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 02:43:47 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35914/2_msa/P35914_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35914/3_mltree/P35914.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35914/4_raxmlng_ancestral/P35914 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677427 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/P35914/2_msa/P35914_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 325 sites WARNING: Sequences tr_B6QGX6_B6QGX6_TALMQ_441960 and tr_A0A093VA65_A0A093VA65_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B6QTB6_B6QTB6_TALMQ_441960 and tr_A0A093XVS8_A0A093XVS8_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W8A2_B2W8A2_PYRTR_426418 and tr_A0A2W1DJ28_A0A2W1DJ28_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A179URQ0_A0A179URQ0_BLAGS_559298 and tr_C5GEG0_C5GEG0_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2RBE6_H2RBE6_PANTR_9598 and sp_Q8TB92_HMGC2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_E9EPX3_E9EPX3_METRA_655844 and tr_A0A0B4IBT2_A0A0B4IBT2_METMF_1276143 are exactly identical! WARNING: Sequences tr_C6HJT4_C6HJT4_AJECH_544712 and tr_F0UJ77_F0UJ77_AJEC8_544711 are exactly identical! WARNING: Sequences sp_P35914_HMGCL_HUMAN_9606 and tr_A0A2R9B522_A0A2R9B522_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FJW7_A0A0E0FJW7_ORYNI_4536 and tr_B8AC86_B8AC86_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FJW7_A0A0E0FJW7_ORYNI_4536 and tr_Q0JNR8_Q0JNR8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H9Z8B6_H9Z8B6_MACMU_9544 and tr_A0A2K6DFK1_A0A2K6DFK1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7X581_G7X581_ASPKW_1033177 and tr_A0A146FLD3_A0A146FLD3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2ZB72_A2ZB72_ORYSI_39946 and tr_Q2RAU5_Q2RAU5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2ZHV1_A2ZHV1_ORYSI_39946 and tr_I1R3T0_I1R3T0_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2ZHV1_A2ZHV1_ORYSI_39946 and tr_A0A0E0RDF0_A0A0E0RDF0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_F4NT96_F4NT96_BATDJ_684364 and tr_A0A177WAV2_A0A177WAV2_BATDE_403673 are exactly identical! WARNING: Sequences tr_F2SKC3_F2SKC3_TRIRC_559305 and tr_A0A178ER47_A0A178ER47_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0D2XAN9_A0A0D2XAN9_FUSO4_426428 and tr_N4TQH4_N4TQH4_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0D2XAN9_A0A0D2XAN9_FUSO4_426428 and tr_X0CNT6_X0CNT6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2XAN9_A0A0D2XAN9_FUSO4_426428 and tr_A0A2H3SRV9_A0A2H3SRV9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_V2YM62_V2YM62_MONRO_1381753 and tr_A0A0W0ETL9_A0A0W0ETL9_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015M415_A0A015M415_9GLOM_1432141 and tr_A0A2H5RCX5_A0A2H5RCX5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2I3MZE1_A0A2I3MZE1_PAPAN_9555 and tr_A0A2K5YVZ8_A0A2K5YVZ8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3NHM1_A0A2I3NHM1_PAPAN_9555 and tr_A0A2K6D4X9_A0A2K6D4X9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3NHM1_A0A2I3NHM1_PAPAN_9555 and tr_A0A2K5XLI6_A0A2K5XLI6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A078HP35_A0A078HP35_BRANA_3708 and tr_A0A0D3B7F5_A0A0D3B7F5_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V4RY63_V4RY63_9ROSI_85681 and tr_A0A2H5N6D9_A0A2H5N6D9_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0F8UPT1_A0A0F8UPT1_9EURO_308745 and tr_A0A2T5M0T8_A0A2T5M0T8_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A091JWQ8_A0A091JWQ8_EGRGA_188379 and tr_A0A091VX88_A0A091VX88_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1S3XN17_A0A1S3XN17_TOBAC_4097 and tr_A0A1U7V1T6_A0A1U7V1T6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4D897_A0A1S4D897_TOBAC_4097 and tr_A0A1U7VC34_A0A1U7VC34_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2N5SCH8_A0A2N5SCH8_9BASI_200324 and tr_A0A2N5VWT8_A0A2N5VWT8_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2U4B170_A0A2U4B170_TURTR_9739 and tr_A0A2Y9P1R6_A0A2Y9P1R6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B170_A0A2U4B170_TURTR_9739 and tr_A0A2Y9SH96_A0A2Y9SH96_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 34 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/P35914/4_raxmlng_ancestral/P35914.raxml.reduced.phy Alignment comprises 1 partitions and 325 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 325 Gaps: 6.39 % Invariant sites: 1.23 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35914/4_raxmlng_ancestral/P35914.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/P35914/3_mltree/P35914.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 82 / 6560 [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: -147637.445671 [00:00:00 -147637.445671] Initial branch length optimization [00:00:00 -146328.007642] Model parameter optimization (eps = 0.100000) [00:00:24] Tree #1, final logLikelihood: -145914.854827 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.226002,0.264948) (0.308935,0.344324) (0.219219,1.059895) (0.245844,2.446260) 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/P35914/4_raxmlng_ancestral/P35914.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35914/4_raxmlng_ancestral/P35914.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35914/4_raxmlng_ancestral/P35914.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35914/4_raxmlng_ancestral/P35914.raxml.log Analysis started: 03-Jun-2021 02:43:47 / finished: 03-Jun-2021 02:44:15 Elapsed time: 27.868 seconds Consumed energy: 2.253 Wh