START OF LOG FILE
#Process_id= 673870

 ---------------------- THE PARAMETERS ----------------------------
input codon file is:            /lsweb/josef_results/selecton/1741769249/DNA.msa
input distribution:             gamma
model used is:                MEC
empirical matrix:                JTT
query sequence is:          1
epsilon for likelihood (precision level):          0.1
branch length optimization:     do
-------------------------
    creating NJ tree 

(10:0.042394,14:0.071882,(((((4:0.063227,8:0.054856):0.022195,(6:0.132054,(5:0.056242,11:0.052688):0.030793):0.010071):0.012156,(12:0.110422,(3:0.051378,7:0.048184):0.038202):0.007712):0.342448,((9:0.038804,((19:0.004027,20:0.000001):0.029872,(2:0.016431,18:0.010125):0.014557):0.004010):0.029096,(15:0.019052,16:0.009621):0.009463):0.073472):0.032133,(13:0.018067,(1:0.018337,17:0.008431):0.004665):0.021350):0.003344);
Iteration Number= 0
---------------------
current best L= -0x1.ae63fca145027p+12

new L After alpha= -0x1.ad21f31a4e6e1p+12
new alpha = 0x1.3ffdf75a7127cp-2

the best current parameters are: alpha=0x1.3ffdf75a7127cp-2, beta=0x1p-1, tr(transition)=0x1.4p+2, tv(transversion)=0x1p+0 f=prob(no selection)=0x1p+0
current best L= -0x1.ad21f31a4e6e1p+12

new L After beta= -0x1.abfaacf8365e3p+12
new beta = 0x1.f4084201fb71ap-1

the best current parameters are: alpha=0x1.3ffdf75a7127cp-2, beta=0x1.f4084201fb71ap-1, tr(transition)=0x1.4p+2, tv(transversion)=0x1p+0 f=prob(no selection)=0x1p+0
current best L= -0x1.abfaacf8365e3p+12

new L After Tr= -0x1.abdda32f7c0abp+12
new tr = 0x1.115008baf053p+2

the best current parameters are: alpha=0x1.3ffdf75a7127cp-2, beta=0x1.f4084201fb71ap-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1p+0 f=prob(no selection)=0x1p+0
current best L= -0x1.abdda32f7c0abp+12

new L After Tv = -0x1.abc2ca7d11938p+12
new Tv = 0x1.6cdc0fd0b4f48p+0

the best current parameters are: alpha=0x1.3ffdf75a7127cp-2, beta=0x1.f4084201fb71ap-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1p+0
current best L= -0x1.abc2ca7d11938p+12

new L After F= -0x1.a5bead662940ap+12
new F = 0x1.d813ff57beb42p-2

******BBL EM*********

current best L= -0x1.a5bead662940ap+12

last best L= -0x1.a5bead662940ap+12
current best L= -0x1.a4715d5a47cd5p+12

last best L= -0x1.a4715d5a47cd5p+12
current best L= -0x1.a42f03d72f99dp+12

last best L= -0x1.a42f03d72f99dp+12
current best L= -0x1.a41db8756d513p+12

last best L= -0x1.a41db8756d513p+12
current best L= -0x1.a4180f15606d8p+12

current best L= -0x1.a5bead662940ap+12
new L After BL = -0x1.a416081adb884p+12 = -0x1.a416081adb884p+12
Iteration Number= 1
---------------------
current best L= -0x1.a416081adb884p+12

new L After alpha= -0x1.a3f00266369bep+12
new alpha = 0x1.d9c2323ec918bp-3

the best current parameters are: alpha=0x1.d9c2323ec918bp-3, beta=0x1.f4084201fb71ap-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3f00266369bep+12

new L After beta= -0x1.a3e2865fad8f7p+12
new beta = 0x1.9506b05703748p-1

the best current parameters are: alpha=0x1.d9c2323ec918bp-3, beta=0x1.9506b05703748p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3e2865fad8f7p+12

new L After Tr= -0x1.a3e2865fad8f7p+12
new tr = 0x1.115008baf053p+2

the best current parameters are: alpha=0x1.d9c2323ec918bp-3, beta=0x1.9506b05703748p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3e2865fad8f7p+12

new L After Tv = -0x1.a3e2865fad8f7p+12
new Tv = 0x1.6cdc0fd0b4f48p+0

the best current parameters are: alpha=0x1.d9c2323ec918bp-3, beta=0x1.9506b05703748p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3e2865fad8f7p+12

new L After F= -0x1.a3e2865fad8f7p+12
new F = 0x1.d813ff57beb42p-2

******BBL EM*********

current best L= -0x1.a3e2865fad8f7p+12

last best L= -0x1.a3e2865fad8f7p+12
current best L= -0x1.a3e1767586775p+12

last best L= -0x1.a3e1767586775p+12
current best L= -0x1.a3e10de7511dp+12

The like in else  = -0x1.a3e10de7511dp+12
current best L= -0x1.a3e2865fad8f7p+12
new L After BL = -0x1.a3e10de7511dp+12 = -0x1.a3e10de7511dp+12
Iteration Number= 2
---------------------
current best L= -0x1.a3e2865fad8f7p+12

new L After alpha= -0x1.a3d279a303e1ap+12
new alpha = 0x1.73068a4ee4593p-3

the best current parameters are: alpha=0x1.73068a4ee4593p-3, beta=0x1.9506b05703748p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3d279a303e1ap+12

new L After beta= -0x1.a3c9bc0be02c6p+12
new beta = 0x1.6c86051a40ceap-1

the best current parameters are: alpha=0x1.73068a4ee4593p-3, beta=0x1.6c86051a40ceap-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c9bc0be02c6p+12

new L After Tr= -0x1.a3c9bc0be02c6p+12
new tr = 0x1.115008baf053p+2

the best current parameters are: alpha=0x1.73068a4ee4593p-3, beta=0x1.6c86051a40ceap-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c9bc0be02c6p+12

new L After Tv = -0x1.a3c9bc0be02c6p+12
new Tv = 0x1.6cdc0fd0b4f48p+0

the best current parameters are: alpha=0x1.73068a4ee4593p-3, beta=0x1.6c86051a40ceap-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c9bc0be02c6p+12

new L After F= -0x1.a3c9bc0be02c6p+12
new F = 0x1.d813ff57beb42p-2

******BBL EM*********

current best L= -0x1.a3c9bc0be02c6p+12

last best L= -0x1.a3c9bc0be02c6p+12
current best L= -0x1.a3c922d0a2483p+12

The like in else  = -0x1.a3c922d0a2483p+12
current best L= -0x1.a3c9bc0be02c6p+12
new L After BL = -0x1.a3c922d0a2483p+12 = -0x1.a3c922d0a2483p+12
Iteration Number= 3
---------------------
current best L= -0x1.a3c9bc0be02c6p+12

new L After alpha= -0x1.a3c7f2b663a09p+12
new alpha = 0x1.4dec4943911abp-3

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.6c86051a40ceap-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c7f2b663a09p+12

new L After beta= -0x1.a3c2d4c23da5dp+12
new beta = 0x1.481237c9f8063p-1

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.481237c9f8063p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c2d4c23da5dp+12

new L After Tr= -0x1.a3c2d4c23da5dp+12
new tr = 0x1.115008baf053p+2

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.481237c9f8063p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c2d4c23da5dp+12

new L After Tv = -0x1.a3c2d4c23da5dp+12
new Tv = 0x1.6cdc0fd0b4f48p+0

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.481237c9f8063p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c2d4c23da5dp+12

new L After F= -0x1.a3c2d4c23da5dp+12
new F = 0x1.d813ff57beb42p-2

******BBL EM*********

current best L= -0x1.a3c2d4c23da5dp+12

last best L= -0x1.a3c2d4c23da5dp+12
current best L= -0x1.a3c2b675158b2p+12

The like in else  = -0x1.a3c2b675158b2p+12
current best L= -0x1.a3c2d4c23da5dp+12
new L After BL = -0x1.a3c2b675158b2p+12 = -0x1.a3c2b675158b2p+12
Iteration Number= 4
---------------------
current best L= -0x1.a3c2d4c23da5dp+12

new L After alpha= -0x1.a3c1c68c1f5ddp+12
new alpha = 0x1.2c87db862c95ap-3

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.481237c9f8063p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c2d4c23da5dp+12

new L After beta= -0x1.a3c2b675158b2p+12
new beta = 0x1.481237c9f8063p-1

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.481237c9f8063p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c2d4c23da5dp+12

new L After Tr= -0x1.a3c2b675158b2p+12
new tr = 0x1.115008baf053p+2

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.481237c9f8063p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c2d4c23da5dp+12

new L After Tv = -0x1.a3c2b675158b2p+12
new Tv = 0x1.6cdc0fd0b4f48p+0

the best current parameters are: alpha=0x1.4dec4943911abp-3, beta=0x1.481237c9f8063p-1, tr(transition)=0x1.115008baf053p+2, tv(transversion)=0x1.6cdc0fd0b4f48p+0 f=prob(no selection)=0x1.d813ff57beb42p-2
current best L= -0x1.a3c2d4c23da5dp+12

new L After F= -0x1.a3c2b675158b2p+12
new F = 0x1.d813ff57beb42p-2

******BBL EM*********

current best L= -0x1.a3c2b675158b2p+12

last best L= -0x1.a3c2b675158b2p+12
current best L= -0x1.a3c2a448c8d9bp+12

The like in else  = -0x1.a3c2a448c8d9bp+12
current best L= -0x1.a3c2d4c23da5dp+12
new L After BL = -0x1.a3c2a448c8d9bp+12 = -0x1.a3c2a448c8d9bp+12
-------------------------
 computing EB_EXP kaks for site 

Calculating posterior and expectation of posterior values for all sites
=========================================
TOTAL RUNNING TIME = 0x1.02aaaaaaaaaabp+4 minutes
=========================================
END OF LOG FILE