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Error in running contigtax assign command on my metaspades assembly #15

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mohitsharma-123 opened this issue Jan 13, 2025 · 0 comments

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(contigtax) mohitsharma@deep:/data/mohitsharma/iiser_metagenomics_project/workflow/L/L_contigtax$ contigtax assign -p 96 L_assembly.tsv.gz L_assembly.taxonomy.tsv
Assigning taxonomy with 96 cpus
Reading L_assembly.tsv.gz: 274792 lines [00:01, 152144.25 lines/s]
NCBI database format is outdated. Upgrading
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...
Loading node names...
2631807 names loaded.
382942 synonyms loaded.
Loading nodes...
2631807 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: ./taxonomy/taxonomy.sqlite ...
2631000 generating entries...
Uploading to ./taxonomy/taxonomy.sqlite

Inserting synonyms: 45000 Traceback (most recent call last):
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/bin/contigtax", line 10, in
sys.exit(main())
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/contigtax/main.py", line 387, in main
args.func(args)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/contigtax/main.py", line 86, in assign_taxonomy
args.taxdir, args.sqlitedb, args.chunksize, args.cpus)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/contigtax/assign.py", line 885, in parse_hits
reportranks, cpus)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/contigtax/assign.py", line 614, in make_lineage_df
ncbi_taxa = init_sqlite_taxdb(taxdir, dbname)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/contigtax/prepare.py", line 218, in init_sqlite_taxdb
ncbi_taxa = NCBITaxa(dbfile=dbfile, taxdump_file=taxdump_file)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 120, in init
self.update_taxonomy_database(taxdump_file)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 129, in update_taxonomy_database
update_db(self.dbfile)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 760, in update_db
upload_data(dbfile)
File "/home/mohitsharma/miniforge-pypy3/envs/contigtax/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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