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hyphaltip merged 5 commits into from
Nov 12, 2026
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v0.9.0 release: results, default release v090, site data, README/About/landing (SEG-off replacement) #337

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c423f51
DRAFT v0.9.0 results: tables, manifests and report tarballs of the de…
hyphaltip Nov 12, 2026
21962ac
DRAFT v0.9.0 release switch: default release v090, README/About/landi…
hyphaltip Nov 12, 2026
a6ef8b6
DRAFT v0.9.0: regenerated site data (loci shards, summary, taxa) for …
hyphaltip Nov 12, 2026
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v0.9.0 results: the curator chose the SEG-off replacement and approve…
hyphaltip Nov 12, 2026
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Merge branch 'main' into v090-results-draft
hyphaltip Nov 12, 2026
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20 changes: 10 additions & 10 deletions README.md
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Expand Up @@ -10,7 +10,7 @@ idiomorph or mating type it is (for example Plus/Minus, MAT1-1/MAT1-2, HD/PR
alleles). Every reference record traces to a publication or a validated
deposit, and every call reports the evidence behind it.

Current release: [`v0.8.1`](https://github.com/stajichlab/MATPredict/releases/tag/v0.8.1) (detection code, database and the data, calls and counts shown on the site are those of the v0.8.1 run).
Current release: [`v0.9.0`](https://github.com/stajichlab/MATPredict/releases/tag/v0.9.0) (detection code, database and the data, calls and counts shown on the site are those of the v0.9.0 run).
Changes: [CHANGELOG.md](CHANGELOG.md).

## Contents
Expand Down Expand Up @@ -245,7 +245,7 @@ not an independent test.

### `matpredict detect`

Every option, policy, preset (`--preset v0.8.1` is what the v0.8.1 run used) and environment variable is listed in [`docs/detect-options.md`](docs/detect-options.md).
Every option, policy, preset (`--preset v0.9.1` is what the v0.9.0 run used) and environment variable is listed in [`docs/detect-options.md`](docs/detect-options.md).

```
matpredict detect --genome GENOME [--proteins PROTEINS] [--taxid TAXID]
Expand Down Expand Up @@ -507,28 +507,28 @@ pixi run -e test pytest -q
## Validation and known limits

Measured results (details in [analysis/INDEX.md](analysis/INDEX.md)). The NCBI public genomes and held-out rows are detection (call) rates from
the v0.8.1 definitive run, not accuracy: no truth set exists for the NCBI public genomes. Subphylum rates count the classes of each subphylum;
the v0.9.0 definitive run, not accuracy: no truth set exists for the NCBI public genomes. Subphylum rates count the classes of each subphylum;
the 12 Basidiomycota genomes suppressed by the shared list (no report) are counted as not called; the nine rust genomes of the allow list (#165) are searched. The ground-truth, typing and hold-out rows are
older measurements and were not repeated for v0.8.1. How each campaign was judged is in
older measurements and were not repeated for v0.9.0. How each campaign was judged is in
[results/2026-10_cleanrun_preparation/](results/2026-10_cleanrun_preparation/).

| Test | Result |
|---|---|
| Zygomycete ground-truth set (23 genomes) | 23/23 loci and idiomorphs |
| Held-out LCG Mucoromycotina genomes (never used in curation) | 549/621 called (v0.8.1 run) |
| Held-out Jena Mucoromycotina genomes | 61/64 called (v0.8.1 run) |
| Held-out LCG Mucoromycotina genomes (never used in curation) | 549/621 called (v0.9.0 run) |
| Held-out Jena Mucoromycotina genomes | 61/64 called (v0.9.0 run) |
| Idiomorph typing validation | 0/540 typed wrong |
| Pezizomycotina hold-out, order radius | 7/7 |
| Ascomycota, 19,415 NCBI public genomes (v0.8.1 run) | 17,618 called (90.7%) |
| Basidiomycota, 3,275 NCBI public genomes (v0.8.1 run) | 2,995 called (91.5%): Agaricomycotina 92.6%, Ustilaginomycotina 97.7%, Pucciniomycotina 86.3% |
| Mucoromycotina, 289 NCBI public genomes (v0.8.1 run) | 258 called (89.3%) |
| Ascomycota, 19,415 NCBI public genomes (v0.9.0 run) | 17,618 called (90.7%) |
| Basidiomycota, 3,275 NCBI public genomes (v0.9.0 run) | 2,995 called (91.5%): Agaricomycotina 92.6%, Ustilaginomycotina 97.7%, Pucciniomycotina 86.3% |
| Mucoromycotina, 289 NCBI public genomes (v0.9.0 run) | 258 called (89.3%) |

Known limits (open items in [analysis/open-questions.md](analysis/open-questions.md)):

- Only three phyla have curated families.
- A genome far from every reference often fails the evidence bar, so an
uncalled genome is weak evidence that the genome has no MAT locus. The full
Ascomycota run (19,415 genomes, v0.8.1) leaves 1,725 uncalled and 72 not run.
Ascomycota run (19,415 genomes, v0.9.0) leaves 1,725 uncalled and 72 not run.
- Fragmented assemblies can split a locus or lose its flanking genes.
- In Mucoromycota, *Absidia* flanking genes are often off-scaffold, and the
gene order of the Lichtheimiaceae is not yet known.
Expand Down
13 changes: 13 additions & 0 deletions results/2026-11-09_v090_ascomycota/MANIFEST.txt
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@@ -0,0 +1,13 @@
v0.9.0 definitive run, ascomycota campaign
commit: 7d73be58826620107fc0ea17436572ad4b2ff160
worktree: /bigdata/stajichlab/jstajich/projects/MATPredict/.claude/worktrees/run-7d73be5
DETECT_ARGS: --preset v0.9.1 --withheld-detail-policy on
tblastn SEG outlier policy: yes
allow list: db/allow.txt (rust genomes searched; large chunk GENOME_TIMEOUT=14400, epyc 8:00:00)
pixi.lock sha256: 675a15123d22857564dbb020592db9075cd60c8bb82f9cbb53a077abb31f4ac9
compute: throttled, 3 chains x 16 CPUs = 48 CPUs in flight (submit_throttled.py); jobs: results/2026-11-09_v090_submit/jobs.tsv; submitted 2026-11-08
replacement (chosen by the curator, 2026-11-12): the 372 genomes whose spans, gene sets, tiers or a locus changed under the tblastn outlier policy were rerun with it OFF on the same frozen code and preset (job 32033862, results/2026-11-09_seg_check2/segoff). reports_all.tar.zst holds those reruns (zz_rerun_segoff/) instead of the 372 SEG-on reports. With them every other span and gene set equals v0.8.1; the differences left are the approved rules and the #302 record (3 Pneumocystis matMi; GCA_052323795.1 outer span +16.7 kb, traced to the #302 record).
tables: scripts/build_cleanrun_tables.py on a hardlinked staging copy (reruns sort last, so they win); baseline columns compare with v0.8.1
determinism: 60 genomes run twice on this commit: identical as sets; one genome lists GAP1/BGL1 in a different order (hash seed; fixed in PR 335)
integrity: all 23,579 reports carry commit 7d73be5, db sha 6953f2e7..., preset v0.9.1, version 0.9.0
approval: the curator approved the outer-span extension of GCA_052323795.1 (+16.7 kb, traced to the #302 Pneumocystis carinii B80 record) on 2026-11-12.
31 changes: 31 additions & 0 deletions results/2026-11-09_v090_ascomycota/by_class.tsv
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class genomes reports called pct_called routing wall_median_s wall_p90_s wall_max_s loci n_label_unsupported tier_dropped tier_dropped_noted margin_fallback vote_collapse polished_model_lost distant_fragment high_supported high_tie_break high_grey outside_scope_high_supported outside_scope_high_tie_break outside_scope_high_grey defective_loci
Sordariomycetes 6016 6012 5628 93.6 lineage:5976; not_searched:36 111 200 738 5754 100 3 0 0 0 0 0 0 0 0 4361 0 0 2203
Eurotiomycetes 3220 3214 3104 96.6 lineage:3210; not_searched:4 100 170 501 3302 10 1 0 0 0 0 0 0 0 0 2057 0 0 1507
Pichiomycetes 2967 2966 2827 95.3 lineage:2652; phylum_fallback:220; direct:91; not_searched:3 20 38 90 3280 29 0 0 0 0 0 0 0 0 0 0 0 0 155
Dothideomycetes 2731 2730 2587 94.8 lineage:2724; not_searched:6 112 190 2092 2705 275 18 0 0 0 0 0 302 11 0 1855 0 0 552
Saccharomycetes 2646 2598 2211 85.1 lineage:2246; phylum_fallback:337; direct:14; not_searched:1 18 41 123 4430 156 0 0 0 0 0 0 0 0 0 0 0 0 300
Lecanoromycetes 479 478 413 86.4 lineage:476; not_searched:2 101 200 386 434 8 0 0 0 0 0 0 0 0 0 260 0 0 179
Leotiomycetes 435 430 399 92.8 lineage:430 116 221 355 414 12 1 0 0 0 0 0 0 0 0 275 0 0 213
Dipodascomycetes 398 397 157 39.5 phylum_fallback:225; lineage:168; not_searched:4 24 47 102 159 3 0 0 0 0 0 0 0 0 0 0 0 0 10
Pezizomycetes 172 172 139 80.8 lineage:169; direct:3 47 109 282 139 2 0 0 0 0 0 0 0 0 0 1 0 0 51
Schizosaccharomycetes 68 67 66 98.5 direct:59; lineage:8 13 32 57 136 0 0 0 0 0 0 0 0 0 0 0 0 0 7
Orbiliomycetes 67 67 4 6.0 phylum_fallback:67 110 157 211 4 0 0 0 0 0 0 0 0 0 0 1 0 0 0
Lipomycetes 59 59 3 5.1 phylum_fallback:59 39 71 141 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0
NA 52 48 29 60.4 phylum_fallback:38; lineage:10 89 165 256 32 1 0 0 0 0 0 0 0 0 0 16 0 0 6
Taphrinomycetes 22 22 5 22.7 lineage:22 11 31 50 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Trigonopsidomycetes 16 16 0 0.0 phylum_fallback:16 20 96 110 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Arthoniomycetes 13 13 8 61.5 lineage:11; not_searched:2 65 106 114 8 0 0 0 0 0 0 0 0 0 0 7 0 0 3
Geoglossomycetes 12 12 6 50.0 lineage:12 102 154 199 6 0 0 0 0 0 0 0 0 0 0 6 0 0 2
Pneumocystomycetes 11 11 9 81.8 lineage:11 6 14 17 9 2 0 0 0 0 0 0 0 0 0 0 0 0 1
Lichinomycetes 10 10 7 70.0 lineage:10 108 181 253 8 1 0 0 0 0 0 0 0 0 0 4 0 0 4
Candelariomycetes 4 4 4 100.0 lineage:4 122 146 146 4 0 0 0 0 0 0 0 0 0 0 1 0 0 2
Sporopachydermiomycetes 4 4 4 100.0 phylum_fallback:4 25 113 113 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0
Alloascoideomycetes 3 3 3 100.0 phylum_fallback:3 51 70 70 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Coniocybomycetes 2 2 2 100.0 lineage:2 92 94 94 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Saitoellomycetes 2 2 0 0.0 lineage:2 9 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Laboulbeniomycetes 1 1 0 0.0 lineage:1 51 51 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Neolectomycetes 1 1 0 0.0 lineage:1 13 13 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Novakomycetes 1 1 0 0.0 lineage:1 28 28 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sareomycetes 1 1 1 100.0 lineage:1 155 155 155 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Xylobotryomycetes 1 1 1 100.0 lineage:1 43 43 43 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Xylonomycetes 1 1 1 100.0 lineage:1 77 77 77 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1
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