"qsub: Unknown option" Problem

Today, a script worked fine under qsub before doesn't work after I made some minor changes.

When I submit it to qsub, the qsub gives me something like:

qsub: Unknown option.


Since the script works fine on my machine, but it can't work in qsub. After some googling, I finally get some clues in from the post: http://www.biac.duke.edu/forums/topic.asp?TOPIC_ID=1284.

Basically, I add one line in my script,

#$local_bin/novoindex -t 2 hg19.nix hg19.fa


As you noticed, I have already made it as comment. This is fine in shell, but qsub will treat it as input option. If I fixed it like,

##$local_bin/novoindex -t 2 hg19.nix hg19.fa

The script works fine again.