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Old 11-26-2013, 07:53 AM   #1
lavik17
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Location: Israel

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Default SOAPdenovo command not found error (linux)

Hi Everyone !
I'm new to this field of genome sequencing and generating contigs.
I've downloaded the latest bin version of SOAPdenovo2 and placed it in a directory in my Desktop.
I've also edited my config file to match my parameters and path to my data set.
My issue is that when I go to the terminal and type the command:

Quote:
SOAPdenovo-63mer
or

Quote:
SOAPdenovo-63mer all -s metasim_config -K 63 -p 1 -o jack>log
I get this error:

Quote:
SOAPdenovo-63mer: command not found
I've checked the permissions (and I'm the admin anyway), and the SOAPdenovo-63mer is located in the same directory where I am, and I've looked at it's properties and it does say its an executable file.

So, what am I missing here ?
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Old 11-26-2013, 08:00 AM   #2
sgcsd
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SOAPdenovo-63mer file should be in a directory in your PATH environment.
you can export the PATH to your SOAPdenovo-63mer file by adding the path of the directory to the path environment

Use:
export PATH=$PATH:/path/to/the/soapdenovo/directory

(of course this will work only in the terminal your export the path and have to do every time you open a new terminal. to avoid this you can place the SOAPdenovo-63mer in any folder accessed by PATH or change the .bashrc file)

or place the SOAPdenovo-63mer in the directory from where you are executing it and use

./SOAPdenovo-63mer
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Old 11-26-2013, 08:03 AM   #3
lavik17
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Great ! Works like a charm !
Thanks!
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Old 07-09-2014, 11:49 AM   #4
BabyFaruda
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Hey! I am having the same problem. How do you find the path for SOAPdenovo? (im using Linux)
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Old 07-09-2014, 11:51 AM   #5
GenoMax
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Quote:
Originally Posted by BabyFaruda View Post
Hey! I am having the same problem. How do you find the path for SOAPdenovo? (im using Linux)
Did you compile the software/do the install (or someone else did)?
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Old 07-09-2014, 12:00 PM   #6
BabyFaruda
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someone did it for me. I think she did the "make".
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Old 07-09-2014, 12:08 PM   #7
GenoMax
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This is probably not going to work but can you first try

Code:
$ which SOAPdenovo-63mer
If you are new to unix (command line) then it may be a good investment to read through this for some UNIX basics. http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

If you are the impatient kind try to see if the command below can locate the program

Code:
$ find ~ -name "SOAPdenovo-63mer" -print
If that does not produce anything then try (could take some time):

Code:
$ find / -name "SOAPdenovo-63mer" -print
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Old 07-09-2014, 12:13 PM   #8
BabyFaruda
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thanks! I got the path from the first code you gave.
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Old 07-09-2014, 01:25 PM   #9
BabyFaruda
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I am experiencing another problem.

I am now working in just 1 path. The SOAPdenovo, the configuration file, and the sequence data are in the same directory.

The command I used is

all -s file.config -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

I got 2 files for the output: the log file (emtpty) and the err file which says

No command 'all' found, did you mean:
Command 'al2' from package 'mono-devel' (main)
Command 'alc' from package 'amule-utils-gui' (universe)
Command 'alc' from package 'amule-adunanza-utils-gui' (universe)
Command 'als' from package 'atool' (universe)
Command 'ali' from package 'mailutils-mh' (universe)
Command 'ali' from package 'nmh' (universe)
Command 'al' from package 'mono-devel' (main)
Command 'axl' from package 'afnix' (universe)
Command 'wall' from package 'bsdutils' (main)
Command 'ale' from package 'ale' (universe)

What should I do?
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Old 07-10-2014, 04:17 AM   #10
GenoMax
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I think you need to do

Code:
$ SOAPdenovo-63mer all -s file.config -K 63 -R -o graph_prefix 1>ass.log 2>ass.err
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Old 07-12-2014, 03:24 AM   #11
laisuliang
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Hi!
I use soapdenovo1.04 and type the command:

./SOAPdenovo pregraph -s a.config -K 31 -d 1 -o test>test.log

after that I only got :test.log
test.edge
test.kmerFreq
these 3 files ,without the test.preGraphBasic file. And I cannot go to the next step. Can someone help me ?
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