/usr/local/bioinformatics/quast-4.5/quast.py --scaffolds -t 24 /home/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa /home/data/20171005_redundans/scaffolds.reduced.fa Version: 4.5, 15ca3b9 System information: OS: Linux-4.4.0-96-generic-x86_64-with-debian-8.9 (linux_64) Python version: 2.7.13 CPUs number: 24 Started: 2017-10-06 22:27:26 Logging to /home/data/quast_results/results_2017_10_06_22_27_26/quast.log CWD: /home/data Main parameters: Threads: 24, scaffolds: true, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... 1 /home/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa ==> 20171004_redundans_scaffolds.reduced 1 breaking scaffolds into contigs: 1 2315 scaffolds (20171004_redundans_scaffolds.reduced) were broken into 2632 contigs (20171004_redundans_scaffolds.reduced_broken) 2 /home/data/20171005_redundans/scaffolds.reduced.fa ==> 20171005_redundans_scaffolds.reduced 2 breaking scaffolds into contigs: 2 2045 scaffolds (20171005_redundans_scaffolds.reduced) were broken into 2389 contigs (20171005_redundans_scaffolds.reduced_broken) 2017-10-06 22:27:34 Running Basic statistics processor... Contig files: 1 20171004_redundans_scaffolds.reduced 2 20171004_redundans_scaffolds.reduced_broken 3 20171005_redundans_scaffolds.reduced 4 20171005_redundans_scaffolds.reduced_broken Calculating N50 and L50... 1 20171004_redundans_scaffolds.reduced, N50 = 17679, L50 = 573, Total length = 40561504, GC % = 36.46, # N's per 100 kbp = 695.24 2 20171004_redundans_scaffolds.reduced_broken, N50 = 15655, L50 = 809, Total length = 40280190, GC % = 36.46, # N's per 100 kbp = 1.82 3 20171005_redundans_scaffolds.reduced, N50 = 16565, L50 = 452, Total length = 29292260, GC % = 36.39, # N's per 100 kbp = 918.03 4 20171005_redundans_scaffolds.reduced_broken, N50 = 14366, L50 = 685, Total length = 29023368, GC % = 36.39, # N's per 100 kbp = 1.36 Drawing Nx plot... saved to /home/data/quast_results/results_2017_10_06_22_27_26/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/data/quast_results/results_2017_10_06_22_27_26/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/data/quast_results/results_2017_10_06_22_27_26/basic_stats/GC_content_plot.pdf Drawing 20171004_redundans_scaffolds.reduced GC content plot... saved to /home/data/quast_results/results_2017_10_06_22_27_26/basic_stats/20171004_redundans_scaffolds.reduced_GC_content_plot.pdf Drawing 20171004_redundans_scaffolds.reduced_broken GC content plot... saved to /home/data/quast_results/results_2017_10_06_22_27_26/basic_stats/20171004_redundans_scaffolds.reduced_broken_GC_content_plot.pdf Drawing 20171005_redundans_scaffolds.reduced GC content plot... saved to /home/data/quast_results/results_2017_10_06_22_27_26/basic_stats/20171005_redundans_scaffolds.reduced_GC_content_plot.pdf Drawing 20171005_redundans_scaffolds.reduced_broken GC content plot... saved to /home/data/quast_results/results_2017_10_06_22_27_26/basic_stats/20171005_redundans_scaffolds.reduced_broken_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2017-10-06 22:27:46 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 2017-10-06 22:27:49 RESULTS: Text versions of total report are saved to /home/data/quast_results/results_2017_10_06_22_27_26/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/data/quast_results/results_2017_10_06_22_27_26/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /home/data/quast_results/results_2017_10_06_22_27_26/report.html PDF version (tables and plots) is saved to /home/data/quast_results/results_2017_10_06_22_27_26/report.pdf Icarus (contig browser) is saved to /home/data/quast_results/results_2017_10_06_22_27_26/icarus.html Log saved to /home/data/quast_results/results_2017_10_06_22_27_26/quast.log Finished: 2017-10-06 22:27:49 Elapsed time: 0:00:23.172880 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!