Metadata
| Status | done |
|---|---|
| Assigned | agent-2727 |
| Agent identity | 46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e |
| Created | 2026-06-24T09:03:01.606384637+00:00 |
| Started | 2026-06-24T22:54:24.525472792+00:00 |
| Completed | 2026-06-25T09:06:10.241319889+00:00 |
| Tags | fig5, sweepga, fastga, frequency32, query-grid, slurm, eval-scheduled |
Description
Run query-grid chop/filter for the Fig5 f32 raw SweepGA/FastGA alignment iteration.
Dependency: use raw f32 many:many PAFs from fig5-sweepga-fastga-frequency32-raw and the merged query-grid pafchop-rs.
Required run shape:
- Work only under paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency32/.
- Chop from raw f32 PAFs directly, not from prior chopped outputs.
- Use pafchop --chunk-mode query-grid --overlap 0 for chop lengths 10000, 5000, 2000. Do not attempt 1000 unless explicitly added later; f16 1kb was cancelled for runtime.
- Use distinct output dirs: chopped_paf_qgrid_l{N}_o0 and filtered_paf_chop_sensitivity_query_grid/l{N}.
- Filter each query-grid chopped PAF with SweepGA: --num-mappings 1:1 --scaffold-jump 0 --scoring ani --overlap 0.
- Use Slurm/job arrays and /dev/shm scratch; do not run heavy chopping/filtering on the head node. Use pigz for compression/decompression.
Validation:
- pigz -t all chopped and filtered PAFs.
- Write sha256 sidecars.
- Record job IDs, hosts, commands, binary paths, binary sha256, chunk mode, length, threads, scratch dir, and status in summary TSVs.
- Write a shifted-boundary audit proving f32 chunks are on the absolute query grid.
Acceptance criteria:
- All 9 required comparison x length filtered outputs exist and validate.
- query_grid_chop_filter_manifest.tsv clearly distinguishes f32 from f16.
- README or notes state the exact f32 settings and point to f16 for comparison.
- Commit with message: feat: fig5-f32-query-grid-chop-filter-rerun (agent-NNN)
Depends on
Required by
Log
- 2026-06-24T22:53:32.742036402+00:00 Lightweight assignment: agent=random-agent-46f6237a (46f6237a), exec_mode=full, context_scope=task, reason=Pipeline Operator best matches the Slurm-heavy chop/filter rerun, with concrete-first execution and strong fit for job orchestration, validation, and file handling.
- 2026-06-24T22:54:24.525476469+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-06-24T22:54:45.740092045+00:00 Starting f32 query-grid chop/filter run: inventorying raw PAFs, scripts, and existing outputs
- 2026-06-24T22:57:34.356253013+00:00 Built pafchop query-grid binary; submitting f32 3x3 Slurm chop/filter array with lengths 10000,5000,2000
- 2026-06-24T22:58:40.046996350+00:00 First array 1706541 failed immediately from wrong pafchop path before work; corrected to repo target/release/pafchop and resubmitting
- 2026-06-24T23:35:56.207702062+00:00 Slurm array 1706550 running on compute node; first six cells active in chop phase, no head-node heavy work
- 2026-06-25T07:13:15.693609522+00:00 Manual intervention after user noticed pafchop was serial: added pafchop --threads implementation in Rust, patched active f32 run script to pass SLURM_CPUS_PER_TASK, rebuilt /moosefs/erikg/phrs/.wg-worktrees/agent-2727/target/release/pafchop (sha256 a8c95c6a1914baca92c83bdca672619cba86344eda59a960959c34fe8350cb37), cancelled obsolete serial array cell 1706550_9, and resubmitted only task index 9 as job 1706559 with 48 CPUs and PAFCHOP_RECORDS_PER_THREAD=32. Eight prior f32 query-grid cells remain completed.
- 2026-06-25T07:13:21.773044406+00:00 Array 1706550 completed 8/9 cells; PAN028 2kb cell was cancelled before finalization, inspecting and preparing single-cell rerun
- 2026-06-25T07:14:18.507120550+00:00 Resubmitted missing PAN028 2kb query-grid cell as single Slurm job 1706560
- 2026-06-25T07:15:28.088475849+00:00 Cancelled duplicate job 1706560 after WG/worker also resubmitted task 9; retained manual 48-thread replacement 1706559_9 on octopus07. Removed 1706560 temp outputs so only one writer remains for PAN028mat_vs_PAN027_joint l2000.
- 2026-06-25T07:45:49.874749248+00:00 Corrected pafchop implementation again: replaced block-per-worker scheduling with a persistent dynamic worker pool where each PAF record is an independent work item and output is emitted deterministically by original line order. Rebuilt active binary /moosefs/erikg/phrs/.wg-worktrees/agent-2727/target/release/pafchop sha256 b1cd0f335206eb0b30d7981a8f608d90ba01d08085b8603bba25cc2425311726. Cancelled bad 1706559 after its temp output was unlinked; resubmitted only task 9 as 1706561 with 48 CPUs, PAFCHOP_QUEUE_DEPTH=384. Current process has 49 threads and is actively using multi-core CPU.
- 2026-06-25T07:58:52.620345013+00:00 Validated: 8/9 f32 query-grid chop/filter cells completed and pigz-tested; PAN028 2kb failed after Slurm cancellations 1706550_9, 1706559_9, 1706560
- 2026-06-25T08:01:10.523795186+00:00 Committed: df2ed37 — feat: fig5-f32-query-grid-chop-filter-rerun (agent-2727); pushed partial 8/9 run metadata and cancellation notes
- 2026-06-25T08:51:18.842637354+00:00 Manual follow-up: Slurm job 1706561_9 completed on octopus07 in 01:02:44 and produced/validated PAN028mat_vs_PAN027_joint l2000 query-grid filtered PAF. Its log shows SweepGA was invoked without --threads and reported cpu:1.0x. Patched query-grid wrappers so future filter invocations pass --threads $THREADS from SLURM_CPUS_PER_TASK; main commit 83a9127 and matching active f32 worktree edit.
- 2026-06-25T09:04:37.731320201+00:00 Validated: final retry 1706561_9 completed PAN028 2kb; collector reports 9 query-grid chopped/filter outputs OK
- 2026-06-25T09:05:20.664683965+00:00 Committed: 2c17cb5 — final retry completed 9/9 f32 query-grid outputs; pushed to remote
- 2026-06-25T09:06:10.241326982+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-06-25T09:17:57.258473884+00:00 PendingEval → Done (evaluator passed; downstream unblocks)