Open palomo11 opened 6 years ago
ursky
commented
6 years ago Well that's not good. Can you give me the lengths of those contigs? The algorithms places weight on each classification based on the length of the contig. So maybe the majority of the length of the bin was classified as Rhodobacteraceae?
palomo11
commented
6 years ago Here is the length of each of those contigs:
RSF33_CG26_100 | 10170
RSF33_CG26_104 | 382479
RSF33_CG26_105 | 75622
RSF33_CG26_106 | 102118
RSF33_CG26_107 | 263163
RSF33_CG26_108 | 63391
RSF33_CG26_109 | 119540
RSF33_CG26_110 | 1685748
RSF33_CG26_111 | 3749
RSF33_CG26_12 | 3424
RSF33_CG26_13 | 1675
RSF33_CG26_17 | 1304
RSF33_CG26_18 | 2397
RSF33_CG26_19 | 6311
RSF33_CG26_21 | 4601
RSF33_CG26_22 | 8056
RSF33_CG26_24 | 1570
RSF33_CG26_28 | 1716
RSF33_CG26_3 | 2962
RSF33_CG26_30 | 9526
RSF33_CG26_33 | 5056
RSF33_CG26_34 | 3417
RSF33_CG26_36 | 2566
RSF33_CG26_37 | 2380
RSF33_CG26_4 | 4326
RSF33_CG26_44 | 3332
RSF33_CG26_45 | 4457
RSF33_CG26_47 | 2519
RSF33_CG26_51 | 2360
RSF33_CG26_53 | 11798
RSF33_CG26_57 | 1482
RSF33_CG26_58 | 2966
RSF33_CG26_59 | 18965
RSF33_CG26_6 | 2243
RSF33_CG26_60 | 2940
RSF33_CG26_61 | 8900
RSF33_CG26_64 | 3828
RSF33_CG26_7 | 8263
RSF33_CG26_72 | 3002
RSF33_CG26_73 | 4783
RSF33_CG26_74 | 3256
RSF33_CG26_75 | 4647
RSF33_CG26_78 | 1545
RSF33_CG26_8 | 2946
RSF33_CG26_83 | 2395
RSF33_CG26_84 | 18201
RSF33_CG26_86 | 1568
RSF33_CG26_87 | 2055
RSF33_CG26_89 | 6728
RSF33_CG26_9 | 1596
RSF33_CG26_90 | 2116
RSF33_CG26_91 | 1602
RSF33_CG26_94 | 1521
RSF33_CG26_95 | 1841
RSF33_CG26_97 | 4154
RSF33_CG26_99 | 4136But any of the contigs of that bin seems to be clasiffied as Rhodobacteraceae
ursky
commented
6 years ago I didn’t catch that. That’s definitely a big, but I can’t figure out how that happens just by eyeballing my code. Can you upload the whole contig taxonomy file and the bin membership of the contigs (any format) so I can try to replicate this?
ursky
commented
6 years ago Actually, hold off. I think I see the issue.
ursky
commented
6 years ago So I was able to find one issue, but I don't believe it could lead to such a grievous error. I am attaching a modified diagnostic script that will output more details about what is going on. You dont have to repeat the analysis. Just run python classify_bins_diagnostic.py contig_taxonomy.tab RSF33_CG26.fa, the contig_taxonomy.tab being the file in the metawrap output, and the second being the problematic bin in fasta format. It will try to classify the bin again, but also print its "thought process". Please report back what it says...
classify_bins_diagnostic.py.gz
palomo11
commented
6 years ago This is the output:
python classify_bins_diagnostic.py contig_taxonomy.tab RSF33_CG26.fa
RSF33_CG26_3 2962 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_6 2243 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_7 8263 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_8 2946 Bacteria;Proteobacteria;Gammaproteobacteria;Methylococcales;Methylococcaceae
RSF33_CG26_9 1596 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_12 3424 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_13 1675 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_17 1304 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Rickettsiaceae
RSF33_CG26_18 2397 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_21 4601 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_22 8056 Bacteria
RSF33_CG26_24 1570 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_28 1716 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_30 9526 Bacteria;Proteobacteria;Betaproteobacteria
RSF33_CG26_33 5056 Bacteria;Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae
RSF33_CG26_34 3417 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_36 2566 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_37 2380 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_44 3332 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_45 4457 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_47 2519 Bacteria;Proteobacteria
RSF33_CG26_51 2360 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_53 11798 Bacteria;Proteobacteria
RSF33_CG26_57 1482 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_58 2966 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_59 18965 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF33_CG26_60 2940 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_61 8900 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_74 3256 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_78 1545 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF33_CG26_83 2395 Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae
RSF33_CG26_86 1568 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_87 2055 Bacteria
RSF33_CG26_89 6728 Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Pseudoalteromonadaceae
RSF33_CG26_90 2116 Bacteria;Proteobacteria;Gammaproteobacteria;Methylococcales;Methylococcaceae;Methylomonas
RSF33_CG26_91 1602 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_94 1521 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas;Nitrosomonas sp. Is79A3
RSF33_CG26_95 1841 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_97 4154 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_99 4136 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae
RSF33_CG26_100 10170 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_105 75622 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_106 102118 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_107 263163 Bacteria
RSF33_CG26_109 119540 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_110 1685748 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF33_CG26_111 3749 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae
{'Bacteria': [2418444, {'Proteobacteria': [2145170, {'Betaproteobacteria': [2106559, {'Burkholderiales': [4136, {'Comamonadaceae': [4136, {}]}], 'Nitrosomonadales': [2092897, {'Nitrosomonadaceae': [2092897, {'Nitrosomonas': [22031, {'Nitrosomonas sp. Is79A3': [1521, {}]}]}]}]}], 'Alphaproteobacteria': [10109, {'Rickettsiales': [1304, {'Rickettsiaceae': [1304, {}]}], 'Rhodobacterales': [3749, {'Rhodobacteraceae': [3749, {}]}], 'Sphingomonadales': [5056, {'Sphingomonadaceae': [5056, {}]}]}], 'Gammaproteobacteria': [14185, {'Alteromonadales': [9123, {'Alteromonadaceae': [2395, {}], 'Pseudoalteromonadaceae': [6728, {}]}], 'Methylococcales': [5062, {'Methylococcaceae': [5062, {'Methylomonas': [2116, {}]}]}]}]}]}]}
RSF33_CG26.fa Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;NitrosomonadaceaeNow,It looks as expected.
palomo11
commented
6 years ago By the way, a similar case happens with RSF29. It was classified as: RSF29.fa Bacteria;Proteobacteria but when I have run the script you sent me it is also classified as Nitrosomonadaceae
RSF29_1 4154 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Oxalobacteraceae
RSF29_2 6722 Bacteria
RSF29_3 13050 Bacteria;Proteobacteria
RSF29_4 11200 Bacteria;Proteobacteria
RSF29_5 6603 uncultured microorganism
RSF29_6 5622 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae
RSF29_7 1858 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_8 10621 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_10 10385 Bacteria;Proteobacteria;Gammaproteobacteria
RSF29_11 6035 Bacteria;Proteobacteria
RSF29_12 2254 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_14 1747 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Alcaligenaceae
RSF29_17 14685 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_18 12946 Bacteria;Proteobacteria
RSF29_19 28797 Bacteria;Proteobacteria
RSF29_21 12271 Bacteria;Proteobacteria
RSF29_22 5575 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_23 7351 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_24 7116 Bacteria;Proteobacteria;Gammaproteobacteria;Aeromonadales;Aeromonadaceae
RSF29_27 16017 Bacteria;Proteobacteria
RSF29_28 11092 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_29 5077 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales
RSF29_30 3742 Bacteria
RSF29_31 9696 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_34 2647 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_35 1434 Bacteria
RSF29_37 8045 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_38 9952 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_39 4679 Bacteria
RSF29_41 8043 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_42 10052 Bacteria
RSF29_45 5161 Bacteria;Proteobacteria
RSF29_46 7532 Bacteria;Proteobacteria
RSF29_47 5663 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_48 11747 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_49 24268 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_51 1609 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_52 9778 Bacteria;Proteobacteria
RSF29_53 3251 Bacteria;Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae
RSF29_56 11717 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_57 16156 Bacteria
RSF29_58 5853 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_59 9464 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales
RSF29_60 5332 Bacteria
RSF29_61 10732 Bacteria;Proteobacteria
RSF29_63 17035 Bacteria;Proteobacteria
RSF29_64 10419 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_65 10364 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales
RSF29_67 1383 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_69 15588 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales
RSF29_70 13017 Bacteria;Proteobacteria
RSF29_74 3547 Bacteria;Proteobacteria;Gammaproteobacteria;uncultured gamma proteobacterium
RSF29_75 5263 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_76 2962 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_77 9110 Bacteria;Proteobacteria
RSF29_79 8696 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_80 10168 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_81 9052 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_82 4206 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales
RSF29_85 1558 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_87 26799 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_89 13562 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_91 6308 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_92 2340 Bacteria;Proteobacteria
RSF29_93 6972 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_94 3540 Bacteria;Proteobacteria
RSF29_95 4709 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_99 7281 Bacteria;Proteobacteria
RSF29_100 2810 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_101 4601 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_106 11648 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_107 3378 Bacteria;Proteobacteria;Gammaproteobacteria
RSF29_109 7467 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_110 9321 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_112 1664 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_113 2034 Bacteria;Proteobacteria;Betaproteobacteria;Rhodocyclales;Rhodocyclaceae;Rugosibacter;Rugosibacter aromaticivorans
RSF29_115 6837 Bacteria;Proteobacteria
RSF29_116 1382 Bacteria;Chlorobi;Chlorobia;Chlorobiales;Chlorobiaceae
RSF29_117 2091 Bacteria
RSF29_120 1658 Bacteria;uncultured bacterium
RSF29_121 3998 Bacteria;Proteobacteria
RSF29_123 10279 Bacteria;Proteobacteria
RSF29_124 7333 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_127 4534 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_129 1441 Bacteria;Proteobacteria;Gammaproteobacteria
RSF29_131 6195 Bacteria;Proteobacteria
RSF29_132 14157 Bacteria;Proteobacteria
RSF29_136 7223 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales
RSF29_138 11739 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_139 6721 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_140 7038 Bacteria;Proteobacteria
RSF29_142 6577 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_143 1808 Bacteria;Proteobacteria
RSF29_144 28266 Bacteria;Proteobacteria
RSF29_145 7168 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales
RSF29_147 3791 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_148 3327 Bacteria;Proteobacteria
RSF29_154 14259 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_155 6355 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_156 12748 Bacteria
RSF29_158 2088 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_159 1282 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas;Nitrosomonas sp. AL212
RSF29_160 15890 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_161 8380 Bacteria;Proteobacteria
RSF29_162 25072 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_166 2656 Bacteria
RSF29_167 1282 Bacteria;Proteobacteria;Betaproteobacteria
RSF29_169 7214 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_170 11502 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_172 24942 Bacteria;Proteobacteria
RSF29_173 3741 Bacteria;Proteobacteria
RSF29_174 1245 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_176 2711 Bacteria;Proteobacteria
RSF29_180 2410 Bacteria;uncultured bacterium
RSF29_181 1499 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_184 4977 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_186 13168 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales
RSF29_187 7535 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Oxalobacteraceae
RSF29_188 6682 Bacteria;Proteobacteria
RSF29_191 2098 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_194 4131 Bacteria;Proteobacteria;Betaproteobacteria;Rhodocyclales;Rhodocyclaceae
RSF29_195 11562 Bacteria;Proteobacteria
RSF29_198 14574 Bacteria;Proteobacteria
RSF29_199 3035 Bacteria;Proteobacteria
RSF29_201 2243 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas
RSF29_203 2079 Bacteria;Cyanobacteria;Synechococcales;Prochloraceae
RSF29_204 2648 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas;Nitrosomonas sp. AL212
RSF29_206 2962 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_210 85860 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
RSF29_213 15893 Bacteria;Proteobacteria
RSF29_215 3853 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae
{'uncultured microorganism': [6603, {}], 'Bacteria': [1090069, {'Chlorobi': [1382, {'Chlorobia': [1382, {'Chlorobiales': [1382, {'Chlorobiaceae': [1382, {}]}]}]}], 'uncultured bacterium': [4068, {}], 'Bacteroidetes': [3251, {'Cytophagia': [3251, {'Cytophagales': [3251, {'Cytophagaceae': [3251, {}]}]}]}], 'Proteobacteria': [1013677, {'Betaproteobacteria': [622921, {'Burkholderiales': [39406, {'Oxalobacteraceae': [11689, {}], 'Alcaligenaceae': [1747, {}]}], 'Nitrosomonadales': [440513, {'Nitrosomonadaceae': [394225, {'Nitrosomonas': [30864, {'Nitrosomonas sp. AL212': [3930, {}]}]}]}], 'Rhodocyclales': [6165, {'Rhodocyclaceae': [6165, {'Rugosibacter': [2034, {'Rugosibacter aromaticivorans': [2034, {}]}]}]}]}], 'Gammaproteobacteria': [31489, {'Aeromonadales': [7116, {'Aeromonadaceae': [7116, {}]}], 'uncultured gamma proteobacterium': [3547, {}], 'Enterobacterales': [5622, {'Enterobacteriaceae': [5622, {}]}]}]}], 'Cyanobacteria': [2079, {'Synechococcales': [2079, {'Prochloraceae': [2079, {}]}]}]}]}
RSF29.fa Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;NitrosomonadaceaeVery strange. Maybe that fixed it then. Try running the full classification now (attaching the script): python classify_bins.py contig_taxonomy.tab FOLDER_WITH_BIN_FILES.
If that still works well and gives you the right results, can you please test one more thing to make sure that fully fixed it before I release a patch? Make sure this new script is executable (chmod +x classify_bins.py), and replace the original script in /miniconda2/bin/metawrap-scripts/classify_bins.py (might be a bit different for you) with the new one. Then re-run the entire metawrap module and see if you still get proper results.
palomo11
commented
6 years ago I have just re-run it and it has worked fine. Thanks!!!
ursky
commented
6 years ago Thank you! The change will be included in metaWRAP v=0.9.4
Hi,
I have run the Classify_bins module on over 100 bins. The output in some of them are correct (as I already double checked with another tool) but at least in one bin that I was expecting a specific taxonomy, the output is different. I have checked the contig_taxonomy.tab and the bin_taxonomy.tab files and this is what I have found for that specific bin.
contig_taxonomy.tab file:
bin_taxonomy.tab file:
I'm pretty sure this bin belongs to Nitrosomonadaceae (ANI of 89% with other Nitrosomonas spp.), and that seems to be also the classfication for most of the contigs, however, the output says a totally different taxonomy.
I have checked in the contig_taxonomy.tab file and there are 319 contigs classified as Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae, but any of them belongs to bin RSF33_CG26.
Any idea of what is going on? I'm not sure if this issue is also happening in other bins...
I'm using metaWRAP v=0.9.