align.seqs segfault with flip=t

Align.seqs is segfaulting for me on 1.31.1 when using flip=t. No problem without it. I’m aligning my sequences to a pcr.seqs processed version of the silva reference database, and the segfault happens nearly immediately.

If this is difficult to reproduce, I will try and come up with a small test case.

From log (I compiled from source):

“Linux version
Using ReadLine
Running 64Bit Version
mothur v.1.31.1
Last updated: 5/29/2013”

I am not seeing that with my test files. Could you email the reference and a small sampling of your sequences, so I can try to track down the issue?

I was unable to reproduce with an EC2 instance today, so it must be something related to my lab workstation, possibly the newer gcc (4.8.1 vs 4.7.3). If I have time to track it down, I will provide more details.