The source of the problem is an obnoxious "phone home" feature of GATK. You can read more here:

http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home

SOLUTION:

As soon as you receive the license file via email, you have to modify the GATK commandline:

$ java ... GenomeAnalysisTK.jar --gatkkey Received.Via.Email.key -et NOET ...

and the error message, plus the annyoing delay, will disappear. You can study these options here:

http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_CommandLineGATK.html

[DETAILS] The warning is due to unavailability of the phone home target server at amazon, 72.21.211.199, which is currently unreachable.

If using a license file is not a viable option, here are details how to track the problem with the aid of linux standard tools.

(A) Do you have an internet connection ? Try

$ ping www.google.com

If yes, does your network reach 72.21.211.199 as well ? This is the the target server where GATK tries to "phone home". You can try

$ ping 72.21.211.199

or better hints why this

$ traceroute 72.21.211.199

From our network, we were only able to trace until 72.21.218.15 while 72.21.218.199 seems to be down or blocked. Both belong actually to amazon.com, Rockville/MD.

(B) If you do not have a working internet connection, you could try setting the http proxy settings via

$ java -Dhttp.proxyHost=proxy.instititue.org -Dhttp.proxyPort=8080 ... -jar GenomeAnalysisTK.jar ...

(B) or better global OS settings. For linux, the system settings are modified via gconftool-2. This post might help:

http://www.linuxquestions.org/questions/linux-software-2/setting-firefox-gnome-and-other-application-proxy-globally-632478/

(C) If you feel adventurous, the exact problem can be traced via linux strace. Just prepend "strace -f -etrace=network" to your linux commandline, and you can watch in detail what happens:

$ strace -f -etrace=network java ... -jar GenomeAnalysisTK.jar ...

[snip]

[pid 14522] connect(82, {safamily=AFINET6, sin6port=htons(443), inetpton(AFINET6, "::ffff:72.21.211.199", &sin6addr), sin6flowinfo=0, sin6scopeid=0}, 28) = -1 EINPROGRESS (Operation now in progress) [pid 14522] getsockopt(82, SOLSOCKET, SO_ERROR, [17179869294], [4]) = 0 INFO 14:24:14,425 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection timed out INFO 14:24:14,426 HttpMethodDirector - Retrying request

[snip]

One can see that the there is a failed socket request to 72.21.211.199, and then the Exception is thrown.