I solved the problem by cat’ing all the pems together:
cat cert.pem chain.pem fullchain.pem >all.pem
openssl pkcs12 -export -in all.pem -inkey privkey.pem -out cert_and_key.p12 -name tomcat -CAfile chain.pem -caname root -password MYPASSWORD
keytool -importkeystore -deststorepass MYPASSWORD -destkeypass MYPASSWORD -destkeystore MyDSKeyStore.jks -srckeystore cert_and_key.p12 -srcstoretype PKCS12 -srcstorepass MYPASSWORD -alias tomcat
keytool -import -trustcacerts -alias root -file chain.pem -keystore MyDSKeyStore.jks -storepass MYPASSWORD
(keytool didn’t know what to do with a PKCS7 formatted key)
I got all the pems from letsencrypt