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