--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 03 20:14:43 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS1/Ebolaaminoresults/L/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)

(Values are saved to the file /opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -37602.28        -37665.08
2     -37601.87        -37664.18
--------------------------------------
TOTAL   -37602.05        -37664.73
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         5.315020    0.038693    4.934347    5.696775    5.308014    145.30    181.02    1.009
r(A<->C){all}   0.096495    0.000038    0.084257    0.108645    0.096229    335.43    420.83    1.002
r(A<->G){all}   0.388345    0.000155    0.363129    0.412202    0.388431    254.85    352.82    1.000
r(A<->T){all}   0.041479    0.000015    0.033841    0.049062    0.041493    403.44    489.67    1.004
r(C<->G){all}   0.023727    0.000022    0.014944    0.033012    0.023560    637.39    681.26    1.001
r(C<->T){all}   0.406444    0.000147    0.381563    0.429240    0.406695    403.45    420.72    1.004
r(G<->T){all}   0.043511    0.000020    0.034716    0.052064    0.043406    466.39    610.07    1.000
pi(A){all}      0.323704    0.000018    0.315287    0.331888    0.323529    356.72    426.60    1.009
pi(C){all}      0.204338    0.000011    0.198016    0.211208    0.204316    396.03    504.73    1.003
pi(G){all}      0.181207    0.000012    0.174715    0.187567    0.181225    308.64    380.18    1.000
pi(T){all}      0.290751    0.000017    0.283197    0.298691    0.290636    399.31    474.72    1.003
alpha{1,2}      0.157536    0.000025    0.147565    0.167020    0.157460    265.60    298.90    1.006
alpha{3}        5.804344    0.893050    4.043328    7.646287    5.719054    655.19    885.04    1.001
pinvar{all}     0.055222    0.000057    0.040702    0.070132    0.055168   1291.26   1302.73    1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.


Setting sumt conformat to Simple



 --- CODEML SUMMARY