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Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
GNU General Public License v3.0
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cannot import name 'reader_cy' from 'pcangsd' #71

Open cnxiaobo94 opened 1 year ago

cnxiaobo94 commented 1 year ago

Hi! Rosemeis, The installation was done as your inst., but a problem occurred as below. Could you please do me a favor?

Traceback (most recent call last): File "/home/xiaobo/bioinformatics/xiaobo_analyses/../pcangsd/pcangsd/pcangsd.py", line 476, in main() File "/home/xiaobo/bioinformatics/xiaobo_analyses/../pcangsd/pcangsd/pcangsd.py", line 147, in main from pcangsd import reader_cy ImportError: cannot import name 'reader_cy' from 'pcangsd' (/home/xiaobo/bioinformatics/pcangsd/pcangsd/pcangsd.py)

Rosemeis commented 1 year ago

Hi,

Can you send me the command that you have used. :-) It could be if you work in a HPC environment that it doesn't use your correct python, see #69

Best, Jonas

cnxiaobo94 commented 1 year ago

python3 ../pcangsd/pcangsd/pcangsd.py --beagle moosePCA.beagle.gz --out moosePCA --threads 8

I used the above command and met a problem like before. After I set an environment path to 'path/to/pcangsd', I used the below command and it worked.

pcangsd --beagle moosePCA.beagle.gz --out moosePCA --threads 8

aguilar-gomez commented 1 year ago

You solved my problem, I was running previous versions of pcangsd with python3 before and this one you have to run direclty