Python not reading partitionfinder pyfile.

[KAIKHO D]

Dear all, 

I have been trying to run partitionfinder but always end up with this issue, i dont know how to go about it, please drop suggestion.

I suppose, python installation in my system is proper with all required dependencies.

This is the path i have followed as given in partition finder tutorial.

python D:\Software\partitionfinder-2.1.1\PartitionFinder.py D:\Software\partitionfinder-2.1.1\examples\nucleotide

I always get this respond

python: can't open file 'D:Softwarepartitionfinder-2.1.1PartitionFinder.py': [Errno 2] No such file or directory

Thanks 

[Rob Lanfear]

Dear Kaikho,

It looks like your terminal is not parsing your filepath properly. I suggest double checking that you are using the correct syntax/character for describing a file path on your system.

The error message tells you that python is looking for a file with no separators in the file path.

Yours,

Rob 

[KAIKHO D]

Thanks Rob,

Earlier i was using Windows but i have shifted to Ubuntu and all works fine now.

Best Regards

D.Kaikho

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[Rose Chai]

Hi Rob and all, I have the same issue as well. I have been trying to run PartitionFinder 2 with Anaconda 3 on windows 10, and so far it has been very unsuccessful. 

I created a conda environment with Anaconda navigator for python 2.7.18 (this is the only version of 2.7 I can get, Anaconda 3 got stuck on "solving environment" whenever I tried to instal a different version of 2.7.x, 2.7.18 seems to be the one Anaconda 3 carries by default).  And I get the respond similar as Kaikho:

python: can't open file 'C:\Users\** Laptop\Desktop\partitionfinder-2.1.1\PartitionFinder.py"C:\Users\** Laptop\Desktop\**\**\data\partitionfinder': [Errno 22] Invalid argument

I have been trying to solve the problem, and it seems like it has something to do with draging and dropping the .py file/folder function not working. Replacing backslash to forwarding slash wasn't working. I choose not to use cmd because I don't know how to start python 2.7.18 in cmd. I have also tried (or attempted to) using the script in this link https://apolo-docs.readthedocs.io/en/latest/software/applications/partitionFinder/2.1.1/

but I'm a very naive user (my python skill is below zero) so didn't even make the script in first line working..

So I think I can say that the current manual for PF 2 about running it in windows system is out of date. I tried the steps in the manual for days and it's not working. I'm a bit depress now. Is there any easy solution to solve my issue? Also, I wonder if you guys are developing a package for using PF 2 in R? Surely there are more ecologists/zoologists using R than using python.....

Thanks.

Xuhong

[Rose Chai]

Hi Rob, please ignore my last message. My PF2 magically decide to work today. I followed the steps for windows in the manual (but not in cmd, instead in conda environment for python 2.7.18), type entre, then this time had a different (but good) error: Could not find the dependency numpy... I then used the code in the second line in this link: https://apolo-docs.readthedocs.io/en/latest/software/applications/partitionFinder/2.1.1/  and all the dependencies were installed. Then I ran the manual steps again and it went well. 

Thanks.

Xuhong

On Monday, August 13, 2018 at 12:37:48 PM UTC+12 rob.l...@gmail.com wrote: