I've had this happen before in my analyses. This is often the result of an unflagged error in your input file - codeml generates a pairwise matrix, one of the initial steps, but doesn't proceed to the ML estimation of omega. I had this happen a while back when my sample names did not conform exactly to Phylip specifications and again when my samples started with a number. My first suggestion would be to shorten the names to 10 characters or less and see what happens. This is easily accomplished with sed:
cat YOURFILE.fa | sed -e s/Updated_Gene_HN//g > YOURFILE.renamed.fa
This reads the file, finds every instance of "Updated_Gene_HN" and replaces it with nothing, globally, then writes the result to a new file. This can be iterated easily in bash, too, if you need it.
I also needed to do some single-rate (i.e., global) omega calculations a couple of weeks ago. I'm pasting my control file below, though it looks like yours is fine. This file executed over 15,000 times, so I'm confident it works :). I've changed the names of the seqfile and outfile; I also provided my own tree.
seqfile = FASTAFILENAME * sequence data filename
treefile = tree.phy * tree structure file name
outfile = FASTAFILENAME.codeml * main result file name
noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
verbose = 1 * 0: concise; 1: detailed, 2: too much
runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
* 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
* ndata = 1
clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
aaRatefile = dat/jones.dat * only used for aa seqs with model=empirical(_F)
* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
model = 0
* models for codons:
* 0:one, 1:b, 2:2 or more dN/dS ratios for branches
* models for AAs or codon-translated AAs:
* 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
* 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
* 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
* 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
* 13:3normal>0
icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
Mgene = 0
* codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
* AA: 0:rates, 1:separate
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 2 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = .5 * initial or fixed omega, for codons or codon-based AAs
fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = 0 * initial or fixed alpha, 0:infinity (constant rate)
Malpha = 0 * different alphas for genes
ncatG = 8 * # of categories in dG of NSsites models
getSE = 1 * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
Small_Diff = .5e-6
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
* fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 0 * 0: simultaneous; 1: one branch at a time
* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.
I hope this resolves your issues. Please respond if you need more help - I use codeml all the time.
Hi Brice, thank you so much for your response.I tried implementing your code after shortening the name length for each sequence. After running the program, the Terminal tells me the following (which is what it said before changing the code and names, but I forgot to include in my original post):
This is bizarre to me, as my tree contains the
CI_7_D1and its branch length when I open it in a text editor.Overall, I am still getting the same output as before with no summary statistics. That being said, I'm wondering if the problem may lie with my input files. I've been constructing/aligning my sequences in MegAlign and exporting as simple fasta files. I'm constructing the tree in MEGA6, which only allows an export file type of .nwk. I was under the impression that a .nwk was equivalent to a .tree file. Could any of this potentially explain my issue?