Pilot validated the MSA-reuse architecture (1 server query, cached &
reused -- server hammering fixed) but Boltz's INPUT a3m parser crashed on
the cached file: KeyError '\x00'. Boltz writes several .a3m files (some
binary); we were grabbing a bad one.
Fix: select the largest a3m that looks like FASTA (starts with '>'), and
strip null bytes before caching. Raise with the candidate list if none
qualifies (so we can see what's there).
Pilot status: MSA caching + reuse confirmed working; this fixes the
a3m-format crash. Re-validate with a 2-drug pilot before the full run.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Junior B.
f74a58aa43