Issue with CAFE Analysis about "Failed to initialize any reasonable values."

[Tingyu Shi]

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."
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,
Shitingyu

[Hahn, Matthew]



Hi,

Did you try removing the top few families? That should be more effective. This is a very deep tree with lots of changes, and simply may not be analyzable via CAFE. 

Matt

On Oct 11, 2024, at 4:43 AM, Tingyu Shi <shitin...@gmail.com> wrote:

Hello,

--
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 on the web visit https://groups.google.com/d/msgid/hahnlabcafe/bde9a6a0-19d5-4f39-a9f7-8d009a2dc172n%40googlegroups.com.

<errorwork.txt>

<tree.txt>

<test3-final.txt>