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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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gappa analyze graft runtime error #6

Closed gavinmdouglas closed 5 years ago

gavinmdouglas commented 5 years ago

Hi @lczech ,

I ran into the below error when running an unusual dataset with EPA-NG (v0.3.4) and GAPPA (v0.1.0).

(Incidentally I just noticed that the version reported by GAPPA is still 0.0.0)

You can download the input jplace file here: https://www.dropbox.com/s/qrx39hy8ahosmx8/epa_result.jplace?dl=1

The command and output:

gappa analyze graft --fully-resolve --jplace-path epa_result.jplace

v0.0.0, (c) 2017-2018 by Lucas Czech and Pierre Barbera

Found 1 jplace files.
terminate called after throwing an instance of 'std::runtime_error'
  what():  Expected end of input while reading Json at 777682:1
Aborted

Although the placed sequences are unusual (they were "clustered" at 100% identity rather than a lower identity as is typically done for 16S sequences, and there are 83,354 in total) I was able to get an output newick tree with gappa tog with the same file and it appears to be in correct JSON format.

Any idea why this is occurring?

lczech commented 5 years ago

Hi @gavinmdouglas,

thanks for reporting the issue. The bug was introduced a few weeks ago while I refactored some code, and it seems I didn't notice so far...

Anyway, it is fixed now, so please use the newly released gappa v0.2.0. It works now with the test file that you sent, so I'm closing the issue. If you still run into trouble, feel free to re-open.

Best Lucas

gavinmdouglas commented 5 years ago

Great, thanks!