Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Align tilt-series additional arguments #1156

Open
FlorianBeckOle opened this issue Jun 26, 2024 · 0 comments
Open

Align tilt-series additional arguments #1156

FlorianBeckOle opened this issue Jun 26, 2024 · 0 comments

Comments

@FlorianBeckOle
Copy link

Describe your problem
get an error when setting additional arguments in Align tilt-series AreTomo job.
Did not work for any add option. I tried -Wbp 1

Environment:

  • OS: sel15
  • MPI runtime: impi/2018.4
  • RELION version: relion5.0-beta-3
  • Memory: 768GB
  • GPU: NVIDIA L40S

Dataset:
-2 tomograms with 60 tilts

Job options:

  • Type of job: Align Tilt Series Aretomo
  • Number of MPI processes: -
  • Number of threads: -
  • Full command
    which relion_python_tomo_align_tilt_series AreTomo --sample-thickness-nanometers 250 --do-tilt-angle-offset-correction --gpu 0 --gpu 1 --gpu 2 --gpu 3 --tilt-series-star-file External/job004/tiltseries_filtered.star --output-directory AlignTiltSeries/job009/ -Wbp 1 --pipeline_control AlignTiltSeries/job009/

Error message:
Currently Loaded Modulefiles:

  1. intel/18.0.5(default) 3) IMOD/4.11.1(default) 5) RELION/5.0-beta-3NC
  2. impi/2018.4(default) 4) ARETOMO/1.3.4
    Usage: -c AreTomo [OPTIONS]
    Try '-c AreTomo --help' for help.
    ╭─ Error ──────────────────────────────────────────────────────────────────────╮
    │ No such option: -W │
    ╰──────────────────────────────────────────────────────────────────────────────╯
    srun: error: hpcl9303: task 0: Exited with exit code 2
    srun: Terminating StepId=559534.0
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant