Better SoFiA-2 error messages in Stimela

[paoloserra]

I ran SoFiA-2 in Stimela (CARACal) on a cube with 10 channels. My S+C settings included smoothing with a spectral boxcar kernel of width 15 channels i.e., more channels than in the cube. That is silly, but it was the default (in CARACal) and so I didn't realise I was about to get in troubles.

Stimela gave the error appended below. The error is not very useful because it does not say what the problem is.

If I run SoFiA-2 with the same settings but outside Stimela I get a more useful error (also appended below).

It would be great to capture the full SoFiA-2 error message in Stimela.

Error message inside Stimela

# ____________________________________________________________________________
# 
#  Running S+C finder
# ____________________________________________________________________________
# 
#   Using the following parameters:
#   - Kernels
#     - spatial:        [0, 3, 6]
#     - spectral:       [0, 3, 7, 15]
#   - Flux threshold:   4.0 * rms
#   - Noise statistic:  median absolute deviation
#   - Flux range:       negative
# 
# Traceback (most recent call last):
#   File "/stimela_mount/code/run.py", line 74, in <module>
#     subprocess.check_call(shlex.split(_runc))
#   File "/usr/lib/python3.8/subprocess.py", line 364, in check_call
#     raise CalledProcessError(retcode, cmd)
# subprocess.CalledProcessError: Command '['sofia', 'sofia_parameters.par']' returned non-zero exit status 7.
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR: /usr/bin/singularity run --workdir /scratch/usd/pserra/Astro/caracal_devel/reduction/.stimela_workdir-17727784154736578 --contain returns error code 1
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR: job failed at 2026-03-06 07:27:57.442357 after 0:00:04.249195
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR: Traceback (most recent call last):
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:   File "/scratch/usd/pserra/Astro/caracal_devel/reduction/caracal-venv-py310/lib/python3.10/site-packages/stimela/recipe.py", line 825, in run
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:     job.run_job()
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:   File "/scratch/usd/pserra/Astro/caracal_devel/reduction/caracal-venv-py310/lib/python3.10/site-packages/stimela/recipe.py", line 495, in run_job
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:     self.job.run(output_wrangler=self.apply_output_wranglers)
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:   File "/scratch/usd/pserra/Astro/caracal_devel/reduction/caracal-venv-py310/lib/python3.10/site-packages/stimela/singularity.py", line 145, in run
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:     utils.xrun(
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:   File "/scratch/usd/pserra/Astro/caracal_devel/reduction/caracal-venv-py310/lib/python3.10/site-packages/stimela/utils/xrun_poll.py", line 285, in xrun
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR:     raise StimelaCabRuntimeError(
2026-03-06 07:27:57 CARACal.Stimela.make_SoFiA-2_mask-field0-iter1 ERROR: stimela.exceptions.StimelaCabRuntimeError: /usr/bin/singularity run --workdir /scratch/usd/pserra/Astro/caracal_devel/reduction/.stimela_workdir-17727784154736578 --contain returns error code 1

Error message outside Stimela

 Running S+C finder
____________________________________________________________________________

  Using the following parameters:
  - Kernels
    - spatial:        0, 3, 6
    - spectral:       0, 3, 7, 15
  - Flux threshold:   5.0 * rms
  - Noise statistic:  median absolute deviation
  - Flux range:       negative


ERROR: Illegal spectral kernel size encountered.
       Terminating with error code 7.