[EMBOSS] Antwort: restrict

[Mehta, Perdeep]

Hi List,

We now have the Rebase locally installed.  Strangely, I see a new error;



"Input nucleotide sequence(s): chr10.fa Uncaught exception:  Allocation failed, insufficient memory available, raised at ajstr.c:2170"



Above example is just for testing with chromosome 10, I plan to do either whole genome (all 23 chromosomes) or do 23 times with each chromosome. I have tested running on a queue with higher memory using following command;



 qsub -q normal-ib /path/restrict -sequence chr10.fa -enzymes hinfI -fragments -outfile chr10.res



Then it threw following error;



"Unable to run job: Script length does not match declared length."

It may not be the restrict problem,  I was just throwing it in here to see if anyone else have had seen such a problem.

Any guess.

Thanks,
perdeep


From: david.bauer at bayerhealthcare.com [mailto:david.bauer at bayerhealthcare.com]
Sent: Tuesday, February 23, 2010 12:56 AM
To: Mehta, Perdeep
Cc: emboss; emboss-bounces at lists.open-bio.org
Subject: Antwort: [EMBOSS] restrict


Hi,

emboss-bounces at lists.open-bio.org schrieb am 23/02/2010 00:21:38:

> I have a few questions on EMBOSS restriction analysis and will
> appreciate any ideas or thoughts on these.
>
> 1. What Rebase file we need to download to get "restrict" working? I
> tried but there are files with different formats.

Go to the /pub/rebase dir on ftp.neb.com.
Download the withrefm.xxx and proto.xxx files
(xxx stands for the version number, just take the latest that's there)
Run rebaseextract -infile withrefm.xxx -protofile proto.xxx
This reformats the neb files for use with emboss. You should now see
4 files embossre.... in the REBASE directory

> 2. Is there a maximum size limit of a nucleotide sequence that I can
> use? Can I use the whole Human genome or at least a full chromosome
> to digest with a particular restriction enzyme?

I'm not sure about the whole genome but I have used it for individual
chromosomes without problems.

> 3. What program can give me the list of all possible fragments
> generated as well? Since I have not seen the output of "restrict",
> perhaps that is already doing that.

You can run restrict with the option -fragments to get them.

Hope this helps,
David.

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