[Jalview-discuss] help - one file keeps saying queuing or job error

[Peter Troshin]

Alternatively you may want to try using Mafft with one of its fast presets. It should be faster than Clustal especially for DNA sequences.

Regards,
Peter


________________________________
From: jalview-discuss-bounces at jalview.org [jalview-discuss-bounces at jalview.org] on behalf of Geoff Barton [gjbarton at dundee.ac.uk]
Sent: 06 March 2012 20:46
To: Jessie Richer; jalview-discuss at jalview.org
Subject: Re: [Jalview-discuss] help - one file keeps saying queuing or job error

That is a large alignment that takes significant resources on our cluster and so will have to wait until there is a slot with sufficient memory.   If you want a faster turn around then you will need to set up your own jabaws server (see www.compbio.dundee.ac.uk/jabaws<http://www.compbio.dundee.ac.uk/jabaws>) so that you can run the alignments locally.

Geoff.




On 06/03/2012 16:59, Jessie Richer wrote:
The longest is around 7000 bases
Sent on the TELUS Mobility network with BlackBerry
________________________________
From: Geoff Barton <gjbarton at dundee.ac.uk><mailto:gjbarton at dundee.ac.uk>
Date: Tue, 6 Mar 2012 16:53:12 +0000
To: Jessie Richer<j.richer3 at mycanadore.ca><mailto:j.richer3 at mycanadore.ca>; <jalview-discuss at jalview.org><mailto:jalview-discuss at jalview.org>
Subject: Re: [Jalview-discuss] help - one file keeps saying queuing or job error

That is a lot of sequences, how long are they?

Geoff.


On 06/03/2012 16:19, Jessie Richer wrote:
Hi
Its DNA sequences and not sure exactly how many.. I'd guess around 700

I started it this morning at 8 am. It is now 1120 and it still says queuing.
Sent on the TELUS Mobility network with BlackBerry
________________________________
From: Geoff Barton <gjbarton at dundee.ac.uk><mailto:gjbarton at dundee.ac.uk>
Date: Tue, 6 Mar 2012 16:05:02 +0000
To: Jessie Richer<j.richer3 at mycanadore.ca><mailto:j.richer3 at mycanadore.ca>
Subject: Re: [Jalview-discuss] help - one file keeps saying queuing or job error

This is odd, the server seems fine and gives almost instantaneous turn-around at the moment.

Are you sending very large problems?

How many sequences are you trying to align, how long are they and are they DNA/RNA or Protein?

Geoff.

On 06/03/2012 13:00, Jessie Richer wrote:

Hello.



I have been trying to run a file to align the sequences using clustal w/ defaults. I get one of two things, either it stays on 'queuing' for days, or its starts 'running' and then says job error.

my file size is 1007 KB



I cant increase the virtual memory since I am using my universities computers and do not have permission to access the program files.



All my sequences are in Capital letters (my first file has small letters in some sequences so i fixed this but am still having the same problem)



Any suggestions? I have run some files that were larger without any problem - minus they took 5-6 hours to complete.



If i need to send the file, it has to be kept confidential (as per my supervisor/professor's request since this is a research project and he has said "data is confidential")







Jessica



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--
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          g.j.barton at dundee.ac.uk<mailto:g.j.barton at dundee.ac.uk>
Tel:+44 1382 385860/388731 (Fax:385764)     www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>

The University of Dundee is registered Scottish charity: No.SC015096


--
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          g.j.barton at dundee.ac.uk<mailto:g.j.barton at dundee.ac.uk>
Tel:+44 1382 385860/388731 (Fax:385764)     www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>

The University of Dundee is registered Scottish charity: No.SC015096


--
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          g.j.barton at dundee.ac.uk<mailto:g.j.barton at dundee.ac.uk>
Tel:+44 1382 385860/388731 (Fax:385764)     www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>

The University of Dundee is registered Scottish charity: No.SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096
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