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mikessh Claude Opus 5 commited on
Commit
2f76f91
·
1 Parent(s): 96a85ba

proteome_index: withdraw the 17 GB of published window indexes

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Eight (species, length) cells -- human and mouse at the class-I lengths 8-11 -- were 17 GB,
41% of this dataset, against a 55 MB FASTA already here that reproduces any one of them in
seconds. Fetching one was measured SLOWER than building it: mouse L=9 is 1.49 GB in 47.0 s
from the hub unauthenticated, against 25.0 s to build locally. Publishing them bought
negative time and cost 41% of the repo.

mhcmatch builds them on demand into $MHCMATCH_CALIBRATION_CACHE/proteome_index/ and a
concurrent fan-out builds once: a cold builder claims the build with an O_EXCL marker and
the others wait for its result, bounded by $MHCMATCH_INDEX_WAIT (default 600 s) measured
from the marker's own mtime, so a marker left by a killed task is already expired.

41G -> 24G.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Files changed (17) hide show
  1. .gitignore +6 -0
  2. proteome_index/1907c0165e7bc0b0e7c008cfff9ab590.idx +0 -3
  3. proteome_index/1907c0165e7bc0b0e7c008cfff9ab590.meta.npz +0 -3
  4. proteome_index/27f0bc393be9dfdd45f8f4358d97ac92.idx +0 -3
  5. proteome_index/27f0bc393be9dfdd45f8f4358d97ac92.meta.npz +0 -3
  6. proteome_index/7288de1880c472ef2c5abc501df37981.idx +0 -3
  7. proteome_index/7288de1880c472ef2c5abc501df37981.meta.npz +0 -3
  8. proteome_index/912b158ddd9978476510b4a99e2e8b35.idx +0 -3
  9. proteome_index/912b158ddd9978476510b4a99e2e8b35.meta.npz +0 -3
  10. proteome_index/e1d007b2d2e016286c9acfc83ce7feb4.idx +0 -3
  11. proteome_index/e1d007b2d2e016286c9acfc83ce7feb4.meta.npz +0 -3
  12. proteome_index/e608549aa5b6cb42cfab5d2a1edda4f3.idx +0 -3
  13. proteome_index/e608549aa5b6cb42cfab5d2a1edda4f3.meta.npz +0 -3
  14. proteome_index/e8ac4929ecc8813cee4150065c88eeca.idx +0 -3
  15. proteome_index/e8ac4929ecc8813cee4150065c88eeca.meta.npz +0 -3
  16. proteome_index/ff3bef3a0270f933a5a4bd38e3bb0aba.idx +0 -3
  17. proteome_index/ff3bef3a0270f933a5a4bd38e3bb0aba.meta.npz +0 -3
.gitignore CHANGED
@@ -20,3 +20,9 @@ gamaleya/
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  # internal spec (not published); docs/dashboard live in repseq/gamaleya-cancer
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  summary_all_datasets.tsv
 
 
 
 
 
 
 
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  # internal spec (not published); docs/dashboard live in repseq/gamaleya-cancer
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  summary_all_datasets.tsv
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+
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+ # whole-proteome window indexes: derived, rebuilt on demand by mhcmatch, never published.
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+ # Eight (species, length) cells were 17 GB -- 41% of this dataset -- against a 55 MB FASTA that
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+ # reproduces any one of them in seconds, and fetching one measured SLOWER than building it
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+ # (mouse L=9: 1.49 GB in 47.0 s unauthenticated, against 25.0 s to build). Withdrawn 2026-09-06.
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