At what point in the process do you get this error? Also have you also signed up for S3 storage, the images are stored in S3 (it is in another tab of the AWS console)

I registed for all of the cloud and storage services. I installed the ec2-api-tools and was authorized successfully (thus my cloud private key, etc. were accepted). I installed s3cmd successfully.
It failed when I typed in PathSeq's "create_ownAMI.com". This is the last step of PathSeq installation. I looked around the web and this supposedly happens when the image is old. The paper was only published a few months ago though... I don't know what this means. Does it meanthe Broad Institute needs to provide a new image? I haven't received an answer from the amazon cloud forum. Thanks!

You may need to explicitly opt-in to use S3. See the AWS console there is a tab for S3 where you enable it. http://aws.amazon.com/console/

Contacted Broad Institute... but their Pathseq contact e-mail generates an immediate automatic bounce msg with a bogus reason why they will not reply (" Ignoring non-text/plain MIME parts"). I guess they want to give the impression of being helpful while automatically bouncing every msg :-(

Tracked down in the paper who was responsible for the cloud implementation and sent a personal e-mail to him, hahaha. Let's see if I get a response...