help - one file keeps saying queuing or job error

Jalview Discussion
1

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

2

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

Geoff.

··· 
-- 
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          [g.j.barton@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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
3

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) so that you can run the alignments locally.

Geoff.

··· 
-- 
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          [g.j.barton@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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
4

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

··· 
-- 
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          [g.j.barton@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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
5

Thanks! My file went through sometime during the night!
Sent on the TELUS Mobility network with BlackBerry

··· 
-- 
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          [g.j.barton@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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
6

Thanks! My file went through sometime during the night!
Sent on the TELUS Mobility network with BlackBerry

··· 
-- 
Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          [g.j.barton@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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@dundee.ac.uk](mailto:g.j.barton@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