/home/sam/programs/quast-5.0.2/quast.py --threads=20 --min-contig=100 --labels=MG1_ets,MG1_sjw,MG2_ets,MG2_sjw,MG3_ets,MG3_sjw,MG5_ets,MG5_sjw,MG6_ets,MG6_sjw,MG7_ets,MG7_sjw --colors #E31A1C,#1F78B4,#33A02C,#6A3D9A,#FF7F00,#800000,#A6CEE3,#B2DF8A,#333300,#CCCC00,#000080,#008080 --ls solid,solid,solid,solid,solid,solid,solid,solid,solid,solid,solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 -t 20 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_ets_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_sjw_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_ets_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_sjw_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_ets_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_sjw_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_ets_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_sjw_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_ets_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_sjw_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_ets_not_aligned_anywhere.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_sjw_not_aligned_anywhere.fasta -o /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned --labels "MG1_ets, MG1_sjw, MG2_ets, MG2_sjw, MG3_ets, MG3_sjw, MG5_ets, MG5_sjw, MG6_ets, MG6_sjw, MG7_ets, MG7_sjw" Started: 2019-04-03 15:35:22 Logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/quast.log CWD: /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons Main parameters: MODE: meta, threads: 20, minimum contig length: 100, minimum alignment length: 65, \ ambiguity: one, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... 1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_ets_not_aligned_anywhere.fasta ==> MG1_ets 2 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_sjw_not_aligned_anywhere.fasta ==> MG1_sjw 3 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_ets_not_aligned_anywhere.fasta ==> MG2_ets 4 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_sjw_not_aligned_anywhere.fasta ==> MG2_sjw 5 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_ets_not_aligned_anywhere.fasta ==> MG3_ets 6 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_sjw_not_aligned_anywhere.fasta ==> MG3_sjw 7 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_ets_not_aligned_anywhere.fasta ==> MG5_ets 8 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_sjw_not_aligned_anywhere.fasta ==> MG5_sjw 9 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_ets_not_aligned_anywhere.fasta ==> MG6_ets 10 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_sjw_not_aligned_anywhere.fasta ==> MG6_sjw 11 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_ets_not_aligned_anywhere.fasta ==> MG7_ets 12 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_sjw_not_aligned_anywhere.fasta ==> MG7_sjw 2019-04-03 15:36:05 Running Basic statistics processor... Contig files: 1 MG1_ets 2 MG1_sjw 3 MG2_ets 4 MG2_sjw 5 MG3_ets 6 MG3_sjw 7 MG5_ets 8 MG5_sjw 9 MG6_ets 10 MG6_sjw 11 MG7_ets 12 MG7_sjw Calculating N50 and L50... 1 MG1_ets, N50 = 580, L50 = 218020, Total length = 407691529, GC % = 44.32, # N's per 100 kbp = 0.00 2 MG1_sjw, N50 = 1160, L50 = 102914, Total length = 637666173, GC % = 42.53, # N's per 100 kbp = 0.00 3 MG2_ets, N50 = 547, L50 = 185251, Total length = 338437560, GC % = 40.75, # N's per 100 kbp = 0.00 4 MG2_sjw, N50 = 921, L50 = 116475, Total length = 562804992, GC % = 39.51, # N's per 100 kbp = 0.00 5 MG3_ets, N50 = 498, L50 = 326988, Total length = 494597962, GC % = 38.49, # N's per 100 kbp = 0.00 6 MG3_sjw, N50 = 1313, L50 = 131507, Total length = 773248418, GC % = 37.28, # N's per 100 kbp = 0.00 7 MG5_ets, N50 = 579, L50 = 132237, Total length = 262161598, GC % = 37.96, # N's per 100 kbp = 0.00 8 MG5_sjw, N50 = 1123, L50 = 63835, Total length = 420250861, GC % = 36.35, # N's per 100 kbp = 0.00 9 MG6_ets, N50 = 564, L50 = 161661, Total length = 298134597, GC % = 40.20, # N's per 100 kbp = 0.00 10 MG6_sjw, N50 = 1142, L50 = 73451, Total length = 477200330, GC % = 38.50, # N's per 100 kbp = 0.00 11 MG7_ets, N50 = 525, L50 = 187326, Total length = 312136624, GC % = 39.74, # N's per 100 kbp = 0.00 12 MG7_sjw, N50 = 1044, L50 = 101880, Total length = 574333428, GC % = 38.19, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/GC_content_plot.pdf Drawing MG1_ets GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG1_ets_GC_content_plot.pdf Drawing MG1_sjw GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG1_sjw_GC_content_plot.pdf Drawing MG2_ets GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG2_ets_GC_content_plot.pdf Drawing MG2_sjw GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG2_sjw_GC_content_plot.pdf Drawing MG3_ets GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG3_ets_GC_content_plot.pdf Drawing MG3_sjw GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG3_sjw_GC_content_plot.pdf Drawing MG5_ets GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG5_ets_GC_content_plot.pdf Drawing MG5_sjw GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG5_sjw_GC_content_plot.pdf Drawing MG6_ets GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG6_ets_GC_content_plot.pdf Drawing MG6_sjw GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG6_sjw_GC_content_plot.pdf Drawing MG7_ets GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG7_ets_GC_content_plot.pdf Drawing MG7_sjw GC content plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/basic_stats/MG7_sjw_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2019-04-03 15:43:27 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 2019-04-03 15:46:02 RESULTS: Text versions of total report are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/report.html PDF version (tables and plots) is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/report.pdf Icarus (contig browser) is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/icarus.html