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 01:57:42 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6VVB1/2_msa/Q6VVB1_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6VVB1/3_mltree/Q6VVB1.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6VVB1/4_raxmlng_ancestral/Q6VVB1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674662 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/Q6VVB1/2_msa/Q6VVB1_nogap_msa.fasta [00:00:00] Loaded alignment with 420 taxa and 395 sites WARNING: Sequences sp_Q8BGX0_TRI23_MOUSE_10090 and tr_G3HXI6_G3HXI6_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BGX0_TRI23_MOUSE_10090 and tr_A0A1U7Q6D0_A0A1U7Q6D0_MESAU_10036 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_G3S4J2_G3S4J2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_K7EUI7_K7EUI7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_K7BY84_K7BY84_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and sp_P36406_TRI23_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_F6WJZ1_F6WJZ1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_A0A2R8M518_A0A2R8M518_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_G7P7M3_G7P7M3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_A0A096MKZ5_A0A096MKZ5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_A0A0D9RTT3_A0A0D9RTT3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_A0A2K5M550_A0A2K5M550_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_A0A2K6D2J5_A0A2K6D2J5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_A0A2K6A039_A0A2K6A039_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QTP4_G1QTP4_NOMLE_61853 and tr_A0A2R8ZUA0_A0A2R8ZUA0_PANPA_9597 are exactly identical! WARNING: Sequences tr_O62463_O62463_CAEEL_6239 and tr_O62464_O62464_CAEEL_6239 are exactly identical! WARNING: Sequences tr_H2QSC5_H2QSC5_PANTR_9598 and sp_Q6VVB1_NHLC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6UAM5_F6UAM5_HORSE_9796 and tr_G3T9J9_G3T9J9_LOXAF_9785 are exactly identical! WARNING: Sequences tr_A0A158NKM3_A0A158NKM3_ATTCE_12957 and tr_F4WWF6_F4WWF6_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NKM3_A0A158NKM3_ATTCE_12957 and tr_A0A195DGC2_A0A195DGC2_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NKM3_A0A158NKM3_ATTCE_12957 and tr_A0A195BLZ2_A0A195BLZ2_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NKM3_A0A158NKM3_ATTCE_12957 and tr_A0A195FC93_A0A195FC93_9HYME_34720 are exactly identical! WARNING: Sequences tr_I3KE63_I3KE63_ORENI_8128 and tr_A0A2I4CHE1_A0A2I4CHE1_9TELE_52670 are exactly identical! WARNING: Sequences tr_F6TPH3_F6TPH3_MACMU_9544 and tr_A0A2K6AM39_A0A2K6AM39_MACNE_9545 are exactly identical! WARNING: Sequences tr_G0N805_G0N805_CAEBE_135651 and tr_G0PAZ9_G0PAZ9_CAEBE_135651 are exactly identical! WARNING: Sequences tr_F1SKT5_F1SKT5_PIG_9823 and tr_A0A2Y9EJN0_A0A2Y9EJN0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A091JPL1_A0A091JPL1_EGRGA_188379 and tr_A0A087QSB5_A0A087QSB5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091KFX4_A0A091KFX4_EGRGA_188379 and tr_A0A091UUL7_A0A091UUL7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091KFX4_A0A091KFX4_EGRGA_188379 and tr_A0A087QP33_A0A087QP33_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091KFX4_A0A091KFX4_EGRGA_188379 and tr_A0A093HLK7_A0A093HLK7_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091KFX4_A0A091KFX4_EGRGA_188379 and tr_A0A091WSX1_A0A091WSX1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091KFX4_A0A091KFX4_EGRGA_188379 and tr_A0A093GGN1_A0A093GGN1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0V1CIM8_A0A0V1CIM8_TRIBR_45882 and tr_A0A0V1KXY4_A0A0V1KXY4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A1S3KUM6_A0A1S3KUM6_SALSA_8030 and tr_A0A060XTI9_A0A060XTI9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226N177_A0A226N177_CALSU_9009 and tr_A0A226PFK8_A0A226PFK8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5KIJ3_A0A2K5KIJ3_CERAT_9531 and tr_A0A2K5XU85_A0A2K5XU85_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3W2P1_A0A2U3W2P1_ODORO_9708 and tr_A0A2U3XM74_A0A2U3XM74_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3W2P1_A0A2U3W2P1_ODORO_9708 and tr_A0A2Y9KRF4_A0A2Y9KRF4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3W2P1_A0A2U3W2P1_ODORO_9708 and tr_A0A384C5C3_A0A384C5C3_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 39 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/Q6VVB1/4_raxmlng_ancestral/Q6VVB1.raxml.reduced.phy Alignment comprises 1 partitions and 395 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 395 Gaps: 50.41 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6VVB1/4_raxmlng_ancestral/Q6VVB1.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/Q6VVB1/3_mltree/Q6VVB1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 99 / 7920 [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: -96300.127828 [00:00:00 -96300.127828] Initial branch length optimization [00:00:00 -76673.840100] Model parameter optimization (eps = 0.100000) [00:00:23] Tree #1, final logLikelihood: -76479.493595 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.051251,0.127692) (0.143534,0.580226) (0.512507,0.825175) (0.292708,1.664681) 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/Q6VVB1/4_raxmlng_ancestral/Q6VVB1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6VVB1/4_raxmlng_ancestral/Q6VVB1.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6VVB1/4_raxmlng_ancestral/Q6VVB1.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q6VVB1/4_raxmlng_ancestral/Q6VVB1.raxml.log Analysis started: 03-Jun-2021 01:57:42 / finished: 03-Jun-2021 01:58:07 Elapsed time: 24.988 seconds Consumed energy: 1.567 Wh