/home/sam/software/quast-4.5/quast.py -t 24 --labels 20180403_pga,20180421_pga,20180810_geo_manual /mnt/owl/Athaliana/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-03 11:05:41.596285/PGA_assembly.fasta /mnt/owl/Athaliana/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/PGA_assembly.fasta /mnt/owl/Athaliana/20180822_phase_genomics_geoduck_Results/geoduck_manual/geoduck_manual_scaffolds.fasta Version: 4.5, 15ca3b9 System information: OS: Linux-4.4.0-130-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64) Python version: 2.7.12 CPUs number: 24 Started: 2018-08-23 07:38:28 Logging to /home/sam/quast_results/results_2018_08_23_07_38_28/quast.log CWD: /home/sam Main parameters: Threads: 24, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... 1 /mnt/owl/Athaliana/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-03 11:05:41.596285/PGA_assembly.fasta ==> 20180403_pga 2 /mnt/owl/Athaliana/20180421_geoduck_hi-c/Results/geoduck_roberts results 2018-04-21 18:09:04.514704/PGA_assembly.fasta ==> 20180421_pga 3 /mnt/owl/Athaliana/20180822_phase_genomics_geoduck_Results/geoduck_manual/geoduck_manual_scaffolds.fasta ==> 20180810_geo_manual 2018-08-23 07:41:53 Running Basic statistics processor... Contig files: 1 20180403_pga 2 20180421_pga 3 20180810_geo_manual Calculating N50 and L50... 1 20180403_pga, N50 = 43382739, L50 = 18, Total length = 2205690888, GC % = 33.92, # N's per 100 kbp = 9142.81 2 20180421_pga, N50 = 43382739, L50 = 18, Total length = 2205690788, GC % = 33.92, # N's per 100 kbp = 9142.81 3 20180810_geo_manual, N50 = 6194822, L50 = 31, Total length = 2205688688, GC % = 33.92, # N's per 100 kbp = 9142.72 Drawing Nx plot... saved to /home/sam/quast_results/results_2018_08_23_07_38_28/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/sam/quast_results/results_2018_08_23_07_38_28/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/sam/quast_results/results_2018_08_23_07_38_28/basic_stats/GC_content_plot.pdf Drawing 20180403_pga GC content plot... saved to /home/sam/quast_results/results_2018_08_23_07_38_28/basic_stats/20180403_pga_GC_content_plot.pdf Drawing 20180421_pga GC content plot... saved to /home/sam/quast_results/results_2018_08_23_07_38_28/basic_stats/20180421_pga_GC_content_plot.pdf Drawing 20180810_geo_manual GC content plot... saved to /home/sam/quast_results/results_2018_08_23_07_38_28/basic_stats/20180810_geo_manual_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2018-08-23 07:47:30 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 2018-08-23 07:49:06 RESULTS: Text versions of total report are saved to /home/sam/quast_results/results_2018_08_23_07_38_28/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/sam/quast_results/results_2018_08_23_07_38_28/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /home/sam/quast_results/results_2018_08_23_07_38_28/report.html PDF version (tables and plots) is saved to /home/sam/quast_results/results_2018_08_23_07_38_28/report.pdf Icarus (contig browser) is saved to /home/sam/quast_results/results_2018_08_23_07_38_28/icarus.html Log saved to /home/sam/quast_results/results_2018_08_23_07_38_28/quast.log Finished: 2018-08-23 07:49:07 Elapsed time: 0:10:39.353635 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!