From jillian.maddoxalumni.unimelb.edu.au  Sun Mar 25 00:25:41 2012
From: Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: Re: Memory and hap_sys problems in crimap
Date: Sun, 25 Mar 2012 00:25:41 -0500

Hi Heidi

I seem to recall that the hapsys message is an original CRI-MAP bug that we
might have fixed for the next version of CRI-MAP that we are developing. If
you can put a compressed version of the problem gen file on an http or ftp
site so that I can download it or e-mail it to me then I can test it with
an intermediate version to see whether it runs. If it does run the we
should be able to send you a CRI-MAP version that will work. If e-mailing
the file please do not have it with a .zip file name - if you use zip to
compress it then please just rename the file to .zap (my ISP automatically
removes .zip files from e-mails).

Regards

 
Jill 
At 03:33 AM 25/03/2012, Heidi Viitaniemi wrote: 

>
>HI, 
> 
>I'm working with SNP data on a F1 half-sib family with 20 offspring from 
>each sire (total 30 sires). Parents and offspring are genotyped for 10 000 
>SNPs. I would like to build a map for these, but so far I'm stuck with 
>memory problems and hap_sys in v2.503. 
> 
>For the memory part I've been trying to adjust the settings on defh.s up 
>and down from what they are there with varying degree of success: I get a 
>warning from glibc with something corrupted and to me this looks more like 
>a problem of the linux than crimap itself. I tried to solve this by 
>removing and compiling crimap again, but I get the same problem still. I 
>get over this problem whendoing twopoint only for 1 chromosome at a time, 
>but I would still like to able to do twopoint for the whole data. 
> 
>When dealing with only 1 chromosome worth of SNPs the twopoint goes fine, 
>but when I start building based on the twopoint I get an error for "Check 
>hap_sys0 systems for intralocus recombinants". Reading the crimap tutorial 
>and documentation hap_sys kind of makes sense to me, but I'm still a bit 
>unsere how the get a around it or where the information of the primary and 
>secondary haplotype systems can be found. I havent specified any hap_sys 
>systems in the .par file, but the hap_sys in the 
>.par file is 1. Any good suggestions on how to get over this problem? 
> 
>All help is wellcome at this point =) 
> 
>Thanks, Heidi Viitaniemi 
> 
>-- 
>______________________________________________ 
> 
>Heidi Viitaniemi PhD student Division of Genetics and Physiology Department 
>of Biology (Vesilinnantie 5) University of Turku 20014 Turku 
> 
>tel: +358-2-3335808 
> 
> 

 
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Jill Maddox 16 Park Square Port Melbourne, 3207 Australia phone: 03 9646
0428 E-mail: jillian.maddoxalumni.unimelb.edu.au

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