Protest failing to complete analysis

[GLFR]

Hello,

I was originally running protest 3.3 but since this error showed up I tried running 3.4 to see if it made any difference. I've now ran protest 3 times and after 10 hours of analysis the same error comes up. On terminal is says "connection interrupted" and on the error log it says "Unable to read the log file: /var/folders/tl/bbnw4bfd6qs2t0mwp7g7pnsh0000gn/T/prottest_5343666072668867500.tmp".

I'm using the GUI on a Mac installed with Yosemite OSX.

Can anybody suggest anything that might help me correct this?

[ktretina]

Were you ever able to solve this issue? I'm having the same one on Linux, so I'd really appreciate an answer. Thanks!

[tilii]

Not sure that you will like this solution, but here goes.

A short answer it that you need an older version of phyml for this work. I don't know exactly how far (or how near) back one needs to go, but 2011 phyml works for sure. You can download it from:

https://launchpad.net/ubuntu/+source/phyml/2:20110919-1

Specifically, you need this file:

https://launchpad.net/ubuntu/+archive/primary/+files/phyml_20110919.orig.tar.gz

After downloading and unpacking, go to the phyml directory and run:

./configure
make

That will create a "phyml" binary in src directory. Copy that binary into "bin" directory of your prottest3 distribution, and rename it into "PhyML_3.0_linux64" (see the README file in that directory for appropriate names if you have something different from x86_64 Linux machine). Lastly, go back to your prottest3 directory and modify the "prottest.properties" file:

global-phyml-exe = false

You can leave global-phyml-exe to be "true" in which case the "phyml" binary compiled in the previous step must be copied to some global directory such as /usr/bin . I assume that you already have a working "phyml" that you don't want to mess with, so the first solution is probably more elegant as it defines a "local" version that only prottest3 will be using.