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 02-Jun-2021 18:17:59 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75306/2_msa/O75306_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75306/3_mltree/O75306.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75306/4_raxmlng_ancestral/O75306 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647079 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/O75306/2_msa/O75306_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 463 sites WARNING: Sequences tr_B6Q737_B6Q737_TALMQ_441960 and tr_A0A093VN36_A0A093VN36_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WCA0_B2WCA0_PYRTR_426418 and tr_A0A2W1HY82_A0A2W1HY82_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G2X1S3_G2X1S3_VERDV_498257 and tr_A0A0G4N324_A0A0G4N324_9PEZI_100787 are exactly identical! WARNING: Sequences tr_C0NBP9_C0NBP9_AJECG_447093 and tr_C6H9Z9_C6H9Z9_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NBP9_C0NBP9_AJECG_447093 and tr_F0UKW2_F0UKW2_AJEC8_544711 are exactly identical! WARNING: Sequences tr_B8NHK7_B8NHK7_ASPFN_332952 and tr_Q2UFF4_Q2UFF4_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NHK7_B8NHK7_ASPFN_332952 and tr_A0A1S9E107_A0A1S9E107_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179ULR1_A0A179ULR1_BLAGS_559298 and tr_C5GBG7_C5GBG7_AJEDR_559297 are exactly identical! WARNING: Sequences tr_E9D9I5_E9D9I5_COCPS_443226 and tr_A0A0J6YD26_A0A0J6YD26_COCIT_404692 are exactly identical! WARNING: Sequences tr_J5JXE5_J5JXE5_BEAB2_655819 and tr_A0A2N6NRB8_A0A2N6NRB8_BEABA_176275 are exactly identical! WARNING: Sequences tr_J3LQ97_J3LQ97_ORYBR_4533 and tr_A0A341PW24_A0A341PW24_WHEAT_4565 are exactly identical! WARNING: Sequences tr_J3LQ97_J3LQ97_ORYBR_4533 and tr_A0A2T7C7D5_A0A2T7C7D5_9POAL_1504633 are exactly identical! WARNING: Sequences sp_Q6ENA1_NDHH_ORYNI_4536 and sp_P0C336_NDHH_ORYSI_39946 are exactly identical! WARNING: Sequences sp_Q6ENA1_NDHH_ORYNI_4536 and tr_I1Q6F5_I1Q6F5_ORYGL_4538 are exactly identical! WARNING: Sequences sp_Q6ENA1_NDHH_ORYNI_4536 and tr_H6CSH7_H6CSH7_9ORYZ_40149 are exactly identical! WARNING: Sequences sp_Q6ENA1_NDHH_ORYNI_4536 and tr_H6CSQ3_H6CSQ3_ORYRU_4529 are exactly identical! WARNING: Sequences sp_Q6ENA1_NDHH_ORYNI_4536 and sp_P0C337_NDHH_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QD14_A2QD14_ASPNC_425011 and tr_G3Y352_G3Y352_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QD14_A2QD14_ASPNC_425011 and tr_A0A319BI14_A0A319BI14_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X520_G7X520_ASPKW_1033177 and tr_A0A146FM18_A0A146FM18_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G2YZC3_G2YZC3_BOTF4_999810 and tr_M7U1W9_M7U1W9_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3MCH4_E3MCH4_CAERE_31234 and tr_A0A261CNN7_A0A261CNN7_9PELO_1503980 are exactly identical! WARNING: Sequences tr_F2SV10_F2SV10_TRIRC_559305 and tr_A0A178F6X7_A0A178F6X7_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0D2X9W5_A0A0D2X9W5_FUSO4_426428 and tr_S0DS89_S0DS89_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_A0A0D2X9W5_A0A0D2X9W5_FUSO4_426428 and tr_N4TX63_N4TX63_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0D2X9W5_A0A0D2X9W5_FUSO4_426428 and tr_X0BWX4_X0BWX4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2X9W5_A0A0D2X9W5_FUSO4_426428 and tr_A0A2H3STG8_A0A2H3STG8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0D2X9W5_A0A0D2X9W5_FUSO4_426428 and tr_A0A2H3HU95_A0A2H3HU95_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A0D2X9W5_A0A0D2X9W5_FUSO4_426428 and tr_A0A2K0W5E2_A0A2K0W5E2_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A0D2X9W5_A0A0D2X9W5_FUSO4_426428 and tr_A0A365N6J6_A0A365N6J6_GIBIN_948311 are exactly identical! WARNING: Sequences tr_F2Q5W1_F2Q5W1_TRIEC_559882 and tr_A0A059JEQ9_A0A059JEQ9_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L8FVV4_L8FVV4_PSED2_658429 and tr_A0A1B8GK55_A0A1B8GK55_9PEZI_342668 are exactly identical! WARNING: Sequences tr_L8FVV4_L8FVV4_PSED2_658429 and tr_A0A1B8CL93_A0A1B8CL93_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A1C9ZP01_A0A1C9ZP01_HORVV_112509 and tr_Q36813_Q36813_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015N1D8_A0A015N1D8_9GLOM_1432141 and tr_A0A2I1GRR5_A0A2I1GRR5_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015N1D8_A0A015N1D8_9GLOM_1432141 and tr_U9SYJ5_U9SYJ5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096NQK6_A0A096NQK6_PAPAN_9555 and tr_A0A2K5ZLM0_A0A2K5ZLM0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0F9ZP98_A0A0F9ZP98_TRIHA_5544 and tr_A0A2T4ANX4_A0A2T4ANX4_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0N0DHX2_A0A0N0DHX2_FUSLA_179993 and tr_I1RA52_I1RA52_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A091J1W5_A0A091J1W5_EGRGA_188379 and tr_A0A099ZZB9_A0A099ZZB9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CUP0_A0A0V1CUP0_TRIBR_45882 and tr_A0A0V0V5A9_A0A0V0V5A9_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CUP0_A0A0V1CUP0_TRIBR_45882 and tr_A0A0V0TPM0_A0A0V0TPM0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100I4I0_A0A100I4I0_ASPNG_5061 and tr_A0A1L9NAU2_A0A1L9NAU2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A140G1X5_A0A140G1X5_TOBAC_4097 and tr_A0A1U8QDY6_A0A1U8QDY6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1V8UR52_A0A1V8UR52_9PEZI_1974281 and tr_A0A1V8SFH6_A0A1V8SFH6_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1Y3BZ29_A0A1Y3BZ29_HELAN_4232 and tr_A0A251VJ91_A0A251VJ91_HELAN_4232 are exactly identical! WARNING: Sequences tr_A0A2H3BQN4_A0A2H3BQN4_9AGAR_1076256 and tr_A0A284R111_A0A284R111_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2G5HL18_A0A2G5HL18_CERBT_122368 and tr_A0A2S6BQE8_A0A2S6BQE8_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2V5IC07_A0A2V5IC07_9EURO_1450541 and tr_A0A2V5IQ20_A0A2V5IQ20_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 49 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/O75306/4_raxmlng_ancestral/O75306.raxml.reduced.phy Alignment comprises 1 partitions and 463 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 463 Gaps: 15.32 % Invariant sites: 0.22 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75306/4_raxmlng_ancestral/O75306.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/O75306/3_mltree/O75306.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 116 / 9280 [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: -127813.170943 [00:00:00 -127813.170943] Initial branch length optimization [00:00:01 -119207.330510] Model parameter optimization (eps = 0.100000) [00:00:44] Tree #1, final logLikelihood: -118392.308354 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.278239,0.371420) (0.389578,0.491528) (0.187955,1.056230) (0.144227,3.512819) 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/O75306/4_raxmlng_ancestral/O75306.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75306/4_raxmlng_ancestral/O75306.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75306/4_raxmlng_ancestral/O75306.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75306/4_raxmlng_ancestral/O75306.raxml.log Analysis started: 02-Jun-2021 18:17:59 / finished: 02-Jun-2021 18:18:47 Elapsed time: 48.162 seconds Consumed energy: 4.076 Wh