Failed to initialize any reasonable values

[Daisy Sotero]

Hi,

I'm currently analyzing a dataset using CAFE5 and came across an issue that I haven’t been able to resolve:

"Families with largest size differentials:
OG0000016: 82
OG0000018: 66
OG0000005: 47
OG0000006: 45
OG0000000: 43
OG0000004: 42
OG0000009: 37
OG0000050: 37
OG0000174: 34
OG0000034: 34
OG0000027: 33
OG0000028: 33
OG0000074: 31
OG0000020: 31
OG0000026: 30
OG0000118: 29
OG0000103: 29
OG0000014: 27
OG0000032: 27
OG0000167: 27

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."

---------------------

I’ve read that others have faced this same problem, but I haven’t found a definitive solution so far. I’ve already tried using the clade_and_size_filter.py script available on GitHub, but the issue remains.

If anyone has encountered this before or has any suggestions on how to fix it, I’d really appreciate your help. I’m attaching my data in case it’s useful for troubleshooting.

Thank you in advance!

Daisy Sotero

[Hahn, Matthew]

Hi Daisy,

You will just have to remove these families from your analysis. They show so much variation in size that an accurate reconstruction of their history is not possible.

Matt

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<Orthogroups.GeneCount_sgCE.txt><SpeciesTree_rooted_sgCE.txt>

[Daisy Sotero]

Thank you for your reply.
I removed these families from my analysis. However, when I rerun the analysis without them, other families appear that also need to be removed. Should I continue removing families until the error no longer occurs?

[Hahn, Matthew]

Yes, that would be best.

To view this discussion visit https://groups.google.com/d/msgid/hahnlabcafe/ddf1f0e8-5168-4e0a-829c-be88b80f7dfbn%40googlegroups.com.

[Daisy Sotero]

Hi,

Following up on the discussion regarding the repeated error messages in CAFE5 about orthogroups with large size differentials: 

I've already run several iterations, each time removing the top problematic OGs, as suggested. However, with each run, new OGs with showing up.

Is there a recommended or safe maximum threshold for the difference between the highest and lowest copy numbers within an OG that I could use to filter them all at once before running the analysis?

Thanks again for the help and support!

[Ben Fulton]

Hi,

This could also indicate an issue with your tree. We generally assume that a branch of length of 1 is about 1 million years, but your tree is much smaller than that which does not leave much time for evolution to occur.

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Ben Fulton

Indiana University