How to set MAX N PID

[davidfstein]

The max pid is incorrectly set. In previous issues there is a suggestion that max pid can be set as an environment variable, but there is no documentation of what this variable should be anywhere nor what version of t_coffee supports this behavior. When t_coffee complains about the max pid it says to set the variable and recompile, but again there is no indication of how to achieve this. How can we properly set the max pid?

[Zefeng-Wu]

I got the same error, but don't know how to solve it.

[marco-mariotti]

I also encountered this problem. See this comment for a solution that works in Ubuntu, and hopefully in all Linux systems.

[mjeltsch]

It is sadly still an issue. I hardly dare to recommend this to my students, even though I would like to. Most of them fail to install it on our university's default Ubuntu distribution. I tried it out just recently (Ubuntu 24.04 LTS with both the stable version T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64.tar.gz and the beta T-COFFEE_installer_Version_13.46.1.b8b01e06_linux_x64.tar.gz), and it still complains. It gets stuck somewhere and takes perhaps one minute before it throws the error with a simple task that normally takes a few seconds. With a more complex alignment, it can take minutes or hours before it throws the error. The workaround helps only if you use the program manually, but we have Python scripts that call t_coffee, and it would be really nice to be able to leave them alone...

Another persisting issue (more an annoyance than a bug) is that t_coffee does not recognize dialign-tx and clustalw when they are installed via the default Ubuntu repositories, because their executables are named differently than t_coffee expects. One has to link them to the expected names to make things work:

sudo apt -y --show-progress install clustalw dialign-tx
sudo ln -s /usr/bin/dialign-tx /bin/dialign-t
sudo ln -s /usr/bin/clustalw /bin/clustalw2

[cnotred]

For some reason the fix on max_n_pid had not made its way into packaging. It is now done in the latest Beta (13.46.13.4e2b3b0d).