search

matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
74 stars 18 forks source link

Fatal error: exception Gtree.Lacking_bark(6591) #219

Closed koadman closed 12 years ago

koadman commented 12 years ago

When running guppy rarefaction or squash but not for pca or compress. The offending jplace file is available from: http://www.cs.wisc.edu/~darling/concat.trim.jplace.bz2

This is using the latest revision on the dev branch.

habnabit commented 12 years ago

I'm able to reproduce this with rarefaction but not squash. How exactly are you running guppy squash on this placefile?

koadman commented 12 years ago

Ooops, the squash error occurred when using two placefiles. The one linked above and this one: http://www.cs.wisc.edu/~darling/concat2.trim.jplace.bz2

Running squash on either one alone completes without error, but isn't very interesting of course... :)

koadman commented 12 years ago

Also troublesome on these placefiles is guppy kr, with --pp I get: Fatal error: exception Placement.No_PP without --pp I get the missing bark error: Fatal error: exception Gtree.Lacking_bark(6591)

seems like it maybe a general parsing error?