Dry Lab / Computational: exit code failure

1. Ranked causes

   1. Missing or mismatched input file pathError occurs immediately at job start, before any real compute.
   2. Uncaught exception in the script logicStack trace visible in the CLI log pointing to a specific line.
   3. Dependency / environment mismatch (wrong package version)Error mentions an unexpected function signature or missing attribute.
   4. Downstream tool in the pipeline failed silently and this step consumed a truncated fileInput file exists but is unexpectedly small or empty.

2. Recovery steps

   1. Re-check the input dataset path for typos or a stale symlinkThe most common single cause of an immediate non-zero exit.
   2. Read the full CLI log / stack trace and fix the reported lineExit-code failures almost always log the true cause; do not guess before reading it.
   3. Pin the environment/container to the exact version specified in the protocolVersion drift between runs is the second most common cause.
   4. Verify the size/checksum of every upstream input file before re-runningCatches a silently truncated upstream step.

3. Controls first

   • Did a known-good control input / fixture exit 0 on the same environment?If no: Environment or script regression — not just this sample's path.
   • Does the CLI log contain a Python/R stack trace or a clear error message?If yes: Fix the specific reported line/module rather than re-running blind.
   • Does the CLI log contain a Python/R stack trace or a clear error message?If no: Check input file existence and environment pinning first.

Diagnose your run

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