/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 --memory-efficient -t 5 /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_3.fasta /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_3.fasta -R /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_ref_3.fasta -o /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3 --labels "meta_contigs_1, meta_contigs_2" Started: 2023-07-07 16:03:37 Logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/quast.log CWD: /home/psgendb/BIRCHDEV/install/quast-5.2.0 Main parameters: MODE: meta, threads: 5, 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 Reference: /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_ref_3.fasta ==> meta_ref_3 Contigs: Pre-processing... 1 /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_3.fasta ==> meta_contigs_1 2 /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_3.fasta ==> meta_contigs_2 2023-07-07 16:03:37 Running Basic statistics processor... Reference genome: meta_ref_3.fasta, length = 64999, num fragments = 1, GC % = 40.73 Contig files: 1 meta_contigs_1 2 meta_contigs_2 Calculating N50 and L50... 1 meta_contigs_1, N50 = 17535, L50 = 2, auN = 18007.5, Total length = 69110, GC % = 40.75, # N's per 100 kbp = 18.81 2 meta_contigs_2, N50 = 16099, L50 = 2, auN = 18221.4, Total length = 63778, GC % = 40.78, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/Nx_plot.pdf Drawing NGx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/NGx_plot.pdf Drawing cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/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/runs_per_reference/meta_ref_3/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/runs_per_reference/meta_ref_3/basic_stats/meta_contigs_2_GC_content_plot.pdf Drawing Coverage histogram (bin size: 4x)... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/coverage_histogram.pdf Drawing meta_contigs_1 coverage histogram (bin size: 4x)... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/meta_contigs_1_coverage_histogram.pdf Drawing meta_contigs_2 coverage histogram (bin size: 4x)... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/meta_contigs_2_coverage_histogram.pdf Done. 2023-07-07 16:03:41 Running Contig analyzer... 1 meta_contigs_1 1 Logging to files /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr... 1 Aligning contigs to the reference 1 quast_libs/minimap2/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N \ 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 5 \ quast_test_output/quast_corrected_input/meta_ref_3.fasta quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_3.fasta \ > quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/minimap_output/meta_contigs_1.coords_tmp \ 2>> quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/contigs_report_meta_contigs_1.stderr 1 Analysis is finished. 2 meta_contigs_2 2 Logging to files /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr... 2 Aligning contigs to the reference 2 quast_libs/minimap2/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N \ 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 5 \ quast_test_output/quast_corrected_input/meta_ref_3.fasta quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_3.fasta \ > quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/minimap_output/meta_contigs_2.coords_tmp \ 2>> quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/contigs_report_meta_contigs_2.stderr 2 Analysis is finished. Creating total report... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/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/runs_per_reference/meta_ref_3/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/runs_per_reference/meta_ref_3/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/runs_per_reference/meta_ref_3/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/misassemblies_frcurve_plot.pdf Done. 2023-07-07 16:03:42 Running NA-NGA calculation... 1 meta_contigs_1, Largest alignment = 27969, NA50 = 17534, NGA50 = 17534, LA50 = 2, LGA50 = 2 2 meta_contigs_2, Largest alignment = 27260, NA50 = 16099, NGA50 = 16099, LA50 = 2, LGA50 = 2 Drawing cumulative plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/aligned_stats/cumulative_plot.pdf Drawing NAx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/aligned_stats/NAx_plot.pdf Drawing NGAx plot... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/aligned_stats/NGAx_plot.pdf Done. 2023-07-07 16:03:43 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 1 Analysis is finished. 2 meta_contigs_2 2 Analysis is finished. Drawing Genome fraction, % histogram... saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/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 16:03:44 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 16:03:47 RESULTS: Text versions of total report are saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/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/runs_per_reference/meta_ref_3/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/runs_per_reference/meta_ref_3/report.html PDF version (tables and plots) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/report.pdf Icarus (contig browser) is saved to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/icarus.html