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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:33:20 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/2_msa/P53675_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/3_mltree/P53675.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/4_raxmlng_ancestral/P53675 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802800 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/2_msa/P53675_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1640 sites WARNING: Sequences tr_M3YUU0_M3YUU0_MUSPF_9669 and tr_F1PHQ0_F1PHQ0_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YUU0_M3YUU0_MUSPF_9669 and tr_G1LYK1_G1LYK1_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YUU0_M3YUU0_MUSPF_9669 and tr_A0A2U3ZD19_A0A2U3ZD19_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YUU0_M3YUU0_MUSPF_9669 and tr_A0A2Y9JVL6_A0A2Y9JVL6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YUU0_M3YUU0_MUSPF_9669 and tr_A0A384CGV2_A0A384CGV2_URSMA_29073 are exactly identical! WARNING: Sequences tr_B2WFT5_B2WFT5_PYRTR_426418 and tr_A0A2W1GKR7_A0A2W1GKR7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_K7CCE3_K7CCE3_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_F7BV85_F7BV85_HORSE_9796 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_A0A287CWD0_A0A287CWD0_ICTTR_43179 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_H0V5M6_H0V5M6_CAVPO_10141 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and sp_Q00610_CLH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_C0MHR2_C0MHR2_PIG_9823 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and sp_P49951_CLH1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_A0A2K5N5L8_A0A2K5N5L8_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_A0A2K6B2Q2_A0A2K6B2Q2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_A0A2R9A770_A0A2R9A770_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_A0A2Y9LHQ9_A0A2Y9LHQ9_DELLE_9749 are exactly identical! WARNING: Sequences tr_H2NV97_H2NV97_PONAB_9601 and tr_A0A2Y9FGX5_A0A2Y9FGX5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A179UE75_A0A179UE75_BLAGS_559298 and tr_C5GFT9_C5GFT9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A088AFV6_A0A088AFV6_APIME_7460 and tr_A0A2A3EGM9_A0A2A3EGM9_APICC_94128 are exactly identical! WARNING: Sequences tr_F4P544_F4P544_BATDJ_684364 and tr_A0A177WFV8_A0A177WFV8_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1QX03_I1QX03_ORYGL_4538 and sp_Q2RBN7_CLH1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G3T424_G3T424_LOXAF_9785 and tr_F7IN80_F7IN80_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3T424_G3T424_LOXAF_9785 and tr_G7PUH3_G7PUH3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3T424_G3T424_LOXAF_9785 and tr_A0A096P4W8_A0A096P4W8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3T424_G3T424_LOXAF_9785 and tr_A0A2K5YCA4_A0A2K5YCA4_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZEW3_H0ZEW3_TAEGU_59729 and tr_A0A218V2S7_A0A218V2S7_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4WYV9_F4WYV9_ACREC_103372 and tr_A0A151XD26_A0A151XD26_9HYME_64791 are exactly identical! WARNING: Sequences tr_G2XND8_G2XND8_BOTF4_999810 and tr_M7U469_M7U469_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_L2GA17_L2GA17_COLFN_1213859 and tr_T0KK29_T0KK29_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M3X4Z2_M3X4Z2_FELCA_9685 and tr_A0A2U3Y9H5_A0A2U3Y9H5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M8A710_M8A710_TRIUA_4572 and tr_A0A3B6KGD4_A0A3B6KGD4_WHEAT_4565 are exactly identical! WARNING: Sequences tr_N4UH02_N4UH02_FUSC1_1229664 and tr_X0CVE2_X0CVE2_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4UH02_N4UH02_FUSC1_1229664 and tr_A0A2H3THK5_A0A2H3THK5_FUSOX_5507 are exactly identical! WARNING: Sequences tr_N4UH02_N4UH02_FUSC1_1229664 and tr_A0A2H3GJB1_A0A2H3GJB1_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W2Q8W4_W2Q8W4_PHYPN_761204 and tr_A0A0W8DE01_A0A0W8DE01_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2Q8W4_W2Q8W4_PHYPN_761204 and tr_W2L890_W2L890_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A091IWI5_A0A091IWI5_EGRGA_188379 and tr_A0A091UKR7_A0A091UKR7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IWI5_A0A091IWI5_EGRGA_188379 and tr_A0A087R026_A0A087R026_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IWI5_A0A091IWI5_EGRGA_188379 and tr_A0A093HC19_A0A093HC19_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091IWI5_A0A091IWI5_EGRGA_188379 and tr_A0A0A0AD00_A0A0A0AD00_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IWI5_A0A091IWI5_EGRGA_188379 and tr_A0A091HUU4_A0A091HUU4_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V0WAJ7_A0A0V0WAJ7_9BILA_92179 and tr_A0A0V1LAN9_A0A0V1LAN9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0VC77_A0A0V0VC77_9BILA_181606 and tr_A0A0V1NJ99_A0A0V1NJ99_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0VC77_A0A0V0VC77_9BILA_181606 and tr_A0A0V0TI53_A0A0V0TI53_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A195EBM7_A0A195EBM7_9HYME_471704 and tr_A0A195FAE3_A0A195FAE3_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S4D5H1_A0A1S4D5H1_TOBAC_4097 and tr_A0A1U7XJ43_A0A1U7XJ43_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3HMW6_A0A1S3HMW6_LINUN_7574 and tr_A0A1S3HP93_A0A1S3HP93_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A226NCB6_A0A226NCB6_CALSU_9009 and tr_A0A226PGH1_A0A226PGH1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SU34_A0A2D0SU34_ICTPU_7998 and tr_A0A2D0SUP0_A0A2D0SUP0_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 50 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/4_raxmlng_ancestral/P53675.raxml.reduced.phy Alignment comprises 1 partitions and 1640 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1640 Gaps: 1.38 % Invariant sites: 1.10 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/4_raxmlng_ancestral/P53675.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/3_mltree/P53675.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 410 / 32800 [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: -389446.794896 [00:00:00 -389446.794896] Initial branch length optimization [00:00:03 -389165.842412] Model parameter optimization (eps = 0.100000) [00:01:24] Tree #1, final logLikelihood: -387454.835501 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.352861,0.444400) (0.290484,0.677397) (0.208722,1.227571) (0.147933,2.637638) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/4_raxmlng_ancestral/P53675.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/4_raxmlng_ancestral/P53675.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/4_raxmlng_ancestral/P53675.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53675/4_raxmlng_ancestral/P53675.raxml.log Analysis started: 04-Jun-2021 13:33:20 / finished: 04-Jun-2021 13:34:59 Elapsed time: 99.584 seconds