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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] No micrographs found at location .../10064/data/*.mrc/*.mrc #16

Closed wlugmayr closed 1 year ago

wlugmayr commented 1 year ago

Describe the bug

When using the interactive Matlab TomoBear version the file extension is duplicated. This worked in older TomoBEAR versions and works with the compiled MATLAb standalone executable.

Project JSON file ribosome_empiar_10064_dynamo.json

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

Error message Error using getOriginalMRCsorTIFs ERROR: No micrographs found at location /gpfs/cssb/software/tutorials/empiar_data/EMPIAR-10064-CTEM/10064/data/.mrc/.mrc

Error in getFileCountChanged (line 2) [file_list, ~] = getOriginalMRCsorTIFs(configuration);

Error in LocalPipeline/execute (line 465) file_count_changed = getFileCountChanged(configuration.general);

Error in runPipeline (line 131) pipeline.execute(starting_tomogram, ending_tomogram, step, gpu);

Error in runTomoBear (line 15) runPipeline(compute_environment, configuration_path, default_configuration_path, starting_tomogram, ending_tomogram, step, gpu);

Error in run_ribosome (line 1) runTomoBear("local", "./ribosome_empiar_10064_dynamo.json", "/gpfs/cssb/software/centos7/x86_64/tomobear/0.2.0/configurations/defaults.json")

To Reproduce Run the tutorial in the MATLAB GUI (matlab/R2022b).

Additional context When using no extensions it gets the error:

INFO:DATA_PATH: /gpfs/cssb/software/tutorials/empiar_data/EMPIAR-10064-CTEM/10064/data/ Error using getUnprocessedTomograms ERROR: Multiple unknown extensions found!

Error in LocalPipeline/execute (line 178) [dynamic_configuration, file_count_changed] = getUnprocessedTomograms(configuration.general, log_file_id);

Error in runPipeline (line 131) pipeline.execute(starting_tomogram, ending_tomogram, step, gpu);

Error in runTomoBear (line 15) runPipeline(compute_environment, configuration_path, default_configuration_path, starting_tomogram, ending_tomogram, step, gpu);

Error in run_ribosome (line 1) runTomoBear("local", "./ribosome_empiar_10064_dynamo.json", "/gpfs/cssb/software/centos7/x86_64/tomobear/0.2.0/configurations/defaults.json")

ArtsemiY commented 1 year ago

Thanks for reporting a bug! I have fixed that in commit 3164620 which is currently under develop branch. You may get dev version from that branch or wait until the next version will be released at the end of the next week. Hope it helps!

ArtsemiY commented 1 year ago

Hi @wlugmayr ! I do apologize that it took much more than expected, but the newly published release v0.3.0 (w/o binary this time) should now solve this issue in the full MATLAB version of the TomoBEAR.

ArtsemiY commented 1 year ago

I assume that this issue was resolved and could be closed, otherwise you are welcome to re-open it.