[Bug] False positive [bio] safeguard trigger on routine RNA-seq statistical analysis

Status Open
Reported on v2.1.278
Maintainer reply None cached
Activity 0 comments · opened Sep 20, 2026

Bug Description
False positive on [bio] — transcriptomics manuscript revision Doctoral work (PPGEBB/UFPR) on host transcriptomic response in chromoblastomycosis. The session had already completed 33 minutes of legitimate work on this same dataset — BH correction, pathway enrichment review, figure/legend edits — and produced a normal, useful result. After that, the safeguard fired on three consecutive turns, all of them plain editorial and statistical review of files already on disk: reading P20_vias_fgsea.tsv and P20_TPM_por_biblioteca.tsv with a short Python heredoc to check p-value adjustment, redundant pathway collapsing, and consistency between tables and text. No new experiments, no protocol, no organism manipulation — host gene expression tables from an already-published pipeline. Rewriting the prompt with explicit academic framing did not change anything, which suggests the trigger is the domain plus data analysis rather than the wording. Blocking routine RNA-seq statistics review makes the model unusable for standard mycology and host-response publication work. Details tag shown: [bio]. Model: Fable 5.1.

Environment Info

  • Platform: linux
  • Terminal: gnome-terminal
  • Version: 2.1.278
  • Feedback ID: 06fc74f5-fa3a-4026-9e7f-e9b7ebc1fd2b

Errors

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