RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 17:48:21 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/2_msa/P51617_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/3_mltree/P51617.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/4_raxmlng_ancestral/P51617 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622645301 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/2_msa/P51617_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 712 sites WARNING: Sequences tr_A0A0E0FHK4_A0A0E0FHK4_ORYNI_4536 and tr_A2WLN3_A2WLN3_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GEK5_A0A0E0GEK5_ORYNI_4536 and tr_A2XE63_A2XE63_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GEK5_A0A0E0GEK5_ORYNI_4536 and tr_A0A0D3FFR8_A0A0D3FFR8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GHF5_A0A0E0GHF5_ORYNI_4536 and tr_B8APB2_B8APB2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GII5_A0A0E0GII5_ORYNI_4536 and tr_A0A0E0PJ24_A0A0E0PJ24_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GII5_A0A0E0GII5_ORYNI_4536 and tr_A0A0N7KKC7_A0A0N7KKC7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0GN21_A0A0E0GN21_ORYNI_4536 and tr_I1QUC2_I1QUC2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GN21_A0A0E0GN21_ORYNI_4536 and tr_A0A0E0QYV6_A0A0E0QYV6_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GN21_A0A0E0GN21_ORYNI_4536 and tr_Q7XEV8_Q7XEV8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0HVD5_A0A0E0HVD5_ORYNI_4536 and tr_A2YGZ3_A2YGZ3_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HVD5_A0A0E0HVD5_ORYNI_4536 and tr_I1Q598_I1Q598_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HVD5_A0A0E0HVD5_ORYNI_4536 and tr_Q5Z9Q3_Q5Z9Q3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0IT42_A0A0E0IT42_ORYNI_4536 and tr_A2XZW7_A2XZW7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IT42_A0A0E0IT42_ORYNI_4536 and tr_I1PS33_I1PS33_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0IT42_A0A0E0IT42_ORYNI_4536 and tr_Q75IN0_Q75IN0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8AC91_B8AC91_ORYSI_39946 and tr_A0A0D9Y6A5_A0A0D9Y6A5_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B8AC91_B8AC91_ORYSI_39946 and tr_Q5NAV8_Q5NAV8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8AZ90_B8AZ90_ORYSI_39946 and tr_A0A0D3G4L1_A0A0D3G4L1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_B8BI46_B8BI46_ORYSI_39946 and tr_A0A0E0R254_A0A0E0R254_ORYRU_4529 are exactly identical! WARNING: Sequences tr_B8BI46_B8BI46_ORYSI_39946 and tr_Q336U5_Q336U5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1NLH8_I1NLH8_ORYGL_4538 and tr_A0A0D3ELA8_A0A0D3ELA8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1NR59_I1NR59_ORYGL_4538 and tr_A0A0D3ET54_A0A0D3ET54_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1NR59_I1NR59_ORYGL_4538 and tr_A0A0D9YDX4_A0A0D9YDX4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1NWM0_I1NWM0_ORYGL_4538 and tr_A0A0E0CDY3_A0A0E0CDY3_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1PRT6_I1PRT6_ORYGL_4538 and sp_Q65XV8_RK176_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1Q5W8_I1Q5W8_ORYGL_4538 and tr_A0A0E0QZN6_A0A0E0QZN6_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1Q5W8_I1Q5W8_ORYGL_4538 and tr_A0A0D3HE48_A0A0D3HE48_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1Q5W8_I1Q5W8_ORYGL_4538 and tr_Q7XE14_Q7XE14_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QVP9_I1QVP9_ORYGL_4538 and tr_A0A0D3HGB9_A0A0D3HGB9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0MSL5_A0A0E0MSL5_ORYRU_4529 and tr_A0A0D3EKM4_A0A0D3EKM4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0MSL5_A0A0E0MSL5_ORYRU_4529 and tr_A0A0D9Y4I2_A0A0D9Y4I2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_M4CSH2_M4CSH2_BRARP_51351 and tr_A0A078HR96_A0A078HR96_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4CZF2_M4CZF2_BRARP_51351 and tr_A0A078HR80_A0A078HR80_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4DXR2_M4DXR2_BRARP_51351 and tr_A0A078GHK9_A0A078GHK9_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4FIK0_M4FIK0_BRARP_51351 and tr_A0A078IAG8_A0A078IAG8_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A067FLW1_A0A067FLW1_CITSI_2711 and tr_V4S5N1_V4S5N1_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078FA69_A0A078FA69_BRANA_3708 and tr_A0A0D3DYK0_A0A0D3DYK0_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078G1N8_A0A078G1N8_BRANA_3708 and tr_A0A0D3BQH7_A0A0D3BQH7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0A0LRA5_A0A0A0LRA5_CUCSA_3659 and tr_A0A1S3BAN7_A0A1S3BAN7_CUCME_3656 are exactly identical! WARNING: Sequences tr_V4V9C8_V4V9C8_9ROSI_85681 and tr_A0A2H5PJ02_A0A2H5PJ02_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2UUZ1_A0A0D2UUZ1_GOSRA_29730 and tr_A0A1U8IPV4_A0A1U8IPV4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1S3Y6W6_A0A1S3Y6W6_TOBAC_4097 and tr_A0A1U7VVM3_A0A1U7VVM3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3YHU3_A0A1S3YHU3_TOBAC_4097 and tr_A0A1U7XPM6_A0A1U7XPM6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZL92_A0A1S3ZL92_TOBAC_4097 and tr_A0A1U7WE19_A0A1U7WE19_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4BGW1_A0A1S4BGW1_TOBAC_4097 and tr_A0A1U7VYV9_A0A1U7VYV9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4C498_A0A1S4C498_TOBAC_4097 and tr_A0A1U7W3U3_A0A1U7W3U3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CSH3_A0A1S4CSH3_TOBAC_4097 and tr_A0A1U7VCE7_A0A1U7VCE7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3U531_A0A1S3U531_VIGRR_3916 and tr_A0A3Q0EWQ9_A0A3Q0EWQ9_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A2D0R070_A0A2D0R070_ICTPU_7998 and tr_A0A2D0R0G6_A0A2D0R0G6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R070_A0A2D0R070_ICTPU_7998 and tr_A0A2D0R1Y5_A0A2D0R1Y5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R070_A0A2D0R070_ICTPU_7998 and tr_A0A2D0R2M1_A0A2D0R2M1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U1M3D1_A0A2U1M3D1_ARTAN_35608 and tr_A0A2U1PWI3_A0A2U1PWI3_ARTAN_35608 are exactly identical! WARNING: Duplicate sequences found: 52 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/4_raxmlng_ancestral/P51617.raxml.reduced.phy Alignment comprises 1 partitions and 712 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 712 Gaps: 45.69 % Invariant sites: 0.42 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/4_raxmlng_ancestral/P51617.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/3_mltree/P51617.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 178 / 14240 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -258995.612325 [00:00:00 -258995.612325] Initial branch length optimization [00:00:02 -241147.124540] Model parameter optimization (eps = 0.100000) [00:00:55] Tree #1, final logLikelihood: -240462.278747 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.120517,0.208219) (0.124109,0.292921) (0.307704,0.789857) (0.447671,1.553620) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/4_raxmlng_ancestral/P51617.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/4_raxmlng_ancestral/P51617.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/4_raxmlng_ancestral/P51617.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51617/4_raxmlng_ancestral/P51617.raxml.log Analysis started: 02-Jun-2021 17:48:21 / finished: 02-Jun-2021 17:49:24 Elapsed time: 62.178 seconds Consumed energy: 3.391 Wh