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research-inventory-files

Research: inventory files and cluster setup

Metadata

Statusdone
Assignedagent-8
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-03-31T21:03:16.997809694+00:00
Started2026-03-31T21:04:28.657005806+00:00
Completed2026-03-31T21:07:06.407118449+00:00
Tagsresearch, eval-scheduled
Eval score0.92
└ blocking impact0.92
└ completeness0.95
└ coordination overhead0.95
└ correctness0.90
└ downstream usability0.93
└ efficiency0.90
└ intent fidelity0.93
└ style adherence0.92

Description

Goal

Read and summarize the key context files for the PHR gene enrichment pipeline.

Files to read

  1. TODO.md — the full task specification (PHR-specific GO enrichment)
  2. subtelomeric_analysis_report.md — current analysis state and findings
  3. OCTOPUS_CLUSTER.md — cluster setup, available tools, job submission

Also check

  • Verify CHM13-HG002.sub-telo-phrs.bed exists and inspect first/last few lines
  • Verify chm13v2.0_RefSeq_Liftoff_v5.2.gff3.gz exists
  • Check if bedtools and R (with clusterProfiler) are available on the head node
  • Check if Angela's xlsx files are present: PHR_Subtelomeric Regions_Summary_March 2026.xlsx, PHR_enrichment_summary.xlsx, PHR_enrichment_all_results.xlsx
  • Check Andrea's annotation path: /moosefs/guarracino/HPRCv2/PHR_III/hprc_annotations/ for CHM13 GFF3

Output

Log a structured summary with:

  • Which files exist and their locations
  • What tools are available on the head node (bedtools, R, clusterProfiler)
  • Whether we need the cluster for any of the 5 steps, or if head node suffices
  • Any missing files or dependencies that need resolving

Validation

  • All file checks are logged with exists/missing status
  • Tool availability is confirmed
  • A clear recommendation on head-node-only vs cluster usage is provided

Depends on

Required by

Log