Failed to initialize any reasonable values

[creo...@naver.com]

Hello everyone,

I encountered the following error message while running CAFE5:

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

The command I used was:

cafe5 -c 8 -t ultrametric.tree -i families.txt -p -k 2 -o 1.cafe_result

I tried removing the top orthogroup families (those with the largest size differences) iteratively several times, but the same error continues to appear.

Has anyone else experienced this issue, or can suggest potential solutions?

[Hahn, Matthew]

Hello,

It may be that your tree is still too deep. Could you possibly share it here?

thanks,

Matt

--
You received this message because you are subscribed to the Google Groups "hahnlab-cafe" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hahnlabcafe...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/hahnlabcafe/c29c57d1-bee2-4756-8329-38cbaec95426n%40googlegroups.com.
<families.txt><ultrametric.tree>

[creo...@naver.com]

Dear Matt.

I have uploaded my ultramatric tree file.

Can short branch length (Prcl-Potr and Tiwe-Tija) be the problem?

Thank you for your support.

Paul.

2025년 8월 18일 월요일 오후 10시 14분 45초 UTC+9에 m...@indiana.edu님이 작성:

[Hahn, Matthew]

Yes, I think those are the problem. Try removing one from each of those pairs and see what happens!

good luck,

Matt

To view this discussion visit https://groups.google.com/d/msgid/hahnlabcafe/7d08db40-199a-4529-b1ed-4b63578acbben%40googlegroups.com.
<ultrametric.tree>

[kavita kumari]

hello everyone,

i am trying to running cafe on 63 species and it always throw the same error fail to initilaise with some families to filter but i already did and also to be clear i have used the make_ultrametrictree.py from the github. i have also run it with sepcifyiny the root age and also without the root age to get the ultrametri tree and then ran the cafe5 but still getting the error. i have attached the species tree file please have look and let me know the possible solutions.

thankyou.