[Errno 2] No such file or directory: (fam file)

[Dan]

Hello, I am trying to use fastStructure on some test data. I use the following command:

python ~/bin/fastStructure/structure.py -K 12 --input=~/filtering/test1/outfiles/test1 --output=~/filtering/test1/test1output

And I get this output:

Traceback (most recent call last):
File "/home/dselech/bin/fastStructure/structure.py", line 171, in <module>
G = parse_bed.load(params['inputfile'])
File "parse_bed.pyx", line 18, in parse_bed.load (parse_bed.c:1630)
handle = open(file+'.fam','r')
IOError: [Errno 2] No such file or directory: '~/filtering/test1/outfiles/test1.fam'

However, I am sure that ~/filtering/test1/outfiles/test1.fam exists. I can open it. The file contains:

1A_0 1A_0 0 0 0 0
1B_0 1B_0 0 0 0 0
1C_0 1C_0 0 0 0 0
1D_0 1D_0 0 0 0 0
2E_0 2E_0 0 0 0 0
2F_0 2F_0 0 0 0 0
2G_0 2G_0 0 0 0 0
2H_0 2H_0 0 0 0 0
3I_0 3I_0 0 0 0 0
3J_0 3J_0 0 0 0 0
3K_0 3K_0 0 0 0 0
3L_0 3L_0 0 0 0 0

Any help or guidance as to what might be producing this error would be appreciated as I can clearly see that I do provide a fam file in the path.

Thanks so much!

[f.pina...@gmail.com]

Hi Dan.
I recall fastStructure being a bit picky with relative paths.
Try replacing the "~" in your command with "/home/your_username" and see if that works.

[Dan]

Did the trick! Thank you SO much!

[f.pina...@gmail.com]

Glad I could help.

Cheers,
Francisco