Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- production_validated_runner_api_slurm_alphacutter
- Storage
- <5
- Strategy
- compiled/binary SIF or shared python312_slim + ext3 overlay
- Next
- Production Ready. Optional hardening: expose uploaded PDB controls and AlphaCutter threshold settings in UI, preserve the mkdssp wrapper/runtime in deployment docs, and add a compact regression test for the bundled PDB.
AlphaCutter source staged from johnnytam100/AlphaCutter rev c1b8a96024f71509ac700ef232f632c13e40a886; source ~17 MB. Slurm jobs 404/405/407 reached real script on bundled PDB but failed on missing pandas, then biopandas, then Python 3.12 dependency compatibility: upstream pins pypstruct==0.1.2 exclude Python >=3.11, pcmap missing, and local overlay pulled NumPy 2.5 causing pyarrow/NumPy ABI conflict. No scientific output produced. 2026-07-05 SOP triage: previous backend Slurm jobs 404/405/407 reached real AlphaCutter code but failed before scientific output due missing pandas/biopandas and Python 3.12 dependency incompatibility: pypstruct excludes Python >=3.11, pcmap missing, and NumPy 2.x/pyarrow ABI conflict. Reclassified from Smoke Pending to Production Blocked until a compatible Python 3.8/3.10 environment exists. 2026-07-09T15:05:38+08:00 SOP promotion: AlphaCutter validated through Ubuntu runner API remote job c93a2723bc0f / Slurm job 587 using staged source /media/nik/seagate_nik/bio_server/tools/alphacutter/source/AlphaCutter, native Python 3.12 target /home/nik/bio_server_venvs/alphacutter_py312_site_20260709, and extracted DSSP runtime /home/nik/bio_server_venvs/alphacutter_runtime. The run completed in 4.132 s on bundled AF-A0A0A2JW93-F1-model_v4.pdb and produced 3 segments: 2 domains, 1 loop, 0 helices, 2 domain PDBs, 1 merged single PDB, mean domain pLDDT 85.4404597526678. Artifacts verified: summary.json, results.csv, alphacutter_summary.csv, alphacutter_output.fasta, alphacutter_result.json, alphacutter_stdout.txt, alphacutter_stderr.txt, input PDB, two AFCT domain PDBs, merged AFCT single PDB, slurm.out, slurm.err. Compatibility patches are runtime-local: mkdssp wrapper converts DSSP 4 stdout to legacy DSSP text and adds a temporary HEADER for chain-only PDBs; run-local AlphaCutter copy replaces scipy.stats.mode string aggregation with pandas mode for SciPy >=1.11.