AreTomo executable was not found

[lmcarreira]

This is a template for reporting bugs. Please fill in as much information as you can.

Describe your problem

I was trying to run the new Relion 5 Tomo but unfortunately it seems not to find AreTomo to perform tilt-series alignements.

Job options:

• Full command (see note.txt in the job directory):
  which relion_python_tomo_align_tilt_series AreTomo --sample-thickness-nanometers 100 --gpu 1 --tilt-series-star-file ExcludeTiltImages/job021/selected_tilt_series.star --output-directory AlignTiltSeries/job028/ --pipeline_control AlignTiltSeries/job028/

Error message:

Please cite the full error message as the example below.

/home/lucarreir/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:177: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use sep='\s+' instead
df = pd.read_csv(
/home/lucarreir/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:194: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing errors and catch exceptions explicitly instead
self.dataframes[key] = df.apply(pd.to_numeric, errors='ignore')
/home/lucarreir/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:177: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use sep='\s+' instead
df = pd.read_csv(
/home/lucarreir/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:194: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing errors and catch exceptions explicitly instead
self.dataframes[key] = df.apply(pd.to_numeric, errors='ignore')
[14:25:31] ERROR: alignment for TS_030 failed with align_tilt_series.py:73
error: AreTomo executable was not found.
Put 'AreTomo' on the PATH to proceed.

[rdrighetto]

Hi @lmcarreira,

You need to make sure that you have AreTomo installed and that the binary is available in your PATH environment variable before launching RELION, as suggested by the error message. Something like this:

export PATH=/path/to/folder/of/AreTomo/:$PATH
(you can add the line above to your ~/.bashrc file to make it persistent)

If you are on an HPC cluster where AreTomo is available as a module, make sure to load that module before launching RELION.

[lmcarreira]

Hi @rdrighetto, thanks for the reply.

• I have AreTomo 1.3.3 installed in /mpcdf/soft/local/AreTomo-1.3.3/
• I also have in PATH environment variable that location (/mpcdf/soft/local/AreTomo-1.3.3/)
• In the .bashrc file I have included the export PATH code (export PATH="/mpcdf/soft/local/AreTomo-1.3.3/:$PATH") and module load AreTomo-1.3.3
• It still does not work.

[rdrighetto]

Are you submitting the job to a cluster e.g. with SLURM? If so, you have to make sure that the AreTomo module (or PATH) is properly loaded in the submission script.

Furthermore, is the binary located in /mpcdf/soft/local/AreTomo-1.3.3/ called just AreTomo or something different, like AreTomo_1.3.4_Cuda118_Feb22_2023 for example?
If there is no binary called simply AreTomo but something different like above, you can create an alias or (better) a link to it and call it AreTomo so that RELION can find it.