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

TIGER with hmmer 3.3.2 gives trusted cutoff error #8

Open
alexweisberg opened this issue May 20, 2023 · 0 comments
Open

TIGER with hmmer 3.3.2 gives trusted cutoff error #8

alexweisberg opened this issue May 20, 2023 · 0 comments

Comments

@alexweisberg
Copy link

When using a --cut_tc filter for hmmsearch, the included hmmer 3.1b2 executables ignore a missing value for the trusted cutoff (TC) field and just dont use it. However if one uses hmmer 3.3.2, then those missing values result in an error:

Error: TC bit thresholds unavailable on model intI_Cterm

The following hmm models in the db are missing a TC field:
ICE.hmm
intI_Cterm.hmm
some of the models in TnpPred_HMM_Profiles.hmm

One fix is to rebuild them with a TC field.

An alternative is to remove the cut_tc filter from the TnpPred hmmsearch in tater.pl as well as from the integron section hmmsearch of integrase_finder.pl

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

No branches or pull requests

1 participant