Hi - I'm having a problem with hyphy crashing when I try and estimate substitution parameters using a local GTR model for each of 4 different partitions, where the overall rate of each gene can vary, and the tree and mean branch lengths are given (and, to make matters worse, there's gamma distributed rate variation between sites). As you can probably tell, the batch file is rather complicated, so it might be a mistake in that causing the problem... though I guess Hyphy shouldn't crash, anyway.

I would submit this to Bugzilla, but can't, because I haven't got the e-mail with my password (I registered about 5 hours ago)..

Maybe I could e-mail you the batch and data files (and the messages.log, though I don't think that helps in this case)?

Thanks,

James

(my e-mail is james.cotton@nhm.ac.uk)

Dear James,

wrote on Jan 24^th, 2006 at 7:48am:

As you can probably tell, the batch file is rather complicated, so it might be a mistake in that causing the problem... though I guess Hyphy shouldn't crash, anyway.

You are quite right - there should not be a crash, even if the batch file has problems.


Quote:

I would submit this to Bugzilla, but can't, because I haven't got the e-mail with my password (I registered about 5 hours ago).. Maybe I could e-mail you the batch and data files (and the messages.log, though I don't think that helps in this case)?

Must be that sendmail died again (Bugzilla uses that to send e-mails), I'll check. If you could compress the batch file and the data into a single archive and send it to any adress at datamonkey.org (they all get forwarded to me, e.g. help at datamonkey org will do), I'll be happy to take a look.

Thanks,
Sergei