If you use the exec command in the NDS window then you might have to wait extremely long:
number of species * execution time of the command (5000 species, 1.5 sec/exec) -> 2 hour waiting.
WHAT TO DO
The only way the to remove the exec command is: run arb_panic on any shell save the database to /tmp/panic.arb edit /tmp/panic.arb search the exec command replace it by the 'echo' command save file test it with 'arb /tmp/panic.arb' If everything works fine save it in your home directory enter 'arb_clean' on any shell remove /tmp/panic.arb
Test your database very carefully because it may not be consistent. Check sequence checksum