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| Output of Data Check for First Full Version of BioCLIP training data (catalog-v1-dev.csv): |
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| [2023-10-25 10:20:12,498] [WARNING] [root] There are 5 kingdoms instead of 3. |
| [2023-10-25 10:20:13,673] [WARNING] [root] 1300744 entries are missing rank kingdom, but have genus label. |
| [2023-10-25 10:20:13,918] [WARNING] [root] 1302578 entries are missing rank phylum, but have genus label. |
| [2023-10-25 10:20:14,168] [WARNING] [root] 2368981 entries are missing rank class, but have genus label. |
| [2023-10-25 10:20:14,402] [WARNING] [root] 1344781 entries are missing rank order, but have genus label. |
| [2023-10-25 10:20:14,637] [WARNING] [root] 1310177 entries are missing rank family, but have genus label. |
| [2023-10-25 10:20:15,065] [WARNING] [root] 24 entries are missing rank phylum, but have family label. |
| [2023-10-25 10:20:15,094] [WARNING] [root] 8759 entries are missing rank class, but have family label. |
| [2023-10-25 10:20:15,123] [WARNING] [root] 111 entries are missing rank order, but have family label. |
| [2023-10-25 10:20:15,233] [WARNING] [root] 67 entries are missing rank class, but have order label. |
| [2023-10-25 10:20:15,254] [WARNING] [root] 253 entries have kingdom and species labels but no genus. |
| [2023-10-25 10:20:15,254] [WARNING] [root] 253 entries have phylum and species labels but no genus. |
| [2023-10-25 10:20:15,255] [WARNING] [root] 173 entries have class and species labels but no genus. |
| [2023-10-25 10:20:15,255] [WARNING] [root] 253 entries have order and species labels but no genus. |
| [2023-10-25 10:20:15,255] [WARNING] [root] 253 entries have family and species labels but no genus. |
| [2023-10-25 10:20:16,644] [WARNING] [root] There are 755133 samples for which the species column may have genus and species. |
| [2023-10-25 10:20:17,199] [WARNING] [root] 2470 species are labeled as '(unidentified)'. |
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| ------------------------------------------------------------------------------------------------------ |
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| Output of Data Check for next iteration where taxon matching was performed (catalog.csv, from pr1): |
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| [2023-10-25 10:25:28,242] [WARNING] [root] There are 7 kingdoms instead of 3. |
| [2023-10-25 10:25:29,234] [WARNING] [root] 14795 entries are missing rank kingdom, but have genus label. |
| [2023-10-25 10:25:29,477] [WARNING] [root] 5824 entries are missing rank phylum, but have genus label. |
| [2023-10-25 10:25:29,719] [WARNING] [root] 15763 entries are missing rank class, but have genus label. |
| [2023-10-25 10:25:29,958] [WARNING] [root] 10550 entries are missing rank order, but have genus label. |
| [2023-10-25 10:25:30,203] [WARNING] [root] 7539 entries are missing rank family, but have genus label. |
| [2023-10-25 10:25:30,470] [WARNING] [root] 296 entries are missing rank kingdom, but have family label. |
| [2023-10-25 10:25:30,495] [WARNING] [root] 272 entries are missing rank phylum, but have family label. |
| [2023-10-25 10:25:30,520] [WARNING] [root] 753 entries are missing rank class, but have family label. |
| [2023-10-25 10:25:30,545] [WARNING] [root] 395 entries are missing rank order, but have family label. |
| [2023-10-25 10:25:30,590] [WARNING] [root] 156 entries are missing rank kingdom, but have order label. |
| [2023-10-25 10:25:30,591] [WARNING] [root] 100 entries are missing rank phylum, but have order label. |
| [2023-10-25 10:25:30,592] [WARNING] [root] 1187 entries are missing rank class, but have order label. |
| [2023-10-25 10:25:30,637] [WARNING] [root] 74 entries have kingdom and species labels but no genus. |
| [2023-10-25 10:25:30,644] [WARNING] [root] 74 entries have phylum and species labels but no genus. |
| [2023-10-25 10:25:30,650] [WARNING] [root] 74 entries have class and species labels but no genus. |
| [2023-10-25 10:25:30,656] [WARNING] [root] 74 entries have order and species labels but no genus. |
| [2023-10-25 10:25:30,662] [WARNING] [root] 74 entries have family and species labels but no genus. |
| [2023-10-25 10:25:31,992] [WARNING] [root] There are 158279 samples for which the species column may have genus and species. |
| Added check for nulls in common column (wasn't an issue in the first iteration): |
| [2023-10-25 11:39:11,384] [WARNING] [root] 915509 entries have null common. They are from ['EOL' 'BIOSCAN']. |
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| ------------------------------------------------------------------------------------------------------ |
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| Output of taxa check for catalog.csv v3.2 (taxa check now also removes duplicate entries for small training) (from pr2): |
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| [2023-10-26 13:44:09,780] [WARNING] [root] There are 7 kingdoms instead of 3. |
| [2023-10-26 13:44:11,325] [WARNING] [root] 160824 entries are missing rank kingdom, but have genus label. |
| [2023-10-26 13:44:11,613] [WARNING] [root] 151405 entries are missing rank phylum, but have genus label. |
| [2023-10-26 13:44:11,910] [WARNING] [root] 161871 entries are missing rank class, but have genus label. |
| [2023-10-26 13:44:12,199] [WARNING] [root] 156405 entries are missing rank order, but have genus label. |
| [2023-10-26 13:44:12,483] [WARNING] [root] 153279 entries are missing rank family, but have genus label. |
| [2023-10-26 13:44:12,782] [WARNING] [root] 315 entries are missing rank kingdom, but have family label. |
| [2023-10-26 13:44:12,809] [WARNING] [root] 289 entries are missing rank phylum, but have family label. |
| [2023-10-26 13:44:12,837] [WARNING] [root] 792 entries are missing rank class, but have family label. |
| [2023-10-26 13:44:12,865] [WARNING] [root] 414 entries are missing rank order, but have family label. |
| [2023-10-26 13:44:12,905] [WARNING] [root] 170 entries are missing rank kingdom, but have order label. |
| [2023-10-26 13:44:12,906] [WARNING] [root] 105 entries are missing rank phylum, but have order label. |
| [2023-10-26 13:44:12,908] [WARNING] [root] 1263 entries are missing rank class, but have order label. |
| [2023-10-26 13:44:12,949] [WARNING] [root] 41 entries have kingdom and species labels but no genus. |
| [2023-10-26 13:44:12,953] [WARNING] [root] 41 entries have phylum and species labels but no genus. |
| [2023-10-26 13:44:12,957] [WARNING] [root] 41 entries have class and species labels but no genus. |
| [2023-10-26 13:44:12,961] [WARNING] [root] 41 entries have order and species labels but no genus. |
| [2023-10-26 13:44:12,965] [WARNING] [root] 41 entries have family and species labels but no genus. |
| [2023-10-26 13:44:14,425] [WARNING] [root] There are 149057 samples for which the species column may have genus and species. |
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| ------------------------------------------------------------------------------------------------------ |
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