Orthology detection using proteinortho

Question

[Ritvik]

Hi,

I can't seem to work out how to use proteinortho, I think the error is related with the path but I have no linux background so I am running it on windows, I get the following error:

C:\proteinortho>proteinortho5.pl -project=test C:\proteinortho\test\C.faa C:\pro
teinortho\test\M.faa
Proteinortho with PoFF version 5.11 - An orthology detection tool
******************************************************************
'system_profiler' is not recognized as an internal or external command,
operable program or batch file.
failed! Use 1 core only
Detected 1 available CPU threads, Detected NCBI BLAST version 2.2.30+
Checking input files

**Step 1**
Generating indices
Building database for 'C:\proteinortho\test\C.faa'      (308 sequences)
The system cannot find the path specified.
Building database for 'C:\proteinortho\test\M.faa'      (40 sequences)
The system cannot find the path specified.

**Step 2**
Running blast analysis: 0% (0/1)The filename, directory name, or volume label sy
ntax is incorrect.
Thread 1 terminated abnormally: Error, could not open file C:\proteinortho\test\
C.faa.vs.C:\proteinortho\test\M.faa.bla: Invalid argument at C:\proteinortho\pro
teinortho5.pl line 883.
Running blast analysis: 0% (0/1)
-> Output written to test.blast-graph

**Step 3**
Clustering by similarity (Proteinortho mode)
'C:\proteinortho\/proteinortho5_clustering' is not recognized as an internal or
external command,
operable program or batch file.
-> Output written to test.proteinortho
Writing graph...
Cleaning edge list...
Could not open file 'test.removed_blast-graph': No such file or directory at C:\
proteinortho\proteinortho5_clean_edges2.pl line 15.
-> Output written to test.proteinortho-graph

All finished.

So can anyone tell me what am I doing wrong. Which path the program can't seem to detect in step 1 as it can very well detect the no. of sequences in the input files. As required, perl, python and blast+ is properly installed as I can get their versions in command prompt. I am just running the test files that come with the program.

Answer 1

[Ritvik]

Actually, proteinortho is not built for Windows and it can only run perfectly on linux.

Answer 2

[nancydong20]

If you are on Windows, the Windows Linux subsystem is really good and Proteinortho works very easily on that.

[JV]

Can confirm that. "Bash on Ubuntu on Windows" is a relatively new feature introduced in Windows 10, and works great. https://msdn.microsoft.com/de-de/commandline/wsl/install_guide. Despite what many tutorials say, it DOES even support graphical user interfaces, you just have to install an X client for windows (such as e.g. Xming) and have it running in the background while you use the ubuntu shell.