Starting QUAST test ./quast.py --test Version: 5.2.0, 3d87c606 System information: OS: Linux-3.10.0-1160.88.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo (linux_64) Python version: 2.7.5 CPUs number: 64 Started: 2023-07-07 16:02:53 Logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast.log NOTICE: Maximum number of threads is set to 16 (use --threads option to set it manually) CWD: /home/psgendb/BIRCHDEV/install/quast-5.2.0 Main parameters: MODE: default, threads: 16, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \ ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000 Reference: /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/reference.fasta.gz ==> reference Contigs: Pre-processing... 1 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/contigs_1.fasta ==> contigs_1 2 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/contigs_2.fasta ==> contigs_2 2023-07-07 16:02:54 Running Basic statistics processor... Reference genome: reference.fasta, length = 10000, num fragments = 1, GC % = 52.07 Contig files: 1 contigs_1 2 contigs_2 Calculating N50 and L50... 1 contigs_1, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 2 contigs_2, N50 = 3360, L50 = 1, auN = 2875.4, Total length = 5460, GC % = 52.44, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/basic_stats/Nx_plot.pdf Drawing NGx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/basic_stats/NGx_plot.pdf Drawing cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/basic_stats/GC_content_plot.pdf Drawing contigs_1 GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/basic_stats/contigs_1_GC_content_plot.pdf Drawing contigs_2 GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/basic_stats/contigs_2_GC_content_plot.pdf Done. 2023-07-07 16:02:57 Running Contig analyzer... Compiling Minimap2 (details are in /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/minimap2/make.log and make.err) 1 contigs_1 2 contigs_2 2 Logging to files /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/contigs_report_contigs_2.stdout and contigs_report_contigs_2.stderr... 1 Logging to files /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/contigs_report_contigs_1.stdout and contigs_report_contigs_1.stderr... 2 Aligning contigs to the reference 1 Aligning contigs to the reference 2 Analysis is finished. 1 Analysis is finished. Creating total report... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Drawing misassemblies by types plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/contigs_reports/misassemblies_frcurve_plot.pdf Done. 2023-07-07 16:03:11 Running NA-NGA calculation... 1 contigs_1, Largest alignment = 2030, NA50 = 1950, NGA50 = 1610, LA50 = 2, LGA50 = 3 2 contigs_2, Largest alignment = 2100, NA50 = 1471, NGA50 = 700, LA50 = 2, LGA50 = 4 Drawing cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/aligned_stats/cumulative_plot.pdf Drawing NAx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/aligned_stats/NAx_plot.pdf Drawing NGAx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/aligned_stats/NGAx_plot.pdf Done. 2023-07-07 16:03:12 Running Genome analyzer... Loaded 10 genomic features of type "gene" Loaded 2 genomic features of type "operon" 1 contigs_1 2 contigs_2 1 Analysis is finished. 2 Analysis is finished. Drawing genomic features cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/genome_stats/features_cumulative_plot.pdf Drawing genomic features FRCurve plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/genome_stats/features_frcurve_plot.pdf Drawing # complete genomic features histogram... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/genome_stats/complete_features_histogram.pdf Drawing operons cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/genome_stats/operons_cumulative_plot.pdf Drawing operons FRCurve plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/genome_stats/operons_frcurve_plot.pdf Drawing # complete operons histogram... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/genome_stats/complete_operons_histogram.pdf Drawing Genome fraction, % histogram... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/genome_stats/genome_fraction_histogram.pdf Done. 2023-07-07 16:03:14 Running GlimmerHMM... Compiling GlimmerHMM (details are in /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_libs/glimmer/src/make.log and make.err) 1 contigs_1 2 contigs_2 2 Genes = 6 unique, 6 total 2 Predicted genes (GFF): /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/predicted_genes/contigs_2_glimmer_genes.gff 1 Genes = 7 unique, 7 total 1 Predicted genes (GFF): /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/predicted_genes/contigs_1_glimmer_genes.gff Done. 2023-07-07 16:03:17 Running GeneMarkS... 1 contigs_1 2 contigs_2 WARNING: License period for GeneMark has ended! To update license, please visit http://exon.gatech.edu/GeneMark/license_download.cgi page and fill in the form. You should choose GeneMarkS tool and your operating system (note that GeneMark is free for non-commercial use). Download the license key and replace your ~/.gm_key with the updated version. After that you can restart QUAST. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2023-07-07 16:03:17 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating PDF with all tables and plots... 2 of 2: Creating Icarus viewers... Done 2023-07-07 16:03:21 RESULTS: Text versions of total report are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/report.html PDF version (tables and plots) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/report.pdf Icarus (contig browser) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/icarus.html Log is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast.log Finished: 2023-07-07 16:03:21 Elapsed time: 0:00:28.449910 NOTICEs: 2; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST! TEST PASSED with WARNINGS! Starting MetaQUAST test /home/psgendb/BIRCHDEV/install/quast-5.2.0/metaquast.py --test Version: 5.2.0, 3d87c606 System information: OS: Linux-3.10.0-1160.88.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo (linux_64) Python version: 2.7.5 CPUs number: 64 Started: 2023-07-07 16:03:22 Logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/metaquast.log NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)! NOTICE: Maximum number of threads is set to 16 (use --threads option to set it manually) Reference(s): /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_ref_1.fasta ==> meta_ref_1 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_ref_2.fasta ==> meta_ref_2 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_ref_3.fasta ==> meta_ref_3 All references were combined in combined_reference.fasta Contigs: Pre-processing... 1 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_contigs_1.fasta ==> meta_contigs_1 2 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_contigs_2.fasta ==> meta_contigs_2 Starting quast.py for the combined reference... /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast.pyc --min-identity 90.0 --combined-ref --colors #E31A1C,#1F78B4 --ls solid,solid --ambiguity-usage all /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_contigs_1.fasta /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_contigs_2.fasta -R /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/combined_reference.fasta -o /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference --labels "meta_contigs_1, meta_contigs_2" Started: 2023-07-07 16:03:22 Logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/quast.log NOTICE: Maximum number of threads is set to 16 (use --threads option to set it manually) CWD: /home/psgendb/BIRCHDEV/install/quast-5.2.0 Main parameters: MODE: meta, threads: 16, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \ ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 Reference: /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/combined_reference.fasta ==> combined_reference Contigs: Pre-processing... 1 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_contigs_1.fasta ==> meta_contigs_1 2 /home/psgendb/BIRCHDEV/install/quast-5.2.0/test_data/meta_contigs_2.fasta ==> meta_contigs_2 2023-07-07 16:03:22 Running Basic statistics processor... Reference genome: combined_reference.fasta, length = 179997, num fragments = 3, GC % = 45.50 Contig files: 1 meta_contigs_1 2 meta_contigs_2 Calculating N50 and L50... 1 meta_contigs_1, N50 = 48458, L50 = 2, auN = 36838.5, Total length = 180190, GC % = 45.35, # N's per 100 kbp = 18.87 2 meta_contigs_2, N50 = 49658, L50 = 2, auN = 38106.6, Total length = 172703, GC % = 45.11, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/GC_content_plot.pdf Drawing meta_contigs_1 GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/meta_contigs_1_GC_content_plot.pdf Drawing meta_contigs_2 GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/meta_contigs_2_GC_content_plot.pdf Drawing Coverage histogram (bin size: 97x)... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/coverage_histogram.pdf Drawing meta_contigs_1 coverage histogram (bin size: 63x)... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/meta_contigs_1_coverage_histogram.pdf Drawing meta_contigs_2 coverage histogram (bin size: 97x)... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/basic_stats/meta_contigs_2_coverage_histogram.pdf Done. 2023-07-07 16:03:28 Running Contig analyzer... 1 meta_contigs_1 2 meta_contigs_2 1 Logging to files /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr... 2 Logging to files /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr... 1 Aligning contigs to the reference 2 Aligning contigs to the reference 1 Analysis is finished. 2 Analysis is finished. Information about interspecies translocations by references for meta_contigs_1 is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/interspecies_translocations_by_refs_meta_contigs_1.info Information about interspecies translocations by references for meta_contigs_2 is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/interspecies_translocations_by_refs_meta_contigs_2.info Drawing Intergenomic misassemblies (found and supposed) metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/intergenomic_misassemblies.pdf Creating total report... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Drawing misassemblies by types plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/misassemblies_frcurve_plot.pdf Done. 2023-07-07 16:03:30 Running NA-NGA calculation... 1 meta_contigs_1, Largest alignment = 55106, NA50 = 37178, LA50 = 2 2 meta_contigs_2, Largest alignment = 49658, NA50 = 27260, LA50 = 3 Drawing cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/aligned_stats/cumulative_plot.pdf Drawing NAx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/aligned_stats/NAx_plot.pdf Done. 2023-07-07 16:03:32 Running Genome analyzer... NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it. NOTICE: No file with operons were provided. Use the -O option if you want to specify it. 1 meta_contigs_1 2 meta_contigs_2 2 Analysis is finished. 1 Analysis is finished. Drawing Genome fraction, % histogram... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/genome_stats/genome_fraction_histogram.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2023-07-07 16:03:33 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating PDF with all tables and plots... 2 of 2: Creating Icarus viewers... Done 2023-07-07 16:03:36 RESULTS: Text versions of total report are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/report.html PDF version (tables and plots) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/report.pdf Icarus (contig browser) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/icarus.html Partitioning contigs into bins aligned to each reference.. processing meta_contigs_1 processing meta_contigs_2 Run QUAST on different references in parallel.. Starting quast.py for the contigs aligned to meta_ref_1... (logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_1/quast.log) Starting quast.py for the contigs aligned to meta_ref_2... (logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_2/quast.log) Starting quast.py for the contigs aligned to meta_ref_3... (logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/quast.log) Starting quast.py for the contigs not aligned anywhere... (logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/quast.log) /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast.pyc --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 -t 16 /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_1_not_aligned_anywhere.fasta /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_2_not_aligned_anywhere.fasta -o /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned --labels "meta_contigs_1, meta_contigs_2" Started: 2023-07-07 16:03:48 Logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/quast.log CWD: /home/psgendb/BIRCHDEV/install/quast-5.2.0 Main parameters: MODE: meta, threads: 16, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \ ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000 Contigs: Pre-processing... 1 /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_1_not_aligned_anywhere.fasta ==> meta_contigs_1 2 /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_2_not_aligned_anywhere.fasta ==> meta_contigs_2 2023-07-07 16:03:48 Running Basic statistics processor... Contig files: 1 meta_contigs_1 2 meta_contigs_2 Calculating N50 and L50... 1 meta_contigs_1, N50 = 1610, L50 = 1, auN = 1409.0, Total length = 2730, GC % = 51.94, # N's per 100 kbp = 0.00 2 meta_contigs_2, N50 = 885, L50 = 1, auN = 885.0, Total length = 885, GC % = 0.00, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/basic_stats/GC_content_plot.pdf Drawing meta_contigs_1 GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/basic_stats/meta_contigs_1_GC_content_plot.pdf Drawing meta_contigs_2 GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/basic_stats/meta_contigs_2_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2023-07-07 16:03:50 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating PDF with all tables and plots... 2 of 2: Creating Icarus viewers... Done 2023-07-07 16:03:51 RESULTS: Text versions of total report are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/report.html PDF version (tables and plots) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/report.pdf Icarus (contig browser) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/not_aligned/icarus.html 2023-07-07 16:03:51 Summarizing results... Drawing # contigs metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/num_contigs.pdf Drawing Largest contig metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Largest_contig.pdf Drawing Total length metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Total_length.pdf Drawing Largest alignment metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Largest_alignment.pdf Drawing Total aligned length metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Total_aligned_length.pdf Drawing Total length (>= 1000 bp) metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Total_length_(ge_1000_bp).pdf Drawing Total length (>= 10000 bp) metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Total_length_(ge_10000_bp).pdf Drawing Total length (>= 50000 bp) metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Total_length_(ge_50000_bp).pdf Drawing # misassemblies metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/num_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for meta_contigs_1... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/meta_contigs_1_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for meta_contigs_2... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/meta_contigs_2_misassemblies.pdf Drawing Misassembled contigs length metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Misassembled_contigs_length.pdf Drawing # mismatches per 100 kbp metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/num_mismatches_per_100_kbp.pdf Drawing # indels per 100 kbp metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/num_indels_per_100_kbp.pdf Drawing # N's per 100 kbp metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/num_Ns_per_100_kbp.pdf Drawing Genome fraction (%) metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Genome_fraction.pdf Drawing Duplication ratio metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/Duplication_ratio.pdf Drawing NGA50 metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/NGA50.pdf Drawing LGA50 metaQUAST summary plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/PDF/LGA50.pdf Text versions of reports and plots for each metric (for all references and assemblies) are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/summary/ Icarus (contig browser) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/icarus.html Extended version of HTML-report (for all references and assemblies) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/report.html MetaQUAST finished. Log is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/metaquast.log Finished: 2023-07-07 16:03:59 Elapsed time: 0:00:36.884689 Total NOTICEs: 8; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST! TEST PASSED!