Repository navigation
results: MAT campaigns — Mucoromycotina publication set; full Basidiomycota and Ascomycota on v0.6.0 - #14
Merged
Conversation
…e trees) 974 genomes (BFD 289, LCG 621, Jena 64) on v0.6.0 (run-7c7ed99): 865/973 called, 911 loci (Plus 482, Minus 425). Locus size between the inner ends of polished flank genes (579 loci, 23 genera) on a pruned genus tree. Synteny of 26 loci (P and M, 13 genera) with clinker and pyGenomeViz. Full-length sexP/sexM tree (IQ-TREE, 526 x 526, JTT+F+R8): sexP and sexM clades hold 0 tips of the other type (UFBoot 40 and 93); the HMG-box tree is still running. Detection reports only (reports_all.tar.zst); runs/ is not committed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya
…on v0.6.1 Regression (panel 166 + Zygo 23) v0.6.0 vs 2026-10-01 candidate: 0 changes. Pilots: 163 Basidiomycota (57 orders), 246 Ascomycota (30 classes). Basidiomycota: 3,270/3,275 reports, 0 failures; 2,982 called (2,745 without PR-only genomes; 1,360 PR calls unverified). Ascomycota: 19,380/19,415 reports, 17,314 called; 20 failures, all genetic code 26 (Alaninales). Alaninales re-run on v0.6.1 (PR #13): 20/20 reports; regression v0.6.1 vs v0.6.0: 0 changes. Report: analysis/2026-10-04_basidiomycota-ascomycota- v060-campaign.md; INDEX and open questions updated (R. toruloides HD open). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya
run-b04a77b (PR #13): 20/20 reports, 15/20 called vs 4/20 miniprot-only; median 457 s vs 34 s per genome. Regression vs v0.6.0: 0 changed loci. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya
…EADME Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Results only; no code or database change.
Mucoromycotina (
results/2026-10-03_mucoromycotina_mat/, reportanalysis/2026-10-03_mucoromycotina-mat-campaign.md)locus_size/). Flank pair differs by lineage.synteny/).Basidiomycota and Ascomycota on v0.6.0 (report
analysis/2026-10-04_basidiomycota-ascomycota-v060-campaign.md)unverified(strict-CAAX only). Most apparent losses vs 2026-09-26 are merges of one interval into one call.results/2026-10-04_alaninales_v061/); regression v0.6.1 vs v0.6.0: 0 changes.reports_all.tar.zst(everydetection_report.yaml+wall_seconds). Per-genome GFF3/FASTA are not committed.Open (curator)
redHDlocus on another contig (26 genomes).🤖 Generated with Claude Code
Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya