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Old 09-16-2010, 10:18 PM   #1
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'Cannot Execute Binary File' issue


Hello-

I have download a 'package' that is meant to be used for genetic research and such...Anyway, i have downloaded the file and when i try to execute the included example, it says cannot execute binary file. i've tried all sorts of permissons/re-downloading/etc. I've pastted the attached readme that I followed EXACTLY, but am still gettin an error.

Here is where i downloaded the file : http://genetics.cs.ucla.edu/eminim/

here is the readme that comes with it:

EMINIM : Expectation-Maximized INtegrative IMputation

0. GETTING STARTED
0.1 Uncompress the package
$ tar xzvf eminim-1-beta.tar.gz
$ cd eminim-1-beta

0.2 Use sample input file to test the software

0.2.1 For human imputation
$ bin/eminim-1-beta -g human/genmap-human.txt -P 0.05 -a rst.h.all -y rst.h.typed -v human/haplos-human.txt human/genos-human.txt

0.2.2 For inbred imputation
$ bin/eminim-1-beta -i -t 1e-6 -l 1e-20 -u 1e-3 -a rst.m.all -y rst.m.typed -v mouse/haplos-mouse.txt human/genos-mouse.txt

1. USAGE AND OPTIONS

1.1. Usage:
eminim-1-beta [options] [haplo_file] [geno_file]

1.2. Required Parameters:
[haplo_file] : input file for reference haplotypes
[geno_file] : input file for target genotypes
(The format of these input files are described in the next sections)

1.3. Selective Options:
-i : inbred/haploid imputation (default: diploid imputation)
-g [genetic_map_file] : use genetic map instead of physical map
-P [fraction of physical map] : combine both physical and genetic map according the scale of genetic map
-t [trans_rate] : intitial transition parameters (default: 3.806)
-l [theta_lower] : lower bound of the transition parameters (default: 0.2)
-u [theta_upper] : upper bound of the transition parameters (default: 20)
-m [mut_rate] : initial mutation parameters (default : 7.78e-4)
-U [mu_upper] : upper bound of mutation parameters (default : 1)
-L [mu_lower] : lower bound of mutation parameters (default : 1e-5)
-N : Do not learn transitional parameters
-M : Do not learn mutational parameters
-T [rel_tol] relative tolerance parameter (default : 1e-3)
-n [max_niter] : maximum number of iterations (default : 100)
-a [aoutfile] : output filename fo

.......and it continues...
 
Old 09-16-2010, 11:14 PM   #2
tommylovell
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Code:
[root@athlonz ~]# cd eminim-1-beta
[root@athlonz eminim-1-beta]# ll
total 20
drwxr-xr-x 2 6201 64 4096 2009-05-16 16:11 bin
-rw-r--r-- 1 6201 64 6385 2009-05-17 03:44 eminim-1-beta.README
drwxr-xr-x 2 6201 64 4096 2009-09-11 23:06 human
drwxr-xr-x 2 6201 64 4096 2009-05-17 02:56 mouse
[root@athlonz eminim-1-beta]# cd bin
[root@athlonz bin]# ll
total 80
-rwxr-xr-x 1 6201 64 76094 2009-09-11 23:23 eminim-1-beta
[root@athlonz bin]# file eminim-1-beta 
eminim-1-beta: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped
[root@athlonz bin]#
It's an x86-64 binary.

Is your system 64-bit or 32-bit?

Do a 'uname -a'

Code:
[root@athlonz bin]# uname -a
Linux athlonz.tomlovell.com 2.6.27.41-170.2.117.fc10.x86_64 #1 SMP Thu Dec 10 10:36:29 EST 2009 x86_64 x86_64 x86_64 GNU/Linux
[root@athlonz bin]#

Last edited by tommylovell; 09-16-2010 at 11:16 PM.
 
Old 09-16-2010, 11:19 PM   #3
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my system is 32...
 
Old 09-16-2010, 11:22 PM   #4
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or more specicially

Linux kkocak-laptop 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 14:24:04 UTC 2010 i686 GNU/Linux
root@kkocak-laptop:~/eminim-1-beta#
 
Old 09-16-2010, 11:54 PM   #5
tommylovell
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There appears to be just the 64-bit download which won't run on your 32-bit OS.

And I think your i686 hardware is 32-bit (someone correct me if I'm wrong), so you can't install a 64-bit OS on it. (There is a section in the output of the 'dmidecode' command that gives processor information. It's greek to me but if you post it as a new post - so it is in the zero replies category - someone can probably tell you if it will support a 64-bit operating system install.)

My hunch is you're 32-bit hardware, can't install a 64-bit OS, and you may be out of luck unless you can obtain a 32-bit version of the app. Sorry. Although there is an email address on that website. Maybe the author would be willing to compile a 32-bit version. That is, if it's practical. That looks like it is probably a pretty heavy duty application and may need 64-bit addressability for the amount of data that it might need to keep in memory...
 
  


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