Cnvnator Error Message

Question

[madkitty]

I wanted to run CNVnator and here is what it says :

./cnvnator -root /output/out.root -chrom X -tree /mybamfile/myfile.bam

-bash: ./cnvnator: No such file or directory

What am I suppose to do ?

Answer 1

[Neilfws]

This is a basic Linux usage issue.

(1) Did you run that command from within the directory which contains cnvnator?

If so, see (2). If not, try again from the correct location, then see (2) if that also fails. If cnvnator were in /home/you/xyz, then either:

 cd /home/you/xyz
 ./cnvnator -root /output/out.root -chrom X -tree /mybamfile/myfile.bam

Or specify the full path from any location:

 /home/you/xyz/cnvnator -root /output/out.root -chrom X -tree /mybamfile/myfile.bam

(2) Is cnvnator executable?

Again assuming that cnvnator is in /home/you/xyz, try:

ls -l /home/you/xyz/cnvnator

Do you see a line beginning with something like:

-rwxr-xr-x

If not, you need to make cnvnator executable:

chmod +x /home/you/xyz/cnvnator

[madkitty]

Thanks for your answer.

First off, I have two files :

 (1) /cnvnator/src/cnvnator.cpp
 (2) /cnvnator/cnvnator2VCF

1. I'm not sure which directory I should used ..
2. Thanks a lot for your help, I did chmod +x and then typed

this:

./cnvnator.cpp -root /home/out.root -chrom X -tree /mybamfile/myfile.bam

The software started but now I have a different issue

./cnvnator.cpp: line 1: //: is a directory
./cnvnator.cpp: line 4: using: command not found
./cnvnator.cpp: line 6: //: is a directory
./cnvnator.cpp: line 10: syntax error near unexpected token `('
./cnvnator.cpp: line 10: `int main(int argc,char *argv[])'

What does that mean ? T.T

[Neilfws]

The file cnvnator.cpp is not an executable program; it's source code. You need to compile the software by following the instructions in the README file, which you should find when you unzip the downloaded software.

[madkitty]

Thanks it worked!