Closed BenoitMorel closed 6 years ago
This alignment seems to have empty columns... --
On Wed, Apr 11, 2018 at 11:42 AM BenoitMorel notifications@github.com wrote:
Hi Diego,
when running ./modeltest-ng -i ENSGT00760000118962.fa -t mp
I get a segfault
3 0x00000000005c399e in __assert_fail ()
4 0x00000000004b08f2 in build_tips_recurse (tree=0x2a64c40, tip_labels=0x1e26020, split_len=6) at consensus.c:927
5 0x00000000004b0662 in build_tips_recurse (split_len=6, tip_labels=0x1e26020, tree=0x1fb39a0) at consensus.c:946
6 build_tips_recurse (split_len=6, tip_labels=0x1e26020, tree=0x1fb2fe0) at consensus.c:946
You can find the fasta file at https://github.com/BenoitMorel/phd_experiments/blob/master/datasets/bugs/modeltest/ENSGT00760000118962.fa
I reproduced the issue when building from the most recent sources, but also with the last binary release.
Benoit
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Thank you Benoit!
This error comes from a bug in pll-modules
, that occurs when the number of taxa is a multiple of 32. I'll fix it, and please update pll-modules in your software if they use split-related functions.
Best, Diego.
Dear David and Diego, thanks a lot for your quick answers. I will temporary exclude multiple of 32 taxa datasets from my analysis. In general, should I filter out empty columns from my MSAs myself before running modeltest? Best, Benoit
Thank you for the report ;)
I will update pll-modules in modeltest later this afternoon, but you can already link manually to the latest modules commit and use your multiple-of-32-taxa MSA. Empty columns are not a problem.
Best, Diego.
It works fine now, thanks a lot!
Hi Diego,
when running
./modeltest-ng -i ENSGT00760000118962.fa -t mp
I get a segfault
You can find the fasta file at https://github.com/BenoitMorel/phd_experiments/blob/master/datasets/bugs/modeltest/ENSGT00760000118962.fa
I reproduced the issue when building from the most recent sources, but also with the last binary release.
Benoit