CAFE
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hahnlab
Lambda: inf & Score: -inf
Hi,
I'm trying to run a simple cafe analysis:
load -i PhyleticProfileHOGs.CafeInput.txt -p 0.01 -t 10 -l log_run1.txt
tree (((((Hmel:0.02,Haoe:0.02):0.1,Herd:0.12):0.05,Eisa:0.17):0.01,Diul:0.18):0.02,Smor:0.2)
lambda -s -t (((((1,1)1,1)1,1)1,1)1,1)
My PhyleticProfileHOGs.CafeInput.txt looks like this:
FAMILYDESC FAMILY Diul Eisa Haoe Herd Hmel Smor
HOG00001 HOG00001 0 0 1 0 1 0
HOG00002 HOG00002 0 0 1 0 1 0
HOG00003 HOG00003 0 0 1 0 1 0
HOG00004 HOG00004 0 0 1 0 1 0
HOG00005 HOG00005 0 0 1 0 1 0
HOG00006 HOG00006 0 0 1 0 1 0
HOG00007 HOG00007 0 0 1 0 1 0
HOG00008 HOG00008 0 0 1 0 1 0
HOG00009 HOG00009 0 0 1 0 1 0
this is the log:
Family information: PhyleticProfileHOGs.CafeInput.txt
Log: log_run1.txt
The number of families is 16650
Root Family size : 1 ~ 121
Family size : 0 ~ 147
P-value: 0.01
Num of Threads: 10
Num of Random: 1000
(((((Hmel:0.02,Haoe:0.02):0.1,Herd:0.12):0.05,Eisa:0.17):0.01,Diul:0.18):0.02,Smor:0.2)
The number of lambdas is 1
Lambda Tree: (((((1,1)1,1)1,1)1,1)1,1)
Empirical Prior Estimation Result: (26 iterations)
Poisson lambda: 0.138451 & Score: 40813.540951
WARNING: Calculated posterior probability for family HOG00001 = 0
Lambda : inf & Score: -inf
.WARNING: Calculated posterior probability for family HOG00001 = 0
Lambda : inf & Score: -inf
.
Lambda Search Result: 0
Lambda : inf & Score: inf
DONE: Lambda Search or setting, for command:
lambda -s -t (((((1,1)1,1)1,1)1,1)1,1)
This the beginning of the report:
Tree:(((((Hmel:0.02,Haoe:0.02):0.1,Herd:0.12):0.05,Eisa:0.17):0.01,Diul:0.18):0.02,Smor:0.2)
Lambda: inf
Lambda tree: (((((1,1)1,1)1,1)1,1)1,1)
# IDs of nodes:(((((Hmel<0>,Haoe<2>)<1>,Herd<4>)<3>,Eisa<6>)<5>,Diul<8>)<7>,Smor<10>)<9>
# Output format for: ' Average Expansion', 'Expansions', 'No Change', 'Contractions', and 'Branch-specific P-values' = (node ID, node ID): (0,2) (1,4) (3,6) (5,8) (7,10)
# Output format for 'Branch cutting P-values' and 'Likelihood Ratio Test': (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
Average Expansion: (0.84036,0.722282) (0,0.755255) (0,1.06871) (0,0.896456) (-1,-0.189369)
Expansion : (13024,11640) (0,11966) (0,13705) (0,12733) (0,652)
nRemain : (3626,5010) (16650,4684) (16650,2945) (16650,3917) (0,10776)
nDecrease : (0,0) (0,0) (0,0) (0,0) (16650,5222)
'ID' 'Newick' 'Family-wide P-value' 'Viterbi P-values' 'cut P-value' 'Likelihood Ratio'
HOG00001 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00002 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00003 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00004 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00005 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00006 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00007 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00008 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
HOG00009 (((((Hmel_1:0.02,Haoe_1:0.02)_0:0.1,Herd_0:0.12)_0:0.05,Eisa_0:0.17)_0:0.01,Diul_0:0.18)_0:0.02,Smor_0:0.2)_1 0.5005 ((-,-),(-,-),(-,-),(-,-),(-,-))
What am I doing wrong?
Thanks for your help Francesco
