Hi there, Jessie.
On 01/02/2012 15:08, Jessie Richer wrote:
I have a big fasta file (nearly 5MB) and when I go to align the
sequences through the Web Alignment tab (I am using Clustal w.
defaults) the dialog box pops up, but does not leave the "align with
ClustalWS - queuing" page.. This has been running almost two hours.
ah - you are not the only one to notice this!
We had a busy time today on our cluster, which revealed some
configuration issues with the new JABAWS 2.0 server that Jalview now
uses. These have been fixed now, so hopefully your jobs will complete soon.
I have used this before for another set of sequences (almost 2MB fasta
file) and had no problems, although it did take about an hour to
load. I Have triied redoing this same sequences but am still getting
the same "align with clustalWS - queuing" page, and it wont move past
this point..
The version of ClustalW that Jalview uses will take a bit of time with
5MB of sequences. You might actually get a good alignment in less time
if you use the MAFFT service. If they are proteins, then you could also
try out Clustal Omega (ClustalO) which is extremely fast and accurate,
and already available in the development version of jalview here:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview_2G.jnlp
I read on increasing the size.. making a backup of a file in program
file, but unfortunatly I can not do this as I am using my unviersities
computers and they have the admin portions blocked out and I can not
access the admin username and password.
Yes. If you are using a locally installed version of Jalview you do need
to have admin rights to change the memory allocation. However, you
should be able to run the webstart version of Jalview with different
memory options.
Default memory settings:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview.jnlp
1 gig of memory:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview_1G.jnlp
2 gigs of memory:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview_2G.jnlp
On each of these links, you'll be ask to 'trust' the Java web start
program's certificate. You need to agree to this, otherwise the program
won't launch on the machine.
If jalview still doesn't launch with one of the big memory links, then
just use a link for a smaller memory setting.
Hope this helps!
Jim
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