Relion 5.0 Aretomo not working

dadmer commented 3 months ago

Describe your problem

Hello, I have an issue trying to align my tomograms using Aretomo in Relion 5. Alignment using Imod works but does not give me satisfactory results, I also have Aretomo previously installed and it works fine.

Environment:

OS: [Ubuntu 22.04.4 LTS]
MPI runtime: [4.1.1]
RELION version [RELION-5.0-beta-2-commit-a0b145
Memory: [128 GB]
GPU: [RTX 3090]

Job options:

Full command :

``which relion_python_tomo_align_tilt_series` AreTomo  --sample-thickness-nanometers 200 --do-tilt-angle-offset-correction  --tilt-series-star-file ExcludeTiltImages/job004/selected_tilt_series.star --output-directory AlignTiltSeries/job034/  --pipeline_control AlignTiltSeries/job034/

Error message:

[12:22:24] ERROR: alignment for Position_11 failed       align_tilt_series.py:70
[12:22:30] ERROR: alignment for Position_15 failed       align_tilt_series.py:70
[12:22:36] ERROR: alignment for Position_16 failed       align_tilt_series.py:70
[12:22:42] ERROR: alignment for Position_21 failed       align_tilt_series.py:70
[12:22:48] ERROR: alignment for Position_22 failed       align_tilt_series.py:70
[12:22:54] ERROR: alignment for Position_5 failed        align_tilt_series.py:70
[12:23:01] ERROR: alignment for Position_6 failed        align_tilt_series.py:70

==================

Thank you very much for your help, David

Amy1809 commented 2 months ago

Hi Daivd, I have the same problem as you where it gives me error of failed alignment at algin_tilti_series.py:70. Do you have any solutions on this now?

dadmer commented 2 months ago

Hello Amy, I haven't find a solution to my issue. To work around this, I run Aretomo externally with the imod output option and copy the generated file to an alignment job made with Imod.

AssmannG commented 3 weeks ago

HI Amy, Hi David,

are you using AreTomo or AreTomo2 ? To use it out of the relion GUI - do you export the PATH of the executable or how are you providing this to relion? ( as there is no option to provide an executable?)

Amy1809 commented 3 weeks ago

HI Amy, Hi David,

are you using AreTomo or AreTomo2 ? To use it out of the relion GUI - do you export the PATH of the executable or how are you providing this to relion? ( as there is no option to provide an executable?)

Hi, I ended up running tilt series alignment in relion using AreTomo. I am sorry that I cannot answer your question.

3dem / relion

Relion 5.0 Aretomo not working #1146