Failed to initialize any reasonable values

[marimaro]

Hello,

I am trying to do an expansion/retraction analysis on a plant genome dataset. I have 10 different species (both monocots and eudicots with different ploidies) and I keep encountering this error (I have already removed a few families that had really high differences in species I was not so interested in).

I don't understand why this is happening, because if I am searching for expansions, this is exactly what I am looking for, right? Many genes in a family in a single species.

Can you please help me in some way? I have used the script clade_and_size_filter.py to filter the dataset and tried different gamma categories values and the error persists.

Thank you in advance!

Families with largest size differentials:
OG0000346: 27
OG0000031: 26
OG0000136: 26
OG0000227: 25
OG0000161: 25
OG0000118: 25
OG0000214: 25
OG0000364: 25
OG0000100: 25
OG0000620: 24
OG0000080: 24
OG0000035: 24
OG0000078: 24
OG0000106: 23
OG0001614: 23
OG0000122: 23
OG0001245: 23
OG0000782: 23
OG0000575: 23
OG0000871: 23

You may want to try removing the top few families with the largest difference
between the max and min counts and then re-run the analysis.

Failed to initialize any reasonable values

[sajjadasaf]

Hello,
I have got same problem. Anybody have solved this issue?

[benfulton]

You may have better luck asking on the mailing list. https://groups.google.com/g/hahnlabcafe

[Rhia15]

Hi, has anyone solved this as I am also experiencing the same problem :) Thank you!

[benfulton]

This error indicates that CAFE couldn't even find a starting point to begin running the optimizer. It could be that your tree is simply too big, and/or your families too variable, for CAFE to make sense of the data. As there is likely to be lots of conflict deep in the tree, an option would be to use sub-clades of the tree in independent runs. Dr. Hahn also says, "You could also try parsimony-based methods (e.g. “Count”), which would be guaranteed to give you something!"

[shitingyu083]

Hello,
I apologize for disturbing you. I encountered the following issue while using CAFE. The error message displayed on the screen is:
"You may want to try removing the top few families with the largest difference between the max and min counts and then re-run the analysis."
"Failed to initialize any reasonable values."
errorwork.txt

Previously, I saw a suggestion to reduce the -l value, so I attempted the following commands:
cafe5 -i test3.txt -t tree.txt -o out -c 16 -l 0.00001 -k 2 -p -a 0.5
and
cafe5 -i test3.txt -t tree.txt -o out -c 16 -l 0.0001 -k 2 -p,
but the error persists. After searching for similar error messages, I didn’t find any successful debugging experiences. I have attached my work log and input files for your reference.
If possible, could you please reply to help resolve the issue?
Thank you!
Best regards,