I got the problem about the out put

[medvedevgroup]

I got the problem about the out put

[LLS007]

cmake .. -DCMAKE_INSTALL_PREFIX=

I want ot ask what's mean of the

[iminkin]

@LLS007 ,

Thanks for opening the issue. I will get back to you shortly.

Thank you,

Ilia Minkin

[LLS007]

I still have the problem bleow, and I use your document of SibeliaZ-1.2.0-Linux/bin
I'm not sure what's the problem of the situation, beacause my data run in my classmate's PC is ok

lychee@lychee:~$ sibeliaz _rebuild.fasta
Constructing the graph...
Threads = 1
Vertex length = 25
Hash functions = 5
Filter size = 17179869184
Capacity = 1
Files:
_rebuild.fasta

terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Command terminated by signal 6
TwoPaco: 0.13 seconds elapsed, 4812 KB memory used
Loading the graph...
error: Can't read the input file
Command exited with non-zero status 1
SibeliaZ-LCB: 0.00 seconds elapsed, 4004 KB memory used
rm: cannot remove './sibeliaz_out/de_bruijn_graph.dbg': No such file or directory
Performing global alignment..
find: ‘./sibeliaz_out/blocks’: No such file or directory
find: ‘./sibeliaz_out/blocks’: No such file or directory
Alignment: 0.01 seconds elapsed, 3896 memory used

[iminkin]

@LLS007 ,

SibeliaZ consists of several programs that have to be installed to work properly. To answer your question:

cmake .. -DCMAKE_INSTALL_PREFIX=

This option sets the path where the binaries will be copied, the path should start after the '=' sign. For example, if you would like to install SibeliaZ to your home directory, you can type:

cmake .. -DCMAKE_INSTALL_PREFIX=~

This command will make sure that SibeliaZ binaries will be copied to your ~/bin directory and will work properly. After running CMake you have to finish the installation by:

make install

To conclude please try to install SibeliaZ by running:

cmake .. -DCMAKE_INSTALL_PREFIX=~
make install

And try running it again. Please let me know if it helps.

[LLS007]

I want to say maybe the problem comes from my Linux's RAM， and I use the sibeliaz -f 0.5 to give the RAM first and solve the problem.

Thanks for your help !