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pcantalupo / annotater

Annotate sequences by BLAST using NCBI taxonomy information
MIT License
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hanging while getting lineage for LXPA01121130.1 #4

Closed pcantalupo closed 6 years ago

pcantalupo commented 6 years ago

Annotater hangs while trying to get lineage from NCBI for LXPA01121130.1. The output says: GetLineage: didn't get valid taxid:<> for GI:LXPA01121130.1 so getting lineage from NCBI

pcantalupo commented 6 years ago

After code fix, the exception that was occurring is revealed (thrown by Bio::DB::EUtilities)

------------- EXCEPTION -------------
MSG: NCBI esummary fatal error: Invalid uid LXPA01121130.1 at position=0
STACK Bio::Tools::EUtilities::parse_data bioperl/Bio-EUtilities/lib/Bio/Tools/EUtilities.pm:327
STACK Bio::Tools::EUtilities::next_DocSum bioperl/Bio-EUtilities/lib/Bio/Tools/EUtilities.pm:909
STACK Bio::DB::EUtilities::next_DocSum bioperl/Bio-EUtilities/lib/Bio/DB/EUtilities.pm:856

The issue was due to an endless do loop since an exception always occurred therefore $@ was always true. I added a limit on the maximum number of eutils requests to fix this issue.

Here is the HTTP response from NCBI if you manually use the eutils HTTP query http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nucleotide&id=LXPA01121130.1&email=pcantalupo%40gmail.com&retmode=text

<eSummaryResult>
<ERROR>Invalid uid LXPA01121130.1 at position=0</ERROR>
</eSummaryResult>