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LKremer / CAFE_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
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AttributeError: 'CAFE_fig' object has no attribute 'lambdas' #2

Closed Matt-BF closed 5 years ago

Matt-BF commented 5 years ago

Hi, I tried parsing my CAFE resultfile, but got an attribute error. Here is the traceback: Traceback (most recent call last): File "../../scripts/CAFE_fig.py", line 509, in main(**vars(args)) File "../../scripts/CAFE_fig.py", line 454, in main c.summary_tree() File "../../scripts/CAFE_fig.py", line 291, in summary_tree min(self.lambdas.values()), max(self.lambdas.values())) AttributeError: 'CAFE_fig' object has no attribute 'lambdas'

I am running python on a conda environment with: pyqt 4.11.4 python 3.5.5 ete3 3.0.0b35

Thanks in advance!

LKremer commented 5 years ago

Hi Matt, would you mind uploading your CAFE result file so I can try to reproduce this issue? Best, Lukas

Matt-BF commented 5 years ago

Sure thing, here it is resultfile.cafe.gz

LKremer commented 5 years ago

Hi @Matt-BF , sorry for the delay, this is just to let you know I'm running into the exact same crash on my computer, so it's either a problem with your CAFE file or my script. I'll see if I can identify what's causing the issue!

LKremer commented 5 years ago

Hi @Matt-BF, thanks for providing your file. I think I was able to fix the issue (see the commit above, the script no longer crashes on my end). Please pull or clone the repo again and try again :)

Matt-BF commented 5 years ago

Hi Lukas, I'm also sorry for the delay. I have just run the script on my desktop and pdf files are being written as expected! Thank you very much for the fix. However, when running the script on a remote server or cluster, ETE3 crashes because of a lack of Xserver support. I will try to find a workaround for this and will report if I find something useful Thanks again!

LKremer commented 5 years ago

Hi Matt, glad to hear that it works for you now! I remember running into the same remote server issues as you, but unfortunately this is out of my control because it's a limitation of ETE3. What you can try to do is using the --dump option to directly write the figures to files instead of displaying them in a window. I think I tried the same in the past and I don't remember if it worked, but it's worth a shot!