stdout.txt (66069 bytes)
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
CIPRES_NP=10
CIPRES_THREADSPP=12
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
running:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
This is RAxML MPI Process Number: 0
This is RAxML MPI Process Number: 1
This is RAxML MPI Process Number: 6
This is RAxML MPI Process Number: 9
This is RAxML MPI Process Number: 3
This is RAxML MPI Process Number: 4
This is RAxML MPI Process Number: 2
This is RAxML MPI Process Number: 7
This is RAxML MPI Process Number: 5
This is RAxML MPI Process Number: 8
You are using a proportion of Invariable sites estimate, although I don't
You are using a proportion of Invariable sites estimate, although I don't
You are using a proportion of Invariable sites estimate, although I don't
You are using a proportion of Invariable sites estimate, although I don't
You are using a proportion of Invariable sites estimate, although I don't
You are using a proportion of Invariable sites estimate, although I don't
You are using a proportion of Invariable sites estimate, although I don't
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
You are using a proportion of Invariable sites estimate, although I don't
You are using a proportion of Invariable sites estimate, although I don't
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
You are using a proportion of Invariable sites estimate, although I don't
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 2
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 11
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 11
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 8
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 11
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 9
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 11
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 7
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 11
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 4
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 11
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 11
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 8
This is the RAxML Master Pthread
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 11
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 8
This is RAxML Worker Pthread Number: 9
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 11
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 7
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 10
This is RAxML Worker Pthread Number: 11
This is RAxML Worker Pthread Number: 9
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 5618 distinct alignment patterns
Found 0 invariant alignment patterns that correspond to 0 columns
Proportion of gaps and completely undetermined characters in this alignment: 85.90%
RAxML rapid bootstrapping and subsequent ML search
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1000 rapid bootstrap inferences and thereafter a thorough ML search
All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories
Likelihood of final tree will be evaluated and optimized under GAMMA+P-Invar
GAMMA+P-Invar Model parameters will be estimated up to an accuracy of 0.0010000000 Log Likelihood units
Partition: 0
Alignment Patterns: 5618
Name: No Name Provided
DataType: AA
Substitution Matrix: VT
Using empirical base frequencies
RAxML was called as follows:
raxmlHPC-HYBRID-AVX -T 12 -s infile -N autoMRE -n result -f a -p 12345 -x 12345 -m PROTCATIVTF -o 001300654,GAX24648,ESK89338,006967043,OPB46261,AAV84602,EEF24858,PRQ42563,AQX45225,011005045,015491435,CCE76660,011084191,002694524,015121405,As_TcsB,001019841,Ca_Sln1,CAA65612,AAB71889,AAC47300,Q9SXL4,002185972,002179622,002185350,001701571,EnvZ,CheA,Sln1
Time for BS model parameter optimization on Process 1: 0.762891 seconds
Time for BS model parameter optimization on Process 0: 0.746691 seconds
Time for BS model parameter optimization on Process 5: 0.742186 seconds
Time for BS model parameter optimization on Process 3: 0.740225 seconds
Time for BS model parameter optimization on Process 8: 0.762233 seconds
Time for BS model parameter optimization on Process 6: 0.740056 seconds
Time for BS model parameter optimization on Process 2: 0.759384 seconds
Time for BS model parameter optimization on Process 7: 0.747713 seconds
Time for BS model parameter optimization on Process 4: 0.744983 seconds
Time for BS model parameter optimization on Process 9: 0.776728 seconds
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[600]: Time 49.746234 seconds, bootstrap likelihood -537769.570660, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[500]: Time 57.243404 seconds, bootstrap likelihood -550445.617726, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[400]: Time 88.701012 seconds, bootstrap likelihood -548607.029713, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[300]: Time 109.103993 seconds, bootstrap likelihood -546222.782722, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[200]: Time 129.892271 seconds, bootstrap likelihood -549698.489358, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[900]: Time 149.072614 seconds, bootstrap likelihood -545336.315583, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[100]: Time 162.177599 seconds, bootstrap likelihood -544406.992513, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[0]: Time 172.286358 seconds, bootstrap likelihood -545674.446658, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[800]: Time 172.848594 seconds, bootstrap likelihood -543002.867770, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[901]: Time 39.139075 seconds, bootstrap likelihood -554469.212942, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[801]: Time 38.129556 seconds, bootstrap likelihood -548620.793079, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[700]: Time 225.001439 seconds, bootstrap likelihood -546125.256027, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[701]: Time 41.088904 seconds, bootstrap likelihood -555182.479147, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[601]: Time 225.755373 seconds, bootstrap likelihood -551655.139957, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[501]: Time 219.158517 seconds, bootstrap likelihood -556382.719118, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[401]: Time 212.014595 seconds, bootstrap likelihood -544113.059085, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[802]: Time 95.796386 seconds, bootstrap likelihood -560824.540137, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[201]: Time 178.451403 seconds, bootstrap likelihood -552622.510741, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[902]: Time 120.389084 seconds, bootstrap likelihood -545480.981212, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[301]: Time 206.264272 seconds, bootstrap likelihood -552044.324269, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[502]: Time 50.633985 seconds, bootstrap likelihood -554581.660686, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[602]: Time 58.548520 seconds, bootstrap likelihood -543703.845298, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[1]: Time 163.696264 seconds, bootstrap likelihood -538983.708276, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[402]: Time 40.046573 seconds, bootstrap likelihood -559971.801537, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[702]: Time 85.681998 seconds, bootstrap likelihood -536598.505568, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[101]: Time 214.380560 seconds, bootstrap likelihood -552164.046421, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[803]: Time 79.783125 seconds, bootstrap likelihood -541502.110085, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[703]: Time 53.448640 seconds, bootstrap likelihood -540619.502082, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[903]: Time 98.973988 seconds, bootstrap likelihood -546791.803401, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[704]: Time 53.437364 seconds, bootstrap likelihood -545260.515190, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[403]: Time 135.376591 seconds, bootstrap likelihood -555763.632324, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[2]: Time 150.478916 seconds, bootstrap likelihood -544339.530264, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[202]: Time 181.202560 seconds, bootstrap likelihood -560324.923451, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[503]: Time 164.753631 seconds, bootstrap likelihood -557027.002805, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[302]: Time 199.724511 seconds, bootstrap likelihood -552566.503532, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[904]: Time 112.574883 seconds, bootstrap likelihood -553048.981970, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[404]: Time 50.567785 seconds, bootstrap likelihood -563452.585591, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[603]: Time 205.688883 seconds, bootstrap likelihood -529582.255824, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[203]: Time 82.771880 seconds, bootstrap likelihood -550462.412043, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[102]: Time 203.801657 seconds, bootstrap likelihood -531800.719787, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[804]: Time 202.873022 seconds, bootstrap likelihood -543593.433869, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[303]: Time 114.004006 seconds, bootstrap likelihood -535525.798287, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[103]: Time 50.812045 seconds, bootstrap likelihood -532478.250894, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[604]: Time 107.131125 seconds, bootstrap likelihood -566361.200564, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[504]: Time 171.416430 seconds, bootstrap likelihood -548328.188184, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[3]: Time 201.134791 seconds, bootstrap likelihood -552589.286919, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[104]: Time 67.227106 seconds, bootstrap likelihood -525918.108658, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[304]: Time 107.222458 seconds, bootstrap likelihood -561139.450819, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[204]: Time 201.250777 seconds, bootstrap likelihood -555150.811802, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[4]: Time 111.254711 seconds, bootstrap likelihood -541736.534515, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[505]: Time 39.242124 seconds, bootstrap likelihood -556613.767110, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[605]: Time 49.674192 seconds, bootstrap likelihood -555369.181175, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[705]: Time 69.703044 seconds, bootstrap likelihood -561872.759473, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[805]: Time 77.775261 seconds, bootstrap likelihood -550771.518239, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[506]: Time 39.990513 seconds, bootstrap likelihood -547549.610520, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[5]: Time 109.302330 seconds, bootstrap likelihood -575063.383600, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[905]: Time 113.447606 seconds, bootstrap likelihood -535628.976753, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[806]: Time 50.864151 seconds, bootstrap likelihood -550057.264140, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[105]: Time 136.984547 seconds, bootstrap likelihood -536984.166799, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[606]: Time 95.113438 seconds, bootstrap likelihood -533793.561559, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[205]: Time 152.206188 seconds, bootstrap likelihood -537356.138068, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[6]: Time 52.986616 seconds, bootstrap likelihood -543513.796731, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[305]: Time 164.239233 seconds, bootstrap likelihood -550565.378079, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[807]: Time 53.121192 seconds, bootstrap likelihood -547419.102440, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[607]: Time 39.951021 seconds, bootstrap likelihood -534898.306790, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[405]: Time 208.195947 seconds, bootstrap likelihood -557023.071071, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[507]: Time 138.506256 seconds, bootstrap likelihood -544018.205229, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[306]: Time 66.298202 seconds, bootstrap likelihood -536388.029596, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[906]: Time 128.544178 seconds, bootstrap likelihood -550105.260647, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[706]: Time 182.643424 seconds, bootstrap likelihood -550286.738868, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[106]: Time 129.064361 seconds, bootstrap likelihood -536501.706172, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[808]: Time 85.600953 seconds, bootstrap likelihood -548314.357893, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[809]: Time 38.581682 seconds, bootstrap likelihood -545612.545169, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[7]: Time 179.258513 seconds, bootstrap likelihood -543935.654921, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[307]: Time 114.417238 seconds, bootstrap likelihood -529863.431013, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[406]: Time 141.722293 seconds, bootstrap likelihood -538459.889800, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[206]: Time 208.792588 seconds, bootstrap likelihood -542514.492513, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[107]: Time 103.655831 seconds, bootstrap likelihood -544823.279276, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[8]: Time 37.924186 seconds, bootstrap likelihood -550587.854475, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[707]: Time 134.765092 seconds, bootstrap likelihood -543550.138799, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[407]: Time 38.055433 seconds, bootstrap likelihood -533640.316048, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[608]: Time 210.469759 seconds, bootstrap likelihood -546114.200100, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[907]: Time 154.496699 seconds, bootstrap likelihood -557888.453543, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[508]: Time 196.128628 seconds, bootstrap likelihood -555726.379205, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[708]: Time 49.369601 seconds, bootstrap likelihood -537747.394580, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[108]: Time 69.593535 seconds, bootstrap likelihood -543001.312346, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[9]: Time 62.066968 seconds, bootstrap likelihood -544938.581805, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[609]: Time 47.213245 seconds, bootstrap likelihood -538770.544925, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[308]: Time 118.769969 seconds, bootstrap likelihood -534965.995356, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[908]: Time 91.783079 seconds, bootstrap likelihood -536272.486928, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[408]: Time 153.068296 seconds, bootstrap likelihood -547734.481583, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[509]: Time 139.651679 seconds, bootstrap likelihood -554355.910225, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[709]: Time 131.823035 seconds, bootstrap likelihood -533217.446063, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[207]: Time 214.189214 seconds, bootstrap likelihood -551861.115733, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[409]: Time 45.235795 seconds, bootstrap likelihood -564474.531782, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[109]: Time 157.762286 seconds, bootstrap likelihood -547387.069780, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[309]: Time 151.684371 seconds, bootstrap likelihood -560826.278832, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[909]: Time 131.151753 seconds, bootstrap likelihood -543006.566416, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[208]: Time 93.899079 seconds, bootstrap likelihood -550859.947299, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[209]: Time 49.327126 seconds, bootstrap likelihood -533290.718596, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[310]: Time 45.202182 seconds, bootstrap likelihood -541187.606018, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[710]: Time 45.752937 seconds, bootstrap likelihood -556644.156010, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[410]: Time 64.552945 seconds, bootstrap likelihood -557615.191554, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[10]: Time 68.958747 seconds, bootstrap likelihood -542395.395740, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[810]: Time 80.231353 seconds, bootstrap likelihood -539568.794829, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[11]: Time 40.907221 seconds, bootstrap likelihood -546023.922811, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[510]: Time 118.319955 seconds, bootstrap likelihood -551991.201724, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[110]: Time 127.781504 seconds, bootstrap likelihood -563921.653503, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[910]: Time 135.427120 seconds, bootstrap likelihood -558954.568446, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[311]: Time 98.529887 seconds, bootstrap likelihood -557729.963759, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[111]: Time 53.696114 seconds, bootstrap likelihood -532038.914766, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[610]: Time 181.628585 seconds, bootstrap likelihood -538027.779904, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[411]: Time 121.107199 seconds, bootstrap likelihood -550025.990843, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[911]: Time 50.547445 seconds, bootstrap likelihood -544130.112391, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[210]: Time 191.455329 seconds, bootstrap likelihood -545609.947945, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[12]: Time 82.759015 seconds, bootstrap likelihood -542237.967038, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[312]: Time 66.289794 seconds, bootstrap likelihood -557197.386341, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[711]: Time 198.091573 seconds, bootstrap likelihood -533768.757547, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[511]: Time 136.439123 seconds, bootstrap likelihood -560756.421269, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[13]: Time 68.737346 seconds, bootstrap likelihood -531719.166179, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[211]: Time 72.568630 seconds, bootstrap likelihood -528057.302792, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[811]: Time 235.352903 seconds, bootstrap likelihood -548454.552242, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[512]: Time 93.641405 seconds, bootstrap likelihood -540891.073055, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[611]: Time 178.693537 seconds, bootstrap likelihood -536142.682876, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[412]: Time 182.538401 seconds, bootstrap likelihood -553633.912737, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[912]: Time 187.249924 seconds, bootstrap likelihood -561192.375078, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[313]: Time 166.543285 seconds, bootstrap likelihood -551439.895604, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[812]: Time 63.806793 seconds, bootstrap likelihood -529456.638597, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[513]: Time 39.700025 seconds, bootstrap likelihood -549700.189564, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[612]: Time 39.656112 seconds, bootstrap likelihood -545174.293235, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[112]: Time 223.708691 seconds, bootstrap likelihood -548260.289977, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[712]: Time 166.816265 seconds, bootstrap likelihood -551663.950368, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[212]: Time 147.857169 seconds, bootstrap likelihood -547075.021263, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[514]: Time 40.923994 seconds, bootstrap likelihood -567782.837392, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[14]: Time 174.616550 seconds, bootstrap likelihood -551563.788689, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[613]: Time 61.861842 seconds, bootstrap likelihood -545262.708283, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[314]: Time 115.519770 seconds, bootstrap likelihood -545959.607303, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[113]: Time 102.873910 seconds, bootstrap likelihood -558666.958684, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[713]: Time 99.062978 seconds, bootstrap likelihood -555189.657784, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[813]: Time 130.902028 seconds, bootstrap likelihood -555464.742788, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[213]: Time 119.818481 seconds, bootstrap likelihood -539164.371601, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[614]: Time 75.785184 seconds, bootstrap likelihood -534965.798753, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[913]: Time 180.264890 seconds, bootstrap likelihood -542592.446560, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[413]: Time 205.829569 seconds, bootstrap likelihood -547590.891908, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[214]: Time 66.709306 seconds, bootstrap likelihood -547459.226007, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[914]: Time 46.941526 seconds, bootstrap likelihood -541434.710318, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[714]: Time 130.713883 seconds, bootstrap likelihood -546932.674242, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[814]: Time 179.361651 seconds, bootstrap likelihood -546725.181925, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[114]: Time 236.260186 seconds, bootstrap likelihood -552945.677366, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[414]: Time 184.435516 seconds, bootstrap likelihood -573288.552219, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[915]: Time 119.723487 seconds, bootstrap likelihood -550036.328096, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[815]: Time 127.052524 seconds, bootstrap likelihood -548585.332782, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[715]: Time 134.788223 seconds, bootstrap likelihood -549414.579574, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[515]: Time 146.304058 seconds, bootstrap likelihood -526716.007345, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[615]: Time 147.513214 seconds, bootstrap likelihood -549274.299495, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[816]: Time 39.185824 seconds, bootstrap likelihood -551931.291022, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[415]: Time 172.392362 seconds, bootstrap likelihood -545374.922274, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[315]: Time 176.792350 seconds, bootstrap likelihood -532363.112251, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[115]: Time 191.324438 seconds, bootstrap likelihood -552258.282509, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[215]: Time 195.660970 seconds, bootstrap likelihood -531877.400479, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[15]: Time 206.836485 seconds, bootstrap likelihood -558209.285253, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[516]: Time 91.847485 seconds, bootstrap likelihood -554264.693204, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[116]: Time 61.955561 seconds, bootstrap likelihood -540079.825812, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[716]: Time 119.539895 seconds, bootstrap likelihood -546571.272558, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[916]: Time 137.894149 seconds, bootstrap likelihood -524022.331267, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[316]: Time 81.165919 seconds, bootstrap likelihood -524972.070118, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[817]: Time 145.815002 seconds, bootstrap likelihood -554000.495371, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[616]: Time 213.030238 seconds, bootstrap likelihood -560762.024217, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[16]: Time 159.809995 seconds, bootstrap likelihood -550937.743201, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[416]: Time 194.391796 seconds, bootstrap likelihood -560083.298593, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[216]: Time 176.249027 seconds, bootstrap likelihood -521912.407045, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[517]: Time 161.554894 seconds, bootstrap likelihood -548354.444078, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[917]: Time 153.867892 seconds, bootstrap likelihood -543433.665611, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[117]: Time 160.012763 seconds, bootstrap likelihood -525989.428941, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[317]: Time 156.481492 seconds, bootstrap likelihood -555203.923851, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[717]: Time 162.363723 seconds, bootstrap likelihood -546268.495450, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[518]: Time 65.769272 seconds, bootstrap likelihood -544306.774878, best rearrangement setting 7
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[818]: Time 162.389719 seconds, bootstrap likelihood -555680.226807, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[417]: Time 154.332085 seconds, bootstrap likelihood -545664.485630, best rearrangement setting 12
Bootstrap[617]: Time 160.581531 seconds, bootstrap likelihood -558611.441154, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[17]: Time 157.390335 seconds, bootstrap likelihood -540333.420430, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[918]: Time 125.754972 seconds, bootstrap likelihood -532191.730145, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[519]: Time 83.330227 seconds, bootstrap likelihood -552561.244314, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[217]: Time 179.087805 seconds, bootstrap likelihood -541840.515760, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[618]: Time 40.514986 seconds, bootstrap likelihood -549421.755510, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[318]: Time 147.324314 seconds, bootstrap likelihood -527009.515912, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[18]: Time 38.189739 seconds, bootstrap likelihood -545785.235188, best rearrangement setting 5
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[118]: Time 200.120510 seconds, bootstrap likelihood -553722.687072, best rearrangement setting 14
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[619]: Time 53.957040 seconds, bootstrap likelihood -536797.810410, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[418]: Time 96.365434 seconds, bootstrap likelihood -534989.859563, best rearrangement setting 9
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[819]: Time 164.369600 seconds, bootstrap likelihood -526654.283347, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[19]: Time 82.240983 seconds, bootstrap likelihood -527997.063887, best rearrangement setting 8
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[718]: Time 227.798833 seconds, bootstrap likelihood -546047.928426, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[119]: Time 51.595773 seconds, bootstrap likelihood -544503.342353, best rearrangement setting 6
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[919]: Time 139.636556 seconds, bootstrap likelihood -549794.802224, best rearrangement setting 11
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[218]: Time 175.576804 seconds, bootstrap likelihood -554320.038263, best rearrangement setting 12
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[419]: Time 112.318811 seconds, bootstrap likelihood -537623.800739, best rearrangement setting 10
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[319]: Time 171.088229 seconds, bootstrap likelihood -548462.664302, best rearrangement setting 13
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[719]: Time 216.943111 seconds, bootstrap likelihood -546092.615039, best rearrangement setting 15
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Bootstrap[219]: Time 212.927619 seconds, bootstrap likelihood -546664.926576, best rearrangement setting 15
Stopped Rapid BS search after 200 replicates with MRE-based Bootstopping criterion
WRF Average of 100 random splits: 2.568074 %
Overall Time for 200 Rapid Bootstraps 3216.884256 seconds
Average Time per Rapid Bootstrap 16.084421 seconds
Starting ML Search ...
Fast ML search on Process 2: Time 1674.862507 seconds
Fast ML search on Process 1: Time 1705.643504 seconds
Fast ML search on Process 3: Time 1740.103840 seconds
Fast ML search on Process 5: Time 1778.605411 seconds
Fast ML search on Process 7: Time 1834.946355 seconds
Fast ML search on Process 8: Time 1923.981456 seconds
Fast ML search on Process 4: Time 1937.135261 seconds
Fast ML optimization finished
Fast ML search on Process 0: Time 2249.787173 seconds
Fast ML search on Process 6: Time 2380.414418 seconds
Fast ML search on Process 9: Time 2381.228527 seconds
Slow ML Search 100 Likelihood: -539549.142138
Slow ML search on Process 1: Time 974.282453 seconds
Slow ML Search 300 Likelihood: -539588.233786
Slow ML search on Process 3: Time 1222.281331 seconds
Thorough ML search on Process 1: Time 851.358199 seconds
processID = 1, bestLH = -539523.405234
Slow ML Search 500 Likelihood: -539555.267137
Slow ML search on Process 5: Time 1833.479987 seconds
Slow ML Search 800 Likelihood: -539594.645779
Slow ML search on Process 8: Time 1760.172022 seconds
Slow ML Search 700 Likelihood: -539564.364340
Slow ML search on Process 7: Time 1952.433157 seconds
Thorough ML search on Process 3: Time 922.579489 seconds
processID = 3, bestLH = -539529.785540
Slow ML Search 200 Likelihood: -539552.114980
Slow ML search on Process 2: Time 2294.014354 seconds
Slow ML Search 0 Likelihood: -539526.703392
Slow ML optimization finished
Slow ML search on Process 0: Time 2025.601615 seconds
Slow ML Search 400 Likelihood: -539674.352399
Slow ML search on Process 4: Time 2466.774244 seconds
Slow ML Search 900 Likelihood: -539631.197765
Slow ML search on Process 9: Time 2068.917600 seconds
Thorough ML search on Process 5: Time 853.586805 seconds
processID = 5, bestLH = -539508.753622
Thorough ML search on Process 8: Time 863.707402 seconds
processID = 8, bestLH = -539531.580502
Thorough ML search on Process 7: Time 868.343139 seconds
processID = 7, bestLH = -539541.149787
Thorough ML search on Process 2: Time 800.239685 seconds
processID = 2, bestLH = -539535.940759
Slow ML Search 600 Likelihood: -539555.858155
Slow ML search on Process 6: Time 2582.503408 seconds
Thorough ML search on Process 0: Time 815.699573 seconds
processID = 0, bestLH = -539507.722978
Thorough ML search on Process 9: Time 747.956101 seconds
processID = 9, bestLH = -539537.717187
Thorough ML search on Process 4: Time 838.116101 seconds
processID = 4, bestLH = -539579.149423
Thorough ML search on Process 6: Time 818.668204 seconds
processID = 6, bestLH = -539518.471436
Final ML Optimization Likelihood: -539507.722978
Model Information:
Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
alpha: 1.648400
invar: 0.000000
Tree-Length: 422.419269
rate A <-> R: 0.834583
rate A <-> N: 0.819222
rate A <-> D: 0.925128
rate A <-> C: 1.662834
rate A <-> Q: 1.489630
rate A <-> E: 1.571977
rate A <-> G: 2.244786
rate A <-> H: 0.646533
rate A <-> I: 0.598954
rate A <-> L: 0.724706
rate A <-> K: 1.003975
rate A <-> M: 1.277922
rate A <-> F: 0.462817
rate A <-> P: 1.839289
rate A <-> S: 4.317169
rate A <-> T: 3.556293
rate A <-> W: 0.369031
rate A <-> Y: 0.363867
rate A <-> V: 3.126612
rate R <-> N: 1.057005
rate R <-> D: 0.507678
rate R <-> C: 0.969161
rate R <-> Q: 3.706116
rate R <-> E: 0.910540
rate R <-> G: 0.882254
rate R <-> H: 3.310623
rate R <-> I: 0.290663
rate R <-> L: 0.563890
rate R <-> K: 6.735276
rate R <-> M: 0.839689
rate R <-> F: 0.284069
rate R <-> P: 0.880246
rate R <-> S: 1.291137
rate R <-> T: 0.898505
rate R <-> W: 1.019983
rate R <-> Y: 0.599251
rate R <-> V: 0.524914
rate N <-> D: 5.283707
rate N <-> C: 0.657885
rate N <-> Q: 2.026715
rate N <-> E: 1.351007
rate N <-> G: 1.621579
rate N <-> H: 4.166924
rate N <-> I: 0.617181
rate N <-> L: 0.275555
rate N <-> K: 2.960717
rate N <-> M: 0.630595
rate N <-> F: 0.339203
rate N <-> P: 0.477627
rate N <-> S: 4.117178
rate N <-> T: 2.612296
rate N <-> W: 0.121598
rate N <-> Y: 0.732534
rate N <-> V: 0.308350
rate D <-> C: 0.152794
rate D <-> Q: 1.113600
rate D <-> E: 6.514078
rate D <-> G: 1.287041
rate D <-> H: 1.442865
rate D <-> I: 0.145342
rate D <-> L: 0.240316
rate D <-> K: 0.976390
rate D <-> M: 0.274004
rate D <-> F: 0.112629
rate D <-> P: 0.720410
rate D <-> S: 1.490086
rate D <-> T: 1.013038
rate D <-> W: 0.167861
rate D <-> Y: 0.500750
rate D <-> V: 0.308919
rate C <-> Q: 0.308444
rate C <-> E: 0.303852
rate C <-> G: 0.741925
rate C <-> H: 1.021773
rate C <-> I: 0.613643
rate C <-> L: 0.946775
rate C <-> K: 0.226660
rate C <-> M: 0.821160
rate C <-> F: 1.139920
rate C <-> P: 0.290879
rate C <-> S: 2.445168
rate C <-> T: 1.180471
rate C <-> W: 1.094282
rate C <-> Y: 1.450943
rate C <-> V: 1.521385
rate Q <-> E: 4.580442
rate Q <-> G: 0.590073
rate Q <-> H: 5.375081
rate Q <-> I: 0.328297
rate Q <-> L: 0.895459
rate Q <-> K: 4.069075
rate Q <-> M: 1.284628
rate Q <-> F: 0.240264
rate Q <-> P: 1.547723
rate Q <-> S: 1.559457
rate Q <-> T: 1.450723
rate Q <-> W: 0.602375
rate Q <-> Y: 0.617470
rate Q <-> V: 0.428089
rate E <-> G: 0.931902
rate E <-> H: 1.099990
rate E <-> I: 0.271332
rate E <-> L: 0.377243
rate E <-> K: 2.910662
rate E <-> M: 0.502385
rate E <-> F: 0.155799
rate E <-> P: 1.017473
rate E <-> S: 1.228644
rate E <-> T: 1.065021
rate E <-> W: 0.282284
rate E <-> Y: 0.391188
rate E <-> V: 0.601130
rate G <-> H: 0.575626
rate G <-> I: 0.194183
rate G <-> L: 0.240616
rate G <-> K: 0.601466
rate G <-> M: 0.400379
rate G <-> F: 0.248352
rate G <-> P: 0.520740
rate G <-> S: 2.059969
rate G <-> T: 0.480570
rate G <-> W: 0.628642
rate G <-> Y: 0.226886
rate G <-> V: 0.416416
rate H <-> I: 0.389159
rate H <-> L: 0.723799
rate H <-> K: 1.215976
rate H <-> M: 0.928418
rate H <-> F: 0.916414
rate H <-> P: 1.235167
rate H <-> S: 1.324547
rate H <-> T: 1.084968
rate H <-> W: 0.423720
rate H <-> Y: 5.216687
rate H <-> V: 0.358586
rate I <-> L: 4.035459
rate I <-> K: 0.419843
rate I <-> M: 4.545028
rate I <-> F: 1.537308
rate I <-> P: 0.323501
rate I <-> S: 0.406611
rate I <-> T: 1.771324
rate I <-> W: 0.376835
rate I <-> Y: 0.580033
rate I <-> V: 10.000000
rate L <-> K: 0.379369
rate L <-> M: 5.400938
rate L <-> F: 2.932276
rate L <-> P: 0.678032
rate L <-> S: 0.602017
rate L <-> T: 0.685272
rate L <-> W: 1.020855
rate L <-> Y: 0.837242
rate L <-> V: 2.384069
rate K <-> M: 1.151735
rate K <-> F: 0.262931
rate K <-> P: 0.935857
rate K <-> S: 1.329706
rate K <-> T: 1.715451
rate K <-> W: 0.393461
rate K <-> Y: 0.526826
rate K <-> V: 0.524515
rate M <-> F: 1.559973
rate M <-> P: 0.333034
rate M <-> S: 0.716569
rate M <-> T: 2.261053
rate M <-> W: 0.987060
rate M <-> Y: 0.732819
rate M <-> V: 2.728754
rate F <-> P: 0.251922
rate F <-> S: 0.744920
rate F <-> T: 0.462769
rate F <-> W: 2.248947
rate F <-> Y: 6.982383
rate F <-> V: 1.145687
rate P <-> S: 2.384594
rate P <-> T: 1.310123
rate P <-> W: 0.290868
rate P <-> Y: 0.324019
rate P <-> V: 0.402442
rate S <-> T: 5.949061
rate S <-> W: 0.456610
rate S <-> Y: 0.641920
rate S <-> V: 0.625649
rate T <-> W: 0.303518
rate T <-> Y: 0.575832
rate T <-> V: 2.302318
rate W <-> Y: 3.050994
rate W <-> V: 0.380488
rate Y <-> V: 0.672362
freq pi(A): 0.084825
freq pi(R): 0.062994
freq pi(N): 0.038293
freq pi(D): 0.057269
freq pi(C): 0.023558
freq pi(Q): 0.045751
freq pi(E): 0.066603
freq pi(G): 0.060043
freq pi(H): 0.030196
freq pi(I): 0.052640
freq pi(L): 0.083990
freq pi(K): 0.043448
freq pi(M): 0.033811
freq pi(F): 0.037302
freq pi(P): 0.044193
freq pi(S): 0.063092
freq pi(T): 0.053828
freq pi(W): 0.022868
freq pi(Y): 0.028020
freq pi(V): 0.067276
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
ML search took 5782.100826 secs or 1.606139 hours
Combined Bootstrap and ML search took 8998.988450 secs or 2.499719 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-40F21EA808D449F28362D24C6055CE77/RAxML_bestTree.result
Found 1 tree in File /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-40F21EA808D449F28362D24C6055CE77/RAxML_bestTree.result
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
WARNING, outgroups are not monophyletic, using first outgroup "001300654"
from the list to root the tree!
Program execution info written to /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-40F21EA808D449F28362D24C6055CE77/RAxML_info.result
All 200 bootstrapped trees written to: /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-40F21EA808D449F28362D24C6055CE77/RAxML_bootstrap.result
Best-scoring ML tree written to: /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-40F21EA808D449F28362D24C6055CE77/RAxML_bestTree.result
Best-scoring ML tree with support values written to: /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-40F21EA808D449F28362D24C6055CE77/RAxML_bipartitions.result
Best-scoring ML tree with support values as branch labels written to: /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-40F21EA808D449F28362D24C6055CE77/RAxML_bipartitionsBranchLabels.result
Overall execution time for full ML analysis: 8999.075867 secs or 2.499743 hours or 0.104156 days