Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Do not validate taxids when using -onlydesc in rfci.pl #70

Open
AntonPetrov opened this issue Jul 8, 2021 · 0 comments
Open

Do not validate taxids when using -onlydesc in rfci.pl #70

AntonPetrov opened this issue Jul 8, 2021 · 0 comments
Assignees
Labels

Comments

@AntonPetrov
Copy link
Member

The following command

rfci.pl -onlydesc -m 'Fix characters in AU line' RF04184

resulted in an error:

ERROR trying to fetch taxids from genbank, reached maximum allowed number of failed attempts (10)

The family was successfully checked in after a few attempts, but in general -onlydesc should have prevented the taxid check.

Seems like the problem is in _commitEntry of Commit.pm.

More logs:

rfci.pl -onlydesc -m 'Fix characters in AU line' RF04184
Successfully loaded local copy of RF04184 through middleware
Successfully loaded SVN copy of RF04184 through middleware
No GO mappings for this family-have you tried to add any?
Look up:
http://www.geneontology.org/ or  http://www.ebi.ac.uk/QuickGO/
Failed to commit family, RF04184: [A repository hook failed: Commit failed (details follow):: Commit blocked by pre-commit hook (exit code 1) with output:
[
    [0] "trunk/Families/RF04184/DESC"
]
trunk/Families/RF04184/DESC[]
[]
ERROR trying to fetch taxids from genbank, reached maximum allowed number of failed attempts (10)
Tried to fetch taxid
-
at rfam-family-pipeline/Rfam/Lib/Bio/Rfam/FamilyIO.pm line 4156.
DBIx::Class::Storage::TxnScopeGuard::DESTROY(): A DBIx::Class::Storage::TxnScopeGuard went out of scope without explicit commit or error. Rolling back. at perl5/lib/perl5/Carp.pm line 291
 at rfam-family-pipeline/Rfam/Lib/Bio/Rfam/SVN/Client.pm line 597.
]
 at rfam-family-pipeline/Rfam/Lib/Bio/Rfam/SVN/Client.pm line 599.
	Bio::Rfam::SVN::Client::commitFamilyDESC(Bio::Rfam::SVN::Client=HASH(0x1cf17c8), "RF04184") called at rfam-family-pipeline/Rfam/Scripts/svn/rfci.pl line 187


Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

2 participants