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 to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" This is RAxML version 8.2.4 released by Alexandros Stamatakis on October 02 2015. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 83 distinct alignment patterns Found 0 invariant alignment patterns that correspond to 0 columns Proportion of gaps and completely undetermined characters in this alignment: 14.79% RAxML rapid bootstrapping and subsequent ML search Using 1 distinct models/data partitions with joint branch length optimization Executing 100 rapid bootstrap inferences and thereafter a thorough ML search All free model parameters will be estimated by RAxML GAMMA+P-Invar model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA+P-Invar Model parameters will be estimated up to an accuracy of 0.0010000000 Log Likelihood units Partition: 0 Alignment Patterns: 83 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: /usr/bin/raxmlHPC-PTHREADS-AVX -T 2 -f a -p 1234 -x 1234 -m GTRGAMMAI -o Kubrickus_heus__K-008 -N 100 -s fromR_2020-02-29.phy -n fromR_2020-02-29 Time for BS model parameter optimization 0.023496 Bootstrap[0]: Time 0.106570 seconds, bootstrap likelihood -2164.789117, best rearrangement setting 10 Bootstrap[1]: Time 0.052927 seconds, bootstrap likelihood -2268.198942, best rearrangement setting 15 Bootstrap[2]: Time 0.070156 seconds, bootstrap likelihood -2241.080238, best rearrangement setting 15 Bootstrap[3]: Time 0.042392 seconds, bootstrap likelihood -2161.098499, best rearrangement setting 12 Bootstrap[4]: Time 0.046080 seconds, bootstrap likelihood -2291.031584, best rearrangement setting 9 Bootstrap[5]: Time 0.030090 seconds, bootstrap likelihood -2146.447469, best rearrangement setting 12 Bootstrap[6]: Time 0.011933 seconds, bootstrap likelihood -2224.764323, best rearrangement setting 14 Bootstrap[7]: Time 0.027090 seconds, bootstrap likelihood -2183.323661, best rearrangement setting 10 Bootstrap[8]: Time 0.042629 seconds, bootstrap likelihood -2165.289470, best rearrangement setting 13 Bootstrap[9]: Time 0.040548 seconds, bootstrap likelihood -2137.134612, best rearrangement setting 14 Bootstrap[10]: Time 0.026023 seconds, bootstrap likelihood -2111.369952, best rearrangement setting 14 Bootstrap[11]: Time 0.043949 seconds, bootstrap likelihood -2299.153401, best rearrangement setting 5 Bootstrap[12]: Time 0.035472 seconds, bootstrap likelihood -2215.208993, best rearrangement setting 9 Bootstrap[13]: Time 0.028707 seconds, bootstrap likelihood -2201.160103, best rearrangement setting 10 Bootstrap[14]: Time 0.033119 seconds, bootstrap likelihood -2078.560725, best rearrangement setting 13 Bootstrap[15]: Time 0.030398 seconds, bootstrap likelihood -2196.048911, best rearrangement setting 6 Bootstrap[16]: Time 0.028995 seconds, bootstrap likelihood -2165.396001, best rearrangement setting 15 Bootstrap[17]: Time 0.039023 seconds, bootstrap likelihood -2152.202204, best rearrangement setting 13 Bootstrap[18]: Time 0.028746 seconds, bootstrap likelihood -2094.952538, best rearrangement setting 9 Bootstrap[19]: Time 0.025039 seconds, bootstrap likelihood -2223.951849, best rearrangement setting 8 Bootstrap[20]: Time 0.030274 seconds, bootstrap likelihood -2146.763856, best rearrangement setting 13 Bootstrap[21]: Time 0.019585 seconds, bootstrap likelihood -2104.342207, best rearrangement setting 10 Bootstrap[22]: Time 0.012893 seconds, bootstrap likelihood -2135.351694, best rearrangement setting 5 Bootstrap[23]: Time 0.033116 seconds, bootstrap likelihood -2285.910283, best rearrangement setting 10 Bootstrap[24]: Time 0.029239 seconds, bootstrap likelihood -2111.153639, best rearrangement setting 14 Bootstrap[25]: Time 0.030926 seconds, bootstrap likelihood -2102.955280, best rearrangement setting 7 Bootstrap[26]: Time 0.040704 seconds, bootstrap likelihood -2133.296040, best rearrangement setting 11 Bootstrap[27]: Time 0.036021 seconds, bootstrap likelihood -2178.895077, best rearrangement setting 11 Bootstrap[28]: Time 0.032972 seconds, bootstrap likelihood -2237.230120, best rearrangement setting 8 Bootstrap[29]: Time 0.035510 seconds, bootstrap likelihood -2155.599867, best rearrangement setting 13 Bootstrap[30]: Time 0.029965 seconds, bootstrap likelihood -2154.511785, best rearrangement setting 6 Bootstrap[31]: Time 0.043369 seconds, bootstrap likelihood -2114.033844, best rearrangement setting 9 Bootstrap[32]: Time 0.025382 seconds, bootstrap likelihood -2155.588622, best rearrangement setting 13 Bootstrap[33]: Time 0.033778 seconds, bootstrap likelihood -2207.067455, best rearrangement setting 8 Bootstrap[34]: Time 0.028880 seconds, bootstrap likelihood -2200.865547, best rearrangement setting 8 Bootstrap[35]: Time 0.029795 seconds, bootstrap likelihood -2137.725150, best rearrangement setting 12 Bootstrap[36]: Time 0.036173 seconds, bootstrap likelihood -2180.430155, best rearrangement setting 5 Bootstrap[37]: Time 0.032380 seconds, bootstrap likelihood -2170.410555, best rearrangement setting 8 Bootstrap[38]: Time 0.028923 seconds, bootstrap likelihood -2044.245831, best rearrangement setting 12 Bootstrap[39]: Time 0.029010 seconds, bootstrap likelihood -2215.467483, best rearrangement setting 13 Bootstrap[40]: Time 0.032432 seconds, bootstrap likelihood -2228.077075, best rearrangement setting 14 Bootstrap[41]: Time 0.031030 seconds, bootstrap likelihood -2112.862357, best rearrangement setting 13 Bootstrap[42]: Time 0.025462 seconds, bootstrap likelihood -2157.311395, best rearrangement setting 10 Bootstrap[43]: Time 0.023408 seconds, bootstrap likelihood -2093.473494, best rearrangement setting 13 Bootstrap[44]: Time 0.030752 seconds, bootstrap likelihood -2131.311530, best rearrangement setting 7 Bootstrap[45]: Time 0.036274 seconds, bootstrap likelihood -2128.230769, best rearrangement setting 14 Bootstrap[46]: Time 0.012846 seconds, bootstrap likelihood -2221.489834, best rearrangement setting 14 Bootstrap[47]: Time 0.030596 seconds, bootstrap likelihood -2184.385398, best rearrangement setting 11 Bootstrap[48]: Time 0.037470 seconds, bootstrap likelihood -2173.660947, best rearrangement setting 11 Bootstrap[49]: Time 0.037977 seconds, bootstrap likelihood -2102.199885, best rearrangement setting 15 Bootstrap[50]: Time 0.011949 seconds, bootstrap likelihood -2126.355442, best rearrangement setting 8 Bootstrap[51]: Time 0.014149 seconds, bootstrap likelihood -2170.996253, best rearrangement setting 5 Bootstrap[52]: Time 0.029001 seconds, bootstrap likelihood -2193.789407, best rearrangement setting 7 Bootstrap[53]: Time 0.031820 seconds, bootstrap likelihood -2240.176495, best rearrangement setting 10 Bootstrap[54]: Time 0.029134 seconds, bootstrap likelihood -2268.934967, best rearrangement setting 7 Bootstrap[55]: Time 0.030229 seconds, bootstrap likelihood -2189.483050, best rearrangement setting 8 Bootstrap[56]: Time 0.028692 seconds, bootstrap likelihood -2073.997393, best rearrangement setting 5 Bootstrap[57]: Time 0.037561 seconds, bootstrap likelihood -2187.288000, best rearrangement setting 12 Bootstrap[58]: Time 0.028358 seconds, bootstrap likelihood -2217.795062, best rearrangement setting 15 Bootstrap[59]: Time 0.031741 seconds, bootstrap likelihood -2120.057442, best rearrangement setting 6 Bootstrap[60]: Time 0.032461 seconds, bootstrap likelihood -2204.033638, best rearrangement setting 9 Bootstrap[61]: Time 0.030620 seconds, bootstrap likelihood -2182.894186, best rearrangement setting 9 Bootstrap[62]: Time 0.038302 seconds, bootstrap likelihood -2203.144416, best rearrangement setting 10 Bootstrap[63]: Time 0.031391 seconds, bootstrap likelihood -2101.592819, best rearrangement setting 12 Bootstrap[64]: Time 0.028786 seconds, bootstrap likelihood -2097.887276, best rearrangement setting 11 Bootstrap[65]: Time 0.028845 seconds, bootstrap likelihood -2057.121464, best rearrangement setting 8 Bootstrap[66]: Time 0.030385 seconds, bootstrap likelihood -2124.074026, best rearrangement setting 13 Bootstrap[67]: Time 0.030762 seconds, bootstrap likelihood -2127.980214, best rearrangement setting 15 Bootstrap[68]: Time 0.031278 seconds, bootstrap likelihood -2144.230425, best rearrangement setting 10 Bootstrap[69]: Time 0.031168 seconds, bootstrap likelihood -2202.957615, best rearrangement setting 13 Bootstrap[70]: Time 0.036494 seconds, bootstrap likelihood -2141.371771, best rearrangement setting 11 Bootstrap[71]: Time 0.036948 seconds, bootstrap likelihood -2135.521467, best rearrangement setting 11 Bootstrap[72]: Time 0.029001 seconds, bootstrap likelihood -2154.606682, best rearrangement setting 13 Bootstrap[73]: Time 0.027887 seconds, bootstrap likelihood -2054.692398, best rearrangement setting 5 Bootstrap[74]: Time 0.033043 seconds, bootstrap likelihood -2121.587241, best rearrangement setting 6 Bootstrap[75]: Time 0.031225 seconds, bootstrap likelihood -2211.966697, best rearrangement setting 11 Bootstrap[76]: Time 0.030361 seconds, bootstrap likelihood -2157.019797, best rearrangement setting 6 Bootstrap[77]: Time 0.030113 seconds, bootstrap likelihood -2157.769669, best rearrangement setting 8 Bootstrap[78]: Time 0.035061 seconds, bootstrap likelihood -2215.272864, best rearrangement setting 13 Bootstrap[79]: Time 0.030556 seconds, bootstrap likelihood -2149.318994, best rearrangement setting 13 Bootstrap[80]: Time 0.032105 seconds, bootstrap likelihood -2204.833933, best rearrangement setting 9 Bootstrap[81]: Time 0.012715 seconds, bootstrap likelihood -2169.369118, best rearrangement setting 10 Bootstrap[82]: Time 0.033153 seconds, bootstrap likelihood -2246.310136, best rearrangement setting 7 Bootstrap[83]: Time 0.033166 seconds, bootstrap likelihood -2154.255306, best rearrangement setting 6 Bootstrap[84]: Time 0.032301 seconds, bootstrap likelihood -2201.559870, best rearrangement setting 15 Bootstrap[85]: Time 0.030059 seconds, bootstrap likelihood -2180.574686, best rearrangement setting 10 Bootstrap[86]: Time 0.029262 seconds, bootstrap likelihood -2214.982757, best rearrangement setting 9 Bootstrap[87]: Time 0.028047 seconds, bootstrap likelihood -2145.823479, best rearrangement setting 5 Bootstrap[88]: Time 0.030104 seconds, bootstrap likelihood -2126.196892, best rearrangement setting 12 Bootstrap[89]: Time 0.031666 seconds, bootstrap likelihood -2195.270708, best rearrangement setting 6 Bootstrap[90]: Time 0.037035 seconds, bootstrap likelihood -2198.451568, best rearrangement setting 13 Bootstrap[91]: Time 0.029502 seconds, bootstrap likelihood -2238.914547, best rearrangement setting 8 Bootstrap[92]: Time 0.032917 seconds, bootstrap likelihood -2126.569791, best rearrangement setting 7 Bootstrap[93]: Time 0.034823 seconds, bootstrap likelihood -2310.011816, best rearrangement setting 11 Bootstrap[94]: Time 0.029660 seconds, bootstrap likelihood -2186.817177, best rearrangement setting 15 Bootstrap[95]: Time 0.036424 seconds, bootstrap likelihood -2196.728738, best rearrangement setting 15 Bootstrap[96]: Time 0.027439 seconds, bootstrap likelihood -2170.289422, best rearrangement setting 5 Bootstrap[97]: Time 0.038204 seconds, bootstrap likelihood -2129.166878, best rearrangement setting 14 Bootstrap[98]: Time 0.033758 seconds, bootstrap likelihood -2176.616021, best rearrangement setting 7 Bootstrap[99]: Time 0.021459 seconds, bootstrap likelihood -2198.785616, best rearrangement setting 10 Overall Time for 100 Rapid Bootstraps 3.235208 seconds Average Time per Rapid Bootstrap 0.032352 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 1.676332 seconds Slow ML Search 0 Likelihood: -2186.697667 Slow ML Search 1 Likelihood: -2186.697668 Slow ML Search 2 Likelihood: -2186.697667 Slow ML Search 3 Likelihood: -2186.697667 Slow ML Search 4 Likelihood: -2186.697668 Slow ML Search 5 Likelihood: -2186.697685 Slow ML Search 6 Likelihood: -2186.697685 Slow ML Search 7 Likelihood: -2186.697685 Slow ML Search 8 Likelihood: -2186.697685 Slow ML Search 9 Likelihood: -2186.697685 Slow ML optimization finished Slow ML search Time: 0.462464 seconds Thorough ML search Time: 0.100085 seconds Final ML Optimization Likelihood: -2186.697682 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: DNA alpha: 0.875736 invar: 0.541245 Tree-Length: 0.123322 rate A <-> C: 3.524215 rate A <-> G: 1.695321 rate A <-> T: 0.431917 rate C <-> G: 0.661875 rate C <-> T: 4.320300 rate G <-> T: 1.000000 freq pi(A): 0.325642 freq pi(C): 0.171561 freq pi(G): 0.233438 freq pi(T): 0.269358 ML search took 2.239178 secs or 0.000622 hours Combined Bootstrap and ML search took 5.474402 secs or 0.001521 hours Drawing Bootstrap Support Values on best-scoring ML tree ... Found 1 tree in File /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bestTree.fromR_2020-02-29 Found 1 tree in File /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bestTree.fromR_2020-02-29 Program execution info written to /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_info.fromR_2020-02-29 All 100 bootstrapped trees written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bootstrap.fromR_2020-02-29 Best-scoring ML tree written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bestTree.fromR_2020-02-29 Best-scoring ML tree with support values written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bipartitions.fromR_2020-02-29 Best-scoring ML tree with support values as branch labels written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bipartitionsBranchLabels.fromR_2020-02-29 Overall execution time for full ML analysis: 5.476693 secs or 0.001521 hours or 0.000063 days