sabifo4
commented
7 months ago Hi there!
Your tree file seems to have the wrong header as you only have one tree in Newick format, not 1,293 trees. In other words, instead of having 9 1293 in your consensAlign.ordered.phylip.treefile file, you should have 9 1. Nevertheless, I can see that you have the results for model M8 in the paml_out.txt file you attach (you can find them from line 463 onward, and I paste them below too):
NSsites Model 8: beta&w>1 (11 categories)
TREE # 1: (1, ((2, (4, 5)), (6, ((7, 9), 8))), 3); MP score: -1
lnL(ntime: 15 np: 23): -3500.924560 +0.000000
10..1 10..11 11..12 12..2 12..13 13..4 13..5 11..14 14..6 14..15 15..16 16..7 16..9 15..8 10..3
0.046279 0.011169 0.006500 0.052531 0.000630 0.038677 0.054104 0.078572 0.115860 0.229059 0.003703 0.052843 0.061416 0.088236 0.021853 2.040912 1.158380 0.819599 1.442637 0.905585 0.194517 0.258267 3.844699
Note: Branch length is defined as number of nucleotide substitutions per codon (not per nucleotide site).
tree length = 0.861431
(1: 0.046279, ((2: 0.052531, (4: 0.038677, 5: 0.054104): 0.000630): 0.006500, (6: 0.115860, ((7: 0.052843, 9: 0.061416): 0.003703, 8: 0.088236): 0.229059): 0.078572): 0.011169, 3: 0.021853);
(Sdro: 0.046279, ((Sfra: 0.052531, (Sint: 0.038677, Spur: 0.054104): 0.000630): 0.006500, (Hpul: 0.115860, ((Mfra: 0.052843, Pdep: 0.061416): 0.003703, Mnud: 0.088236): 0.229059): 0.078572): 0.011169, Spal: 0.021853);
Detailed output identifying parameters
kappa (ts/tv) = 2.04091
Frequency parameters:
0.26204 (T) 0.18540 (C) 0.32634 (A) 0.22621 (G)
Parameters in M8 (beta&w>1):
p0 = 0.90559 p = 0.19452 q = 0.25827
(p1 = 0.09441) w = 3.84470
MLEs of dN/dS (w) for site classes (K=11)
p: 0.09056 0.09056 0.09056 0.09056 0.09056 0.09056 0.09056 0.09056 0.09056 0.09056 0.09441
w: 0.00000 0.00076 0.01038 0.05682 0.18875 0.43116 0.71245 0.90915 0.98676 0.99981 3.84470
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
10..1 0.046 954.0 339.0 0.7520 0.0142 0.0189 13.5 6.4
10..11 0.011 954.0 339.0 0.7520 0.0034 0.0046 3.3 1.5
11..12 0.007 954.0 339.0 0.7520 0.0020 0.0027 1.9 0.9
12..2 0.053 954.0 339.0 0.7520 0.0161 0.0214 15.4 7.3
12..13 0.001 954.0 339.0 0.7520 0.0002 0.0003 0.2 0.1
13..4 0.039 954.0 339.0 0.7520 0.0119 0.0158 11.3 5.3
13..5 0.054 954.0 339.0 0.7520 0.0166 0.0221 15.8 7.5
11..14 0.079 954.0 339.0 0.7520 0.0241 0.0321 23.0 10.9
14..6 0.116 954.0 339.0 0.7520 0.0355 0.0473 33.9 16.0
14..15 0.229 954.0 339.0 0.7520 0.0703 0.0934 67.0 31.7
15..16 0.004 954.0 339.0 0.7520 0.0011 0.0015 1.1 0.5
16..7 0.053 954.0 339.0 0.7520 0.0162 0.0216 15.5 7.3
16..9 0.061 954.0 339.0 0.7520 0.0188 0.0251 18.0 8.5
15..8 0.088 954.0 339.0 0.7520 0.0271 0.0360 25.8 12.2
10..3 0.022 954.0 339.0 0.7520 0.0067 0.0089 6.4 3.0
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Sdro)
Pr(w>1) post mean +- SE for w
28 S 0.631 2.761
42 L 0.899 3.551
126 S 0.526 2.451
129 Q 0.904 3.564
139 K 0.927 3.632
150 S 0.900 3.555
205 P 0.934 3.652
221 S 0.769 3.168
248 T 0.772 3.177
249 M 0.875 3.480
255 M 0.500 2.362
259 M 0.509 2.389
279 G 0.551 2.514
290 P 0.811 3.290
304 L 0.983* 3.795
305 E 0.785 3.214
308 S 0.915 3.598
310 I 0.998** 3.838
320 K 0.536 2.483
406 Q 0.532 2.457
407 G 0.977* 3.779
409 I 0.634 2.771
411 L 0.912 3.588
414 G 0.805 3.273
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Sdro)
Pr(w>1) post mean +- SE for w
24 S 0.574 2.154 +- 1.353
28 S 0.806 2.836 +- 1.192
42 L 0.955* 3.310 +- 0.942
126 S 0.744 2.643 +- 1.238
129 Q 0.955* 3.326 +- 0.972
139 K 0.968* 3.360 +- 0.927
142 S 0.520 1.994 +- 1.343
150 S 0.955* 3.322 +- 0.960
157 L 0.688 2.493 +- 1.333
166 V 0.572 2.147 +- 1.355
167 E 0.591 2.205 +- 1.356
204 S 0.670 2.440 +- 1.345
205 P 0.971* 3.375 +- 0.925
211 D 0.634 2.331 +- 1.350
221 S 0.883 3.091 +- 1.109
237 K 0.505 1.951 +- 1.334
246 G 0.544 2.066 +- 1.352
248 T 0.885 3.097 +- 1.108
249 M 0.941 3.278 +- 1.002
255 M 0.689 2.501 +- 1.339
259 M 0.696 2.521 +- 1.337
279 G 0.726 2.614 +- 1.322
285 Q 0.628 2.313 +- 1.352
289 P 0.678 2.463 +- 1.341
290 P 0.906 3.171 +- 1.080
295 F 0.699 2.515 +- 1.304
299 Q 0.653 2.387 +- 1.348
302 T 0.563 2.121 +- 1.352
303 N 0.599 2.227 +- 1.356
304 L 0.993** 3.443 +- 0.857
305 E 0.892 3.123 +- 1.100
306 A 0.592 2.205 +- 1.353
308 S 0.962* 3.346 +- 0.945
310 I 0.999** 3.460 +- 0.841
316 T 0.564 2.123 +- 1.353
320 K 0.751 2.662 +- 1.231
393 G 0.588 2.192 +- 1.353
404 A 0.646 2.368 +- 1.351
405 P 0.640 2.351 +- 1.353
406 Q 0.713 2.572 +- 1.328
407 G 0.991** 3.437 +- 0.867
409 I 0.808 2.843 +- 1.191
411 L 0.959* 3.341 +- 0.967
414 G 0.902 3.160 +- 1.088
416 S 0.598 2.225 +- 1.354
418 Q 0.584 2.183 +- 1.426
422 M 0.525 2.010 +- 1.344
423 G 0.657 2.404 +- 1.350
429 L 0.501 1.943 +- 1.340
The grid
p0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950
p : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900
q : 0.100 0.300 0.500 0.700 0.900 1.100 1.300 1.500 1.700 1.900
ws: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500
Posterior on the grid
p0: 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.131 0.735 0.134
p : 0.073 0.173 0.237 0.244 0.173 0.071 0.020 0.006 0.002 0.001
q : 0.055 0.032 0.061 0.073 0.088 0.109 0.123 0.138 0.153 0.167
ws: 0.001 0.261 0.598 0.072 0.052 0.014 0.002 0.000 0.000 0.000I ran CODEML on my PC with the header changed and it ran without issues. The printed messages on the terminal when running model 8 are the following:
NSsites Model 8: beta&w>1
TREE # 1
(1, ((2, (4, 5)), (6, ((7, 9), 8))), 3); MP score: -1
initial w for M8:NSbetaw>1 reset.
ntime & nrate & np: 15 5 23
Qfactor_NS = 0.759931
Out..
lnL = -3500.924560
2265 lfun, 27180 eigenQcodon, 373725 P(t)
BEBing (dim = 4). This may take several minutes.
Calculating f(x_h|w): 10 categories 20 w sets.
Calculating f(X), the marginal likelihood.
log(fX) = -3507.727807 S = -3242.366064 -261.361327
Calculating f(w|X), posterior probabilities of site classes.
did 253 / 253 patterns 5:10
Time used: 5:10I believe that you just thought that the did 253 / 253 patterns was an error, but this is just a message printed on the terminal to let you know how many site patterns have been parsed on your input file.
Hope this helps!
Hello, when running codeml (paml v4.10.7) on MacBook Pro M1, the program quits during NSsites Model 8 with the following error:
error: edid 253 / 253 patterns 4:02(base) ~/desktop/paml$I've included the output from running the codeml command, the control file, and the multiple sequence alignment, and the tree. Any help would be greatly appreciated. err.txt paml_out.txt consensAlign.ordered.phylip.txt consensAlign.ordered.phylip.treefile.txt codeml.ctl.txt