harvest-fig5-wfmash — octopus01:/moosefs/erikg/phrs

Metadata

Status	done
Assigned	`agent-2756`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-06-25T16:25:49.682060085+00:00
Started	2026-06-25T16:49:31.317225203+00:00
Completed	2026-06-25T16:56:12.757936769+00:00
Tags	`eval-scheduled`
Eval score	0.88
└ blocking impact	0.95
└ completeness	0.83
└ constraint fidelity	0.85
└ coordination overhead	0.91
└ correctness	0.85
└ downstream usability	0.90
└ efficiency	0.93
└ intent fidelity	0.86
└ style adherence	0.91

Description

Inspect Slurm job 1706563 from fig5-wg-wfmash-filtered-graph-untangle-pilot, collect the runtime command manifest and odgi untangle focus summaries from paper_prep/_brainstorming/fig5_whole_genome_graph_untangle_pilot/summaries/, and decide whether the WFMASH graph is valid enough to run the configured sweepga_fastga_f32_l2000 follow-on row. Implement directly — do not decompose further.

Validation

Slurm job 1706563 final state recorded with stdout/stderr reviewed
If successful, summaries/wfmash_p95_updated_bin_l2000.focus_summary.tsv and focus_segments.tsv are promoted or summarized in a tracked report
chr9q/chr3q, PAR X/Y, and acrocentric-control patterns are compared explicitly
Decision to run or not run sweepga_fastga_f32_l2000 is documented with rationale

## Description
Inspect Slurm job 1706563 from fig5-wg-wfmash-filtered-graph-untangle-pilot, collect the runtime command manifest and odgi untangle focus summaries from paper_prep/_brainstorming/fig5_whole_genome_graph_untangle_pilot/summaries/, and decide whether the WFMASH graph is valid enough to run the configured sweepga_fastga_f32_l2000 follow-on row. Implement directly — do not decompose further.

## Validation
- [ ] Slurm job 1706563 final state recorded with stdout/stderr reviewed
- [ ] If successful, summaries/wfmash_p95_updated_bin_l2000.focus_summary.tsv and focus_segments.tsv are promoted or summarized in a tracked report
- [ ] chr9q/chr3q, PAR X/Y, and acrocentric-control patterns are compared explicitly
- [ ] Decision to run or not run sweepga_fastga_f32_l2000 is documented with rationale

Depends on

Required by

done .flip-harvest-fig5-wfmash

Log

2026-06-25T16:27:53.961953393+00:00 Dependency rewired per user: harvest/review should wait for fig5-2kb-direct-similarity-pilot, not the graph/seqwish pilot. Graph pilot is being de-emphasized/stopped; final harvest should evaluate existing-alignment direct similarity outputs.
2026-06-25T16:49:31.317229291+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-06-25T16:49:39.189089199+00:00 Starting harvest of Slurm 1706563 WFMASH graph untangle pilot artifacts.
2026-06-25T16:51:55.976610842+00:00 Reviewed sacct state and Slurm stdout/stderr for 1706563; found no focus summaries because the graph/ODGI path did not complete.
2026-06-25T16:53:20.728809612+00:00 Drafted tracked harvest report with Slurm states, stderr review, command manifest summary, missing focus outputs, control comparison, and no-run decision.
2026-06-25T16:54:42.872261528+00:00 Validated: task-specific criteria met in HARVEST_WFMASH_JOB_1706563.md; no code/build changes required for this documentation harvest.
2026-06-25T16:55:25.257222328+00:00 Committed: ad69e0c — pushed to remote
2026-06-25T16:56:12.757944864+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-06-25T17:05:41.282113466+00:00 PendingEval → Done (evaluator passed; downstream unblocks)