Fix arguments and paths for make_msa.sh

[alephreish]

This fixes several issues in how make_msa.sh is run from preprocessing.py:

• Enables non-empty database_params.sequencedb which in my interpretation was originally meant to provide the path to the database files
• Makes it possible to use absolute paths for database_params.command
• Fixes the bug in how subprocess.run() is used in preprocessing.py: it's a bad practice to create the entire command string by simply stitching together the command and the arguments. search_command = f"./{command} {fasta_file} {out_dir} {num_cpus} {ram_gb} {search_base} {template_database}" implied six arguments to make_msa.sh but the script in fact expected five: this issue was masked by the fact that search_base = model_runner.config.database_params.sequencedb is an empty string in base.yaml.
• Fixes Error in the protein example #32

This commit does not fix several other issues in make_msa.sh: e.g. it breaks if any of the paths have spaces.