Open lmcarreira opened 2 months ago
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.
Hi @rdrighetto, thanks for the reply.
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.
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:
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 passingerrors
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. Usesep='\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 passingerrors
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.