Permission denied error when running Topaz wrapper in cryoSPARC



Dear all,

I followed the instructions that has given in the new cryosparc version for running topaz, but eventually I got this error.

Does it has do anything with the directory permission where the topaz is installed ?

Any suggestions are welcome,


Hi @eswar909

Insufficient permissions can cause the error you are experiencing. It is recommended to try running the command chmod +rx <TOPAZ_EXECUTABLE_PATH> in the Terminal where <TOPAZ_EXECUTABLE_PATH> is the Topaz path input into the cryoSPARC job.

If the output of this command is chmod: cannot access '<TOPAZ_EXECUTABLE_PATH>': Permission denied, then the permissions on the directory holding the Topaz executable must be altered. To appropriately alter the directory permissions, run the command chmod +x <TOPAZ_EXECUTABLE_PATH_DIRECTORY> in the Terminal where <TOPAZ_EXECUTABLE_PATH_DIRECTORY> is the path to the directory holding the Topaz executable. This path should be identical to <TOPAZ_EXECUTABLE_PATH> except topaz at the end is removed.

The above command may also output a chmod: permission denied error in which case

DIR=/; for i in a b c d e f; do DIR=$DIR$i/; chmod +x $DIR; done

will set the permission for all folders in <TOPAZ_EXECUTABLE_PATH_DIRECTORY> assuming this path is in the form “/a/b/c/d/e/f”.

If the output is chmod: changing permissions of '/a/': Operation not permitted, simply move the remove “a” from the list after “i” and add it immediately after “DIR=/” and add a “/” afterwards. This command should then look like

DIR=/a/; for i in b c d e f; do DIR=$DIR$i/; chmod +x $DIR; done

If the above don’t work, further permissions may be required, in which case try doing the above again, except replace “+x” and +rx" in the commands with “+rwx”.


Hi @jyoo,

Yes, your correct, limited disk permission caused the error, I made directory accessible and its working.

Thanks for your help,