Question: Orthology detection using proteinortho
0
gravatar for Ritvik
4.8 years ago by
Ritvik30
Ritvik30 wrote:

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. 

 

proteinortho orthology • 2.4k views
ADD COMMENTlink modified 2.6 years ago by nancydong2080 • written 4.8 years ago by Ritvik30
1
gravatar for Ritvik
4.8 years ago by
Ritvik30
Ritvik30 wrote:

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

ADD COMMENTlink written 4.8 years ago by Ritvik30
1
gravatar for nancydong20
2.6 years ago by
nancydong2080
nancydong2080 wrote:

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

ADD COMMENTlink written 2.6 years ago by nancydong2080

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by JV380
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