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KudryashevLab / TomoBEAR

TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.
https://github.com/KudryashevLab/TomoBEAR/wiki
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[BUG] Could not open file ./configurations/defaults.json. #17

Open wlugmayr opened 1 year ago

wlugmayr commented 1 year ago

Describe the bug

A default run in an empty project directory (not in the TomoBEAR install directory gives the error message above but it continues working

Project JSON file

        "data_path": "/gpfs/cssb/software/tutorials/empiar_data/EMPIAR-10064-CTEM/10064/data/*.mrc",
       "processing_path": ".",

Error message

jobid : 790785

Loading tomobear/0.2.0 Loading requirement: aretomo/1.3.3 gctf/1.18.0 imod/4.11.21 mcr/9.10 motioncor2/1.5.0 INFO: startup... Warning: Executing startup failed in matlabrc. This indicates a potentially serious problem in your MATLAB setup, which should be resolved as soon as possible. Error detected was: MATLAB:fileread:cannotOpenFile Could not open file ./configurations/defaults.json. No such file or directory. 3dmod -h: Aborted INFO: PROCESSING STEP 1:MetaData INFO: PROCESSING STEP 2:CreateStacks :