Frequently Asked Questions

Content

openSSL

I’m getting an SSL: CERTIFICATE_VERIFY_FAILED error

If you encounter an SSL error like SSL: CERTIFICATE_VERIFY_FAILED, you may need to enable the SSL mofule for Python or update the certifications. It depends on your OS or distribution.

  • Mac OS you need to find run Install Certificates.command, usually found in the folder where Python has been installed.

On Linux, you may need to update the certificates:

  • Debian: run update-ca-certificates --fresh and export the environment variable SSL_CERT_DIR=/etc/ssl/certs.
  • Arch Linux: install the ca-certificates* packages, e.g. pacman -S ca-certificates*
It is also possible to update the certificates via pip:
  • run pip install --upgrade certifi

SQLite

sqlite3.OperationalError: near "ON": syntax error during import

ncbi-taxonomist aborts with an error message similar as shown below:

Traceback (most recent call last):
  File "/tools/python/3.7.4/bin/ncbi-taxonomist", line 93, in <module>
    main()
  File "/tools/python/3.7.4/bin/ncbi-taxonomist", line 58, in main
    ncbitaxonomist.db.dbimporter.import_stdin(nt.db)
  File "/tools/python/3.7.4/lib/python3.7/site-packages/ncbitaxonomist/db/dbimporter.py", line 95, in import_stdin
    commit(db, taxa, names)
  File "/tools/python/3.7.4/lib/python3.7/site-packages/ncbitaxonomist/db/dbimporter.py", line 34, in commit
    db.add_taxa(taxa)
  File "/tools/python/3.7.4/lib/python3.7/site-packages/ncbitaxonomist/db/dbmanager.py", line 69, in add_taxa
    self.taxa.insert(self.connection, values)
  File "/tools/python/3.7.4/lib/python3.7/site-packages/ncbitaxonomist/db/table/taxa.py", line 39, in insert
    connection.cursor().executemany(stmt, taxavalues)
sqlite3.OperationalError: near "ON": syntax error

Possible solution 1

The taxonomic database uses an old ncbi-taxonomist database scheme. In this case, you need to rebuild the database using a current version of ncbi-taxonomist.

Possible solution 2

This has been reported earlier (issue 2).

ncbi-taxonomist uses a PostgreSQL-style UPSERT introduced to SQLite 3.24.0. You need a recent Python version (>= Python 3.8) and SQlite version >= 3.24.0. You can use the available containers if you can’t update Python or SQLite.

If none of these solutions work for you, please open an issue.