/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 2 quast_libs/minimap2/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N \ 100 -s 65 -z 200 --mask-level 1 --min-occ 200 -g 2500 --score-N 2 --cs -t 8 quast_test_output/quast_corrected_input/combined_reference.fasta \ quast_test_output/quast_corrected_input/meta_contigs_2.fasta > quast_test_output/combined_reference/contigs_reports/minimap_output/meta_contigs_2.coords_tmp \ 2>> quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_2.stderr 1 quast_libs/minimap2/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N \ 100 -s 65 -z 200 --mask-level 1 --min-occ 200 -g 2500 --score-N 2 --cs -t 8 quast_test_output/quast_corrected_input/combined_reference.fasta \ quast_test_output/quast_corrected_input/meta_contigs_1.fasta > quast_test_output/combined_reference/contigs_reports/minimap_output/meta_contigs_1.coords_tmp \ 2>> quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_1.stderr 1 Alignments: quast_test_output/combined_reference/contigs_reports/alignments_meta_contigs_1.tsv 2 Alignments: quast_test_output/combined_reference/contigs_reports/alignments_meta_contigs_2.tsv 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