Aligning contigs to reference... Aligning contigs to the reference Filtering alignments... Parsing coords... Loading reference... Loaded [meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa] Total Regions: 1 Total Region Length: 64999 Analyzing contigs... CONTIG: NODE_3_length_27260_cov_310.524_ID_9332986 (27260bp) Best alignment score: 27257.3 (LEN: 27260, IDY: 99.99), Total number of alignments: 1 One align captures most of this contig: 7597 34856 | 1 27260 | 27260 27260 | 99.99 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_3_length_27260_cov_310.524_ID_9332986 CONTIG: NODE_4_length_16099_cov_310.325_ID_9343456 (16099bp) Best alignment score: 16099.0 (LEN: 16099, IDY: 100.00), Total number of alignments: 1 One align captures most of this contig: 36665 52763 | 1 16099 | 16099 16099 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_4_length_16099_cov_310.325_ID_9343456 CONTIG: NODE_5_length_10428_cov_300.989_ID_9343584 (10428bp) Best alignment score: 10428.0 (LEN: 10428, IDY: 100.00), Total number of alignments: 1 One align captures most of this contig: 54572 64999 | 1 10428 | 10428 10428 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_5_length_10428_cov_300.989_ID_9343584 CONTIG: NODE_6_length_6988_cov_303.415_ID_9341226 (6988bp) Best alignment score: 6985.9 (LEN: 6988, IDY: 99.97), Total number of alignments: 1 One align captures most of this contig: 25 7012 | 1 6988 | 6988 6988 | 99.97 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_6_length_6988_cov_303.415_ID_9341226 CONTIG: NODE_8_length_817_cov_651.256_ID_9343784 (817bp) Best alignment score: 813.0 (LEN: 817, IDY: 99.51), Total number of alignments: 2 This contig has 2 significant alignments. [An ambiguously mapped contig] Using only first of these alignment (option --ambiguity-usage is set to "one"): Alignment: 52709 53525 | 1 817 | 817 817 | 99.51 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_8_length_817_cov_651.256_ID_9343784 Skipping alignment 34802 35618 | 1 817 | 817 817 | 98.65 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_8_length_817_cov_651.256_ID_9343784 CONTIG: NODE_9_length_729_cov_671.122_ID_9343806 (729bp) Best alignment score: 729.0 (LEN: 729, IDY: 100.00), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 53899 54626 | 728 1 | 728 728 | 98.9 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_9_length_729_cov_671.122_ID_9343806 One align captures most of this contig: 35991 36719 | 729 1 | 729 729 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_9_length_729_cov_671.122_ID_9343806 CONTIG: NODE_11_length_694_cov_336.263_ID_9343406 (694bp) Best alignment score: 693.0 (LEN: 694, IDY: 99.86), Total number of alignments: 1 One align captures most of this contig: 6958 7651 | 1 694 | 694 694 | 99.86 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_11_length_694_cov_336.263_ID_9343406 CONTIG: NODE_29_length_219_cov_25.5122_ID_8985538 (763bp) Best alignment score: 204.0 (LEN: 208, IDY: 98.08), Total number of alignments: 4 Looking for the best set of alignments (out of 4 total alignments) The best set is below. Score: 532.9, number of alignments: 4, unaligned bases: 37 This contig is misassembled. Real Alignment 1: 7777 7983 | 1 207 | 207 207 | 90.82 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_29_length_219_cov_25.5122_ID_8985538 Extensive misassembly (relocation, inconsistency = 13950) between these two alignments Real Alignment 2: 21946 22153 | 427 220 | 208 208 | 98.08 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_29_length_219_cov_25.5122_ID_8985538 Extensive misassembly (relocation, inconsistency = 14984) between these two alignments Real Alignment 3: 6775 6961 | 428 610 | 187 183 | 91.44 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_29_length_219_cov_25.5122_ID_8985538 Extensive misassembly (relocation, inconsistency = -1863) between these two alignments Real Alignment 4: 5124 5251 | 636 763 | 128 128 | 96.88 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_29_length_219_cov_25.5122_ID_8985538 Analyzing coverage... Writing SNPs into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/minimap_output/meta_contigs_2.used_snps Analysis is finished! Founded SNPs were written into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/minimap_output/meta_contigs_2.used_snps Results: Local Misassemblies: 0 Misassemblies: 3 Relocations: 3 Translocations: 0 Inversions: 0 Scaffold gap extensive misassemblies: 0 Scaffold gap local misassemblies: 0 Misassembled Contigs: 1 Misassembled Contig Bases: 763 Misassemblies Inter-Contig Overlap ("Extra" Aligned Bases): 0 Unaligned Contigs: 0 + 0 part Half Unaligned Contigs with Misassemblies: 0 Unaligned Bases in Fully and Partially Unaligned Contigs: 0 Ambiguously Mapped Contigs: 1 Total Bases in Ambiguously Mapped Contigs: 817 "Extra" Aligned Bases in Ambiguously Mapped Contigs: 0 Note that --allow-ambiguity option was set to "one" and only first alignment per each of these contigs was used (there is no "extra" aligned bases). Covered Bases in Reference: 62795 Raw Aligned Bases in Assembly: 63741 Total Aligned Bases in Assembly (with "Extras"): 63741 SNPs: 42 Insertions: 6 Deletions: 10