Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- ready
- Storage
- <5
- Strategy
- shared python312_slim.sif + lichen_py312_site + ablang2_py312_site + palm_py312_site + real LICHEN Model/model_weights.pt
- Next
- Production Ready for scoped LICHEN light-chain generation and light-chain perplexity mode using real model weights. Optional expansion: expose richer generation/filtering controls.
No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged LICHEN repo, Zenodo weights, SIF/artifacts/runner. Upstream needs PyTorch plus antibody tooling such as ANARCII/AbLang2 and separate model weights; shared PyTorch antibody SIF/overlay is preferred over a one-off per-tool SIF. Kept Smoke Pending. 2026-07-05 18:21 +08:00 backend re-audit: no staged LICHEN repo, Zenodo weights, SIF, artifacts, or runner found under shared backend root. Kept Smoke Pending. 2026-07-06 21:01 +08:00 implementation attempt: cloned oxpig/LICHEN to /media/nik/seagate_nik/bio_server/tools/lichen/source/LICHEN rev e25474e. Installed LICHEN 1.0.1 no-deps into /media/nik/seagate_nik/bio_server/envs/lichen_py312_site and verified imports with shared python312_slim.sif plus palm_py312_site (torch 2.4.1+cpu, pandas, Bio, LICHEN class). Zenodo record 15917096 lists Model.zip 94,236,081 bytes and Data.zip 66,272,551 bytes; Model.zip transfer started but stalled at about 21 MB, so no real model-weight Slurm generation smoke was submitted. 2026-07-06 21:34 +08:00 continuation: resumed official Zenodo Model.zip download but transfer remained very slow and was stopped cleanly at 39 MB partial file to avoid leaving background work. No model extraction or Slurm smoke submitted. 2026-07-06 22:18 +08:00 continuation: Python streaming resume advanced official Zenodo Model.zip from ~39 MB to 52,080,796 bytes, but the server closed the transfer before the expected 94,236,081 bytes. Partial file retained at /media/nik/seagate_nik/bio_server/models/lichen/Model.zip; no extraction or Slurm smoke submitted. 2026-07-06 23:06 +08:00 continuation: LICHEN Model.zip remains partial at 52,080,796 bytes after repeated official Zenodo resume attempts; no extraction or smoke submitted. 2026-07-07 00:14 +08:00 continuation: completed official Zenodo Model.zip download at 94,236,081 bytes, verified archive, extracted Model/model_weights.pt (101,736,258 bytes), staged ANARCII 2.0.8 small dependencies into lichen_py312_site, and reused shared ablang2_py312_site plus palm_py312_site with python312_slim.sif. Direct Slurm job 477 at /media/nik/seagate_nik/bio_server/runs/lichen/smoke_20260707_001236 loaded real weights, generated a light chain, and produced light_perplexity 1.28 with summary.json and results.csv. Promoted to Runner Adapter Pending pending web runner adapter/API wiring. 2026-07-08T00:33:06+08:00 SOP runner-adapter pass: added real backend adapter using shared python312_slim.sif, lichen_py312_site, ablang2_py312_site, palm_py312_site, and real model_weights.pt. Ubuntu runner API job cb7b111e4b6d / Slurm job 528 passed light_generation plus light_perplexity with generated_light_length=107 and perplexity=1.28, produced generated_light_chains.fasta, results.csv, lichen_runtime.json, job.log, slurm.out, and zero-byte slurm.err. Also isolated shared-SIF PYTHONPATH per tool to avoid overlay cross-contamination.