Staging reference data: the four tiers of bootstrap

Every reference table is fetched on first use, so none of this is required. bootstrap moves the download earlier, which is what a compute node with no outbound network needs. Each tier is a superset of the need above it, and each is independent of the others — pass several in one call.

call	size	what it stages, and who reads it
mhcmatch bootstrap	~16 MB	the isalgo/pmhc_data ligand panel, both tiers. Store.from_pmhc and therefore every presentation path. --tier full|shortlist takes one instead of both
--proteome human,mouse	51 MB	reference proteomes (human UP000005640 37 MB, mouse UP000000589 14 MB); also accepts a pathogen stem. Read by source, genes and the mimicry scan
--reference	~115 MB	the corpora, the tested-neoantigen database, the mimicry references and the expression tables — everything rank, neoag and mimicry read. This is the one a cluster wants: one call, and the run is offline-complete

There is no index tier, because there is nothing left worth staging. Peptide origin search – what source, genes, the cassette safety screen and the mimicry annotation all ultimately ask – runs on one seqtree.TextIndex per proteome, built from the FASTA the row above already fetches. Measured on the human proteome (147,506 records, 69,578,135 residues): 0.7 s to build, 0.6 GB peak RSS, answering every peptide length and every substitution radius from that one build.

What it replaced was one index per query length: ~65 s and 12.6 GB peak for the first, ~5.5 GB apiece on disk, and ~82 GB for the fifteen lengths class II admits. That cost is what an --index flag, a proteome_index/ cache directory, an O_EXCL build marker and a $MHCMATCH_INDEX_WAIT timeout all existed to manage; all four are gone with it. A fan-out needs no hand-off now, because the race-free design is the one with nothing to race on – at 0.7 s, rebuilding costs less than agreeing about who rebuilds.

Note

--proteome takes a plain comma-separated list of names — human,mouse, or a pathogen stem. There are no per-length specs: the two-separator grammar this page used to document went with the per-length index described above, and cmd_bootstrap splits on commas only.