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) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 03-Jun-2021 14:58:10 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43187/2_msa/O43187_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43187/3_mltree/O43187.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43187/4_raxmlng_ancestral/O43187 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622721490 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/O43187/2_msa/O43187_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 625 sites WARNING: Sequences tr_A0A0E0FNK2_A0A0E0FNK2_ORYNI_4536 and tr_A0A0E0MYH4_A0A0E0MYH4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FNK2_A0A0E0FNK2_ORYNI_4536 and tr_A0A0D9YAY1_A0A0D9YAY1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0FNK2_A0A0E0FNK2_ORYNI_4536 and tr_Q5ZB74_Q5ZB74_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0FVU4_A0A0E0FVU4_ORYNI_4536 and tr_A0A0E0N522_A0A0E0N522_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GA92_A0A0E0GA92_ORYNI_4536 and tr_B8AFU8_B8AFU8_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GKQ0_A0A0E0GKQ0_ORYNI_4536 and tr_A0A0E0NT10_A0A0E0NT10_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GKQ0_A0A0E0GKQ0_ORYNI_4536 and tr_A0A0D9Z577_A0A0D9Z577_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0I2G9_A0A0E0I2G9_ORYNI_4536 and tr_I1QEA8_I1QEA8_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0I2G9_A0A0E0I2G9_ORYNI_4536 and tr_A0A0E0QA19_A0A0E0QA19_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0I2G9_A0A0E0I2G9_ORYNI_4536 and tr_A0A0D3GSJ3_A0A0D3GSJ3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0I2G9_A0A0E0I2G9_ORYNI_4536 and tr_A0A0E0ALK2_A0A0E0ALK2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0I2G9_A0A0E0I2G9_ORYNI_4536 and tr_Q7F1I0_Q7F1I0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0IW23_A0A0E0IW23_ORYNI_4536 and tr_A0A0E0R254_A0A0E0R254_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IW23_A0A0E0IW23_ORYNI_4536 and tr_Q336U5_Q336U5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2Z0M3_A2Z0M3_ORYSI_39946 and tr_I1QNH6_I1QNH6_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2Z0M3_A2Z0M3_ORYSI_39946 and tr_A0A0E0QQN2_A0A0E0QQN2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2Z0M3_A2Z0M3_ORYSI_39946 and tr_A0A0E0B2A5_A0A0E0B2A5_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2ZA86_A2ZA86_ORYSI_39946 and tr_I1QVY6_I1QVY6_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2ZA86_A2ZA86_ORYSI_39946 and tr_A0A0D3HGM1_A0A0D3HGM1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2ZA86_A2ZA86_ORYSI_39946 and tr_A0A0E0BDT0_A0A0E0BDT0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B8A9G0_B8A9G0_ORYSI_39946 and tr_I1NRQ0_I1NRQ0_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8A9G0_B8A9G0_ORYSI_39946 and tr_A0A0E0N2G9_A0A0E0N2G9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_B8A9G0_B8A9G0_ORYSI_39946 and tr_A0A0D3EU15_A0A0D3EU15_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_B8A9G0_B8A9G0_ORYSI_39946 and tr_A0A0D9YF03_A0A0D9YF03_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B8A9G0_B8A9G0_ORYSI_39946 and tr_Q5JN60_Q5JN60_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8AKP4_B8AKP4_ORYSI_39946 and tr_Q10NG8_Q10NG8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8AWI6_B8AWI6_ORYSI_39946 and tr_A0A0D3G262_A0A0D3G262_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1NTE3_I1NTE3_ORYGL_4538 and tr_A0A0D3EWB5_A0A0D3EWB5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0NI99_A0A0E0NI99_ORYRU_4529 and tr_A3A9F2_A3A9F2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_M4E776_M4E776_BRARP_51351 and tr_A0A078FP69_A0A078FP69_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4EB73_M4EB73_BRARP_51351 and tr_A0A078H9K5_A0A078H9K5_BRANA_3708 are exactly identical! WARNING: Sequences tr_T1ME10_T1ME10_TRIUA_4572 and tr_A0A3B6B3V5_A0A3B6B3V5_WHEAT_4565 are exactly identical! WARNING: Sequences tr_T1N4D9_T1N4D9_TRIUA_4572 and tr_A0A3B6NNH7_A0A3B6NNH7_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067GSE1_A0A067GSE1_CITSI_2711 and tr_V4TJD4_V4TJD4_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078GHY8_A0A078GHY8_BRANA_3708 and tr_A0A0D3AXF9_A0A0D3AXF9_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0D2R2Q2_A0A0D2R2Q2_GOSRA_29730 and tr_A0A1U8MPK2_A0A1U8MPK2_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2SQF1_A0A0D2SQF1_GOSRA_29730 and tr_A0A1U8KAV1_A0A1U8KAV1_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2SXF6_A0A0D2SXF6_GOSRA_29730 and tr_A0A1U8M4J4_A0A1U8M4J4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1S3X1N3_A0A1S3X1N3_TOBAC_4097 and tr_A0A1U7YL41_A0A1U7YL41_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZPD4_A0A1S3ZPD4_TOBAC_4097 and tr_A0A1U7Y3S8_A0A1U7Y3S8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4C6E3_A0A1S4C6E3_TOBAC_4097 and tr_A0A1U7YB72_A0A1U7YB72_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CMH8_A0A1S4CMH8_TOBAC_4097 and tr_A0A1U7WKX2_A0A1U7WKX2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CT11_A0A1S4CT11_TOBAC_4097 and tr_A0A1U7WI73_A0A1U7WI73_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3TMS8_A0A1S3TMS8_VIGRR_3916 and tr_A0A3Q0EUC6_A0A3Q0EUC6_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_A0A1U8H9M8_A0A1U8H9M8_CAPAN_4072 and tr_A0A2G3CB03_A0A2G3CB03_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2P6PPC0_A0A2P6PPC0_ROSCH_74649 and tr_A0A2P6PPC3_A0A2P6PPC3_ROSCH_74649 are exactly identical! WARNING: Sequences tr_A0A2P6PPC0_A0A2P6PPC0_ROSCH_74649 and tr_A0A2P6SQ56_A0A2P6SQ56_ROSCH_74649 are exactly identical! WARNING: Duplicate sequences found: 50 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/O43187/4_raxmlng_ancestral/O43187.raxml.reduced.phy Alignment comprises 1 partitions and 625 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 625 Gaps: 42.00 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43187/4_raxmlng_ancestral/O43187.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/O43187/3_mltree/O43187.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 157 / 12560 [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: -253431.786354 [00:00:00 -253431.786354] Initial branch length optimization [00:00:01 -250460.847113] Model parameter optimization (eps = 0.100000) [00:00:51] Tree #1, final logLikelihood: -249729.961865 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.088186,0.240548) (0.114646,0.250902) (0.296487,0.714092) (0.500681,1.474599) 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/O43187/4_raxmlng_ancestral/O43187.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43187/4_raxmlng_ancestral/O43187.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43187/4_raxmlng_ancestral/O43187.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43187/4_raxmlng_ancestral/O43187.raxml.log Analysis started: 03-Jun-2021 14:58:10 / finished: 03-Jun-2021 14:59:08 Elapsed time: 58.025 seconds Consumed energy: 5.110 Wh