Metadata
| Status | done |
|---|---|
| Assigned | agent-2617 |
| Agent identity | 46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e |
| Created | 2026-06-20T16:50:43.412182335+00:00 |
| Started | 2026-06-20T18:12:07.120670052+00:00 |
| Completed | 2026-06-20T18:30:23.492609089+00:00 |
| Tags | eval-scheduled |
| Eval score | 0.90 |
| └ blocking impact | 0.93 |
| └ completeness | 0.88 |
| └ constraint fidelity | 0.85 |
| └ coordination overhead | 0.89 |
| └ correctness | 0.90 |
| └ downstream usability | 0.91 |
| └ efficiency | 0.85 |
| └ intent fidelity | 0.75 |
| └ style adherence | 0.94 |
Description
The whole-genome Fig5 sweepGA correction is blocked because /moosefs/pangenomes/washu_pedigree/PAN011.fa.gz and PAN011.fa.gz.fai returned input/output errors on Slurm compute node octopus07 during jobs 1704278 and 1704279. Provide or repair a readable full whole-genome PAN011 assembly plus index; do not substitute the 500 kb telomeric-window FASTA.\n\n## Validation\n- [ ] gzip -t /moosefs/pangenomes/washu_pedigree/PAN011.fa.gz passes on a Slurm compute node\n- [ ] head /moosefs/pangenomes/washu_pedigree/PAN011.fa.gz.fai shows PAN011#1 and PAN011#2 full-chromosome records on a Slurm compute node\n- [ ] A full-assembly path usable by paper_prep/_brainstorming/pedigree_whole_genome_sweepga_joint_parent/scripts/prepare_inputs.py is documented
Depends on
Required by
Log
- 2026-06-20T18:11:27.064650049+00:00 Lightweight assignment: agent=random-agent-46f6237a (46f6237a), exec_mode=full, context_scope=task, reason=This is a concrete filesystem/data-repair prerequisite, so the Pipeline Operator is the best fit for checking the broken PAN011 assembly, repairing or replacing it with a readable full-genome copy plus index, and documenting the usable path.
- 2026-06-20T18:12:03.425351416+00:00 Coordinator diagnosis: file metadata/stat and first bytes of PAN011.fa.gz can be read, but PAN011.fa.gz.fai and PAN011.fa.gz.gzi small reads hang/timeout, and Slurm job 1704279 hit gzip Input/output error on PAN011.fa.gz. This points to MooseFS data chunk availability/corruption, not Unix permissions. Dependency direction fixed so this prerequisite can be handled before retrying the whole-genome sweepGA task.
- 2026-06-20T18:12:07.120673919+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-06-20T18:12:32.627201660+00:00 Starting PAN011 full-assembly restore: checking target files, downstream input expectations, and Slurm availability
- 2026-06-20T18:20:47.832408387+00:00 Canonical /moosefs/pangenomes/washu_pedigree/PAN011 files reproduce Input/output error; noninteractive sudo unavailable; rebuilding full PAN011 assembly from public WashU v1.1 diploid source into writable recovery path
- 2026-06-20T18:27:39.676196025+00:00 Validated recovered full assembly on octopus07: job 1704283 completed 0:0; gzip -t passed; .fai head starts PAN011#1#chr1 and PAN011#2#chr1 with 46 full-chromosome records. Canonical /moosefs/pangenomes path still fails job 1704284 with Input/output error; cannot replace guarracino-owned files without owner/admin.
- 2026-06-20T18:29:37.926875056+00:00 Committed: 19f19c9 — restored full PAN011 assembly at /moosefs/erikg/phrs/recovery/prereq-restore-readable/PAN011.fa.gz and documented recovery/validation scripts
- 2026-06-20T18:29:58.566255427+00:00 Pushed commit 19f19c9 to origin/wg/agent-2617/prereq-restore-readable
- 2026-06-20T18:30:23.492618086+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-06-20T18:36:14.153786833+00:00 PendingEval → Done (evaluator passed; downstream unblocks)