/home/sam/programs/quast-5.0.2/quast.py --threads=20 --min-contig=100 --labels=ets,sjw /home/sam/data/metagenomics/P_generosa/emma_assemblies/contigs.fa /home/sam/data/metagenomics/P_generosa/final.contigs.fa Version: 5.0.2 System information: OS: Linux-4.4.0-145-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64) Python version: 2.7.12 CPUs number: 24 Started: 2019-04-08 09:47:17 Logging to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/quast.log CWD: /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison 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 /home/sam/data/metagenomics/P_generosa/emma_assemblies/contigs.fa ==> ets 2 /home/sam/data/metagenomics/P_generosa/final.contigs.fa ==> sjw 2019-04-08 09:49:54 Running Basic statistics processor... Contig files: 1 ets 2 sjw Calculating N50 and L50... 1 ets, N50 = 566, L50 = 230075, Total length = 412748178, GC % = 44.29, # N's per 100 kbp = 0.00 2 sjw, N50 = 1413, L50 = 308641, Total length = 2243059881, GC % = 39.32, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/basic_stats/GC_content_plot.pdf Drawing ets GC content plot... saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/basic_stats/ets_GC_content_plot.pdf Drawing sjw GC content plot... saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/basic_stats/sjw_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2019-04-08 09:52:47 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 2019-04-08 09:54:03 RESULTS: Text versions of total report are saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/report.html PDF version (tables and plots) is saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/report.pdf Icarus (contig browser) is saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/icarus.html Log is saved to /home/sam/analyses/20190408_metagenomics_pgen_quast_comparison/quast_results/results_2019_04_08_09_47_17/quast.log Finished: 2019-04-08 09:54:03 Elapsed time: 0:06:45.649379 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!