Use of use_precomputed_msas

Hello

Like others, here in Calmip computation center, we have trouble trying to run alphafold on our HPC cluster, because of the MSAs step: data files are on an nfs-based filesystem and performances are low, the host memory is satured with nfs caching, sometimes the wole machine is stuck because of alphafold running... No solution as the ones explained here https://github.com/soedinglab/hh-suite/wiki#running-hhblits-efficiently-on-a-computer-cluster can be applied.

So, the idea would be to run the MSAs stage on some specialized hardware, then copying the output directory to the cluster for the GPU-based step. It seems to be possible doing only the GPU-based stage, thanks to the `--use_precomputed_msas` flag. But how to isolate the MSAs stage ? Is it sufficient running "by hand" the `jackhmmer` and `hhblits` codes, and how to generate the `features.pkl` file needed for the second stage ?

Thanks !
Emmanuel C.