HyPhy message board - Tipdate function

jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	Re: Tipdate function Reply #15 - Mar 29^th, 2007 at 10:48am Dear Sergei, I found the error, this sequence 8247228Hum don't have the date, I removed it and the tipdate's function runs correct. Thanks your advice and sorry this newbie error. Every day the HYPHY package surprises me, a very good software, congratulations HYPHY team. Cheers, Jackson
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jackson

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Re: Tipdate function
Reply #16 - Mar 29^th, 2007 at 1:02pm

Dear Sergei,

It forgives me if this error will be plus an error newbie.
I tried to run the new options that you wrote in your post, but the HYPHY returned this error , the log is below:

/HYPHY 0.9920070328beta(MP) for Linux on x86_64\
***************** TYPES OF STANDARD ANALYSES *****************
   (1) Basic Analyses
   (2) Codon Selection Analyses
   (3) Compartmentalization
   (4) Data File Tools
   (5) Miscellaneous
   (6) Model Comparison
   (7) Molecular Clock
   (8) Phylogeny Reconstruction
   (9) Positive Selection
   (10) Recombination
   (11) Selection/Recombination
   (12) Relative Rate
   (13) Relative Ratio
   (14) Substitution Rates

Please select type of analyses you want to list (or press ENTER to process custom batch file):7
***************** FILES IN 'Molecular Clock' *****************
   (1) Test for the presence of a global molecular clock with DATED sequences. Evolutionary rates and dates for internal nodes are estimated as well. This analysis is effectively an extended version of Andrew Rabmaut's TipDate methodogoly.
   (2) Test for the presence of a global molecular clock on the tree using its root (the resulting clock tree is unrooted, but one of the root branches can be divided in such a way as to enforce the clock).
   (3) Test for the presence of a local molecular clock. Every subtree of the given tree is subjected to the clock constraint, while the remainder of the tree is free of the clock constraint.
   (4) Test for the presence of a global molecular clock on the tree. The tree is rooted at every possible branch.
   (5) Infer dates of ancestral nodes for a sample of DATED sequences using a rate-distribution genetic algorithm to allow for multiple substituion rates. This is a frequentist alternative to the relaxed clock analyses implemented by Drummond and Rambaut in BEAST. [MPI Enabled]
   (6) Process a .samples file generated with GADatedClock

Please select the file you want to use (or press ENTER to return to the list of analysis types):5

(/root/HYPHY/TemplateBatchFiles/) Locate a nucleotide data file:/root/NSP4orfdatedmafftseqrootedtree.phy
   +--------------------------+
   | Select a standard model. |
   +--------------------------+
   (CUSTOM):Custom 4x4 reversible model (defined as in 010023) with choice of several equilibrium frequencies options.
   (F81):Felsenstein 81 (F81).Rate heterogeneity (and HM spatial correlation) optional.
   (F84):Felsenstein 84. Rate heterogeneity (and HM spatial correlation) optional.
   (F84P):Felsenstein 84, compatible with PHYLIP's dnaml version. User chooses ts/tv ratio. Rate heterogeneity (and HM spatial correlation) optional.
   (GRM):General Reversible Model.Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).
   (HKY85):Hasegawa et al.,1985. Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).
   (JC69):Jukes-Cantor 1969.Rate heterogeneity (and HM spatial correlation) optional.
   (K2P):Kimura 2 parameter (K2P).Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).
   (K3ST):Kimura(1981) 3 substitution type model. Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).
   (NRM):Non reversible model, constrained to have observed counts as its equilibrium frequencies. 11 parameters (8 rate parameteres + 3 frequency parameters).
   (NRM+FREQS):Non reversible model, NOT constrained to have observed counts as its equilibrium frequencies. 11 parameters.
   (TRN):Tamura and Nei 1993. Local or global parameters. Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).

Please type in the abbreviation for the model you want to use:custom

Please enter a 6 character model designation (e.g:010010 defines HKY85):010010
+-------------+
|Model Options|
+-------------+
   (1):[Local] All model parameters are estimated independently for each branch.
   (2):[Global] Model parameters are shared by all branches, branch lengths are estimated independently.
   (3):[Global w/variation] Model parameters are shared by all branches, branch lengths come from a user-chosen distribution, whose parameters are estimated.
   (4):[Global w/variation+HM] Model parameters are shared by all branches, branch lengths come from a user-chosen distribution, whose parameters is estimated; rates at adjacent sites are correlated via a simple Hidden Markov model with an autocorrelation parameter lambda.

Please choose an option (or press q to cancel selection):3
+-------------------+
|Choose Distribution|
+-------------------+
   (1):[Gamma] Gamma distribution with shape parameter alpha. Mean: alpha, variance: 1/alpha.
   (2):[Beta] Two-parameter beta distrubution. Mean: betaP/(betaQ+betaP), variance: betaP*betaQ/((betaP+betaQ)^2 (betaP+betaQ+1)).
   (3):[Normal(x>0)] Two-parameter normal distrubution restriced to x>0. Mean parameter: mu, variance parameter: sigma^2.
   (4):[Log normal] Unit mean log normal distribution with parameter sigma. Variance: 1/[exp(sigma^2)-1].
   (5):[Gamma+Inv] Gamma distribution with shape parameter alpha and mean 1/(1-P) and a zero rate class for invariable sites with weight P.
   (6):[Gamma Quadratures] Gamma distribution with shape parameter alpha. Mean: alpha, variance: 1/alpha. Discretized using Gauss-Laguerre quadratures, matching 2N-1 moments, with N = the number of rate classes.
   (7):[Inv Class] A mixture of point masses at 0 and 1, with proportions P and (1-P). Mean: (1-P), variance P(1-P). Parameters: P - the proportion of invariable sites.
   (8):[General Discrete] Unit mean general discrete.
   (9):[Beta-Gamma] Gamma distribution with shape parameter alpha partitioned by a beta distribution.
   (10):[Beta-Lognormal] Mean one log normal distribution with parameter sigma, partitioned by the beta. Variance: 1/[exp(sigma^2)-1].
   (11):[Normal(x>0) mod Beta] Normal (x>0) distribution with parameter sigma, partitioned by the beta. Mean parameter: mu, variance parameter: sigma^2.
   (12):[Beta-Uniform] Mean 1 piecewise uniform on [0,1] and [1,R] partitioned by the beta.
   (13):[Uniform] Mean 1 piecewise uniform on [0,1] and [1,R].
   (14):[Beta-(Gamma+Inv)] Mixture of gamma mod beta and an invariant class partitioned by the beta.

Please choose an option (or press q to cancel selection):5

How many rate classes should we have?4
+---------------+
|Rate Parameters|
+---------------+
   (1):[Estimated] Rate parameters are inferred by maximum likelihood.
   (2):[User] Rate parameters are fixed at user specified values

Please choose an option (or press q to cancel selection):2
Enter the rate for AC (relative to AG rate):7.10000
+-----------------------+
|Equilibrium Frequencies|
+-----------------------+
   (1):[Observed] Nucleotide frequencies collected from the data file will be used as equilibrium frequencies.
   (2):[Equal] Equal (.25) frequencies are used as equilibrium frequencies
   (3):[Custom] Define your own vector of frequencies.

Please choose an option (or press q to cancel selection):1

A tree was found in the data file:
(13Hum1995:4120.2,(107Hum2002:0,((((12Hum2004:0,(11Hum2004:0,(((((((4Hum1999:0,(
123Cap1998:0,239Can1980:7.17531):2.18521):154.789,((((((((((((((((((((((((((((((
((((2Hum2000:4.91975,118Lam1981:3.16657):1.00259,242Equ1976:0.54289):1.67751,77H
um1993:1.81005):1.04422,(((((1Sim1958:1.73424,19Hum2004:1.55462):1.86337,(((((((
((((((((((((((((((((((((((((((((((((((((3hum2000:0,282Hum2002:0.019575):0.057103
6,14Hum2002:0.0425057):0,15Hum2000:0):0.364404,16Hum2001:0.133973):0,180Hum1990:
0):0.00106258,179Hum1990:0):0.00282136,181Hum1990:0):0.0290651,110Hum1998:0):0.0
0500024,274Hum2003:0):0.00299513,169Hum1998:0):0.00439328,155Hum1997:0):0.017498
3,289Hum2001:0):0.0017609,171Hum1998:0):0.00310972,275Hum2003:0):0.00267115,170H
um1998:0):0.002041,164Hum1998:0):0.00204142,167Hum1998:0):0.00202064,156Hum1997:
0):0.00191157,272Hum2003:0):0.00433435,264Hum2004:0):0.00100582,166Hum1998:0):2.
00307e-06,168Hum1996:0):0.0262291,(((82Hum1996:0,((((95Hum1996:0,112Hum1999:0.01
62303):0.00529217,279Hum2002:0):0,287Hum2001:0):0,286Hum2002:0):0.00310414):8.12
184e-05,85Hum1997:0):0.004212,91Hum1996:0):0.00762451):0,276Hum2003:0):0.0048001
4,87Hum1996:0):0.0773933,206Hum1978:0):0.0115426,(130Hum1980:0.0296187,(267Hum20
04:0.0317216,268Hum2004:0.016421):0.0167293):0.00215788):0.0109373,202Hum1995:0.
0130884):0.0593484,((209Hum1993:0,((210Hum1994:0,(211Hum1994:0.00190364,212Hum19
95:0):2.085e-06):0.00855432,235Hum1994:0.000207175):0):0.0001328,220Hum1995:0):0
.00676737):0.000622239,233Hum1974:0):0.00309869,((84Hum1996:0.00196616,89Hum1997
:0):0.0103962,(((((((((127Hum1990:0.000341553,(128Hum1991:0.00407388,129Hum1991:
0):0.00586837):0.00183738,139Hum1990:0.011653):0.00335238,((159Hum1997:0.0013182
9,((161Hum1997:0,236Hum1997:0.00403527):0.00406097,237Hum1997:0):0.00298694):0.0
0155052,162Hum1997:0.000307539):0.00928197):0.00205181,(207Hum1994:0,208Hum1994:
0.0040529):0.00592305):0,134Hum1990:0):0.00308755,141Hum1986:0.00372256):0.00240
187,138Hum1989:0.00192639):0.00178473,201Hum1989:0):0.0357136,132Hum1983:0.02533
04):0.00844376):0.00161787):0.000861525,232Hum1996:0.00783089):0.000390435,(135H
um1981:0.00388288,(271Hum2003:0.0149456,277Hum2003:0.00107206):0.00886243):0.005
40648):0.000649812,((194Hum1985:0.00199558,196Hum1985:0.00205918):0,195Hum1985:0
):0.00197891):0.000694978,(((((70Hum1992:0.00379096,73Hum1991:0.00482068):0,71Hu
m1992:0):0.00772346,74Hum1991:0.00417174):0,72Hum1992:0):0.000147237,75Hum1990:0
):0.00183163):0.00643038,((124Hum1995:0,125Hum1995:0.00404394):0.00332144,154Hum
1997:0.00332664):0.00477916):0.000185696,160Hum1997:0):0.0055867,111Hum1993:0):0
.0542895,178Hum1990:0):0,(136Hum1977:0,203Hum1993:0.0756656):0.0709806):0.158305
,176Hum1980:0):0,((((131Hum1981:0,((((((133Hum1982:0.0942778,254Hum1975:0.093833
1):0.0624907,231Hum1998:0):0.0510279,(((((182Hum1988:0,(183Hum1988:0,184Hum1988:
0.00394963):0.00657816):0.00113508,185Hum1988:0):0.0196337,204Hum1992:0):0.03968
19,255Hum1982:0):0,205Hum1981:0):0.166457):0.0709423,261Hum1988:0):0.092376,142H
um1992:0.30933):0,260Hum1990:0):0.0121973):0.0568728,262Hum1987:0):0,263Hum1986:
0):0.0536069,253Hum1981:0):0.0187805):0.105537,(17Hum1997:0.129449,177Hum1984:0)
:0.0834963):0.465497,((((5Hum2003:0,6Hum2001:0.207129):0.511905,(7Hum2000:0,53Po
r2004:0.215376):0.923543):0.832293,(109Hum1997:0.251246,175Hum1986:0):0.401185):
0,68Hum1995:0):0.93743):1.47251,(((((9Bov2005:0.204165,51Por2004:0):0.0811759,11
4Hum1990:0):0.859461,238Por1987:0.58979):1.45801,(106Por1980:0.227754,(243Equ197
5:0.0747096,((244Por1987:0.0842832,246Por1987:0.122436):0.134412,252Por1976:0):0
.104454):0.134456):2.22517):0.255884,21Hum1997:2.65024):0.258209):0.84812,((((11
3Hum2000:0.0151591,(((122Rab1996:0.119551,290Lap2004:0):0.0764512,248Lap1988:0.0
203089):0,251Rot1984:0):0.0704559):0.063765,247Lap1988:0):2.71223,(119Rab2001:0.
17806,120Rab2001:0):2.76861):0.0773764,121Rab2001:2.74894):0.9595):0.2607,(240Eq
u1981:2.48731,241Equ1981:2.47287):1.14142):0.155344):0.768818,249Lap1978:2.66):0
.682119,(50Sim1990:0.0626322,172Bov1981:0):2.31971):0.672659,117Bov2001:1.36566)
:0.889501):1.40815,98Hum1996:0):0.241922,108Hum1998:0):0,140Hum1992:0):0.990655,
63Hum1997:0):0.0114751,257Hum1993:0):0,42Hum1997:0):0.361657,151Hum1996:0):0,67H
um1995:0):0.302637,20Hum2004:5.50543):0.943886,65Hum1996:0):0.00945965,283Hum200
2:0):0.147208,187Hum1994:0):0.022128,100Hum1996:0):0.00523764,69Hum1996:0):0.014
3003,105hum1996:0):0,234Hum1996:0):0,78Hum1990:1.54561):0.615906,278Hum2002:0):0
.317713,8Hum1997:0):0.326008,64Hum1996:0):0,258Hum1981:0):0.234658,24Hum1997:0):
0.245123,256Hum1993:0):0,((((((79Hum1990:0,(153Hum1997:0,(291Mur1982:2.35224,292
Mur1981:0.271833):241.812):39.9998):12.3761,173Bov1973:0):10.9326,(((101Hum1996:
0,((137Hum1980:7.62351,245Por1987:0):3.90022,250Lap1983:0):3.70695):0,152Hum1997
:0):1.1622,186Hum1976:0):44.2382):0,193Hum1981:0):0.99991,189Hum1993:0):1.29879,
192Hum1982:0):2.39156):9.45341,190Hum1992:0):0.991022,191Hum1983:0):5.42061,62Hu
m1982:0):0,43Hum1997:0):0,144Lap1978:0):23.3456,56Fel1993:0):0):222.876,55Fel199
3:0):1.31013,57Fel1993:0):3.86669,61Fel1989:0):0,(116Hum2000:466.916,126Hum1992:
120.895):732.074):564.737,58Fel1993:0):672.1):0):0,174Bov1973:0):3238.72,145Hum1
993:3858.34):10540.1,115Hum1998:0):0))

Would you like to use it:(Y/N)?Y

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jackson

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Posts: 30
São Paulo, Brazil
Gender: male

Re: Tipdate function
Reply #17 - Mar 29^th, 2007 at 1:07pm

Cont.

      +-----------+
|Date Format|
+-----------+
   (1):[TipDate] Taxon names include sampling dates, e.g. ((s1_85,s2_90),t_83)
   (2):[Branch Lengths] Branch lengths are the sampling dates, e.g. ((s1:85,s2:90),t:83)
Please choose an option (or press q to cancel selection):1
What units are the dates measured in (e.g. months. This is only used for reporting the results.)?years
Read the following dates:
13Hum1995: 1995 years
107Hum2002:    2002 years
12Hum2004: 2004 years
11Hum2004: 2004 years
4Hum1999: 1999 years
123Cap1998:    1998 years
239Can1980:    1980 years
2Hum2000: 2000 years
118Lam1981:    1981 years
242Equ1976:    1976 years
77Hum1993: 1993 years
1Sim1958: 1958 years
19Hum2004: 2004 years
3hum2000: 2000 years
282Hum2002:    2002 years
14Hum2002: 2002 years
15Hum2000: 2000 years
16Hum2001: 2001 years
180Hum1990:    1990 years
179Hum1990:    1990 years
181Hum1990:    1990 years
110Hum1998:    1998 years
274Hum2003:    2003 years
169Hum1998:    1998 years
155Hum1997:    1997 years
289Hum2001:    2001 years
171Hum1998:    1998 years
275Hum2003:    2003 years
170Hum1998:    1998 years
164Hum1998:    1998 years
167Hum1998:    1998 years
156Hum1997:    1997 years
272Hum2003:    2003 years
264Hum2004:    2004 years
166Hum1998:    1998 years
168Hum1996:    1996 years
82Hum1996: 1996 years
95Hum1996: 1996 years
112Hum1999:    1999 years
279Hum2002:    2002 years
287Hum2001:    2001 years
286Hum2002:    2002 years
85Hum1997: 1997 years
91Hum1996: 1996 years
276Hum2003:    2003 years
87Hum1996: 1996 years
206Hum1978:    1978 years
130Hum1980:    1980 years
267Hum2004:    2004 years
268Hum2004:    2004 years
202Hum1995:    1995 years
209Hum1993:    1993 years
210Hum1994:    1994 years
211Hum1994:    1994 years
212Hum1995:    1995 years
235Hum1994:    1994 years
220Hum1995:    1995 years
233Hum1974:    1974 years
84Hum1996: 1996 years
89Hum1997: 1997 years
127Hum1990:    1990 years
128Hum1991:    1991 years
129Hum1991:    1991 years
139Hum1990:    1990 years
159Hum1997:    1997 years
161Hum1997:    1997 years
236Hum1997:    1997 years
237Hum1997:    1997 years
162Hum1997:    1997 years
207Hum1994:    1994 years
208Hum1994:    1994 years
134Hum1990:    1990 years
141Hum1986:    1986 years
138Hum1989:    1989 years
201Hum1989:    1989 years
132Hum1983:    1983 years
232Hum1996:    1996 years
135Hum1981:    1981 years
271Hum2003:    2003 years
277Hum2003:    2003 years
194Hum1985:    1985 years
196Hum1985:    1985 years
195Hum1985:    1985 years
70Hum1992: 1992 years
73Hum1991: 1991 years
71Hum1992: 1992 years
74Hum1991: 1991 years
72Hum1992: 1992 years
75Hum1990: 1990 years
124Hum1995:    1995 years
125Hum1995:    1995 years
154Hum1997:    1997 years
160Hum1997:    1997 years
111Hum1993:    1993 years
178Hum1990:    1990 years
136Hum1977:    1977 years
203Hum1993:    1993 years
176Hum1980:    1980 years
131Hum1981:    1981 years
133Hum1982:    1982 years
254Hum1975:    1975 years
231Hum1998:    1998 years
182Hum1988:    1988 years
183Hum1988:    1988 years
184Hum1988:    1988 years
185Hum1988:    1988 years
204Hum1992:    1992 years
255Hum1982:    1982 years
205Hum1981:    1981 years
261Hum1988:    1988 years
142Hum1992:    1992 years
260Hum1990:    1990 years
262Hum1987:    1987 years
263Hum1986:    1986 years
253Hum1981:    1981 years
17Hum1997: 1997 years
177Hum1984:    1984 years
5Hum2003: 2003 years
6Hum2001: 2001 years
7Hum2000: 2000 years
53Por2004: 2004 years
109Hum1997:    1997 years
175Hum1986:    1986 years
68Hum1995: 1995 years
9Bov2005: 2005 years
51Por2004: 2004 years
114Hum1990:    1990 years
238Por1987:    1987 years
106Por1980:    1980 years
243Equ1975:    1975 years
244Por1987:    1987 years
246Por1987:    1987 years
252Por1976:    1976 years
21Hum1997: 1997 years
113Hum2000:    2000 years
122Rab1996:    1996 years
290Lap2004:    2004 years
248Lap1988:    1988 years
251Rot1984:    1984 years
247Lap1988:    1988 years
119Rab2001:    2001 years
120Rab2001:    2001 years
121Rab2001:    2001 years
240Equ1981:    1981 years
241Equ1981:    1981 years
249Lap1978:    1978 years
50Sim1990: 1990 years
172Bov1981:    1981 years
117Bov2001:    2001 years
98Hum1996: 1996 years
108Hum1998:    1998 years
140Hum1992:    1992 years
63Hum1997: 1997 years
257Hum1993:    1993 years
42Hum1997: 1997 years
151Hum1996:    1996 years
67Hum1995: 1995 years
20Hum2004: 2004 years
65Hum1996: 1996 years
283Hum2002:    2002 years
187Hum1994:    1994 years
100Hum1996:    1996 years
69Hum1996: 1996 years
105hum1996:    1996 years
234Hum1996:    1996 years
78Hum1990: 1990 years
278Hum2002:    2002 years
8Hum1997: 1997 years
64Hum1996: 1996 years
258Hum1981:    1981 years
24Hum1997: 1997 years
256Hum1993:    1993 years
79Hum1990: 1990 years
153Hum1997:    1997 years
291Mur1982:    1982 years
292Mur1981:    1981 years
173Bov1973:    1973 years
101Hum1996:    1996 years
137Hum1980:    1980 years
245Por1987:    1987 years
250Lap1983:    1983 years
152Hum1997:    1997 years
186Hum1976:    1976 years
193Hum1981:    1981 years
189Hum1993:    1993 years
192Hum1982:    1982 years
190Hum1992:    1992 years
191Hum1983:    1983 years
62Hum1982: 1982 years
43Hum1997: 1997 years
144Lap1978:    1978 years
56Fel1993: 1993 years
55Fel1993: 1993 years
57Fel1993: 1993 years
61Fel1989: 1989 years
116Hum2000:    2000 years
126Hum1992:    1992 years
58Fel1993: 1993 years
174Bov1973:    1973 years
145Hum1993:    1993 years
115Hum1998:    1998 years
(/root/HYPHY/TemplateBatchFiles/) Save the best model to:/root/NSP4bestmodel

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Cheers,
Jackson
Ps: Sorry the long post.

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Tipdate function Reply #18 - Apr 2^nd, 2007 at 11:22am Dear Jackson, Hmm - seems like a bug in the single-processor version of my analysis. Let me check and get back to you. Cheers, Sergei
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jackson

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Posts: 30
São Paulo, Brazil
Gender: male

Re: Tipdate function
Reply #19 - Apr 10^th, 2007 at 11:43am

Quote:

I have finally added the multiple rate (relaxed) molecular clock to today's build in the form of two new files under the Molecular Clock rubrik of Standard Analyses - GADatedClock.bf, GADatedClockProcessor.bf. In a nutshell, this method uses a GA to allocate multiple rates to tree branches which still enforcing a dated molecular clock. This is in unpublished (yet) method, but I will be writing some documentation on it shortly.

Cheers,
Sergei

Hi Serguei,

I obtained success in making to function HYPHY in mpi, below I am the result of the MPITeste.bf.

mpirun -machinefile /etc/hosts.equiv -nodes 8 -allcpus -v ./HYPHYMPI BatchFiles/MPITest.bf
running /usr/ports/distfiles/HYPHY/./HYPHYMPI on 10000 LINUX ch_p4 processors
Created /home/jackson/PI14876
Password:
Password:
Password:
Password:
Password:
Password:
Password:
Running a HYPHY-MPI test

Detected 8 computational nodes
Polling slave nodes...
Polling node 2...
OK
Polling node 3...
OK
Polling node 4...
OK
Polling node 5...
OK
Polling node 6...
OK
Polling node 7...
OK
Polling node 8...
OK

Measuring simple job send/receieve throughput...
Node    2 sent/received 10401.2 batch jobs per second
Node    3 sent/received 3853.6 batch jobs per second
Node    4 sent/received 3832.2 batch jobs per second
Node    5 sent/received 927.8 batch jobs per second
Node    6 sent/received 878 batch jobs per second
Node    7 sent/received 1214.2 batch jobs per second
Node    8 sent/received 1172 batch jobs per second

Measuring relative computational performance...
Master node reference index: 2167176
Slave node 1 index: 2205320.    101.76% relative to the master
Slave node 2 index:    725773. 33.49% relative to the master
Slave node 3 index:    728118. 33.60% relative to the master
Slave node 4 index:    468882. 21.64% relative to the master
Slave node 5 index:    474804. 21.91% relative to the master
Slave node 6 index:    674083. 31.10% relative to the master
Slave node 7 index:    661110. 30.51% relative to the master

But, i tried to run the GADatedClock.bf in mpi, because the menu of Molecular Clock show the GADatedClock.bf is MPI enable,but it don't realize this analysis in mpi, only in the local machine. Why this?

Cheers,
Jackson Lima

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Tipdate function Reply #20 - Apr 10^th, 2007 at 12:21pm Dear Jackson, Try running the file on a small dataset - the way the current version is implemented, large datasets will tie up the master node for some time (fitting the standard TipDate function). Cheers, Sergei
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jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	Re: Tipdate function Reply #21 - Apr 11^th, 2007 at 10:29am Dear Sergei, The Hyphy's Tipdate function is implemented in MPI for large dataset?? I tried to run the GADatedClock.bf on dataset with 29 sequences, but, yet, it ran on the local machine or master node. Cheers, Jackson Lima
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Tipdate function Reply #22 - Apr 11^th, 2007 at 12:49pm Dear Jackson, The analysis is MPI enabled - I am not sure why only the master node would be used, especially since the MPITest.bf ran fine. Once the analysis gets into the GA phase it should spread across all the nodes. Sorry for your troubles! Did the 29 sequence analysis finish on the master? Cheers, Sergei
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jackson

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I love YaBB 1G - SP1!

Posts: 30
São Paulo, Brazil
Gender: male

Re: Tipdate function
Reply #23 - Apr 12^th, 2007 at 7:32am

Dear Sergei,

I cancelled the analysis. I tried to run the GABranchFiles that have in your site, after one day, the analysis don't over, seems me that it stopped to the computation, entering in hibernation's state. In the Top, don't it showed me the HYPHYMPI.

It stopped in this part: [Starting the GA with 2 rate classes.]

mpirun -machinefile /etc/hosts.equiv -nodes 8 -allcpus -v ./HYPHYMPI GABranchFiles/ModelSelectorBranchLocal.bf
running /usr/ports/distfiles/HYPHY_Source/./HYPHYMPI on 10000 LINUX ch_p4 processors
Created /usr/ports/distfiles/HYPHY_Source/PI26641
Password:
Password:
Password:
Password:
Password:
Password:
Password:

+-------------------+
|Choose Genetic Code|
+-------------------+

   (1):[Universal] Universal code. (Genebank transl_table=1).
   (2):[Vertebrate mtDNA] Vertebrate mitochondrial DNA code. (Genebank transl_table=2).
   (3):[Yeast mtDNA] Yeast mitochondrial DNA code. (Genebank transl_table=3).
   (4):[Mold/Protozoan mtDNA] Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spiroplasma code. (Genebank transl_table=4).
   (5):[Invertebrate mtDNA] Invertebrate mitochondrial DNA code. (Genebank transl_table=5).
   (6):[Ciliate Nuclear] Ciliate, Dasycladacean and Hexamita Nuclear code. (Genebank transl_table=6).
   (7):[Echinoderm mtDNA] Echinoderm mitochondrial DNA code. (Genebank transl_table=9).
   (8):[Euplotid Nuclear] Euplotid Nuclear code. (Genebank transl_table=10).
   (9):[Alt. Yeast Nuclear] Alternative Yeast Nuclear code. (Genebank transl_table=12).
   (10):[Ascidian mtDNA] Ascidian mitochondrial DNA code. (Genebank transl_table=13).
   (11):[Flatworm mtDNA] Flatworm mitochondrial DNA code. (Genebank transl_table=14).
   (12):[Blepharisma Nuclear] Blepharisma Nuclear code. (Genebank transl_table=15).

Please choose an option (or press q to cancel selection):1

(/usr/ports/distfiles/HYPHY_Source/GABranchFiles/) Codon file to analyze:Example/lysozyme.nex

A tree was found in the data file:
(((((LANGUR_SEN_SVE,LANGUR_TOB_TFR,DOUC_LANGUR_PNE),PROBISCIS_NLA),COLOBUS_CGU_C
AN),(((BABOON_PCY,MANGABEY_CAT),RHESUS_MMU),ALLEN_ANI,(TALAPOIN_MTA,(PATAS_EPA,V
ERVET_CAE)))),(((HUMAN,CHIMP_BONOBO_GORILLA),ORANGUTAN_PPY),GIBBON_GGO),(SQUIRRE
L_M,(TAMARIN_SOE,MARMOSET_CJA)))

Would you like to use it:(Y/N)?Y

Nucleotide a 6-character model string specification (e.g. HKY85 = 010010):?010010
[Preliminary Step 1] A total of 33 branches. Fitting a nucleotide model to approximate branch lengths...
[Preliminary Step 2] Nucleotide LogL = -1062.28
[Preliminary Step 3] Base model has 44 parameters. Log-L = -1038.75. Mean dN/dS = 0.571926

[Starting the GA with 2 rate classes.]

Sorry for these newbies questions.

Cheers,
      Jackson

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