Metadata
| Status | done |
|---|---|
| Assigned | agent-2715 |
| Agent identity | 46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e |
| Created | 2026-06-24T09:02:11.361090335+00:00 |
| Started | 2026-06-24T09:03:48.004218998+00:00 |
| Completed | 2026-06-24T22:44:47.085864806+00:00 |
| Tags | fig5, sweepga, fastga, frequency32, slurm, eval-scheduled |
| Eval score | 0.91 |
| └ blocking impact | 0.86 |
| └ completeness | 0.93 |
| └ constraint fidelity | 0.85 |
| └ coordination overhead | 0.83 |
| └ correctness | 0.95 |
| └ downstream usability | 0.84 |
| └ efficiency | 0.90 |
| └ intent fidelity | 0.83 |
| └ style adherence | 0.93 |
Description
Run a new Fig5 whole-genome SweepGA/FastGA f32 raw alignment iteration.
Goal: reproduce the f16 raw many:many whole-genome alignment matrix at FastGA k-mer frequency 32 so downstream query-grid chop/filter panels can compare f16 vs f32.
Required run shape:
- Create a distinct package: paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency32/. Do not overwrite f16 outputs.
- Use the same comparisons and full whole-genome FASTA input symlinks as the f16 package.
- Run SweepGA/FastGA on Slurm only, not on the head node.
- Command semantics: /home/erikg/.cargo/bin/sweepga --fastga --fastga-frequency 32 --num-mappings many:many --scaffold-jump 0 --temp-dir /dev/shm/... --output-file <query.fa> <target.fa>.
- Use /dev/shm scratch for SweepGA/FastGA, with logs proving the scratch path.
- Use the current installed sweepGA binary and record which/realpath/version/sha256 plus --check-fastga output.
- Produce raw PAFs named clearly with frequency32_many_many_j0.
Validation:
- gzip/pigz test every raw PAF.
- Write sha256 sidecars.
- Write summaries/slurm_jobs.tsv, summaries/sweepga_binary.tsv, summaries/fastga_binary.tsv, summaries/input_manifest.tsv, and a raw candidate-window chr3 support summary comparable to f16.
Acceptance criteria:
- All three whole-genome comparison raw PAFs exist, validate, and have sha256 sidecars.
- README documents this as the f32 iteration and explicitly references the f16 package for comparison.
- No heavy alignment work is run on the head node.
- Commit with message: feat: fig5-sweepga-fastga-frequency32-raw (agent-NNN)
Depends on
Required by
Log
- 2026-06-24T09:02:56.998958870+00:00 Lightweight assignment: agent=random-agent-46f6237a (46f6237a), exec_mode=full, context_scope=task, reason=The task is a concrete Slurm-backed pipeline run with validation and artifact bookkeeping, which best matches the Pipeline Operator role and a full-write execution mode.
- 2026-06-24T09:03:48.004223566+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-06-24T09:04:06.060862857+00:00 Starting f32 SweepGA/FastGA package setup; first mirroring f16 inputs and scripts.
- 2026-06-24T09:06:32.818720397+00:00 Prepared frequency32 package skeleton, binary provenance, and whole-genome input manifest; submitting Slurm raw matrix.
- 2026-06-24T15:07:22.163821916+00:00 Frequency32 Slurm jobs still running after 6h; PAN027mat_vs_PAN010 completed FastGA and is streaming final gzip; other two remain in FastGA.
- 2026-06-24T17:09:01.021922900+00:00 Frequency32 raw matrix status after 8h: PAN027mat_vs_PAN010 completed and validated; PAN027pat_vs_PAN011 and PAN028mat_vs_PAN027 still running in FastGA on Slurm.
- 2026-06-24T18:09:18.409012492+00:00 Frequency32 status after 9h: one raw PAF complete/validated; two jobs still RUNNING in FastGA on Slurm with no error markers.
- 2026-06-24T19:09:42.668084552+00:00 Frequency32 status after 10h: one raw PAF complete/validated; two Slurm jobs still RUNNING in FastGA with unchanged logs and no error markers.
- 2026-06-24T20:09:55.643584338+00:00 Frequency32 status after 11h: one raw PAF complete/validated; PAN027pat_vs_PAN011 and PAN028mat_vs_PAN027 still RUNNING in FastGA on Slurm.
- 2026-06-24T21:08:48.349550962+00:00 Frequency32 status after 12h: PAN027mat complete/validated; PAN027pat completed SweepGA and is streaming final gzip; PAN028 still converting FastGA output.
- 2026-06-24T22:42:32.968574687+00:00 Validated: all three frequency32 raw PAFs exist locally, gzip/sha256 checks passed, summaries and README are staged for commit
- 2026-06-24T22:43:14.015710770+00:00 Committed: eebb5c8 — feat: fig5-sweepga-fastga-frequency32-raw (agent-2715)
- 2026-06-24T22:43:58.259986096+00:00 Pushed: eebb5c8 to origin/wg/agent-2715/fig5-sweepga-fastga-frequency32-raw
- 2026-06-24T22:44:47.085872971+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-06-24T22:53:22.880838495+00:00 PendingEval → Done (evaluator passed; downstream unblocks)