[2024-05-25 08:21:36,859] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-05-25 08:21:36,859] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-05-25 08:21:36,860] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-05-25 08:21:36,862] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-05-25 08:21:36,862] 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}} [2024-05-25 08:21:36,862] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-25 08:21:36,898] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-05-25 08:21:36,898] multiqc [INFO ] This is MultiQC v1.9 [2024-05-25 08:21:36,898] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-25 08:21:36,898] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/40/bccc8253e49f8dc82ee55d89e96d86/merged [2024-05-25 08:21:36,898] multiqc [INFO ] Template : default [2024-05-25 08:21:36,898] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-05-25 08:21:36,898] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/40/bccc8253e49f8dc82ee55d89e96d86/merged [2024-05-25 08:21:36,899] 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 [2024-05-25 08:21:36,899] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-46989446/tmpqx24l9f3 [2024-05-25 08:21:37,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H22N7DRX5_n01_ARF7_01_fastqc.html [2024-05-25 08:21:37,026] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H22N7DRX5_n01_ARF7_01_fastqc.html [2024-05-25 08:21:37,099] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H22N7DRX5_n01_undetermined_fastqc.html [2024-05-25 08:21:37,106] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H22N7DRX5_n01_undetermined_fastqc.html [2024-05-25 08:21:37,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H22N7DRX5_n02_ARF7_01_fastqc.html [2024-05-25 08:21:37,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H22N7DRX5_n02_ARF7_01_fastqc.html [2024-05-25 08:21:37,230] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H22N7DRX5_n02_undetermined_fastqc.html [2024-05-25 08:21:37,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H22N7DRX5_n02_undetermined_fastqc.html [2024-05-25 08:21:37,766] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-25 08:21:37,768] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-25 08:21:37,775] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2024-05-25 08:21:37,777] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2024-05-25 08:21:37,779] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-05-25 08:21:37,783] multiqc [DEBUG ] No samples found: conpair [2024-05-25 08:21:37,788] multiqc [DEBUG ] No samples found: peddy [2024-05-25 08:21:37,793] multiqc [DEBUG ] No samples found: somalier [2024-05-25 08:21:37,798] multiqc [DEBUG ] No samples found: methylQA [2024-05-25 08:21:37,806] multiqc [DEBUG ] No samples found: mosdepth [2024-05-25 08:21:37,810] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-05-25 08:21:37,814] multiqc [DEBUG ] No samples found: qualimap [2024-05-25 08:21:37,818] multiqc [DEBUG ] No samples found: preseq [2024-05-25 08:21:37,823] multiqc [DEBUG ] No samples found: quast [2024-05-25 08:21:37,828] multiqc [DEBUG ] No samples found: qorts [2024-05-25 08:21:37,832] multiqc [DEBUG ] No samples found: rna_seqc [2024-05-25 08:21:37,837] multiqc [DEBUG ] No samples found: rockhopper [2024-05-25 08:21:37,841] multiqc [DEBUG ] No samples found: rsem [2024-05-25 08:21:37,852] multiqc [DEBUG ] No samples found: rseqc [2024-05-25 08:21:37,856] multiqc [DEBUG ] No samples found: busco [2024-05-25 08:21:37,861] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-05-25 08:21:37,865] multiqc [DEBUG ] No samples found: disambiguate [2024-05-25 08:21:37,870] multiqc [DEBUG ] No samples found: supernova [2024-05-25 08:21:37,882] multiqc [DEBUG ] No samples found: deeptools [2024-05-25 08:21:37,887] multiqc [DEBUG ] No samples found: sargasso [2024-05-25 08:21:37,892] multiqc [DEBUG ] No samples found: verifybamid [2024-05-25 08:21:37,896] multiqc [DEBUG ] No samples found: mirtrace [2024-05-25 08:21:37,900] multiqc [DEBUG ] No samples found: happy [2024-05-25 08:21:37,905] multiqc [DEBUG ] No samples found: mirtop [2024-05-25 08:21:37,911] multiqc [DEBUG ] No samples found: homer [2024-05-25 08:21:37,916] multiqc [DEBUG ] No samples found: macs2 [2024-05-25 08:21:37,919] multiqc [DEBUG ] No samples found: theta2 [2024-05-25 08:21:37,924] multiqc [DEBUG ] No samples found: snpeff [2024-05-25 08:21:37,931] multiqc [DEBUG ] No samples found: gatk [2024-05-25 08:21:37,935] multiqc [DEBUG ] No samples found: htseq [2024-05-25 08:21:37,940] multiqc [DEBUG ] No samples found: bcftools [2024-05-25 08:21:37,945] multiqc [DEBUG ] No samples found: featureCounts [2024-05-25 08:21:37,951] multiqc [DEBUG ] No samples found: fgbio [2024-05-25 08:21:37,963] multiqc [DEBUG ] No samples found: dragen [2024-05-25 08:21:37,968] multiqc [DEBUG ] No samples found: dedup [2024-05-25 08:21:37,973] multiqc [DEBUG ] No samples found: damageprofiler [2024-05-25 08:21:37,995] multiqc [DEBUG ] No samples found: biobambam2 [2024-05-25 08:21:38,000] multiqc [DEBUG ] No samples found: mtnucratio [2024-05-25 08:21:38,002] multiqc [DEBUG ] No samples found: picard [2024-05-25 08:21:38,006] multiqc [DEBUG ] No samples found: prokka [2024-05-25 08:21:38,010] multiqc [DEBUG ] No samples found: samblaster [2024-05-25 08:21:38,019] multiqc [DEBUG ] No samples found: samtools [2024-05-25 08:21:38,023] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-05-25 08:21:38,028] multiqc [DEBUG ] No samples found: bamtools [2024-05-25 08:21:38,032] multiqc [DEBUG ] No samples found: jellyfish [2024-05-25 08:21:38,039] multiqc [DEBUG ] No samples found: vcftools [2024-05-25 08:21:38,044] multiqc [DEBUG ] No samples found: longranger [2024-05-25 08:21:38,048] multiqc [DEBUG ] No samples found: stacks [2024-05-25 08:21:38,053] multiqc [DEBUG ] No samples found: varscan2 [2024-05-25 08:21:38,066] multiqc [DEBUG ] No samples found: bbmap [2024-05-25 08:21:38,071] multiqc [DEBUG ] No samples found: bismark [2024-05-25 08:21:38,076] multiqc [DEBUG ] No samples found: biscuit [2024-05-25 08:21:38,080] multiqc [DEBUG ] No samples found: hicexplorer [2024-05-25 08:21:38,085] multiqc [DEBUG ] No samples found: hicup [2024-05-25 08:21:38,090] multiqc [DEBUG ] No samples found: hicpro [2024-05-25 08:21:38,094] multiqc [DEBUG ] No samples found: salmon [2024-05-25 08:21:38,098] multiqc [DEBUG ] No samples found: kallisto [2024-05-25 08:21:38,103] multiqc [DEBUG ] No samples found: slamdunk [2024-05-25 08:21:38,107] multiqc [DEBUG ] No samples found: star [2024-05-25 08:21:38,112] multiqc [DEBUG ] No samples found: hisat2 [2024-05-25 08:21:38,116] multiqc [DEBUG ] No samples found: tophat [2024-05-25 08:21:38,121] multiqc [DEBUG ] No samples found: bowtie2 [2024-05-25 08:21:38,125] multiqc [DEBUG ] No samples found: bowtie1 [2024-05-25 08:21:38,129] multiqc [DEBUG ] No samples found: snpsplit [2024-05-25 08:21:38,134] multiqc [DEBUG ] No samples found: kat [2024-05-25 08:21:38,138] multiqc [DEBUG ] No samples found: leehom [2024-05-25 08:21:38,142] multiqc [DEBUG ] No samples found: adapterRemoval [2024-05-25 08:21:38,147] multiqc [DEBUG ] No samples found: clipandmerge [2024-05-25 08:21:38,151] multiqc [DEBUG ] No samples found: cutadapt [2024-05-25 08:21:38,155] multiqc [DEBUG ] No samples found: flexbar [2024-05-25 08:21:38,160] multiqc [DEBUG ] No samples found: kaiju [2024-05-25 08:21:38,164] multiqc [DEBUG ] No samples found: kraken [2024-05-25 08:21:38,169] multiqc [DEBUG ] No samples found: malt [2024-05-25 08:21:38,173] multiqc [DEBUG ] No samples found: trimmomatic [2024-05-25 08:21:38,178] multiqc [DEBUG ] No samples found: sickle [2024-05-25 08:21:38,182] multiqc [DEBUG ] No samples found: skewer [2024-05-25 08:21:38,186] multiqc [DEBUG ] No samples found: sortmerna [2024-05-25 08:21:38,190] multiqc [DEBUG ] No samples found: biobloomtools [2024-05-25 08:21:38,195] multiqc [DEBUG ] No samples found: fastq_screen [2024-05-25 08:21:38,199] multiqc [DEBUG ] No samples found: afterqc [2024-05-25 08:21:38,204] multiqc [DEBUG ] No samples found: fastp [2024-05-25 08:21:38,290] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-05-25 08:21:38,291] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H22N7DRX5_n01_undetermined' [2024-05-25 08:21:38,291] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H22N7DRX5_n02_undetermined' [2024-05-25 08:21:38,348] multiqc [DEBUG ] No samples found: pycoqc [2024-05-25 08:21:38,352] multiqc [DEBUG ] No samples found: minionqc [2024-05-25 08:21:38,357] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-05-25 08:21:38,361] multiqc [DEBUG ] No samples found: clusterflow [2024-05-25 08:21:38,366] multiqc [DEBUG ] No samples found: bcl2fastq [2024-05-25 08:21:38,371] multiqc [DEBUG ] No samples found: interop [2024-05-25 08:21:38,375] multiqc [DEBUG ] No samples found: ivar [2024-05-25 08:21:38,380] multiqc [DEBUG ] No samples found: flash [2024-05-25 08:21:38,384] multiqc [DEBUG ] No samples found: seqyclean [2024-05-25 08:21:38,384] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-05-25 08:21:38,384] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-05-25 08:21:38,385] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-05-25 08:21:38,391] multiqc [INFO ] Compressing plot data [2024-05-25 08:21:38,449] multiqc [INFO ] Report : multiqc_report.html [2024-05-25 08:21:38,449] multiqc [INFO ] Data : multiqc_data [2024-05-25 08:21:38,449] multiqc [DEBUG ] Moving data file from '/state/partition1/job-46989446/tmpqx24l9f3/multiqc_data' to '/vast/gencore/GENEFLOW/work/40/bccc8253e49f8dc82ee55d89e96d86/merged/multiqc_data' [2024-05-25 08:21:38,604] multiqc [INFO ] MultiQC complete