/usr/local/bioinformatics/quast-4.5/quast.py --scaffolds -t 24 /home/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa /home/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa /home/data/20171003_redundans_01/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: 2017-10-05 14:28:51 Logging to /home/data/quast_results/results_2017_10_05_14_28_51/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/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa ==> Oly_Redundans_Output_scaffolds.reduced 1 breaking scaffolds into contigs: 1 114 scaffolds (Oly_Redundans_Output_scaffolds.reduced) were broken into 32 contigs (Oly_Redundans_Output_scaffolds.reduced_broken) 2 /home/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa ==> Oly_Redundans_Output_Try_2_scaffolds.reduced 2 breaking scaffolds into contigs: 2 188612 scaffolds (Oly_Redundans_Output_Try_2_scaffolds.reduced) were broken into 209699 contigs (Oly_Redundans_Output_Try_2_scaffolds.reduced_broken) 3 /home/data/20171003_redundans_01/scaffolds.reduced.fa ==> 20171003_redundans_01_scaffolds.reduced 3 breaking scaffolds into contigs: 3 2315 scaffolds (20171003_redundans_01_scaffolds.reduced) were broken into 2632 contigs (20171003_redundans_01_scaffolds.reduced_broken) 2017-10-05 14:30:58 Running Basic statistics processor... Contig files: 1 Oly_Redundans_Output_scaffolds.reduced 2 Oly_Redundans_Output_scaffolds.reduced_broken 3 Oly_Redundans_Output_Try_2_scaffolds.reduced 4 Oly_Redundans_Output_Try_2_scaffolds.reduced_broken 5 20171003_redundans_01_scaffolds.reduced 6 20171003_redundans_01_scaffolds.reduced_broken Calculating N50 and L50... 1 Oly_Redundans_Output_scaffolds.reduced, N50 = 682, L50 = 40, Total length = 85207, GC % = 36.24, # N's per 100 kbp = 17127.70 2 Oly_Redundans_Output_scaffolds.reduced_broken, N50 = 639, L50 = 13, Total length = 21590, GC % = 36.07, # N's per 100 kbp = 0.00 3 Oly_Redundans_Output_Try_2_scaffolds.reduced, N50 = 4175, L50 = 32022, Total length = 513841258, GC % = 35.90, # N's per 100 kbp = 1019.31 4 Oly_Redundans_Output_Try_2_scaffolds.reduced_broken, N50 = 3545, L50 = 38434, Total length = 503440027, GC % = 35.90, # N's per 100 kbp = 37.83 5 20171003_redundans_01_scaffolds.reduced, N50 = 17679, L50 = 573, Total length = 40561504, GC % = 36.46, # N's per 100 kbp = 695.24 6 20171003_redundans_01_scaffolds.reduced_broken, N50 = 15655, L50 = 809, Total length = 40280190, GC % = 36.46, # N's per 100 kbp = 1.82 Drawing Nx plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/GC_content_plot.pdf Drawing Oly_Redundans_Output_scaffolds.reduced GC content plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/Oly_Redundans_Output_scaffolds.reduced_GC_content_plot.pdf Drawing Oly_Redundans_Output_scaffolds.reduced_broken GC content plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/Oly_Redundans_Output_scaffolds.reduced_broken_GC_content_plot.pdf Drawing Oly_Redundans_Output_Try_2_scaffolds.reduced GC content plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/Oly_Redundans_Output_Try_2_scaffolds.reduced_GC_content_plot.pdf Drawing Oly_Redundans_Output_Try_2_scaffolds.reduced_broken GC content plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/Oly_Redundans_Output_Try_2_scaffolds.reduced_broken_GC_content_plot.pdf Drawing 20171003_redundans_01_scaffolds.reduced GC content plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/20171003_redundans_01_scaffolds.reduced_GC_content_plot.pdf Drawing 20171003_redundans_01_scaffolds.reduced_broken GC content plot... saved to /home/data/quast_results/results_2017_10_05_14_28_51/basic_stats/20171003_redundans_01_scaffolds.reduced_broken_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2017-10-05 14:32:19 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 2017-10-05 14:32:45 RESULTS: Text versions of total report are saved to /home/data/quast_results/results_2017_10_05_14_28_51/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/data/quast_results/results_2017_10_05_14_28_51/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_05_14_28_51/report.html PDF version (tables and plots) is saved to /home/data/quast_results/results_2017_10_05_14_28_51/report.pdf Icarus (contig browser) is saved to /home/data/quast_results/results_2017_10_05_14_28_51/icarus.html Log saved to /home/data/quast_results/results_2017_10_05_14_28_51/quast.log Finished: 2017-10-05 14:32:46 Elapsed time: 0:03:54.594816 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!