/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 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta -R /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 -o /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03 --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 15:34:03 Logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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 Reference: /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 ==> alpha_proteobacterium_SCGC_AAA076_C03 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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.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_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta ==> MG7_sjw 2019-04-03 15:34:04 Running Basic statistics processor... Reference genome: alpha_proteobacterium_SCGC_AAA076_C03.fasta__1, length = 1967776, num fragments = 46, GC % = 36.69 WARNING: Reference genome is fragmented. You may consider rerunning QUAST using --fragmented option. QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from # misassemblies). 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 = 1045, L50 = 507, Total length = 1918817, GC % = 37.02, # N's per 100 kbp = 0.00 2 MG1_sjw, N50 = 2219, L50 = 280, Total length = 2927725, GC % = 37.38, # N's per 100 kbp = 0.00 3 MG2_ets, N50 = 789, L50 = 650, Total length = 1608131, GC % = 37.43, # N's per 100 kbp = 0.00 4 MG2_sjw, N50 = 3448, L50 = 142, Total length = 2451480, GC % = 38.14, # N's per 100 kbp = 0.00 5 MG3_ets, N50 = 819, L50 = 607, Total length = 1541528, GC % = 37.40, # N's per 100 kbp = 0.00 6 MG3_sjw, N50 = 9999, L50 = 34, Total length = 2521786, GC % = 42.49, # N's per 100 kbp = 0.00 7 MG5_ets, N50 = 729, L50 = 629, Total length = 1395509, GC % = 37.36, # N's per 100 kbp = 0.00 8 MG5_sjw, N50 = 7172, L50 = 57, Total length = 1806777, GC % = 38.25, # N's per 100 kbp = 0.00 9 MG6_ets, N50 = 935, L50 = 601, Total length = 1939046, GC % = 37.15, # N's per 100 kbp = 0.00 10 MG6_sjw, N50 = 1880, L50 = 381, Total length = 3207999, GC % = 37.41, # N's per 100 kbp = 0.00 11 MG7_ets, N50 = 825, L50 = 615, Total length = 1665161, GC % = 37.17, # N's per 100 kbp = 0.00 12 MG7_sjw, N50 = 2243, L50 = 258, Total length = 2731850, GC % = 37.34, # 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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/basic_stats/Nx_plot.pdf Drawing NGx plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/basic_stats/NGx_plot.pdf Drawing cumulative plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/basic_stats/MG7_sjw_GC_content_plot.pdf Done. 2019-04-03 15:34:10 Running Contig analyzer... 1 MG1_ets 1 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG1_ets.stdout and contigs_report_MG1_ets.stderr... 1 Aligning contigs to the reference 2 MG1_sjw 2 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG1_sjw.stdout and contigs_report_MG1_sjw.stderr... 3 MG2_ets 2 Aligning contigs to the reference 4 MG2_sjw 3 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG2_ets.stdout and contigs_report_MG2_ets.stderr... 4 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG2_sjw.stdout and contigs_report_MG2_sjw.stderr... 3 Aligning contigs to the reference 4 Aligning contigs to the reference 5 MG3_ets 5 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG3_ets.stdout and contigs_report_MG3_ets.stderr... 6 MG3_sjw 5 Aligning contigs to the reference 6 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG3_sjw.stdout and contigs_report_MG3_sjw.stderr... 7 MG5_ets 6 Aligning contigs to the reference 7 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG5_ets.stdout and contigs_report_MG5_ets.stderr... 7 Aligning contigs to the reference 8 MG5_sjw 8 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG5_sjw.stdout and contigs_report_MG5_sjw.stderr... 8 Aligning contigs to the reference 9 MG6_ets 9 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG6_ets.stdout and contigs_report_MG6_ets.stderr... 10 MG6_sjw 9 Aligning contigs to the reference 10 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG6_sjw.stdout and contigs_report_MG6_sjw.stderr... 10 Aligning contigs to the reference 11 MG7_ets 12 MG7_sjw 11 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG7_ets.stdout and contigs_report_MG7_ets.stderr... 12 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG7_sjw.stdout and contigs_report_MG7_sjw.stderr... 12 Aligning contigs to the reference 11 Aligning contigs to the reference 2 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG1_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG1_sjw.stderr 12 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG7_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG7_sjw.stderr 6 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG3_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG3_sjw.stderr 5 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG3_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG3_ets.stderr 1 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG1_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG1_ets.stderr 3 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG2_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG2_ets.stderr 8 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG5_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG5_sjw.stderr 7 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG5_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG5_ets.stderr 4 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG2_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG2_sjw.stderr 10 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_sjw_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG6_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG6_sjw.stderr 11 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG7_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG7_ets.stderr 9 /home/sam/programs/quast-5.0.2/quast_libs/minimap2/minimap2 -c -x asm5 -B5 -O4,16 \ --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 \ --score-N 2 --cs -t 1 quast_results/results_2019_04_03_08_23_17/quast_corrected_input/alpha_proteobacterium_SCGC_AAA076_C03.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_ets_to_alpha_proteobacterium_SCGC_AAA076_C03.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/minimap_output/MG6_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/contigs_report_MG6_ets.stderr 3 Analysis is finished. 1 Analysis is finished. 9 Analysis is finished. 6 Analysis is finished. 4 Analysis is finished. 8 Analysis is finished. 7 Analysis is finished. 11 Analysis is finished. 5 Analysis is finished. 2 Analysis is finished. 12 Analysis is finished. 10 Analysis is finished. Creating total report... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Drawing misassemblies by types plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/contigs_reports/misassemblies_frcurve_plot.pdf Done. 2019-04-03 15:34:30 Running NA-NGA calculation... 1 MG1_ets, Largest alignment = 7851, NA50 = 965, NGA50 = 948, LA50 = 534, LGA50 = 559 2 MG1_sjw, Largest alignment = 21617, NA50 = 1330, NGA50 = 2646, LA50 = 444, LGA50 = 187 3 MG2_ets, Largest alignment = 4290, NA50 = 717, NGA50 = 579, LA50 = 691, LGA50 = 969 4 MG2_sjw, Largest alignment = 25499, NA50 = 1823, NGA50 = 2923, LA50 = 269, LGA50 = 165 5 MG3_ets, Largest alignment = 4025, NA50 = 759, NGA50 = 600, LA50 = 643, LGA50 = 959 6 MG3_sjw, Largest alignment = 37889, NA50 = 1586, NGA50 = 3828, LA50 = 225, LGA50 = 109 7 MG5_ets, Largest alignment = 3373, NA50 = 665, NGA50 = 458, LA50 = 671, LGA50 = 1186 8 MG5_sjw, Largest alignment = 41962, NA50 = 3470, NGA50 = 2732, LA50 = 113, LGA50 = 140 9 MG6_ets, Largest alignment = 7657, NA50 = 855, NGA50 = 840, LA50 = 634, LGA50 = 651 10 MG6_sjw, Largest alignment = 27640, NA50 = 999, NGA50 = 2251, LA50 = 658, LGA50 = 241 11 MG7_ets, Largest alignment = 4881, NA50 = 762, NGA50 = 634, LA50 = 643, LGA50 = 860 12 MG7_sjw, Largest alignment = 22331, NA50 = 1493, NGA50 = 2597, LA50 = 378, LGA50 = 181 Drawing cumulative plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/aligned_stats/cumulative_plot.pdf Drawing NAx plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/aligned_stats/NAx_plot.pdf Drawing NGAx plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/aligned_stats/NGAx_plot.pdf Done. 2019-04-03 15:34:31 Running Genome analyzer... NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it. NOTICE: No file with operons were provided. Use the -O option if you want to specify it. 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 7 Analysis is finished. 3 Analysis is finished. 8 Analysis is finished. 1 Analysis is finished. 6 Analysis is finished. 5 Analysis is finished. 11 Analysis is finished. 4 Analysis is finished. 9 Analysis is finished. 2 Analysis is finished. 10 Analysis is finished. 12 Analysis is finished. Drawing Genome fraction, % histogram... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/genome_stats/genome_fraction_histogram.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2019-04-03 15:34:33 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 15:34:43 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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/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/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/icarus.html