Apache SSL Converting itermediateCA.cer to crt with openssl
There are two common certificate encoding types. If you can read the "----BEGIN CERTIFICATE----" then it's PEM encoded. If not, DER (binary) encoded. Trying to convert with the openssl x509 command specifying the wrong encoding will produce the error you got.
If certificate file is DER encoded (binary)
openssl x509 -inform DER -in certificate.cer -out certificate.crt
If certificate is PEM encoded (human readable)
openssl x509 -inform PEM -in certificate.cer -out certificate.crt