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 14:20:53 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P31040/2_msa/P31040_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P31040/3_mltree/P31040.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P31040/4_raxmlng_ancestral/P31040 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805653 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/P31040/2_msa/P31040_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 664 sites WARNING: Sequences tr_E3RDZ9_E3RDZ9_PYRTT_861557 and tr_B2WDQ3_B2WDQ3_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3RDZ9_E3RDZ9_PYRTT_861557 and tr_A0A2W1GKD4_A0A2W1GKD4_9PLEO_45151 are exactly identical! WARNING: Sequences tr_J3KL57_J3KL57_COCIM_246410 and tr_A0A0J6YRK3_A0A0J6YRK3_COCIT_404692 are exactly identical! WARNING: Sequences tr_A7UWT5_A7UWT5_NEUCR_367110 and tr_G4UCE2_G4UCE2_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q292E4_Q292E4_DROPS_46245 and tr_B4GDN2_B4GDN2_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NTR8_B8NTR8_ASPFN_332952 and tr_Q2U4B1_Q2U4B1_ASPOR_510516 are exactly identical! WARNING: Sequences tr_J5K0V1_J5K0V1_BEAB2_655819 and tr_A0A0A2W1I9_A0A0A2W1I9_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A0E0GJZ6_A0A0E0GJZ6_ORYNI_4536 and tr_B8B729_B8B729_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GJZ6_A0A0E0GJZ6_ORYNI_4536 and tr_A0A0E0Q3S1_A0A0E0Q3S1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GJZ6_A0A0E0GJZ6_ORYNI_4536 and tr_A0A0E0AK20_A0A0E0AK20_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GJZ6_A0A0E0GJZ6_ORYNI_4536 and sp_Q6ZDY8_SDHA_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QEZ7_A2QEZ7_ASPNC_425011 and tr_G3Y2B9_G3Y2B9_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QEZ7_A2QEZ7_ASPNC_425011 and tr_A0A319AS23_A0A319AS23_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F4P8I9_F4P8I9_BATDJ_684364 and tr_A0A177WVX9_A0A177WVX9_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9WWR1_F9WWR1_ZYMTI_336722 and tr_A0A1X7RFW3_A0A1X7RFW3_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F9XAC6_F9XAC6_ZYMTI_336722 and tr_A0A1X7RSM2_A0A1X7RSM2_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2SJ90_F2SJ90_TRIRC_559305 and tr_A0A178F329_A0A178F329_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0D2XCC1_A0A0D2XCC1_FUSO4_426428 and tr_X0D9R6_X0D9R6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2XCC1_A0A0D2XCC1_FUSO4_426428 and tr_A0A2H3T5A7_A0A2H3T5A7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_S0DST7_S0DST7_GIBF5_1279085 and tr_A0A365MQG5_A0A365MQG5_GIBIN_948311 are exactly identical! WARNING: Sequences tr_M2T9D7_M2T9D7_COCH5_701091 and tr_W6YPE3_W6YPE3_COCCA_930089 are exactly identical! WARNING: Sequences tr_V2XJM2_V2XJM2_MONRO_1381753 and tr_A0A0W0FU34_A0A0W0FU34_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RDR6_W2RDR6_PHYPN_761204 and tr_A0A0W8CNF5_A0A0W8CNF5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RDR6_W2RDR6_PHYPN_761204 and tr_W2M498_W2M498_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015KTZ6_A0A015KTZ6_9GLOM_1432141 and tr_A0A2I1EYQ5_A0A2I1EYQ5_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015KTZ6_A0A015KTZ6_9GLOM_1432141 and tr_A0A2H5U282_A0A2H5U282_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A078GZX6_A0A078GZX6_BRANA_3708 and tr_A0A078IV31_A0A078IV31_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A078GZX6_A0A078GZX6_BRANA_3708 and tr_A0A0D3D8D6_A0A0D3D8D6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094DTU1_A0A094DTU1_9PEZI_1420912 and tr_A0A1B8GH13_A0A1B8GH13_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094DTU1_A0A094DTU1_9PEZI_1420912 and tr_A0A1B8CJM7_A0A1B8CJM7_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A094DTU1_A0A094DTU1_9PEZI_1420912 and tr_A0A1B8FA64_A0A1B8FA64_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_V4SED1_V4SED1_9ROSI_85681 and tr_A0A2H5NRL5_A0A2H5NRL5_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0B4HXH2_A0A0B4HXH2_METMF_1276143 and tr_A0A0D9P9S6_A0A0D9P9S6_METAN_1291518 are exactly identical! WARNING: Sequences tr_A0A0F8XRV8_A0A0F8XRV8_9EURO_308745 and tr_A0A2T5LYS2_A0A2T5LYS2_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V0X3G4_A0A0V0X3G4_9BILA_92179 and tr_A0A0V1LID5_A0A0V1LID5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A117E3A0_A0A117E3A0_ASPNG_5061 and tr_A0A1L9N922_A0A1L9N922_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A165AFL7_A0A165AFL7_9HOMO_1314777 and tr_A0A166IY68_A0A166IY68_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3YKI8_A0A1S3YKI8_TOBAC_4097 and tr_A0A1U7Y5Z6_A0A1U7Y5Z6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226NFK0_A0A226NFK0_CALSU_9009 and tr_A0A226P9V0_A0A226P9V0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3C869_A0A2H3C869_9AGAR_1076256 and tr_A0A284QV24_A0A284QV24_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2V5IAE3_A0A2V5IAE3_9EURO_1450541 and tr_A0A2V5GV31_A0A2V5GV31_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 41 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/P31040/4_raxmlng_ancestral/P31040.raxml.reduced.phy Alignment comprises 1 partitions and 664 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 664 Gaps: 6.01 % Invariant sites: 8.58 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P31040/4_raxmlng_ancestral/P31040.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/P31040/3_mltree/P31040.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: -171323.814881 [00:00:00 -171323.814881] Initial branch length optimization [00:00:01 -170799.118922] Model parameter optimization (eps = 0.100000) [00:00:35] Tree #1, final logLikelihood: -170387.510800 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.309127,0.251896) (0.362212,0.462374) (0.175854,1.266112) (0.152808,3.481526) 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/P31040/4_raxmlng_ancestral/P31040.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P31040/4_raxmlng_ancestral/P31040.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P31040/4_raxmlng_ancestral/P31040.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P31040/4_raxmlng_ancestral/P31040.raxml.log Analysis started: 04-Jun-2021 14:20:53 / finished: 04-Jun-2021 14:21:35 Elapsed time: 41.449 seconds