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fig5-whole-genome-wfmash-p95-updated-bin

Rerun Fig5 whole-genome wfmash p95 with updated ~/bin binary

Metadata

Statusdone
Assignedagent-2636
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-21T09:56:15.271615907+00:00
Started2026-06-21T09:58:58.397794654+00:00
Completed2026-06-21T10:57:51.028344242+00:00
Tagspedigree, fig5, wfmash, updated-binary, p95, whole-genome-alignment, raw-paf, chr3-homology, eval-scheduled
Eval score0.97
└ blocking impact0.95
└ completeness0.96
└ constraint fidelity0.85
└ coordination overhead0.97
└ correctness0.97
└ downstream usability0.98
└ efficiency0.94
└ intent fidelity0.91
└ style adherence0.97

Description

Input context:

  • Prior wfmash package: paper_prep/_brainstorming/pedigree_whole_genome_wfmash_p95/.
  • Prior wfmash evidence review: paper_prep/_brainstorming/fig5_whole_genome_wfmash_p95_evidence_review/REPORT.md.
  • Prior corrected whole-genome sweepGA package for shared inputs: paper_prep/_brainstorming/pedigree_whole_genome_sweepga_joint_parent/.
  • Recovered full assemblies: /moosefs/erikg/phrs/recovery/fig5-whole-genome-joint-parent-sweepga/.

User update: Use the newly updated local wfmash binary, not plain PATH lookup:

  • Required binary: /home/erikg/bin/wfmash
  • Expected realpath at task creation: /export/local/home/erikg/bin/wfmash-v0.24.2-12-ge040aa10
  • Expected version at task creation: v0.24.2-12-ge040aa10
  • Expected sha256 at task creation: 14a6d5c7ac7be8890e904d11121341df118fad0c11193d0e91a9899e18a53d60 Plain wfmash is unsafe because this shell still finds stale Guix 0.12.5 first.

Task: Rerun the Fig5 whole-genome wfmash direct-alignment test using the updated /home/erikg/bin/wfmash binary. This is a fresh provenance-controlled rerun, not reuse of the prior task-built v0.24.2 binary.

Comparisons:

  • PAN027pat_vs_PAN011_joint
  • PAN027mat_vs_PAN010_joint
  • PAN028mat_vs_PAN027_joint Use the same full whole-genome haplotype/joint-parent definitions as the prior corrected packages. Do not substitute window-only, chromosome-only, arm-only, or telomeric-only alignments. Candidate-window slicing is posthoc only.

Required runs:

  • Slurm, parallelizable across comparisons.
  • Primary literal run: /home/erikg/bin/wfmash -p 95 -t $THREADS -B /dev/shm/... TARGET.fa QUERY.fa > OUT.paf.
  • Use /dev/shm or node-local scratch through -B, stage target/query FASTAs there, bgzip raw PAFs, and copy back.
  • Record which, explicit path, realpath, --version, sha256sum, and first relevant help lines for the binary actually used.
  • Optional: rerun the permissive config (-p 95 -w 1k -l 1k -n 50 -f -M) if it can finish cheaply, but the primary decision must be based on the literal -p 95 raw PAFs.

Output package: Create paper_prep/_brainstorming/pedigree_whole_genome_wfmash_p95_updated_bin/ with README, config, scripts, logs, summaries, and ignored raw PAF paths/checksums. Required summaries:

  • summaries/wfmash_binary.tsv
  • summaries/wfmash_jobs.tsv
  • summaries/paf_file_summary.tsv
  • summaries/candidate_window_support.tsv

Acceptance:

  • All three whole-genome literal -p 95 wfmash runs complete, or failures are diagnosed with Slurm logs and exact next commands.
  • The package states whether the updated /home/erikg/bin/wfmash recovers chr3-target raw PAF rows for the PAN027 and PAN028 chr9 candidate windows.
  • Exact command logs prove /home/erikg/bin/wfmash or its realpath was used and -B /dev/shm/... was used.
  • No submission/ files are modified and no Fig5 schematic is created.

Depends on

Required by

Log