finalize-fig5-raw — octopus01:/moosefs/erikg/phrs

Metadata

Status	failed
Assigned	`agent-2842`
Agent identity	`46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e`
Created	2026-06-27T11:41:16.046190924+00:00
Started	2026-06-27T11:58:59.350571254+00:00
Tags	`eval-scheduled`
Failure reason	Attempted finalization but Slurm arrays 1706840-1706845 were still incomplete: at 2026-06-27T13:47Z two tasks from 1706840 were running, six array ranges were pending, only 15 shard metadata files and 13 temp gzip shard outputs existed, and zero final-named shard outputs existed. The finalizer requires all 906 shard rows to be OK, so running it now would fail or assemble incomplete data. Recorded recovery notes and current state in commit 437139f.

Description

Finalize the submitted Slurm arrays for fig5-raw-manymany-impg-similarity-2kb-sharded. File scope: paper_prep/_brainstorming/fig5_raw_manymany_impg_similarity_2kb_sharded/outputs/, metadata/, manifests/shard_completion_manifest.tsv, manifests/assembled_outputs.tsv, summaries/, REPORT.md only. Implement directly — do not decompose further.

Arrays submitted by the parent task: 1706840,1706841,1706842,1706843,1706844,1706845. Run the existing finalizer after all shards complete:

python3 paper_prep/_brainstorming/fig5_raw_manymany_impg_similarity_2kb_sharded/scripts/finalize_2kb_sharded_impg.py

Validation

All 906 shard rows in manifests/shard_completion_manifest.tsv have state OK
Six assembled compressed outputs exist under outputs/assembled/, one per required method x comparison
Assembled outputs have one header each and nonzero data rows
Summary tables exist: per_window_target_similarity_support.tsv, top_interchromosomal_targets.tsv, all_interchromosomal_targets.tsv, chr9q_chr3q_windows.tsv, par_controls.tsv, acrocentric_controls.tsv, full_genome_target_pattern_tracks.tsv
REPORT.md updated with final Slurm completion state, output paths, and row counts

## Description
Finalize the submitted Slurm arrays for fig5-raw-manymany-impg-similarity-2kb-sharded. File scope: paper_prep/_brainstorming/fig5_raw_manymany_impg_similarity_2kb_sharded/outputs/, metadata/, manifests/shard_completion_manifest.tsv, manifests/assembled_outputs.tsv, summaries/, REPORT.md only. Implement directly — do not decompose further.

Arrays submitted by the parent task: 1706840,1706841,1706842,1706843,1706844,1706845. Run the existing finalizer after all shards complete:

python3 paper_prep/_brainstorming/fig5_raw_manymany_impg_similarity_2kb_sharded/scripts/finalize_2kb_sharded_impg.py

## Validation
- [ ] All 906 shard rows in manifests/shard_completion_manifest.tsv have state OK
- [ ] Six assembled compressed outputs exist under outputs/assembled/, one per required method x comparison
- [ ] Assembled outputs have one header each and nonzero data rows
- [ ] Summary tables exist: per_window_target_similarity_support.tsv, top_interchromosomal_targets.tsv, all_interchromosomal_targets.tsv, chr9q_chr3q_windows.tsv, par_controls.tsv, acrocentric_controls.tsv, full_genome_target_pattern_tracks.tsv
- [ ] REPORT.md updated with final Slurm completion state, output paths, and row counts

Depends on

Required by

open .flip-finalize-fig5-raw

✉ Messages 2 messages (2 unread)

#1codex2026-06-27T12:05:09.434177514+00:00read

For plotting summaries, reduce IMPG similarity output to the single best target hit per 2 kb query/target window. Keep all raw/all-hit assembled output and all_interchromosomal_targets.tsv for audit/debug, but per_window_target_similarity_support.tsv and full_genome_target_pattern_tracks.tsv should choose the best similarity/support record per window, with deterministic tie-breaking documented. Do not plot multiple overlapping hits per window as separate tracks unless explicitly requested.

#2finalize-fig5-raw2026-06-27T12:15:42.881786799+00:00read

Acknowledged — I will keep assembled raw/all-hit outputs and all_interchromosomal_targets.tsv intact, then collapse per_window_target_similarity_support.tsv and full_genome_target_pattern_tracks.tsv to one deterministic best record per 2 kb window and document the tie-break in REPORT.md.

Log

2026-06-27T11:58:00.868067779+00:00 Lightweight assignment: agent=random-agent-46f6237a (46f6237a), exec_mode=full, context_scope=task, reason=This is a concrete pipeline finalization task with file updates and validation, which best matches the Pipeline Operator’s execution-oriented style.
2026-06-27T11:58:59.350576434+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-06-27T11:59:15.439192446+00:00 Starting finalization: checking Slurm arrays and existing shard outputs before running finalizer
2026-06-27T12:00:14.044113380+00:00 Waiting for Slurm arrays 1706840-1706845 to complete before final assembly; current scheduler state still has running/pending tasks
2026-06-27T12:03:54.549535304+00:00 Still waiting on Slurm completion; as of latest check arrays have pending/running jobs and only initial shard temp outputs exist
2026-06-27T12:05:09.755493517+00:00 User requirement added 2026-06-27: plotting summaries must keep/select the best similarity hit per 2 kb window. Preserve all-hit output separately for audit, but per-window plotting tables/tracks should reduce to one best record per window with documented deterministic tie-breaking.
2026-06-27T12:15:14.171349997+00:00 Confirmed slow shards are active via impg logs; will normalize tmp shard filenames after completion because job script leaves .tmp.<job>_<task>.gz names while finalizer expects final .tsv.gz paths
2026-06-27T12:26:23.049490259+00:00 Slurm wait continues: first array still has two active long shards, with no failed states observed
2026-06-27T12:47:34.879298576+00:00 Still waiting after roughly one hour on first-array dense shards; logs continue to update and no Slurm failures are present
2026-06-27T13:08:40.894975533+00:00 Extended wait: first Slurm array still has two long-running dense shards; finalizer not run because required all-OK shard state is not attainable yet
2026-06-27T13:48:34.528089481+00:00 Validation blocked: shard_completion_manifest cannot reach 906 OK rows because Slurm arrays 1706840-1706845 remain active/pending; finalizer not run against incomplete shards
2026-06-27T13:48:34.696532903+00:00 Committed blocked finalization handoff: 437139f — pushed to remote
2026-06-27T13:49:18.858657966+00:00 Task marked as failed: Attempted finalization but Slurm arrays 1706840-1706845 were still incomplete: at 2026-06-27T13:47Z two tasks from 1706840 were running, six array ranges were pending, only 15 shard metadata files and 13 temp gzip shard outputs existed, and zero final-named shard outputs existed. The finalizer requires all 906 shard rows to be OK, so running it now would fail or assemble incomplete data. Recorded recovery notes and current state in commit 437139f.