/home/sam/programs/quast-5.0.2/quast.py --threads=20 --min-contig=100 --labels=redundans_sb_01,redundans_sb_02,redundans_sjw_01,redundans_sjw_02,redundans_sjw_03,soap_bgi_01,pbjelly_sjw_01 /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa /mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa /mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa /mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa /mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta Version: 5.0.2 System information: OS: Linux-4.4.0-210-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64) Python version: 2.7.12 CPUs number: 24 Started: 2021-05-21 09:36:34 Logging to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/quast.log CWD: /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons Main parameters: MODE: default, threads: 20, minimum contig length: 100, minimum alignment length: 65, \ ambiguity: one, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... 1 /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa ==> redundans_sb_01 2 /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa ==> redundans_sb_02 3 /mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa ==> redundans_sjw_01 4 /mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa ==> redundans_sjw_02 5 /mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa ==> redundans_sjw_03 6 /mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa ==> soap_bgi_01 7 /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta ==> pbjelly_sjw_01 2021-05-21 09:39:20 Running Basic statistics processor... Contig files: 1 redundans_sb_01 2 redundans_sb_02 3 redundans_sjw_01 4 redundans_sjw_02 5 redundans_sjw_03 6 soap_bgi_01 7 pbjelly_sjw_01 Calculating N50 and L50... 1 redundans_sb_01, N50 = 251, L50 = 1513, Total length = 968128, GC % = 34.28, # N's per 100 kbp = 3121.49 2 redundans_sb_02, N50 = 3852, L50 = 36149, Total length = 546928670, GC % = 35.91, # N's per 100 kbp = 957.75 3 redundans_sjw_01, N50 = 16546, L50 = 453, Total length = 29303793, GC % = 36.39, # N's per 100 kbp = 917.67 4 redundans_sjw_02, N50 = 17679, L50 = 573, Total length = 40561504, GC % = 36.46, # N's per 100 kbp = 695.24 5 redundans_sjw_03, N50 = 16998, L50 = 1724, Total length = 111139362, GC % = 36.34, # N's per 100 kbp = 626.41 6 soap_bgi_01, N50 = 3635, L50 = 54072, Total length = 776306190, GC % = 35.82, # N's per 100 kbp = 17634.69 7 pbjelly_sjw_01, N50 = 11531, L50 = 29266, Total length = 1252987201, GC % = 36.51, # N's per 100 kbp = 6456.30 Drawing Nx plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/GC_content_plot.pdf Drawing redundans_sb_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/redundans_sb_01_GC_content_plot.pdf Drawing redundans_sb_02 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/redundans_sb_02_GC_content_plot.pdf Drawing redundans_sjw_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/redundans_sjw_01_GC_content_plot.pdf Drawing redundans_sjw_02 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/redundans_sjw_02_GC_content_plot.pdf Drawing redundans_sjw_03 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/redundans_sjw_03_GC_content_plot.pdf Drawing soap_bgi_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/soap_bgi_01_GC_content_plot.pdf Drawing pbjelly_sjw_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/basic_stats/pbjelly_sjw_01_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2021-05-21 09:42:26 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 2021-05-21 09:43:34 RESULTS: Text versions of total report are saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/report.html PDF version (tables and plots) is saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/report.pdf Icarus (contig browser) is saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/icarus.html Log is saved to /home/sam/analyses/20210521_olur_quast_scaffold_assembly-comparisons/quast_results/results_2021_05_21_09_36_33/quast.log Finished: 2021-05-21 09:43:34 Elapsed time: 0:07:00.318177 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!