I got the problem about the out put

[LLS007]

when I ues the doucument called SibeliaZ-1.2.0-Linux

I ues the commond follow this ./sibeliaz -t 6 /home/lychee/dissertation/ZKV_99cutoff.fasta

however there get some probelms Constructing the graph... Threads = 6 Vertex length = 25 Hash functions = 5 Filter size = 17179869184 Capacity = 1 Files: /home/lychee/dissertation/ZKV_99cutoff.fasta

Command terminated by signal 9 TwoPaco: 5.64 seconds elapsed, 1727848 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, 3884 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: 0.02 seconds elapsed, 3868 memory used

I'm not sure what's the problems is

[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 !