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

edit here of the current issues I had the following error message :

./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[])'

Following errors come out :

 1)  // C/C++ includes
 2)  #include <iostream> 
 3) #include <fstream> 
 4) using namespace std; 

 6) // Application includes
 7) #include "AliParser.hh"
 8) #include "HisMaker.hh"

 10) int main(int argc,char *argv[])
 11) {

To my understanding :

• Line 1 and 6 are due to the fact the program reads a command a path to directory
• Line 4 .. he doesn't find using

• Line 10 and 11 he doesn't like the declaration of variable int.

  I'm clueless from here .. I typed earlier /cnvnator.cpp, if I remove the "cpp" it doesn't work, I think the way I type the command line is wrong..