Emboss Needle() Warning: “Sequence Character Not Found In Ajseqcvtks” …?

Question

[a1ultima]

I am using EMBOSSwin's needle() command line function which performs pairwise global alignments, but I encounter a strange warning.

So I have 24 pairs of amino acid sequences that need aligning, I run the needle() command from python using "subprocess.call()" - whilst this process occurs (seemingly smoothly) I get the following warning:

Warning: Sequence character string not found in ajSeqCvtKS

Can anybody explain what this means?

I must make it clear: this question has been asked outside of BioStar in an email: http://www.mail-archive.com/[e-mail]/msg01959.html