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 03-Jun-2021 02:09:32 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00571/2_msa/O00571_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00571/3_mltree/O00571.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00571/4_raxmlng_ancestral/O00571 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675372 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/O00571/2_msa/O00571_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 662 sites WARNING: Sequences sp_Q9VHP0_DDX3_DROME_7227 and tr_B4HL39_B4HL39_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3GSH5_G3GSH5_CRIGR_10029 and tr_Q8K5D5_Q8K5D5_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q1DJF0_DED1_COCIM_246410 and tr_A0A0J7BG47_A0A0J7BG47_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QHG5_B6QHG5_TALMQ_441960 and tr_A0A093VHB0_A0A093VHB0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2J8WIR6_A0A2J8WIR6_PONAB_9601 and sp_O00571_DDX3X_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8WIR6_A0A2J8WIR6_PONAB_9601 and tr_G1LJW1_G1LJW1_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2J8WIR6_A0A2J8WIR6_PONAB_9601 and tr_G7Q2J2_G7Q2J2_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8WIR6_A0A2J8WIR6_PONAB_9601 and tr_M3WY95_M3WY95_FELCA_9685 are exactly identical! WARNING: Sequences tr_C0NAF4_C0NAF4_AJECG_447093 and sp_A6R3L3_DED1_AJECN_339724 are exactly identical! WARNING: Sequences sp_Q9P6U9_DED1_NEUCR_367110 and tr_G4UGA3_G4UGA3_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8N9S2_B8N9S2_ASPFN_332952 and sp_Q2UGK3_DED1_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N9S2_B8N9S2_ASPFN_332952 and tr_A0A1S9DZJ4_A0A1S9DZJ4_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A2I3RHJ0_A0A2I3RHJ0_PANTR_9598 and tr_A0A2R9C932_A0A2R9C932_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FTF1_F9FTF1_FUSOF_660025 and tr_A0A0D2XDN9_A0A0D2XDN9_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FTF1_F9FTF1_FUSOF_660025 and tr_N4TP04_N4TP04_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FTF1_F9FTF1_FUSOF_660025 and tr_X0D377_X0D377_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FTF1_F9FTF1_FUSOF_660025 and tr_A0A2H3TFA0_A0A2H3TFA0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9FAA0_E9FAA0_METRA_655844 and tr_A0A0D9P3P1_A0A0D9P3P1_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6H4W7_C6H4W7_AJECH_544712 and tr_F0UIQ5_F0UIQ5_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0J3X5_A0A0E0J3X5_ORYNI_4536 and tr_A0A0E0RAK2_A0A0E0RAK2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0J3X5_A0A0E0J3X5_ORYNI_4536 and sp_Q2R1M8_RH52C_ORYSJ_39947 are exactly identical! WARNING: Sequences sp_A2QI25_DED1_ASPNC_425011 and tr_G7X6S4_G7X6S4_ASPKW_1033177 are exactly identical! WARNING: Sequences sp_A2QI25_DED1_ASPNC_425011 and tr_A0A100IA64_A0A100IA64_ASPNG_5061 are exactly identical! WARNING: Sequences sp_A2QI25_DED1_ASPNC_425011 and tr_A0A146FID4_A0A146FID4_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A0A1D5Q9J1_A0A1D5Q9J1_MACMU_9544 and tr_A0A2I3LNN5_A0A2I3LNN5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q9J1_A0A1D5Q9J1_MACMU_9544 and tr_A0A2K6BVJ6_A0A2K6BVJ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q9J1_A0A1D5Q9J1_MACMU_9544 and tr_A0A2K6AJS4_A0A2K6AJS4_MANLE_9568 are exactly identical! WARNING: Sequences tr_B8B879_B8B879_ORYSI_39946 and sp_Q6Z4K6_RH52B_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1R1F4_I1R1F4_ORYGL_4538 and tr_A0A0E0F7G8_A0A0E0F7G8_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1R1F4_I1R1F4_ORYGL_4538 and tr_A0A0D3HNP9_A0A0D3HNP9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G2YXE8_G2YXE8_BOTF4_999810 and tr_M7TRN8_M7TRN8_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SGT2_F2SGT2_TRIRC_559305 and tr_A0A178F3P1_A0A178F3P1_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3Y8M6_G3Y8M6_ASPNA_380704 and tr_A0A319AHR1_A0A319AHR1_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F2PW21_F2PW21_TRIEC_559882 and tr_A0A059J7G6_A0A059J7G6_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0PDY0_L0PDY0_PNEJ8_1209962 and tr_A0A0W4ZVM7_A0A0W4ZVM7_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_L8FX65_L8FX65_PSED2_658429 and tr_A0A094E691_A0A094E691_9PEZI_1420912 are exactly identical! WARNING: Sequences tr_U5GYA1_U5GYA1_USTV1_683840 and tr_A0A2X0ML95_A0A2X0ML95_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A044SSK0_A0A044SSK0_ONCVO_6282 and tr_A0A182E425_A0A182E425_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067FU12_A0A067FU12_CITSI_2711 and tr_V4S6V3_V4S6V3_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A0F8XAN6_A0A0F8XAN6_9EURO_308745 and tr_A0A2T5M8X0_A0A2T5M8X0_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0G4NX86_A0A0G4NX86_PENCA_1429867 and tr_A0A1V6R185_A0A1V6R185_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0V1D6R6_A0A0V1D6R6_TRIBR_45882 and tr_A0A0V0WF57_A0A0V0WF57_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D6R6_A0A0V1D6R6_TRIBR_45882 and tr_A0A0V1KXN4_A0A0V1KXN4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D6R6_A0A0V1D6R6_TRIBR_45882 and tr_A0A0V1PBU2_A0A0V1PBU2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S4A7G6_A0A1S4A7G6_TOBAC_4097 and tr_A0A1U7W4Y3_A0A1U7W4Y3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1Q3EB86_A0A1Q3EB86_LENED_5353 and tr_A0A1Q3EBA0_A0A1Q3EBA0_LENED_5353 are exactly identical! WARNING: Sequences tr_A0A1V8UR37_A0A1V8UR37_9PEZI_1974281 and tr_A0A1V8T7X0_A0A1V8T7X0_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1V8UR37_A0A1V8UR37_9PEZI_1974281 and tr_A0A1V8TCC0_A0A1V8TCC0_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1Y1XSF5_A0A1Y1XSF5_9FUNG_1314790 and tr_A0A1Y1YTA1_A0A1Y1YTA1_9FUNG_1314790 are exactly identical! WARNING: Sequences tr_A0A2G4T3B3_A0A2G4T3B3_9FUNG_1340429 and tr_A0A367JD36_A0A367JD36_9FUNG_86630 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/O00571/4_raxmlng_ancestral/O00571.raxml.reduced.phy Alignment comprises 1 partitions and 662 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 662 Gaps: 17.53 % Invariant sites: 6.19 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00571/4_raxmlng_ancestral/O00571.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/O00571/3_mltree/O00571.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 166 / 13280 [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: -184202.721143 [00:00:00 -184202.721143] Initial branch length optimization [00:00:01 -183239.058990] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -182903.975593 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.225283,0.119990) (0.211565,0.256474) (0.260962,0.998407) (0.302190,2.177969) 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/O00571/4_raxmlng_ancestral/O00571.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00571/4_raxmlng_ancestral/O00571.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00571/4_raxmlng_ancestral/O00571.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O00571/4_raxmlng_ancestral/O00571.raxml.log Analysis started: 03-Jun-2021 02:09:32 / finished: 03-Jun-2021 02:10:17 Elapsed time: 45.118 seconds Consumed energy: 2.851 Wh