/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_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta -R /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_corrected_input/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 -o /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02 --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 15:31:44 Logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 ==> Flavobacterium_sp._SCGC_AAA160_P02 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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.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_Flavobacterium_sp._SCGC_AAA160_P02.fasta ==> MG7_sjw 2019-04-03 15:31:46 Running Basic statistics processor... Reference genome: Flavobacterium_sp._SCGC_AAA160_P02.fasta__1, length = 2544614, num fragments = 80, GC % = 31.79 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 = 743, L50 = 1103, Total length = 2503583, GC % = 32.80, # N's per 100 kbp = 0.00 2 MG1_sjw, N50 = 4593, L50 = 223, Total length = 5600353, GC % = 32.40, # N's per 100 kbp = 0.00 3 MG2_ets, N50 = 646, L50 = 1172, Total length = 2237516, GC % = 33.09, # N's per 100 kbp = 0.00 4 MG2_sjw, N50 = 5117, L50 = 166, Total length = 4280858, GC % = 31.78, # N's per 100 kbp = 0.00 5 MG3_ets, N50 = 708, L50 = 1119, Total length = 2377305, GC % = 32.99, # N's per 100 kbp = 0.00 6 MG3_sjw, N50 = 8739, L50 = 108, Total length = 5056949, GC % = 32.34, # N's per 100 kbp = 0.00 7 MG5_ets, N50 = 510, L50 = 906, Total length = 1331382, GC % = 32.96, # N's per 100 kbp = 0.00 8 MG5_sjw, N50 = 3014, L50 = 128, Total length = 3602542, GC % = 33.11, # N's per 100 kbp = 0.00 9 MG6_ets, N50 = 653, L50 = 1234, Total length = 2424450, GC % = 33.21, # N's per 100 kbp = 0.00 10 MG6_sjw, N50 = 4063, L50 = 226, Total length = 4561220, GC % = 32.15, # N's per 100 kbp = 0.00 11 MG7_ets, N50 = 588, L50 = 1232, Total length = 2055500, GC % = 32.87, # N's per 100 kbp = 0.00 12 MG7_sjw, N50 = 4497, L50 = 212, Total length = 4147737, GC % = 32.34, # 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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/basic_stats/MG7_sjw_GC_content_plot.pdf Done. 2019-04-03 15:31:58 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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG1_sjw.stdout and contigs_report_MG1_sjw.stderr... 2 Aligning contigs to the reference 3 MG2_ets 3 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG2_ets.stdout and contigs_report_MG2_ets.stderr... 3 Aligning contigs to the reference 4 MG2_sjw 4 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG2_sjw.stdout and contigs_report_MG2_sjw.stderr... 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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG3_sjw.stdout and contigs_report_MG3_sjw.stderr... 6 Aligning contigs to the reference 7 MG5_ets 7 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG5_sjw.stdout and contigs_report_MG5_sjw.stderr... 8 Aligning contigs to the reference 10 MG6_sjw 10 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG6_sjw.stdout and contigs_report_MG6_sjw.stderr... 10 Aligning contigs to the reference 11 MG7_ets 11 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG7_ets.stdout and contigs_report_MG7_ets.stderr... 11 Aligning contigs to the reference 12 MG7_sjw 12 Logging to files /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG7_sjw.stdout and contigs_report_MG7_sjw.stderr... 12 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/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG6_ets.stdout and contigs_report_MG6_ets.stderr... 9 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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG1_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG1_sjw.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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG2_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG2_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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG3_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG3_sjw.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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG1_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG1_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG1_ets.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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG3_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG3_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG3_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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG6_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG6_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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG2_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG2_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG5_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG5_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG5_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG5_ets.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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG6_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG6_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_ets_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG7_ets.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG7_ets.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/Flavobacterium_sp._SCGC_AAA160_P02.fasta__1 \ quast_results/results_2019_04_03_08_23_17/quast_corrected_input/MG7_sjw_to_Flavobacterium_sp._SCGC_AAA160_P02.fasta \ > quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/minimap_output/MG7_sjw.coords_tmp \ 2>> quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/contigs_report_MG7_sjw.stderr 7 Analysis is finished. 9 Analysis is finished. 5 Analysis is finished. 12 Analysis is finished. 11 Analysis is finished. 6 Analysis is finished. 8 Analysis is finished. 3 Analysis is finished. 4 Analysis is finished. 1 Analysis is finished. 2 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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/contigs_reports/misassemblies_frcurve_plot.pdf Done. 2019-04-03 15:32:19 Running NA-NGA calculation... 1 MG1_ets, Largest alignment = 3633, NA50 = 595, NGA50 = 584, LA50 = 1289, LGA50 = 1323 2 MG1_sjw, Largest alignment = 18818, NA50 = 401, NGA50 = 3340, LA50 = 1690, LGA50 = 218 3 MG2_ets, Largest alignment = 2819, NA50 = 526, NGA50 = 471, LA50 = 1362, LGA50 = 1671 4 MG2_sjw, Largest alignment = 33804, NA50 = 883, NGA50 = 3579, LA50 = 666, LGA50 = 197 5 MG3_ets, Largest alignment = 2929, NA50 = 584, NGA50 = 546, LA50 = 1293, LGA50 = 1441 6 MG3_sjw, Largest alignment = 31861, NA50 = 395, NGA50 = 5547, LA50 = 1097, LGA50 = 133 7 MG5_ets, Largest alignment = 2087, NA50 = 439, LA50 = 1034 8 MG5_sjw, Largest alignment = 5815, NA50 = 355, NGA50 = 960, LA50 = 1582, LGA50 = 706 9 MG6_ets, Largest alignment = 3286, NA50 = 532, NGA50 = 510, LA50 = 1446, LGA50 = 1562 10 MG6_sjw, Largest alignment = 18545, NA50 = 902, NGA50 = 3709, LA50 = 739, LGA50 = 189 11 MG7_ets, Largest alignment = 2377, NA50 = 498, NGA50 = 419, LA50 = 1373, LGA50 = 1908 12 MG7_sjw, Largest alignment = 33492, NA50 = 1246, NGA50 = 3943, LA50 = 545, LGA50 = 184 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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/aligned_stats/NGAx_plot.pdf Done. 2019-04-03 15:32:21 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 11 Analysis is finished. 3 Analysis is finished. 8 Analysis is finished. 5 Analysis is finished. 1 Analysis is finished. 6 Analysis is finished. 7 Analysis is finished. 9 Analysis is finished. 2 Analysis is finished. 12 Analysis is finished. 4 Analysis is finished. 10 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/Flavobacterium_sp._SCGC_AAA160_P02/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 15:32:23 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 15:32:35 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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/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/Flavobacterium_sp._SCGC_AAA160_P02/icarus.html