pangolin --add-assignment-cache fails with "NameError: name 'CalledProcessError' is not defined"

[GorgonVZ]

Dear pangos, I just tried to install the assignment cache using, but I get the Error Message pasted to the very end of this message. Can you give me any advice how to solve this? Am I running a misscompiled installation?

Command I used: conda activate pangolin /home/pcr/anaconda3/envs/pangolin/bin/pangolin --add-assignment-cache

Versions I use: pangolin already latest release (v4.0.6) pangolin-data already latest release (v1.8) constellations already latest release (v0.1.10) scorpio already latest release (v0.3.17) pangolin-data already latest release (v1.8) constellations already latest release (v0.1.10) UShER (v0.5.4)

I am mostly interested in the "add-assignment-cache" feature, because I would like to have acccess to the most "up to date" usher tree. This brings me to my question/feature request... Is it possible to update the pangolin_data repository more regularly than this is the case right now? Actually 15 days are a quite long timeperiod if one tries to find the most recent viral-lineages around.

Thanks in advance and for the amazing work you are doing! You are awsome!

################################################################################## /home/pcr/anaconda3/envs/pangolin/bin/pangolin --add-assignment-cache Traceback (most recent call last): File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/site-packages/pangolin/utils/update.py", line 82, in install_pangolin_assignment import pangolin_assignment ModuleNotFoundError: No module named 'pangolin_assignment'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/site-packages/pangolin/utils/update.py", line 61, in git_lfs_install stderr=subprocess.DEVNULL) File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/subprocess.py", line 488, in run with Popen(*popenargs, **kwargs) as process: File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/subprocess.py", line 800, in init restore_signals, start_new_session) File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/subprocess.py", line 1551, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'git-lfs': 'git-lfs'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/pcr/anaconda3/envs/pangolin/bin/pangolin", line 8, in sys.exit(main()) File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/site-packages/pangolin/command.py", line 113, in main update.install_pangolin_assignment() File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/site-packages/pangolin/utils/update.py", line 86, in install_pangolin_assignment git_lfs_install() File "/home/pcr/anaconda3/envs/pangolin/lib/python3.7/site-packages/pangolin/utils/update.py", line 62, in git_lfs_install except CalledProcessError as e: NameError: name 'CalledProcessError' is not defined ################################################################################################

[AngieHinrichs]

Hi @GorgonVZ, it looks like your conda environment needs to be updated since it does not have git-lfs:

FileNotFoundError: [Errno 2] No such file or directory: 'git-lfs': 'git-lfs'

Can you try running these commands?

conda activate pangolin
conda update --update-all pangolin

Then try pangolin --add-assignment-cache again? Thanks!

[GorgonVZ]

Hi @AngieHinrichs, thanks that solved my issue! Nevertheless, do you think it's feasible to update usher's reference-tree in shorter time intervals to, be more up to date? Thanks, GVZ

[AngieHinrichs]

Hi @GorgonVZ -- yes, it has been a few weeks. I'm hoping there will be another release of pango-designation by the end of this week, and then @aineniamh and I can update pangolin-data with the new release.