I have the following mummer command, when run in terminal it redirects both output and error (log) to separate files.

mummer -mum Reference.fasta Query.fasta > output.txt 2> err.txt

However the same command when called inside a php as below, it only prints output but not error (log).

shell_exec("mummer -mum '$ref_dest' '$sub_dest' > output.txt 2> err.txt");

Please let me know what has to done.

Thanks, Karthic K