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lczech / gappa

A toolkit for analyzing and visualizing phylogenetic (placement) data
GNU General Public License v3.0
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Error handling EPA-NG jplace output file #20

Closed erikrikarddaniel closed 1 year ago

erikrikarddaniel commented 1 year ago

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):

Found 1 jplace file
terminate called after throwing an instance of 'std::runtime_error'
  what():  Invalid characters at 1:8543: '0.8590006000'.
Aborted (core dumped)

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

lczech commented 1 year ago

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 gappa examine graft works for me with it... Sorry for that, "works for me" is not very helpful... Did you use the latest release of gappa? Which OS are you on?

One could imagine that two tools from the same group would use the same library to parse the files... ;-)

Haha yes of course, we want to achieve that, and so far, it has worked :-)

Cheers and so long Lucas

erikrikarddaniel commented 1 year ago

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.

lczech commented 1 year ago

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.