Memory error when using phyml with a custom model

[halabikeren]

Hi,

I get a memory error upon executing phyml on the attached alignment with the attached custom aa matrix.

*** Error in `phyml': free(): invalid next size (fast): 0x0000556389604930 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7fd579ffd489]
phyml(+0x94ec5)[0x556387e4dec5]
phyml(+0x120e89)[0x556387ed9e89]
phyml(+0x307d)[0x556387dbc07d]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fd579f9e3d5]
phyml(+0x3dce)[0x556387dbcdce]

Best,
Keren

example.zip

[stephaneguindon]

I was unable to reproduce this issue with the latest stable release (Summer 2020) and the following command-line options:
./phyml -i aln.phy -d aa -m custom --aa_rate_file=./model.PAML
Did you use different version of PhyML and/or other command-line options?

I attach the tree and stats files obtained.

aln.phy_phyml_tree.txt
aln.phy_phyml_stats.txt

[halabikeren]

Thank you for the quick response!

Yes, I have used the default version available via conda install, which is 3.3.20190909.
Here are additional steps to reproduce the issue:

1. I used the CLI, but on interactive mode.
2. Like you, I used AA alphabet and custom model, which were selected using the interactive mode screen.
3. I used provided the full paths to the files (the issue is not reproducible when using the relative paths).

Best,
Keren

[stephaneguindon]

Can you please try with 3.3.20200621, i.e., the latest release? Thanks.