQA [2024-03-14 04:39:57,121] multiqc [DEBUG ] No samples found: mosdepth [2024-03-14 04:39:57,125] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-03-14 04:39:57,129] multiqc [DEBUG ] No samples found: qualimap [2024-03-14 04:39:57,134] multiqc [DEBUG ] No samples found: preseq [2024-03-14 04:39:57,138] multiqc [DEBUG ] No samples found: quast [2024-03-14 04:39:57,143] multiqc [DEBUG ] No samples found: qorts [2024-03-14 04:39:57,148] multiqc [DEBUG ] No samples found: rna_seqc [2024-03-14 04:39:57,152] multiqc [DEBUG ] No samples found: rockhopper [2024-03-14 04:39:57,157] multiqc [DEBUG ] No samples found: rsem [2024-03-14 04:39:57,169] multiqc [DEBUG ] No samples found: rseqc [2024-03-14 04:39:57,174] multiqc [DEBUG ] No samples found: busco [2024-03-14 04:39:57,178] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-03-14 04:39:57,183] multiqc [DEBUG ] No samples found: disambiguate [2024-03-14 04:39:57,188] multiqc [DEBUG ] No samples found: supernova [2024-03-14 04:39:57,201] multiqc [DEBUG ] No samples found: deeptools [2024-03-14 04:39:57,205] multiqc [DEBUG ] No samples found: sargasso [2024-03-14 04:39:57,210] multiqc [DEBUG ] No samples found: verifybamid [2024-03-14 04:39:57,215] multiqc [DEBUG ] No samples found: mirtrace [2024-03-14 04:39:57,219] multiqc [DEBUG ] No samples found: happy [2024-03-14 04:39:57,224] multiqc [DEBUG ] No samples found: mirtop [2024-03-14 04:39:57,230] multiqc [DEBUG ] No samples found: homer [2024-03-14 04:39:57,235] multiqc [DEBUG ] No samples found: macs2 [2024-03-14 04:39:57,239] multiqc [DEBUG ] No samples found: theta2 [2024-03-14 04:39:57,244] multiqc [DEBUG ] No samples found: snpeff [2024-03-14 04:39:57,251] multiqc [DEBUG ] No samples found: gatk [2024-03-14 04:39:57,255] multiqc [DEBUG ] No samples found: htseq [2024-03-14 04:39:57,261] multiqc [DEBUG ] No samples found: bcftools [2024-03-14 04:39:57,265] multiqc [DEBUG ] No samples found: featureCounts [2024-03-14 04:39:57,271] multiqc [DEBUG ] No samples found: fgbio [2024-03-14 04:39:57,284] multiqc [DEBUG ] No samples found: dragen [2024-03-14 04:39:57,289] multiqc [DEBUG ] No samples found: dedup [2024-03-14 04:39:57,294] multiqc [DEBUG ] No samples found: damageprofiler [2024-03-14 04:39:57,316] multiqc [DEBUG ] No samples found: biobambam2 [2024-03-14 04:39:57,322] multiqc [DEBUG ] No samples found: mtnucratio [2024-03-14 04:39:57,324] multiqc [DEBUG ] No samples found: picard [2024-03-14 04:39:57,329] multiqc [DEBUG ] No samples found: prokka [2024-03-14 04:39:57,333] multiqc [DEBUG ] No samples found: samblaster [2024-03-14 04:39:57,341] multiqc [DEBUG ] No samples found: samtools [2024-03-14 04:39:57,346] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-03-14 04:39:57,351] multiqc [DEBUG ] No samples found: bamtools [2024-03-14 04:39:57,356] multiqc [DEBUG ] No samples found: jellyfish [2024-03-14 04:39:57,363] multiqc [DEBUG ] No samples found: vcftools [2024-03-14 04:39:57,368] multiqc [DEBUG ] No samples found: longranger [2024-03-14 04:39:57,373] multiqc [DEBUG ] No samples found: stacks [2024-03-14 04:39:57,377] multiqc [DEBUG ] No samples found: varscan2 [2024-03-14 04:39:57,391] multiqc [DEBUG ] No samples found: bbmap [2024-03-14 04:39:57,396] multiqc [DEBUG ] No samples found: bismark [2024-03-14 04:39:57,401] multiqc [DEBUG ] No samples found: biscuit [2024-03-14 04:39:57,406] multiqc [DEBUG ] No samples found: hicexplorer [2024-03-14 04:39:57,410] multiqc [DEBUG ] No samples found: hicup [2024-03-14 04:39:57,415] multiqc [DEBUG ] No samples found: hicpro [2024-03-14 04:39:57,419] multiqc [DEBUG ] No samples found: salmon [2024-03-14 04:39:57,424] multiqc [DEBUG ] No samples found: kallisto [2024-03-14 04:39:57,429] multiqc [DEBUG ] No samples found: slamdunk [2024-03-14 04:39:57,433] multiqc [DEBUG ] No samples found: star [2024-03-14 04:39:57,438] multiqc [DEBUG ] No samples found: hisat2 [2024-03-14 04:39:57,442] multiqc [DEBUG ] No samples found: tophat [2024-03-14 04:39:57,447] multiqc [DEBUG ] No samples found: bowtie2 [2024-03-14 04:39:57,451] multiqc [DEBUG ] No samples found: bowtie1 [2024-03-14 04:39:57,456] multiqc [DEBUG ] No samples found: snpsplit [2024-03-14 04:39:57,460] multiqc [DEBUG ] No samples found: kat [2024-03-14 04:39:57,465] multiqc [DEBUG ] No samples found: leehom [2024-03-14 04:39:57,469] multiqc [DEBUG ] No samples found: adapterRemoval [2024-03-14 04:39:57,474] multiqc [DEBUG ] No samples found: clipandmerge [2024-03-14 04:39:57,478] multiqc [DEBUG ] No samples found: cutadapt [2024-03-14 04:39:57,482] multiqc [DEBUG ] No samples found: flexbar [2024-03-14 04:39:57,487] multiqc [DEBUG ] No samples found: kaiju [2024-03-14 04:39:57,492] multiqc [DEBUG ] No samples found: kraken [2024-03-14 04:39:57,496] multiqc [DEBUG ] No samples found: malt [2024-03-14 04:39:57,501] multiqc [DEBUG ] No samples found: trimmomatic [2024-03-14 04:39:57,505] multiqc [DEBUG ] No samples found: sickle [2024-03-14 04:39:57,510] multiqc [DEBUG ] No samples found: skewer [2024-03-14 04:39:57,514] multiqc [DEBUG ] No samples found: sortmerna [2024-03-14 04:39:57,519] multiqc [DEBUG ] No samples found: biobloomtools [2024-03-14 04:39:57,523] multiqc [DEBUG ] No samples found: fastq_screen [2024-03-14 04:39:57,528] multiqc [DEBUG ] No samples found: afterqc [2024-03-14 04:39:57,533] multiqc [DEBUG ] No samples found: fastp [2024-03-14 04:39:57,649] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2024-03-14 04:39:57,764] multiqc [DEBUG ] No samples found: pycoqc [2024-03-14 04:39:57,769] multiqc [DEBUG ] No samples found: minionqc [2024-03-14 04:39:57,773] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-03-14 04:39:57,778] multiqc [DEBUG ] No samples found: clusterflow [2024-03-14 04:39:57,783] multiqc [DEBUG ] No samples found: bcl2fastq [2024-03-14 04:39:57,788] multiqc [DEBUG ] No samples found: interop [2024-03-14 04:39:57,811] multiqc [DEBUG ] No samples found: ivar [2024-03-14 04:39:57,819] multiqc [DEBUG ] No samples found: flash [2024-03-14 04:39:57,829] multiqc [DEBUG ] No samples found: seqyclean [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-03-14 04:39:57,830] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-03-14 04:39:57,844] multiqc [INFO ] Compressing plot data [2024-03-14 04:39:58,030] multiqc [INFO ] Report : multiqc_report.html [2024-03-14 04:39:58,030] multiqc [INFO ] Data : multiqc_data [2024-03-14 04:39:58,030] multiqc [DEBUG ] Moving data file from '/state/partition1/job-44067593/tmpi00fjgmo/multiqc_data' to '/vast/gencore/GENEFLOW/work/e5/082816ed8286413532f49e56026108/1/multiqc_data' [2024-03-14 04:39:58,199] multiqc [INFO ] MultiQC complete