t_coffee troubleshooting "MAX_N_PID exceed"

Question

[merzanaeem007]

Hello everyone,

I recently downloaded t_coffee multiple alignment tool and exploring its usage, however I keep on getting the error "MAX_N_PID value exceeded (current: 260000 requested: 434668)" recompile changing the value or setenv MAX_N_PID_4_TCOFFEE=434668. I tried running the setenv MAX_N_PID_4_TCOFFEE=434668 command but got the error "-sh:18 setenv: not found". there appears to be a solution in this link https://groups.google.com/g/tcoffee/c/sO8Kd5NjA5A however with my limited knowledge about linux shell and understanding code I wasn't able to implement it. I'm running an ubuntu machine, if anyone could explain how I could implement the solution or suggest how I could fix the issue I would totally appreciate it :)

PS: I tried the web version of t_coffee however there's a limitation on the number of sequences I could upload hence (unfortunately) its not an option for me.

Answer 1

[Mensur Dlakic]

I don't think you will fix this by changing environmental variables like you attempted. I think you need to recompile the whole program to allow for larger number of sequences. You get the package from here and inside the file coffee_defines.h change the 260000 to something larger, say 500000. Run the ./install script after that and it should create a new t_coffee that will be able to work with larger number of sequences. There is a more detailed description on how to do all of this on their website.

I will mention that aligning >400000 sequences in any program will take a very long time, and it may not be practical to wait for it. You may need to consider using fewer sequences.