At first glance:-

• $parseblast1 should be $parseblast[1]

• $parseblast{0} should be $parseblast[0]

• $ARGV1 should be $ARGV[1]

• $assemblast1 should be $assemblast[1]

• [doc://each] returns key <b>and</b> value, I suspect you might need [doc://keys]

• each(%assemblast) should be each(%assem)

Further points:-

• You should indent your code to make it easier to determine the logic employed.

• Use the three-argument from of open, lexical file handles and check for success, e.g. open my $fh, '<', '/path/to/file' or die "open failed: $!\n";

They may be other problems but clear up the ones above and the debugging task will get smaller.

Update: OP added code tags, fixed some of the subscripting problems and indented code while I was posting so much of my advice is moot.