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fig5-whole-genome-sweepga-qa-closeout

QA closeout for corrected Fig5 whole-genome sweepGA tests

Metadata

Statusdone
Assignedagent-2626
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-06-20T16:31:06.230056997+00:00
Started2026-06-21T00:31:54.133976975+00:00
Completed2026-06-21T00:36:04.877505057+00:00
Tagspedigree, fig5, sweepga, qa, closeout, correction, chopped-paf, pipeline-correction, whole-genome-alignment, no-window-fallback, eval-scheduled, devshm-scratch
Eval score0.95
└ blocking impact0.97
└ completeness0.95
└ coordination overhead0.95
└ correctness0.95
└ downstream usability0.95
└ efficiency0.93
└ intent fidelity0.89
└ style adherence0.95

Description

Input:

  • Handoff: paper_prep/_brainstorming/PEDIGREE_SWEEPGA_HANDOFF_2026-06-20.md.
  • Corrected package from fig5-whole-genome-joint-parent-sweepga.
  • Evidence decision package from fig5-whole-genome-sweepga-evidence-review.

Task: QA the corrected Fig5 sweepGA work. Verify full whole-genome input/alignment, joint parent targets, /dev/shm sweepGA/FastGA scratch, raw whole-genome many:many preservation, chopped PAF before filtering, and 1:1 diagnostic labeling. A chromosome-only, arm-only, or 500 kb-window run is not acceptable.

Output:

  • paper_prep/_brainstorming/fig5_whole_genome_sweepga_closeout/QA_REPORT.md.
  • Optional closeout addendum in _brainstorming linking task IDs and output directories.

Acceptance:

  • QA report gives pass/fail for six issues: full whole-genome input/alignment, joint parent target, /dev/shm sweepGA scratch, raw many:many preservation, chopped PAF before filtering, and 1:1 diagnostic labeling.
  • QA verifies summaries/input_manifest.tsv, summaries/chop_manifest.tsv, and Slurm logs/manifests for /dev/shm scratch.
  • QA states the current Fig5 evidence source, or says no corrected direct sweepGA source is acceptable yet.
  • No submission/ files are modified.

Depends on

Required by

Log