MEME analysis crashes

[harturchin]

This small MEME analysis starts successfully then crashes with the error message below. Input file is attached (fasta, 21 sequences, with Newick string); it runs correctly in other apps on the data monkey (GARD, aBSREL) but not in MEME. I guess it is a problem with an undefined branch length or rate caused by the data themselves?

Thanks!
Mike

Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model

• Log(L) = -7579.97
• non-synonymous/synonymous rate ratio for test = 0.5739
  Error:
  meme.site_tree_bsrel.Node1 is not a valid likelihood function/data set filter/tree topology/tree node in call to SetParameter(
  Function call stack
  1 : Set parameter MODEL of meme.site_tree_bsrel.Node1 to meme.bsrel

---

2 : ExecuteCommands in string "SetParameter (id."+model.ApplyModelToTree.list[model.ApplyModelToTree.b]+",MODEL,"+model.ApplyModelToTree.apply_model+")" using basepath /home/datamonkey/datamonkey-js-test/app/meme/../../.hyphy/res/TemplateBatchFiles/libv3/models/.

3 : model.ApplyModelToTree("meme.site_tree_bsrel",meme.trees[meme.partition_index],None,meme.model_to_branch_bsrel)

3.3.Zp1_Primates.txt

[spond]

Dear @harturchin,

Thank for reporting this issue. I have seen this error before and thought we had fixed it (it has to do with tree rerooting). Essentially, you Newick string has an extraneous set of (), which results in the "root branch" like shown in the attached screenshot

You can get this dataset to run right away simply by removing the outermost () from the Newick string.

Best,
Sergei

[harturchin]

Whoops! Thanks Sergei!

[spond]

Dear @harturchin,

No problem. Datamonkey should handle it, however. So, I'll keep the issue open.

Best,
Sergei

[rdvelazquez]

This now works fine with the hyphy develop branch. Datamonkey will be able to handle this type of file once version 2.4.0 of hyphy is released and datamonkey is upgraded to use the new version.