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fig5-minimap2-harvest-active-slurm

Harvest active minimap2 Fig5 Slurm PAFs and finish chop/sweep

Metadata

Statusdone
Assignedagent-2660
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-22T07:11:31.130844602+00:00
Started2026-06-22T07:12:42.488607481+00:00
Completed2026-06-22T21:50:07.288190656+00:00
Tagspedigree, fig5, minimap2, pafchop, sweepga, slurm, eval-scheduled
Eval score0.78
└ blocking impact0.71
└ completeness0.75
└ constraint fidelity0.55
└ coordination overhead0.80
└ correctness0.77
└ downstream usability0.86
└ efficiency0.72
└ intent fidelity0.72
└ style adherence0.85

Description

The previous long-run minimap2 task closed while Slurm jobs 1704357, 1704358, and 1704359 were still running and no raw PAFs had been copied back. Do not treat that as a negative result.

Task:

  • Inspect current squeue/sacct state for jobs 1704357-1704359. If any are still running, monitor until they complete or hit their 24h wall time; do not cancel them.
  • Work in the existing package paper_prep/_brainstorming/pedigree_whole_genome_minimap2_asm5_allchains_longrun_chop_sweep/ from the agent-2652 branch/package, preserving provenance.
  • Refresh raw PAF status using the package scripts. If completed raw PAFs exist, summarize raw chr3 support for the PAN027/PAN028 Fig5 chr9 candidate windows.
  • If raw PAFs are complete, run 10kb pafchop-rs (l10000_o0) and then sweepGA PAF filtering on the chopped minimap2 PAFs for many:many and 4:many with --scaffold-jump 0, using /home/erikg/.cargo/bin/sweepga and /dev/shm scratch as appropriate.
  • Update README, logs, checksums/manifests, and summaries/minimap2_chop_sweep_chr3_support_summary.tsv with direct yes/no/not_evaluable answers.

Acceptance:

  • Direct answer: did minimap2 raw PAF emit chr3 target rows overlapping the PAN027/PAN028 chr9 windows?
  • Direct answer: if yes, did 10kb chopping plus sweepGA PAF filtering retain/catch chr3 homology?
  • Keep submission/ unchanged.
  • Do not overwrite the completed -f16 SweepGA package; reference it only for comparison.

Depends on

Required by

Log