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Trinotate / Trinotate.github.io

web documentation for Trinotate
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Loading Swiss-Prot database is throwing format warning #23

Closed bifxcore closed 5 years ago

bifxcore commented 5 years ago

Trinotate/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --uniprot_index Trinotate.TaxonomyIndex

is throwing

Trinotate.TaxonomyIndex:13785: expected 3 columns but found 2 - filling the rest with NULL

brianjohnhaas commented 5 years ago

Probably fine, unless the issue is due to a truncated embl file. If the sprot fasta file has the expected number of entries, it's likely fine.

You could try rerunning the boilerplate build in a new directory and see if the error repeats.

Best

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On Thu, Jul 25, 2019, 1:27 AM Seattle BioMed notifications@github.com wrote:

Trinotate/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --uniprot_index Trinotate.TaxonomyIndex

is throwing

Trinotate.TaxonomyIndex:13785: expected 3 columns but found 2 - filling the rest with NULL

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bifxcore commented 5 years ago

The sprot fasta looks fine. I just re-ran the boilerplate build in a new directory and got no errors, so all is good.

Thank you very much for your help (and for providing this software!).