ModuleNotFoundError: No module named 'pcangsd.pcangsd'; 'pcangsd' is not a package

[IgnasiLucas]

After installing successfully, when I run pcangsd I get the following error:

Traceback (most recent call last): File "/home/joiglu/.conda/envs/bio/bin/pcangsd", line 5, in <module> from pcangsd.pcangsd import main ModuleNotFoundError: No module named 'pcangsd.pcangsd'; 'pcangsd' is not a package

I think this is related to the naming of the pcangsd.py file inside pcangsd folder, as described in the link below:

https://stackoverflow.com/questions/54333865/python-no-module-named-error-package-is-not-a-package

[Rosemeis]

Can you write the command that prompted the error? :-)

/Jonas

[IgnasiLucas]

Yes, the error appeared as soon as I run pcangsd, like:

pcangsd -h

I also noticed that the pcangsd executable is a text file containing this:

#!/home/joiglu/.conda/envs/bio/bin/python3.12
#-- coding: utf-8 --
import re
import sys
from pcangsd.pcangsd import main
if name == 'main':
sys.argv[0] = re.sub(r'(-script.pyw|.exe)?$', '', sys.argv[0])
sys.exit(main())`

And if I edit it and substitute from pcangsd.pcangsd import main for from pcangsd import main, then, the command pcangsd -h does show the help without error, but it becomes unable to import "admixture" when I run pcangsd --beagle input.beagle.gz. The error that shows then is this:

-------------------------------------
PCAngsd v1.35
Jonas Meisner and Anders Albrechtsen.
Using 1 thread(s).
-------------------------------------

Traceback (most recent call last):
File "/home/joiglu/.conda/envs/bio/bin/pcangsd", line 8, in
sys.exit(main())
^^^^^^
File "/home/joiglu/software/PCANGSD/pcangsd/pcangsd.py", line 145, in main
from pcangsd import admixture
ImportError: cannot import name 'admixture' from 'pcangsd' (/home/joiglu/software/PCANGSD/pcangsd/pcangsd.py)

It's not that I expect to fix the problem by editing the executable, but I was trying to understand the problem. Thanks for your help.

[johannabeam]

Hi, I am having a similar problem and cannot get pcangsd to run.
I am using the following code:

python /path/to/pcangsd/pcangsd/pcangsd.py -b GL_YBCH_hz.beagle.gz -e 4 -t 10 -o pcangsd_YBCH_hz

And keep getting errors such as the following:

Traceback (most recent call last):
  File "/path/to/pcangsd/pcangsd/pcangsd.py", line 552, in <module>
    main()
  File "/path/to/pcangsd/pcangsd/pcangsd.py", line 145, in main
    from pcangsd import admixture
ImportError: cannot import name 'admixture' from 'pcangsd' (/path/to/pcangsd/pcangsd/pcangsd.py)

I have confirmed that admixture.py is in that /pcangsd/pcangsd/ directory.
Any insight you have would be greatly appreciated. Thanks!

[Rosemeis]

Hi Johanna,

If you have installed pcangsd as described on the GitHub, it is only available as a command-line program pcangsd. There are some older tutorials which show python /path/to/pcangsd/pcangsd/pcangsd.py, but you need to simply just use pcangsd -b GL_YBCH_hz.beagle.gz -e 4 -t 10 -o pcangsd_YBCH_hz. Sorry! :-)

Let me know if it helped!

Best,
Jonas

[johannabeam]

Gosh, I just forgot a line of the install code! Thanks for letting me know; it's running fine now!