./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) make -C quast_libs/minimap2 >> quast_libs/minimap2/make.log 2>> quast_libs/minimap2/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 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 8 \ quast_test_output/quast_corrected_input/reference.fasta quast_test_output/quast_corrected_input/contigs_1.fasta \ > quast_test_output/contigs_reports/minimap_output/contigs_1.coords_tmp 2>> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr 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 8 \ quast_test_output/quast_corrected_input/reference.fasta quast_test_output/quast_corrected_input/contigs_2.fasta \ > quast_test_output/contigs_reports/minimap_output/contigs_2.coords_tmp 2>> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr 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) make -C quast_libs/glimmer/src >> quast_libs/glimmer/src/make.log 2>> quast_libs/glimmer/src/make.err 1 contigs_1 2 contigs_2 1 quast_libs/glimmer/glimmerhmm quast_test_output/predicted_genes/tmp/tmp35b2CI/0.fasta \ -d quast_libs/glimmer/trained/arabidopsis -g -o quast_test_output/predicted_genes/tmp/tmp35b2CI/0.gff \ >> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 2>> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 2 quast_libs/glimmer/glimmerhmm quast_test_output/predicted_genes/tmp/tmpR74k6u/0.fasta \ -d quast_libs/glimmer/trained/arabidopsis -g -o quast_test_output/predicted_genes/tmp/tmpR74k6u/0.gff \ >> quast_test_output/predicted_genes/contigs_2_glimmer.stderr 2>> quast_test_output/predicted_genes/contigs_2_glimmer.stderr 1 quast_libs/glimmer/glimmerhmm quast_test_output/predicted_genes/tmp/tmp35b2CI/1.fasta \ -d quast_libs/glimmer/trained/arabidopsis -g -o quast_test_output/predicted_genes/tmp/tmp35b2CI/1.gff \ >> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 2>> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 2 quast_libs/glimmer/glimmerhmm quast_test_output/predicted_genes/tmp/tmpR74k6u/1.fasta \ -d quast_libs/glimmer/trained/arabidopsis -g -o quast_test_output/predicted_genes/tmp/tmpR74k6u/1.gff \ >> quast_test_output/predicted_genes/contigs_2_glimmer.stderr 2>> quast_test_output/predicted_genes/contigs_2_glimmer.stderr 1 quast_libs/glimmer/glimmerhmm quast_test_output/predicted_genes/tmp/tmp35b2CI/2.fasta \ -d quast_libs/glimmer/trained/arabidopsis -g -o quast_test_output/predicted_genes/tmp/tmp35b2CI/2.gff \ >> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 2>> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 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 1 perl quast_libs/genemark/linux_64/gmsn.pl --name contigs_1 --clean --out quast_test_output/predicted_genes/tmp/tmp1V6Yw2 \ quast_test_output/quast_corrected_input/contigs_1.fasta > quast_test_output/predicted_genes/contigs_1_genemark.stderr \ 2> quast_test_output/predicted_genes/contigs_1_genemark.stderr 2 perl quast_libs/genemark/linux_64/gmsn.pl --name contigs_2 --clean --out quast_test_output/predicted_genes/tmp/tmpUnRcZG \ quast_test_output/quast_corrected_input/contigs_2.fasta > quast_test_output/predicted_genes/contigs_2_genemark.stderr \ 2> quast_test_output/predicted_genes/contigs_2_genemark.stderr The tool returned non-zero. See quast_test_output/predicted_genes/contigs_1_genemark.stderr for stderr. The tool returned non-zero. See quast_test_output/predicted_genes/contigs_2_genemark.stderr for stderr. 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!