Error in gene neighborhoods

mattb112885 / clusterDbAnalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes

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Error in gene neighborhoods #70

Open leoliuzhenshan opened 8 years ago

leoliuzhenshan commented 8 years ago

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: index Would anyone please help me to figure out what wrong with it?Thanks.

mattb112885 commented 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.

Can you post here the command line options you used when the problem occurred?
Does the tree show correctly if you use --display (and not --savepng)?
Did the image files with neighborhoods actually get created? They should be in /tmp/ (or the value of parent of the results of tempfile.mkdtemp() ) in a directory with a random name (do a ls -l to get files by date and look for one created around when you ran the code)

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

leoliuzhenshan commented 8 years ago

Thank you Matt, for your kindly reply. This is the command to create the tree : 111

and the tree display correctly: 222 333

And then I create the image of neighborhoods of the gene with the command: 444

the eroor occurred. But many image files with neighborhoods were generated in the /tmp/ directory.

Best, Liu zhenshan

mattb112885 commented 8 years ago

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

leoliuzhenshan commented 8 years ago

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/.

mattb112885 commented 8 years ago

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

working_neighborhoods

Best

Matt