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Old 12-26-2014, 11:55 AM   #1
suhalsuhaimi
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Location: US

Join Date: Dec 2014
Posts: 5
Talking how to create output directory folder on velvet

Hi all, i'm new here. I already download velvet 1.2.10. After I extract that file, I store it at Desktop/BioTool/velvet.

I try to follow all the command as what manual wrote. The manual wrote like this:

> make
> ./velveth
> ./velvetg
> ./velveth sillyDirectory 21 -shortPaired data/test_reads.fa
> ./velvetg sillyDirectory


I wrote command like this:

[email protected]:~$ echo `export PATH=$PATH:~/Desktop/BioTool/velvet` >> ~/.bashrc

[email protected]:~$ > make
[email protected]:~$ > ./velveth
[email protected]:~$ > ./velvetg
[email protected]:~$ > ./velveth my_velvet_output 21 -shortPaired data/J99.fa
my_velvet_output: command not found

How do I create an output folder? Please help me.
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Old 12-26-2014, 01:37 PM   #2
GenoMax
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If you run ./velveth by itself if should produce output for some basic help on screen. It is not apparent if you were able to see that (and have removed it in the post above).

If you did not then you are going to likely need to add execute permissions to the velvet executables. You can do that by

Code:
$ chmod a+x velveth velvetg
Verify that you are able to get the help output by running

Code:
$ ./velveth
Then you can run command to start analysis.
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Old 12-27-2014, 09:10 AM   #3
suhalsuhaimi
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Join Date: Dec 2014
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Thank for you quick reply GenoMax. I already add your cmd like this:

[email protected]:~$ echo `export PATH=$PATH:~/Desktop/BioTool/velvet` >> ~/.bashrc
[email protected]:~$ chmod a+x velveth velvetg
[email protected]:~$ ./velveth
[email protected]:~$ ln -s /path/to/Desktop/BioTool/velvet/project/folder/J99.fasta
ln: failed to create symbolic link ‘./J99.fasta’: File exists
[email protected]:~$ ln -s /path/to/Desktop/BioTool/velvet/project/J99.fasta
[email protected]:~$ ln -s /path/to/Desktop/BioTool/velvet/project/HPAG1.fasta
[email protected]:~$ ./velveth my_velvet_folder 21 -shortPaired data/J99.fa
[email protected]:~$ ./velvetg
[email protected]:~$ ./velvetg my_velvet_output
[email protected]:~$ ./velveth my_velvet_output 35 -fasta -shortPaired -separate J99.fa HPAG1.fa
[email protected]:~$ ./velvetg my_velvet_output -clean yes -exp_cov 21 -cov_cutoff 2.81 -min_contig_lgth 200

while i'm doing this. There is no feedback from SLUM and doesn't appear any basic held when I type ./velveth or ./velvetg

And the output folder that I want to create is my_velvet_output. I did not see this folder appear in my velvet file. When I create this output folder, it should appear in my velvet file, right? If i'm wrong, please correct me.

one more thing, why I cannot locate my fasta file into my velvet folder. Is there any other correct cmd tht I need to use?

Please help me....
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Old 12-27-2014, 11:21 AM   #4
mastal
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Posts: 662
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Velvet will not create the output directory for you.

You need to create a directory ($ mkdir my_velvet_output) where you want the velvet output to go, and give the name of that directory when you run velveth and velvetg.

Note that velveth produces 3 files that are used by velvetg, so you need to give the name of the same directory when you run velvetg subsequent to running velveth.

Also note that if you do more than one run of velvet using the same directory for your output, it will overwrite the files.

But if you are not seeing anything when you type ./velveth or ./velvetg,
then velvet isn't installed properly.
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Old 12-27-2014, 08:28 PM   #5
suhalsuhaimi
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Join Date: Dec 2014
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Thank mastal, that folder name appear now at home/my_velvet_output, but where should I store my sequence. It is in home same as my_velvet_output or in my velvet folder at Desktop/BioTool/velvet

I try to cmd it again and it's appear like this:

[email protected]:~$ echo `export PATH=$PATH:/Desktop/BioTool/velvet` >> ~/.bashrc
[email protected]:~$ chmod a+x velveth velvetg
[email protected]:~$ >./velveth
[email protected]:~$ >./velveth my_velvet_output
my_velvet_output: command not found

when I try to call ./velveth my_velvet_output is an error appear.

how do I solve this problem?
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Old 12-28-2014, 05:04 AM   #6
GenoMax
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Quote:
Originally Posted by suhalsuhaimi View Post
[email protected]:~$ >./velveth
If that produces no help output on screen then something is wrong with compilation of velvet program.

When you did "make" in the source code directory did you see any error(s)?

Can you post the output of the following command?

Code:
$ file velveth velvetg
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