CRI-MAP Users Forum Posted mail
From  Fri Nov  4 13:39:07 2011
From: "Chunsheng He" <>
Postmaster: Processed by the Listmaster
To: Multiple Recipients of <>
Subject: RE: RE: A bug, I found,Help
Date: Fri, 04 Nov 2011 13:39:07 -0500

Hi Yan-Fa,

Here are my suggestions:

1) You cannot run Cri-Map in this way: "./crimap chrname prepare > out".
The program will just freeze there and produce no output. Cri-Map prepare
is a program that need to run in an interactive manner, which means
type"./crimap chrname prepare" and then answer all its answers one by one.
If you don't like this interactive manner, try 'lispcri' as Jill has

2) You also told us you have sib-pairs. For the sib-pairs, you need to make 
sure the parental genotypes are available in them. Cri-Map is not a 
full-likelihood program and it does not require allele freq information. It 
will give you inaccurate (under-estimated) map distance if parental data are 
missing. If that's the case, I suggest you to use sib_map (multipoint marker 
distance estimation from sib pair data) in the ASPEX (or Allegro/Genehunter 
instead) to get unbiased results. 


Statistical Genetics Lab 
Rockefeller University 

-----Original Message----- 
.From: Jill Maddox [] 
.Sent: Thursday, November 03, 2011 7:40 PM 
.To: Multiple Recipients of 
.Subject: Re:RE: A bug, I found,Help 

Hi Yan fa

If you wish to redirect output from prepare to see noninheritances then
there are 2 ways to do it.

1. The easiest way to do it is to use the lispcri program that can also be
compiled when you compile CRI-MAP. lispcri chrn prepare > chrn.prepare
assuming lispcri is in your path. The fact that you are prefixing crimap
with ./ suggests that it isn't. There are lots of tutorials on the web re
how to set your path. For this to work you need to make sure there is not a
dat file for chrn already in the directory. If there is then then unless
you indicate that it is to be overwritten this part of prepare won't run
again and lispcri will appear to hang. Once you are sure that there is no
dat file in the directory you can run prepare.

2. The other way to do it is to use crimap. You will have to set up an
input file (e.g. chrn.answers) with the answers to the questions that
normally occur when running prepare. If there is already a dat file in the
directory then the easiest thing to do is delete it before running prepare.
Otherwise there will be an extra question that you need to answer Y to.
crimap chrn prepare chrn.prepare


Jill At 06:06 PM 3/11/2011, 孙艳发 wrote:

>Hi, Zhiliang 
>and everyone 
>Thank you for you kind help. I checked my  file 
>format, there was no problem.  But I do not how 
>I set the parameter in the file well. 20 
>full-sib in my .gen file, about 500 
>individuals,the number of markers was about 46700. 
>Thank you for help. 
>Best wishes. 
>Yan fa 
>At 2011-11-03 11:41:10,"Hu, Zhiliang [AN S]"  wrote: 
> >Yan-fa, 
> >It doesn't sound like a "bug" but input file 
> format or parameter problem.  Please double 
> check them out; or post them here if the problem persists. 
> >Zhiliang 
> >-----Original Message----- 
> >.From: ËïÑŞ·¢ [] 
> >.Sent: Wednesday, November 02, 2011 10:34 PM 
> >.To: Multiple Recipients of 
> >.Subject: A bug, I found,Help 
> >Dear,Green: 
> >    When I used  crimap_2.503a_inc_doc.tar.gz 
> (Mar 12, 2009) in unix 64-bit system,  the 
> command of ./crimap chrname prepare > out, I 
> only found an empty text, no information in the 
> text. I do not how can I read the full 
> information in the terminal. Please help me! 
> >                     Sun Yan-fa 


Jill Maddox 16 Park Square Port Melbourne, 3207 Australia phone: 03 9646
0428 E-mail:


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