Wrap Augustus rerun extraction in timeout-safe error handling

[hyphaltip]

_augustus_rerun called _extract() without any error handling, meaning a timed-out or truncated Augustus output file in the second pass would crash the entire run. The first-pass extraction already had a try/except guard; the second pass was missing it.

Change

• _augustus_rerun extraction loop (funannotate-BUSCO2.py ~L1502): wrapped _extract(mainout, plain_name) and _extract(mainout, plain_name, aa=False) in the same try/except Exception block used by the first-pass loop, logging a warning and skipping the offending file rather than propagating the exception.

try:
    self._extract(self.mainout, plain_name)
    self._extract(self.mainout, plain_name, aa=False)
except Exception as e:
    _logger.warning(
        'Failed to extract proteins from %s (possibly truncated by timeout), skipping: %s'
        % (plain_name, e)
    )

This makes timeout resilience consistent across both Augustus passes.

[Copilot]

Pull request overview

This PR addresses issue #1169 where Augustus can hang indefinitely during BUSCO-based training by introducing a per-job timeout that kills long-running Augustus subprocesses and allows the overall run to continue.

Changes:

• Added --augustus_timeout to funannotate-BUSCO2.py and enforced per-job timeouts in threaded Augustus execution (with timing/timeout summary logging).
• Forwarded a new funannotate predict CLI option (--augustus_BUSCO_timeout) into the BUSCO2 wrapper as --augustus_timeout.
• Documented the new behavior and flags in CHANGES.md.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

File	Description
funannotate/predict.py	Adds a new CLI flag and forwards it to the BUSCO2 subprocess invocation.
funannotate/aux_scripts/funannotate-BUSCO2.py	Implements per-job Augustus timeouts, kill logic, and post-run timing/timeout logging.
CHANGES.md	Documents the new timeout feature and related CLI options.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.