CAFE5 running error: Invalid lambda index set for 1

[Pu Shi]

Hello,

When I run the CAFE5 with the code: "-i cafe.input.tsv -t 14aatree.fa -y 14aa_lambda.fa -k 3 -o report_14aa/" , the "Invalid lambda index set for 1" will occur. And when I use the speice name like "speice:1" , the error would occur with the "Invalid lambda index set for

 speice". 

After that, I let the CAFE5 calculate the lambda with code " cafe5 -i cafe.input.tsv -t 14aatree.fa -k 3 -l 0.01 -o report_14aa/" , but the error "Failed to initialize any reasonable values" came out. So I'd like to know where are the mistakes in my code.

The cafe.input.tsv, 14aatree.fa, 14aa_lambda.fa, 14aa_lambda_speicename.fa , and the error are  in the attachment. 

Looking forward your reply.

Best Wishes!

[Hahn, Matthew]

Hi,

It seems that your tree is quite long, and your families are highly variable (with some not likely existing in the root). So I would suggest using only a subset of species and families.

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 on the web visit https://groups.google.com/d/msgid/hahnlabcafe/cb8948e2-5e2a-4edb-9f82-5228834ea00fn%40googlegroups.com.
<14aa_lambda_speicename.fa><error.txt><14aatree.fa><cafe.input.tsv><14aa_lambda.fa>

[Pu Shi]

Hi,

Thanks for your reply, and I just used 14 speices to run the CAFE5, it seems like fine in other researchers CAFE5, and I had removed the family with more than 100 orthologs, the error came the same.

So whether is it better to use the CAFE4?

best wishes!

[Hahn, Matthew]

Sorry, but it’s not the number of species, but how distantly related they are. Likewise, it’s not the size of families, but the variance in copy-number that is the issue.

matt

To view this discussion on the web visit https://groups.google.com/d/msgid/hahnlabcafe/02c72f51-6659-43b6-97d8-d078ddcfa7cfn%40googlegroups.com.