After multiple cycles of deleting families, rerunning cafe5 still reports errors.

[guo23e]

Hello, may I ask if there is any solution to this error? (I have deleted [the relevant data] twice already.) Here is my code and the error message.
cafe5 -i gene_family_filter.txt -t tree.txt -o out -c 16 -l 0.00001 -k 2 -p
Families with largest size differentials:
OG0000437: 52
OG0000073: 51
OG0000172: 51
OG0000267: 51
OG0000181: 50
OG0000123: 47
OG0000143: 47
OG0000132: 47
OG0000173: 47
OG0000204: 46
OG0001965: 46
OG0000160: 46
OG0000322: 45
OG0001079: 44
OG0000130: 44
OG0000265: 44
OG0000456: 44
OG0000241: 44
OG0000139: 44
OG0004072: 44
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
Best regards,

[benfulton]

I am seeing many people get this error when their trees are very short. CAFE assumes that a branch length of 1 represents 1 million years, so if you have a tree with a total depth of 0.01, that would only represent about 10,000 years and there would most likely be no evolution to speak of.