HMMER MSAs aren't saved and repeated when running with --use_precomputed_msas=True

I separated the MSA part and am doing it with ProtreinFold on CPU. After this I run AlphaFold on GPU with:
` --use_precomputed_msas=True`

Alphafold correctly identifies all jackhammer alignments but repeats a bunch of HMMER alignments which on ocasion can take quite some time.

I suspect this is happening because HMMER output is always directed to TMPDIR and is deleted after running all MSAs, causing AlphaFold to repeat it. I also suspect HMMER output isn't needed as long as you have all the .sto's, last one being uniprot_hits.sto

Is there any way to manually disable HMMER and start with the step:
`run_alphafold.py:191] Running model model_1_multimer_v3_pred_0 on K7R_CENPF`

Example HMMER repeat alignments:
```
hmmbuild.py:121] Launching subprocess ['/usr/bin/hmmbuild', '--hand', '--amino', '/scratch/tmp_AF/K7R_CENPF_10174/tmp_82megdk/output.hmm', '/scratch/tmp_AF/K7R_CENPF_10174/tmp_82megdk/query.msa']
I0206 16:20:13.699746 23223541839680 utils.py:36] Started hmmbuild query
I0206 16:20:16.644826 23223541839680 hmmbuild.py:128] hmmbuild stdout:
# hmmbuild :: profile HMM construction from multiple sequence alignments
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
...
utils.py:40] Finished hmmbuild query in 2.945 seconds
I0206 16:20:16.661780 23223541839680 hmmsearch.py:103] Launching sub-process ['/usr/bin/hmmsearch', '--noali', '--cpu', '8', '--F1', '0.1', '--F2', '0.1', '--F3', '0.1', '--incE', '100', '-E', '100', '--domE', '100', '--incdomE', '100', '-A', '/scratch/tmp_AF/K7R_CENPF_10174/tmpksyfr5el/output.sto', '/scratch/tmp_AF/K7R_CENPF_10174/tmpksyfr5el/query.hmm', '/wynton/group/gladstone/users/apelin/alphafold_DBs/pdb_seqres/pdb_seqres.txt']
I0206 16:20:16.697458 23223541839680 utils.py:36] Started hmmsearch (pdb_seqres.txt) query
I0206 16:22:01.650443 23223541839680 utils.py:40] Finished hmmsearch (pdb_seqres.txt) query in 104.952 seconds
```