Sequences must be in the same order as well
while I was waiting for your reply As workaround I downloaded files on my VM using gsutil and changed inputs file pointing to local files instead of gs://bucket path.
I'm getting some java error now.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: Do not use this function to merge dictionaries with different sequences in them. Sequences must be in the same order as well. Found  and [....
Error is attached.