Hi Rainer - you should really post this to the list !
Hello Jim,
i fear, i need your help:
I cannot start an Alignment WebService at Dundee.
Always get a job error.....
hmm - the services are working, so something else must be wrong...
Thanks for your assistance.
1. Can you view this URL ?
http://www.compbio.dundee.ac.uk/jabaws/
If the above doesn't work, then you have a network problem...
2. Can you open the Jalview Java Console (from Tools menu) - close and restart Jalview (the window should open the next time Jalview starts), and then when you try the alignment again, send me the contents of that panel along with the sequences you tried to align. Remember to tell me which service you were trying, too!
Jim.
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On 13/03/2012 16:49, Rainer Merkl wrote:
Rainier - it seems our cluster is really busy at the moment, and a scheduler tweak might be needed to ensure that very important jobs get through 
If you needed this alignment yesterday, I suggest you download your own Jabaws server instance from http://www.compbio.dundee.ac.uk/jabaws/ - it should work out of the box if you have VMWare installed on your machine, and all you need do is add the URL to the Jalview webservice server list in the Preferences dialog (http://www.jalview.org/help/html/webServices/webServicesPrefs.html).
Sorry about this!
Jim.
ps. your job will go through eventually, if you can wait.
pps. Tom and Chris - I've cc'ed you because it looks like the jpredBig jobs may be choking the cluster... time to use a token ?
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On 20/03/2012 10:51, Rainer Merkl wrote:
Jim Procter wrote:
Hi Rainier.
On 20/03/2012 09:44, Rainer Merkl wrote:
MSA Programs hang. Tried MAFFT with default parameters.
Find enclosed the MSA and below the content of the Jalview
Java Console.
Thanks - I just checked, and whatever problem seems to have
cleared itself. Could you try it again ?
Jim.
I have rebootet my windows 7 system.
I tried to start mafft. This is the console output.
Jalview Desktop 2.7
Build Date: 28 September 2011
Java version: 1.6.0_25
amd64 Windows 7 6.1
INFO - Constructing news reader.
INFO - Initialising googletracker for usage stats.
INFO - Completed construction of reader.
INFO - Saved last read date as 17-Oct-2011 18:00:00
Building ws menu again Thread[Thread-23,6,main]
The Window Align with Mafft states it is queuing and thats it....
Align with MafftWS using service hosted at http://www.compbio.dundee.ac.uk/jabaws
Alignment of G:\science\Pap_Trp\PabBTrpE_comb.fa
Job details
Job Output:
This is actually what the 'Queuing' means 
However, I understand your frustration and we'll see what we can do - would you like to submit an enhancement/new feature request at issues.jalview.org ?
Jim.
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On 20/03/2012 11:41, Rainer Merkl wrote:
Could you somehow indicate that the job was started and that one has to wait? Such a message will (hopefully) avoid such annoying mails as i send them now and then.