Comments (1)
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>
from annotater.
Related Issues (11)
- getting multiple "print() on closed filehandle TMPOUT" messages HOT 1
- blastdbcmd errors during Taxonomy step
- EXCEPTION: Bio::Root::Exception MSG: Response Error Too Many Requests HOT 1
- getting integer values for the Description column in Report.txt HOT 1
- Exception error when testing Taxonomy.t HOT 1
- Confirm that use of BLAST's `-max_target_seqs` is intentional
- implement baculovirus filter and other methods to flag/eliminate suspect hits
- BLAST error: No alias or index file found for database
- Rapsearch outputs illegal evalues
- BLAST database error during Taxonomy step
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from annotater.