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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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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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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This is probably not going to work but can you first try
Code:$ which SOAPdenovo-63mer
If you are the impatient kind try to see if the command below can locate the program
Code:$ find ~ -name "SOAPdenovo-63mer" -print
Code:$ find / -name "SOAPdenovo-63mer" -print
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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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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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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:
SOAPdenovo-63mer
SOAPdenovo-63mer all -s metasim_config -K 63 -p 1 -o jack>log
SOAPdenovo-63mer: command not found
So, what am I missing here ?
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