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Help! sqlite3.IntegrityError: UNIQUE constraint failed: synonym.spname, synonym.taxid #1

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PKUIEE opened this issue Dec 3, 2022 · 0 comments

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@PKUIEE
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PKUIEE commented Dec 3, 2022

diamond_add_taxonomy NR.out --taxdump_filename /gpfs/share/home/2201112334/00database/09NCBI.taxonomy/taxdump.tar.gz --output_file NR.tax.out
Loading node names...
2472128 names loaded.
287948 synonyms loaded.
Loading nodes...
2472128 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /gpfs/share/home/2201112334/.etetoolkit/taxa.sqlite ...
2472000 generating entries...
Uploading to /gpfs/share/home/2201112334/.etetoolkit/taxa.sqlite

Inserting synonyms: 20000 Traceback (most recent call last):
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/bin/diamond_add_taxonomy", line 12, in
sys.exit(annotate_diamond())
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/click/core.py", line 1137, in call
return self.main(*args, **kwargs)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/click/core.py", line 1062, in main
rv = self.invoke(ctx)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/click/core.py", line 763, in invoke
return __callback(*args, **kwargs)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/diamond_add_taxonomy/cli.py", line 45, in annotate_diamond
annotater = TaxIDExpander(taxdb_filename=taxdb_filename, taxdump_filename=taxdump_filename)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/diamond_add_taxonomy/taxid_utils.py", line 26, in init
self.ncbi = NCBITaxa(taxdump_file=taxdump_filename)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 106, in init
self.update_taxonomy_database(taxdump_file)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 131, in update_taxonomy_database
update_db(self.dbfile, taxdump_file)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 760, in update_db
upload_data(dbfile)
File "/gpfs/share/home/2201112334/miniconda3/envs/diamond/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 802, in upload_data
db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))
sqlite3.IntegrityError: UNIQUE constraint failed: synonym.spname, synonym.taxid

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