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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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phyluce_probe_get_multi_merge_table syntax error #231

Closed RaulGoch closed 3 years ago

RaulGoch commented 3 years ago

I am running into the following error:

phyluce_probe_get_multi_merge_table - INFO - Creating database

Traceback (most recent call last):

  File "/miniconda3/envs/phyluce-1.7.1/bin/phyluce_probe_get_multi_merge_table", line 147, in <module>

    main()

  File "/miniconda3/envs/phyluce-1.7.1/bin/phyluce_probe_get_multi_merge_table", line 129, in main

    conn, c = create_match_database(args.output, organisms, args.base_taxon)

  File "/miniconda3/envs/phyluce-1.7.1/bin/phyluce_probe_get_multi_merge_table", line 85, in create_match_database

    c.execute(query)

sqlite3.OperationalError: near "-": syntax error

Any Idea of what might be the issue?

brantfaircloth commented 3 years ago

Are the dashes/hyphens on the taxon names? If so, that is potentially the problem. Try to replace those with underscores or use just letters [followed by numbers if you want] as the taxon name. The tutorial taxon names are one way to do this (e.g. triCas1, agrPla2, etc.).

RaulGoch commented 3 years ago

Hi Brant,

yes! I think it was that. I changed the taxa name to only letters and numbers and all worked just fine. Thanks!

brantfaircloth commented 3 years ago

Excellent.