segmentation fault

[antunderwood]

I've been trying to run this on Mac OSX and get a seg fault

....
subprocess.CalledProcessError: Command 'gubbins -r -v snps_vs_HO.fas.gaps.vcf -t snps_vs_HO.fas.iteration_1 -p snps_vs_HO.fas.gaps.phylip -m 3 snps_vs_HO.fas' returned non-zero exit status -11

Any ideas why this may be?

[aldertzomer]

Same issue here, Ubuntu 14.04, input is an alignment of the core genome of 61 campylobacter isolates. No indication what went wrong. I can provide the sequences on request. Gubbins does work on a test genome alignment of 9 isolates. The 61 isolates alignment does contain gap characters (---). Could that be an issue?

[aldertzomer]

Issue goes away if I remove all positions with gap characters in the alignment

[andrewjpage]

Hi,
Would it be possible for you to send the error message and your alignment to gubbins@sanger.ac.uk and I'll see if I can track down the problem. I've recently pushed out some updates to both gubbins and fastml, so it might be fixed already (hopefully).
Regards,
Andrew