t_coffee still fails on a standard Ubuntu 24.04 LTS install

Thu, 18 Sep 2025 00:00:00 +0000

The bug in t_coffee, reported on https://github.com/cbcrg/tcoffee/issues/27#issuecomment-1355339411, is still an issue after many years. I hardly dare to recommend t_coffee to my students, even though I would like to, because it is otherwise an excellent and very powerful program. Most of them fail to install it on our university’s default Ubuntu distribution (“Cubbli”), which is atm Ubuntu 24.04. I tried it out myself just recently (Ubuntu 24.04 LTS with both the version provided by the default Ubuntu repository via the package manager and the stable and beta versions from https://tcoffee.org/Projects/tcoffee/index.html (stable COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64.tar.gz and beta T-COFFEE_installer_Version_13.46.1.b8b01e06_linux_x64.tar.gz). All of them still complain with –ERROR: MAX_N_PID exceeded. It gets stuck somewhere and takes approximately one minute before it throws the error, even with a simple task that normally takes a few seconds. With a more complex alignment, it can take minutes or hours before the error is thrown. The workaround is to set the environment variable before every run, i.e., you replace t_coffee with a shell script that calls the renamed t_coffee after setting the environment parameter MAX_N_PID_4_TCOFFEE to something big (like /proc/sys/kernel/pid_max). The issue is explained in the Github link above. See also https://github.com/cbcrg/tcoffee/issues/47 . Another workaround is to recompile with a different MAX_N_PID, which is rather straightforward; see also here https://github.com/cbcrg/tcoffee :

T_coffee on Michael’s Domain

t_coffee still fails on a standard Ubuntu 24.04 LTS install