Question: Very anomalous dN/dS output trouble in PAML
0
gravatar for munna.uppal
5.2 years ago by
munna.uppal10
United States
munna.uppal10 wrote:

Hi all,

First off, Happy Thanksgiving to the Biostars community! I've been working in PAML to generate a single dn/ds (or, omega) value for an alignment of 16 sequences. However, despite everything I try, I cannot get a single estimate of omega for the alignment in the output file. What I end up getting looks like this:

CI_7_D1             
CI_8_D1              0.0565 (0.0089 0.1581)
CI_9_D1              0.1516 (0.0024 0.0160) 0.0533 (0.0081 0.1521)

---------

Each time I run Codeml, even with aligned sequences for a different protein using a different tree, I also get the following output in the terminal (not the output file itself):

"Seq #1 (CI_7_D1) is missing in the tree." (CI_7_D1 is the name of the first sequence).

The thing is, it isn't missing from the tree. The following is the first line from my .nwk file:

"((((((((('CI_14_D1':0.00185424,KJ672615:0.00123049):0.00000000,'CI_7_D1':0.00185089):"

---------

The following is the relevant input for my Codeml ctl file:

runmode = 0, seqtype = 1, CodonFreq = 2, model = 0, NSsites = 0

fix_kappa = 0, kappa = 1, fix_omega = 0, omega = 1, ncatG = 10

--------

Can anyone tell me what the potential issue may be here? I've honestly tried exhausting every resource that I could find online, but it seems that my type of problem isn't one that has been presented to the PAML support community. Any and all help would be greatly appreciated. 

Thank you,

Munna

alignment gene software error • 2.1k views
ADD COMMENTlink modified 5.0 years ago by Andre Elias80 • written 5.2 years ago by munna.uppal10
3
gravatar for Siva
5.2 years ago by
Siva1.7k
United States
Siva1.7k wrote:

It seems to me that the sequence names in your tree file and the alignment file are not identical. From what you posted, the sequence name in your tree file has single quotes:

"((((((((('CI_14_D1':0.00185424,KJ672615:0.00123049):0.00000000,'CI_7_D1':0.00185089):"

In the CODEML error line, the sequence name in the alignment does not have single quotes:

"Seq #1 (CI_7_D1) is missing in the tree." (CI_7_D1 is the name of the first sequence).

Please check if you have identical sequence names in both the tree file and the alignment file. 

As for the result, what you are seeing is a partial result file. CODEML program failed to run. If it runs without any error, you will see the following lines in your result file.

Detailed output identifying parameters
kappa (ts/tv) =  4.81815
omega (dN/dS) =  0.85620

 

 

 

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Siva1.7k
0
gravatar for Andre Elias
5.0 years ago by
Andre Elias80
Rio de Janeiro, Brazil
Andre Elias80 wrote:

Yes, PAML can be sensitive to very simple things.

Like the other answer said, if you add " or ' to your sequence names in your tree file (if you're creating your tree file using Figtree, it will add the quotation marks automatically), PAML programs will not recognize the name of the sequences in the tree file.

 

ADD COMMENTlink written 5.0 years ago by Andre Elias80
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