segfault when using -g with ensembl gff3 about cufflinks HOT 3 CLOSED

That GFF3 file seems badly formatted, the essential attribute "Parent" is spelled "PARENT" which is incorrect (these attributes are case sensitive according to the GFF3 specification).
Simply transforming the file with something like perl -pe 's/(NAME|PARENT)=/\L\u$1=/g' should fix this. I suspect TopHat just failed silently at loading that annotation (i.e. no transcript features were actually loaded).

from cufflinks.

Sounds like it's a bad GFF file (shame on ensembl...) but I don't think a segfault is the best response.
Perhaps an error message with the location in the input would head off this kind of question in the future?

from cufflinks.

I fully agree. I have added some code checking for situations like this, hopefully it's going to make its way in to the next release.

from cufflinks.