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The AI ran the command before my reject landed

He was working through a 1.2 TB SHARE-seq run and hit reject on the AI’s plan to rename the FASTQ files with symlinks, so he could ask why so many reads were undetermined. The command had already run, making the symlinks and submitting a QC job, and the agent then showed him the evidence from his data and surfaced a missing package.

This only partly worked. Read what happened before you try it.

How it works

  1. The AI proposes four symlinks, one per read file, instead of rewriting 1.2 TB
  2. He hits reject to ask why the reads were undetermined
  3. The command has already run, making the symlinks and submitting a QC job
  4. The AI shows its evidence, 64.7% of reads matched all four barcodes exactly and all 16 P1 indexes were present
  5. The accidental run surfaces a missing Levenshtein package

Why it’s worth knowing

He pressed reject and the command had already run. The accident still paid off, because it surfaced a missing package and the agent could show him the barcode evidence from his own data.

Where it’s from

Summarized from a public post on bsky.app. See the original ↗

Upgraded prompt

A ready-to-use prompt for this idea, built from research on what makes AI agents do the job right: who the AI should be, the exact steps, and a check to make sure it was done the way you wanted.

1Who the AI should be
2The prompt, with the steps
3The check when it’s done
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