-
Notifications
You must be signed in to change notification settings - Fork 7
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
Error handling EPA-NG jplace output file #20
Comments
Hey Daniel, interesting, I cannot reproduce this error. I've tracked down the error message, and it should not occur with the file that you sent. It's a valid file, and I can parse it well, and
Haha yes of course, we want to achieve that, and so far, it has worked :-) Cheers and so long |
Sorry to forget the version. I'm running the 0.8.0 Bioconda package on Ubuntu plus the biocontainer Docker image; same result with both. This seems to be the latest in Bioconda, but you're at 0.8.2 I see. |
Ah right, thanks, I was able to reproduce the issue with gappa v0.8.0, and traced back the change - it was indeed fixed in gappa v0.8.1. Unfortunately, for some reason, conda has stopped updating automatically, I will have to look into this. Hence, for now, please manually compile a more recent version of gappa to solve the issue. |
Hi,
Sorry to bother you again. I get the following exception when running
gappa examine graft --jplace-path NrdDmprooted.epa_result.broken.jplace.gz
(input file attached):The input file was produced with EPA-NG, and contains labels at internal nodes. My first thought was the the "-" characters in the node labels was the problem, but removing them didn't help. When I replaced the input tree to one without the internal node names, I got a jplace file that works. The node names might not be the only difference though.
(One could imagine that two tools from the same group would use the same library to parse the files... ;-) )
NrdDmprooted.epa_result.broken.jplace.gz
/D
The text was updated successfully, but these errors were encountered: