Hello,
I ran the command for phyloFit using my multi aligned file from
clustal omega in fasta format and a newick tree, and i got the .mod
file
command: phyloFit --tree clustal_omega_tree.nwk clustal_omega.fasta >
phyloFit.mod
Extracting sufficient statistics ...
Compacting sufficient statistics ...
Fitting tree model to clustal_omega.fasta using REV ...
numpar = 9
Done. log(likelihood) = -741.651633 numeval=13
Writing model to phyloFit.mod ...
Done.
When i try to run the phastCons using this command : phastCons
clustal_omega.fasta phyloFit.mod > phastCons.wig
i get an error: ERROR: no match for reference sequence in tree.
Why is that? Any suggestion will do...thanks
Hi Dimitris.
Your post is a little off-topic for Jalview's discussion list but see below for my suggestion:
Hello,
I ran the command for phyloFit using my multi aligned file from
clustal omega in fasta format and a newick tree, and i got the .mod
file
command: phyloFit --tree clustal_omega_tree.nwk clustal_omega.fasta >
phyloFit.mod
Extracting sufficient statistics ...
Compacting sufficient statistics ...
Fitting tree model to clustal_omega.fasta using REV ...
numpar = 9
Done. log(likelihood) = -741.651633 numeval=13
Writing model to phyloFit.mod ...
Done.
When i try to run the phastCons using this command : phastCons
clustal_omega.fasta phyloFit.mod > phastCons.wig
i get an error: ERROR: no match for reference sequence in tree.
Why is that? Any suggestion will do...thanks
First check whether the sequence IDs in phyloFit.mod match the IDs in clustal_omega.fasta. Different tools have different ID requirements, and some will clip the ID string in their results if the input ID was too long.
It's also possible that phastCons has different requirements for IDs - make sure the IDs begin with a letter and are only alphanumeric. For Jalview's services, we always rename the Sequence IDs before submission to avoid this problem!
Hope that helps...
Jim.
ยทยทยท
On 29/06/2020 13:41, Dimitris Hatzopoulos wrote:
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