/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... (logging to /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/quast.log) 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) 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!