Start: Sun Jun 13 16:51:04 CDT 2021 /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast.py --eukaryote --scaffolds --threads 32 -o /local/genbank/workspace/reads.all3.spades1.55/quast_results /local/genbank/workspace/reads.all3.spades1.55/scaffolds.fasta Version: 4.6.3 System information: OS: Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo (linux_64) Python version: 2.7.5 CPUs number: 64 Started: 2021-06-13 16:51:04 Logging to /local/genbank/workspace/reads.all3.spades1.55/quast_results/quast.log CWD: /local/genbank/workspace/reads.all3.spades1.55 Main parameters: Threads: 32, eukaryotic: true, scaffolds: true, minimum contig length: 500, ambiguity: one, \ threshold for extensive misassembly size: 1000 Contigs: Pre-processing... /local/genbank/workspace/reads.all3.spades1.55/scaffolds.fasta ==> scaffolds breaking scaffolds into contigs: 79558 scaffolds (scaffolds) were broken into 82508 contigs (scaffolds_broken) 2021-06-13 16:52:36 Running Basic statistics processor... Contig files: 1 scaffolds 2 scaffolds_broken Calculating N50 and L50... 1 scaffolds, N50 = 3404, L50 = 9959, Total length = 201162385, GC % = 56.26, # N's per 100 kbp = 28.67 2 scaffolds_broken, N50 = 3199, L50 = 10718, Total length = 201101205, GC % = 56.26, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/GC_content_plot.pdf Drawing scaffolds GC content plot... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/scaffolds_GC_content_plot.pdf Drawing scaffolds_broken GC content plot... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/scaffolds_broken_GC_content_plot.pdf Drawing Coverage histogram (bin size: 1x)... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/coverage_histogram.pdf Drawing scaffolds coverage histogram (bin size: 1x)... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/scaffolds_coverage_histogram.pdf Drawing scaffolds_broken coverage histogram (bin size: 1x)... saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/basic_stats/scaffolds_broken_coverage_histogram.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2021-06-13 16:54:00 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating Icarus viewers... 2 of 2: Creating PDF with all tables and plots... Done 2021-06-13 16:54:20 RESULTS: Text versions of total report are saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/report.html PDF version (tables and plots) is saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/report.pdf Icarus (contig browser) is saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/icarus.html Log saved to /local/genbank/workspace/reads.all3.spades1.55/quast_results/quast.log Finished: 2021-06-13 16:54:20 Elapsed time: 0:03:16.189371 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST! Finish: Sun Jun 13 16:54:20 CDT 2021