Very anomalous dN/dS output trouble in PAML

Question

[munna.uppal]

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

Answer 1

[Siva]

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
        ^_____^

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

Answer 2

[Andre Elias]

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.