conda package doesn't have pplacer_threads option?

[CJREID]

Hi Rhys,

I'm using aviary via the conda package and I've been having gtdbtk run out of memory with the default setting of 48 threads for pplacer so I tried to set it lower on the command line --pplacer_threads 1 but I get this error.

usage: aviary [--version] [--verbosity VERBOSITY] [--log LOG]
              {assemble,recover,annotate,diversity,cluster,viral,complete,isolate,batch,configure}
              ...
aviary: error: unrecognized arguments: --pplacer_threads 1

I've also noticed that when I print the help, the option is not there. I also tried with the -p option and got the same error. The parameter seems to be present in all the .smk files and a number of python scripts within the package but just doesn't work as a command line option.

Cheers,
Cam

[rhysnewell]

Hey Cam,

That's because --placer_threads is no longer a command line argument. It was deprecated awhile ago, the help message of aviary reflects it but the docs are out of date. The pplacer_threads variables are now set via the max_threads cli argument. We just automatically cap pplacer out at 48 threads because that software has a deadlock when given more CPU. Just figured it would be easier for the user to not worry about manually setting the amount of pplacer threads they want every time

Cheers,
Rhys

[CJREID]

Ah ok, yeah I read here that pplacer uses (or appears to use) PARENT_MEMORY * (N_CHILDREN + 1) GB. So whatever I set it'll run out because the memory that the rule takes is the same as what the slurm job requests? Or am I misunderstanding?