Installation issues #19
Comments
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Could you give some information about your operating system? Could you also paste the conda channel order and conda version? You may get that information by the command |
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Change back to import each function from ete3 import Tree, faces, AttrFace, TreeStyle, NodeStyle and instead fix so that conda installation (won´t crashing on importing faces). |
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@standage I tested the same command as you with the public FSC200 genome and it worked fine
This is whats in my conda environment. ( |
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@standage I´m looking into this issue. It would be great to get some more details about your operating system and installed packages similar to what Caroline posted above. I cannot replicate your problem using default installations in conda. |
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Sorry for the delayed response, I am trying to catch up after a 3-day holiday weekend. I am using CentOS 7 and Conda 4.8.3. See my setup below. I have tried several configurations and methods of installing CanSNPer2 and ETE3 beside what is shown below, but I continue to have issues. I have found some of the issue threads mentioned above, but I confirmed from the Python interpreter that PyQt5 is installed correctly. |
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If I run the same step without the |
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Thank you @standage I am trying to recreate your bug, would it be possible for you to try ete3 directly in python to see if we can pinpoint the problem. What happens if you run the command ete3.NodeStyle() in a python terminal after importing ete3? python
If that is still giving you an error try instead: (which is how it is solved in CanSNPer)
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Seems you have the old channel order. Bioconda changed this last year to be dependent on conda-forge. Please follow the instructions here to correct it and then re-run
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I fixed the channel order, but I'm getting the same result. |
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Hello again! I've been digging through this again, but unable to find root cause. Any luck on your end? |
xref from CanSNPer1: adrlar/CanSNPer#28 were @standage mention the following issue with installing CanSNPer2.
I was able to install CanSNPer2 in a new Conda environment, and download the Ft database. But unfortunately I get the following error when I run it on an Ft sample.
$ CanSNPer2 --database francisella_tularensis.db Ft.fna Run 1 alignments to references using progressiveMauve Traceback (most recent call last): File "/home/standage/anaconda3/envs/cansnper2/lib/python3.7/site-packages/CanSNPer2/modules/CanSNPer2.py", line 379, in run final_snp,message,called = self.create_tree(SNPS,self.query_name,called_snps,self.save_tree,min_required_hits=self.min_required_hits,strictness=self.strictness) File "/home/standage/anaconda3/envs/cansnper2/lib/python3.7/site-packages/CanSNPer2/modules/CanSNPer2.py", line 218, in create_tree final_snp = newickTree.draw_ete3_tree(SNPS,called_snps,save_tree,summary=summary) File "/home/standage/anaconda3/envs/cansnper2/lib/python3.7/site-packages/CanSNPer2/modules/NewickTree.py", line 288, in draw_ete3_tree nstyle = ete3.NodeStyle() AttributeError: module 'ete3' has no attribute 'NodeStyle' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/standage/anaconda3/envs/cansnper2/bin/CanSNPer2", line 10, in sys.exit(main()) File "/home/standage/anaconda3/envs/cansnper2/lib/python3.7/site-packages/CanSNPer2/CanSNPerTree.py", line 164, in main CanSNPer2_obj.run(database=args.database) File "/home/standage/anaconda3/envs/cansnper2/lib/python3.7/site-packages/CanSNPer2/modules/CanSNPer2.py", line 407, in run raise CanSNPer2Error("A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)") CanSNPer2.modules.CanSNPer2.CanSNPer2Error: 'A file did not run correctly exit CanSNPer2 (use --keep_going to continue with next file!)'The text was updated successfully, but these errors were encountered: