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CoBrALab / RABIES

fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/en/stable/
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An error occurred while using RABIES preprocessing: subprocess.CalledProcessError #381

Open JianhuiFeng06 opened 3 months ago

JianhuiFeng06 commented 3 months ago

Describe the bug When I use the example dataset and run the preprocessing command rabbies preprocess test_dataset/ preprocess_outputs/ --TR 1.0s --no_STC, the error occurs: subprocess.CalledProcessError: Command 'install_DSURQE.sh /home/jhfeng/.local/share/rabies' returned non-zero exit status 6.

The installation command I used was: pip install rabies， and my environment already satisfies other dependencies I'm not sure if there was some error when I installed

Attach log file 2024-08-27 15:26:18,962 - root - INFO - SOME FILES FROM THE DEFAULT TEMPLATE ARE MISSING. THEY WILL BE INSTALLED BEFORE FURTHER PROCESSING. 2024-08-27 15:27:32,921 - root - WARNING - % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0curl: (6) Could not resolve host: repo.mouseimaging.ca Warning: Problem : timeout. Will retry in 1 seconds. 5 retries left. 0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0curl: (6) Could not resolve host: repo.mouseimaging.ca Warning: Problem : timeout. Will retry in 2 seconds. 4 retries left. 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0curl: (6) Could not resolve host: repo.mouseimaging.ca Warning: Problem : timeout. Will retry in 4 seconds. 3 retries left. 0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0curl: (6) Could not resolve host: repo.mouseimaging.ca Warning: Problem : timeout. Will retry in 8 seconds. 2 retries left. 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0curl: (6) Could not resolve host: repo.mouseimaging.ca Warning: Problem : timeout. Will retry in 16 seconds. 1 retries left. 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0curl: (6) Could not resolve host: repo.mouseimaging.ca

Traceback (most recent call last): File "/home/jhfeng/anaconda3/envs/mouse/bin/rabies", line 3, in execute_workflow() File "/home/jhfeng/anaconda3/envs/mouse/lib/python3.9/site-packages/rabies/run_main.py", line 501, in execute_workflow install_DSURQE(log) File "/home/jhfeng/anaconda3/envs/mouse/lib/python3.9/site-packages/rabies/run_main.py", line 718, in install_DSURQE rc = run_command(f'install_DSURQE.sh {rabies_path}', verbose=True) File "/home/jhfeng/anaconda3/envs/mouse/lib/python3.9/site-packages/rabies/preprocess_pkg/utils.py", line 896, in run_command process = subprocess.run( File "/home/jhfeng/anaconda3/envs/mouse/lib/python3.9/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'install_DSURQE.sh /home/jhfeng/.local/share/rabies' returned non-zero exit status 6.

Gab-D-G commented 3 months ago

Hi @JianhuiFeng06 , I would highly recommend trying the containerized installation of the pipeline through Docker/Apptainer https://rabies.readthedocs.io/en/latest/installation.html#container-singularity-docker. You are attempting a local installation, which will likely require lots of troubleshooting.