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 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”.