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Hi there,
I try to install inStrain using conda,
got this error by calling inStrain -h
File "/home/dell/.conda/envs/instrain/bin/inStrain", line 19, in <module>
import inStrain.controller
File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/controller.py", line 20, in <module>
import inStrain.profile
File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/profile/__init__.py", line 5, in <module>
import inStrain.profile.profile_controller
File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/profile/profile_controller.py", line 14, in <module>
import inStrain.SNVprofile
File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/SNVprofile.py", line 21, in <module>
import inStrain.profile.profile_utilities
File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/profile/profile_utilities.py", line 27, in <module>
import inStrain.GeneProfile
File "/home/dell/.conda/envs/instrain/lib/python3.8/site-packages/inStrain/GeneProfile.py", line 26, in <module>
from Bio.codonalign.codonalphabet import default_codon_table
ModuleNotFoundError: No module named 'Bio.codonalign.codonalphabet'
I have tryied reinstall biopython==1.73, 1.74 or 1.78, all gave same error,
any suggestion on this,
thanks.
Liu
The text was updated successfully, but these errors were encountered:
I also got that issue, but it got solved when I reinstalled inStrain using Conda. conda remove inStrain conda install -c bioconda inStrain
I hope that works for you.
This problem happens with Biopython version > 1.74. Are you sure that your attempts to download v1.74 were successful? You can check by typing "python" "import Bio" "print(Bio.version)"
You can also try and alter the version using the command pip install biopython=1.74
Hi,
I try to reinstall as ecvanderwijk suggested and now it worked. Could be the install of biopython version issue, not properly installed.
thank you both.
Hi there,
I try to install inStrain using conda,
got this error by calling inStrain -h
I have tryied reinstall biopython==1.73, 1.74 or 1.78, all gave same error,
any suggestion on this,
thanks.
Liu
The text was updated successfully, but these errors were encountered: