Open leoliuzhenshan opened 8 years ago
Hello,
I have not seen this particular problem before, can you try a few things for me? It will help me to tell where the problem is. It may be a bug in ETE (in which case we may need to file a bug report with them) but lets try a few things first.
I'm also assuming you have access to an X server. Another thing that may be useful -- does db_displayTree.py work for you?
Best
Matt
Thank you Matt, for your kindly reply.
This is the command to create the tree :
and the tree display correctly:
And then I create the image of neighborhoods of the gene with the command:
the eroor occurred. But many image files with neighborhoods were generated in the /tmp/ directory.
Best, Liu zhenshan
Thank you Liu. Based on the outputs in the above images, my first guess is that this is somehow due to the polytony (identical proteins) in the tree. If you produce an alignment that does not have identical proteins in it and try to run the same neighborhood tree command, do you still see the problem occurring?
One other question -- what version of ETE are you running?
I will play with it in the VM this weekend and see if I can produce the problem on my end.
Best
Matt
Dear Matt:
I tried your suggestion to create a bifurcating tree and run the same neighborhood tree command and the same error occurred. The version of ETE is 2.3.10.
If this command doesn't work, I can still use the pictures in the /tmp/.
Hi Liu, I was able to reproduce this problem but I only observed it with ETE 2.3 -- it didn't happen when I ran it with 2.2rev1014 (which was the current version when ITEP was published).
I will try to fix the script to work with newer versions, but as a workaround you can install the version of ETE I know works using:
(sudo) easy_install -U ete2==2.2rev1014
Best
Matt
Hi,I encountered a problem when I run the db_makeNeighborhoodTree.py script to check the neighborhood of one gene. I have installed all the dependencies ITEP required and created one nwk tree. The error message is like that:
Would anyone please help me to figure out what wrong with it?Thanks.