How to automate Keystore generation using the java keystore tool? w/o user interaction
Try this:
keytool -genkey -noprompt \
-alias alias1 \
-dname "CN=mqttserver.ibm.com, OU=ID, O=IBM, L=Hursley, S=Hants, C=GB" \
-keystore keystore \
-storepass password \
-keypass password
don't forget -noprompt, otherwise you will be asked to input Yes or No
See the full documentation about command line or by typing keytool without any arguments.
Specifically you may want to look options -storepass password -keypass password