First, check if you gave the right arguments to the script because your command looks incorrect. Try this:

orthomclBlastParser my_blast_results my_orthomcl_dir/compliantFasta >> my_orthomcl_dir/similarSequences.txt

Next, check and make sure you properly ran orthomclAdjustFasta and produced correctly formatted sequences prior to running your blast job. Last, and most importantly, don't run jobs as root.

See Orthomclblastparser Problems In Orthomcl Programs to a similar question; looks like the same issue.