Aligning contigs to reference... Aligning contigs to the reference Filtering alignments... Parsing coords... Loading reference... Loaded [meta_ref_1_Lactobacillus_plantarum_22_55k.fa] Loaded [meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa] Loaded [meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa] Total Regions: 3 Total Region Length: 179997 Analyzing contigs... CONTIG: contigs_not_from_here (1120bp) This contig is unaligned. (1120 bp) Unaligned bases: 1120 (number of Ns: 0) CONTIG: another_contig_not_from_here (1610bp) This contig is unaligned. (1610 bp) Unaligned bases: 1610 (number of Ns: 0) CONTIG: NODE_6_length_49658_cov_2.58581 (48458bp) Best alignment score: 37170.6 (LEN: 37178, IDY: 99.98), Total number of alignments: 2 Looking for the best set of alignments (out of 2 total alignments) The best set is below. Score: 48197.2, number of alignments: 2, unaligned bases: 0 This contig is misassembled. Real Alignment 1: 43683 54962 | 11280 1 | 11280 11280 | 99.97 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_6_length_49658_cov_2.58581 Extensive misassembly (relocation, inconsistency = 1200) between these two alignments Real Alignment 2: 5305 42482 | 48458 11281 | 37178 37178 | 99.98 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_6_length_49658_cov_2.58581 CONTIG: NODE_8_length_182_cov_2.81102 (1152bp) Best alignment score: 638.0 (LEN: 638, IDY: 100.00), Total number of alignments: 5 Looking for the best set of alignments (out of 5 total alignments) Skipping redundant alignments after choosing the best set of alignments Skipping redundant alignment 3645 3826 | 182 1 | 182 182 | 100.0 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_8_length_182_cov_2.81102 Skipping redundant alignment 6775 6960 | 182 1 | 186 182 | 91.4 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_8_length_182_cov_2.81102 The best set is below. Score: 1020.1, number of alignments: 3, unaligned bases: 51 This contig is misassembled. Real Alignment 1: 3395 3573 | 182 5 | 179 178 | 91.62 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_8_length_182_cov_2.81102 Scaffold gap between these two alignments, gap lengths difference (reference vs assembly) = 1020 (extensive) Real Alignment 2: 1717 2354 | 840 203 | 638 638 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_8_length_182_cov_2.81102 Extensive misassembly (interspecies translocation) between these two alignments Real Alignment 3: 3112 3396 | 868 1152 | 285 285 | 99.65 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_8_length_182_cov_2.81102 CONTIG: NODE_15_length_55106_cov_26.0999 (55106bp) Best alignment score: 55106.0 (LEN: 55106, IDY: 100.00), Total number of alignments: 1 One align captures most of this contig: 4893 59998 | 1 55106 | 55106 55106 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_15_length_55106_cov_26.0999 CONTIG: NODE_18_length_714_cov_2.71927 (714bp) Best alignment score: 713.0 (LEN: 714, IDY: 99.86), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 1 123 | 251 373 | 123 123 | 99.19 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_18_length_714_cov_2.71927 One align captures most of this contig: 78 791 | 1 714 | 714 714 | 99.86 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_18_length_714_cov_2.71927 CONTIG: NODE_25_length_832_cov_317.008 (832bp) Best alignment score: 832.0 (LEN: 832, IDY: 100.00), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 3386 3573 | 195 5 | 188 191 | 92.19 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_25_length_832_cov_317.008 One align captures most of this contig: 6129 6960 | 832 1 | 832 832 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_25_length_832_cov_317.008 CONTIG: NODE_30_length_694_cov_43.795 (694bp) Best alignment score: 694.0 (LEN: 694, IDY: 100.00), Total number of alignments: 3 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 3824 4517 | 1 694 | 694 694 | 93.96 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_30_length_694_cov_43.795 Skipping alignment 3575 4268 | 1 694 | 694 694 | 93.63 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_30_length_694_cov_43.795 One align captures most of this contig: 6958 7651 | 1 694 | 694 694 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_30_length_694_cov_43.795 CONTIG: NODE_32_length_1057_cov_298.503 (1057bp) Best alignment score: 1056.0 (LEN: 1057, IDY: 99.91), Total number of alignments: 3 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 737 1793 | 1 1057 | 1057 1057 | 96.32 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_32_length_1057_cov_298.503 Skipping alignment 493 1544 | 6 1057 | 1052 1052 | 90.68 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_32_length_1057_cov_298.503 One align captures most of this contig: 3868 4924 | 1 1057 | 1057 1057 | 99.91 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_32_length_1057_cov_298.503 CONTIG: NODE_33_length_929_cov_25.7529 (929bp) Best alignment score: 929.0 (LEN: 929, IDY: 100.00), Total number of alignments: 1 One align captures most of this contig: 844 1772 | 1 929 | 929 929 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_33_length_929_cov_25.7529 CONTIG: NODE_34_length_3898_cov_294.65 (3898bp) Best alignment score: 3896.8 (LEN: 3898, IDY: 99.97), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 1 79 | 3349 3427 | 79 79 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_34_length_3898_cov_294.65 One align captures most of this contig: 25 3922 | 1 3898 | 3898 3898 | 99.97 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_34_length_3898_cov_294.65 CONTIG: NODE_35_length_850_cov_25.8629 (850bp) Best alignment score: 836.0 (LEN: 850, IDY: 98.35), Total number of alignments: 3 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 3654 4232 | 273 850 | 579 578 | 93.94 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_35_length_850_cov_25.8629 Skipping alignment 720 1101 | 469 850 | 382 382 | 97.64 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_35_length_850_cov_25.8629 One align captures most of this contig: 3 852 | 1 850 | 850 850 | 98.35 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_35_length_850_cov_25.8629 CONTIG: NODE_37_length_747_cov_199.488 (747bp) Best alignment score: 747.0 (LEN: 747, IDY: 100.00), Total number of alignments: 3 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 3824 4566 | 1 743 | 743 743 | 93.98 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_37_length_747_cov_199.488 Skipping alignment 3575 4287 | 1 713 | 713 713 | 93.27 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_37_length_747_cov_199.488 One align captures most of this contig: 6958 7704 | 1 747 | 747 747 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_37_length_747_cov_199.488 CONTIG: NODE_38_length_862_cov_88.5167 (862bp) Best alignment score: 843.0 (LEN: 862, IDY: 97.80), Total number of alignments: 3 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 3575 4436 | 1 862 | 862 862 | 94.77 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_38_length_862_cov_88.5167 Skipping alignment 3824 4685 | 1 862 | 862 862 | 93.52 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_38_length_862_cov_88.5167 One align captures most of this contig: 6958 7819 | 1 862 | 862 862 | 97.8 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_38_length_862_cov_88.5167 CONTIG: NODE_39_length_1141_cov_25.1602 (1141bp) Best alignment score: 1141.0 (LEN: 1141, IDY: 100.00), Total number of alignments: 1 One align captures most of this contig: 2300 3440 | 1 1141 | 1141 1141 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_39_length_1141_cov_25.1602 CONTIG: NODE_40_length_987_cov_309.523 (987bp) Best alignment score: 987.0 (LEN: 987, IDY: 100.00), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 2066 3036 | 1 972 | 971 972 | 91.21 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_40_length_987_cov_309.523 One align captures most of this contig: 5197 6183 | 1 987 | 987 987 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_40_length_987_cov_309.523 CONTIG: NODE_41_length_17535_cov_311.913 (17535bp) Best alignment score: 17530.5 (LEN: 17534, IDY: 99.98), Total number of alignments: 3 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 34802 35618 | 817 1 | 817 817 | 98.77 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_41_length_17535_cov_311.913 Skipping alignment 53899 54626 | 17534 16807 | 728 728 | 98.9 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_41_length_17535_cov_311.913 One align captures most of this contig: 35992 53525 | 17534 1 | 17534 17534 | 99.98 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_41_length_17535_cov_311.913 CONTIG: NODE_42_length_11102_cov_303.126 (11102bp) Best alignment score: 11093.2 (LEN: 11101, IDY: 99.93), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 35992 36719 | 2 729 | 728 728 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_42_length_11102_cov_303.126 One align captures most of this contig: 53899 64999 | 2 11102 | 11101 11101 | 99.93 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_42_length_11102_cov_303.126 CONTIG: NODE_43_length_3427_cov_1.72301 (3427bp) Best alignment score: 3426.0 (LEN: 3427, IDY: 99.97), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 1 79 | 3349 3427 | 79 79 | 100.0 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_43_length_3427_cov_1.72301 One align captures most of this contig: 25 3451 | 1 3427 | 3427 3427 | 99.97 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_43_length_3427_cov_1.72301 CONTIG: NODE_44_length_27969_cov_310.914 (27969bp) Best alignment score: 27957.8 (LEN: 27969, IDY: 99.96), Total number of alignments: 2 Skipping these alignments as insignificant (option --ambiguity-score is set to "0.99"): Skipping alignment 52709 53525 | 817 1 | 817 817 | 99.51 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_44_length_27969_cov_310.914 One align captures most of this contig: 7650 35618 | 27969 1 | 27969 27969 | 99.96 | meta_ref_3_Lactobacillus_reuteri_F275_Kitasato_55_65k.fa NODE_44_length_27969_cov_310.914 Analyzing coverage... Writing SNPs into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/minimap_output/meta_contigs_1.used_snps Analysis is finished! Founded SNPs were written into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/combined_reference/contigs_reports/minimap_output/meta_contigs_1.used_snps Results: Local Misassemblies: 0 Misassemblies: 2 Relocations: 1 Translocations: 0 Interspecies translocations: 1 Inversions: 0 Potentially Misassembled Contigs (i/s translocations): 0 Possible Misassemblies: 0 Scaffold gap extensive misassemblies: 1 Scaffold gap local misassemblies: 0 Misassembled Contigs: 2 Misassembled Contig Bases: 49610 Misassemblies Inter-Contig Overlap ("Extra" Aligned Bases): 0 Unaligned Contigs: 2 + 0 part Half Unaligned Contigs with Misassemblies: 0 Unaligned Bases in Fully and Partially Unaligned Contigs: 2730 Ambiguously Mapped Contigs: 0 Total Bases in Ambiguously Mapped Contigs: 0 "Extra" Aligned Bases in Ambiguously Mapped Contigs: 0 Note that --allow-ambiguity option was set to "all" and each of these contigs was used several times (there are "extra" aligned bases). Covered Bases in Reference: 172091 Raw Aligned Bases in Assembly: 177407 Total Aligned Bases in Assembly (with "Extras"): 177407 SNPs: 79 Insertions: 3 Deletions: 4