Hello
I am having a problem with JalView (the install anywhere version).
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.
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…
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.
Help! Any ideas why it will not move past the queuing page? is there a size limit to the fasta file? Could there be a problem with the CLustal program that is not allowing me to move forward?
Any Help would be greatly appreciated and as soon as possible so I can continue to move forward…
Thanks!!
Jess
Hi there, Jessie.
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