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Error in gene tree processing #3
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Thank you for reporting! Would it be possible to share your input trees? |
Hello, thank you for the quick reply. Not the exact same tree, but another tree which produces the same error. It is the reconciled tree from Notung v2.9.1.5.
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Thank you. This looks like a gene tree. I need a species tree too to reproduce the error. |
Oh, my apologies. Below you can find the species tree used.
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Oops, I needed .parsable file too for the NOTUNG input. Could you also tell me the full |
Here is the parsable file and also the command used. Should've shared these too, sorry.
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I couldn't reproduce the error... Could you share the all inputs as a zipped file? Copying-and-pasting may cause some troubles. I can fix apparent errors such as the missing semi-colon in the species tree, but there may be something more. |
Here it is: |
I couldn't reproduce the error still but found that the species tree contains non-labeled nodes. I've just updated the radte to return an error for the format violation. Could you retry with the latest radte.r? You should be able to get the correct outputs (below) if the species tree was properly labeled, for example, with the following command.
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The update seemed to have worked. Indeed it pointed out the format violation and after fixing it it works good. 👍 Thank you very much for the help! |
Hello,
First of all let me thank you for setting up this tool, been searching for something like it before. I tried to follow the tutorial provided with my own dataset and provided the same parameters as in the the tutorial, but got the following error message:
What do you think I am doing wrong?
Cheers
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