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 02-Jun-2021 14:08:33 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34949/2_msa/P34949_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34949/3_mltree/P34949.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34949/4_raxmlng_ancestral/P34949 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622632113 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/P34949/2_msa/P34949_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 423 sites WARNING: Sequences tr_A0A0E1RWF9_A0A0E1RWF9_COCIM_246410 and tr_A0A0J7AZN5_A0A0J7AZN5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WJ39_B2WJ39_PYRTR_426418 and tr_A0A2W1D3T3_A0A2W1D3T3_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3RFM0_G3RFM0_GORGO_9595 and sp_P34949_MPI_HUMAN_9606 are exactly identical! WARNING: Sequences tr_C6HT72_C6HT72_AJECH_544712 and tr_F0USY6_F0USY6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0IIT4_A0A0E0IIT4_ORYNI_4536 and tr_A2Z0W7_A2Z0W7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IIT4_A0A0E0IIT4_ORYNI_4536 and tr_A0A0D3H6E6_A0A0D3H6E6_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0J531_A0A0E0J531_ORYNI_4536 and tr_A2ZFV6_A2ZFV6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0J531_A0A0E0J531_ORYNI_4536 and tr_I1R1F9_I1R1F9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0J531_A0A0E0J531_ORYNI_4536 and tr_A0A0E0RAL2_A0A0E0RAL2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0J531_A0A0E0J531_ORYNI_4536 and tr_A0A0D3HNQ9_A0A0D3HNQ9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0K0J3Y0_A0A0K0J3Y0_BRUMA_6279 and tr_A0A0N4TP76_A0A0N4TP76_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0J3Y0_A0A0K0J3Y0_BRUMA_6279 and tr_A0A0R3QUK4_A0A0R3QUK4_9BILA_42155 are exactly identical! WARNING: Sequences tr_A2QRK4_A2QRK4_ASPNC_425011 and tr_G3YHJ0_G3YHJ0_ASPNA_380704 are exactly identical! WARNING: Sequences tr_F4P4N2_F4P4N2_BATDJ_684364 and tr_A0A177WG67_A0A177WG67_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1NJX4_I1NJX4_ORYGL_4538 and tr_A0A0D3EJ62_A0A0D3EJ62_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_F9X0M3_F9X0M3_ZYMTI_336722 and tr_A0A1X7RGZ1_A0A1X7RGZ1_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2SP97_F2SP97_TRIRC_559305 and tr_A0A178F1S0_A0A178F1S0_TRIRU_5551 are exactly identical! WARNING: Sequences tr_M4EYY7_M4EYY7_BRARP_51351 and tr_A0A078FHG5_A0A078FHG5_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4FDL0_M4FDL0_BRARP_51351 and tr_A0A078I0X7_A0A078I0X7_BRANA_3708 are exactly identical! WARNING: Sequences tr_N4UPL2_N4UPL2_FUSC1_1229664 and tr_X0CSK2_X0CSK2_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_V2X688_V2X688_MONRO_1381753 and tr_A0A0W0FB66_A0A0W0FB66_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PZD5_W2PZD5_PHYPN_761204 and tr_A0A0W8CXW1_A0A0W8CXW1_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PZD5_W2PZD5_PHYPN_761204 and tr_W2KVB3_W2KVB3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015IMS9_A0A015IMS9_9GLOM_1432141 and tr_A0A2I1G1F5_A0A2I1G1F5_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015IMS9_A0A015IMS9_9GLOM_1432141 and tr_U9TCG9_U9TCG9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2K6WBK9_A0A2K6WBK9_ONCVO_6282 and tr_A0A182EBA0_A0A182EBA0_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0A1NBG4_A0A0A1NBG4_9FUNG_58291 and tr_A0A367JY13_A0A367JY13_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A164VD74_A0A164VD74_9HOMO_1314777 and tr_A0A165Z273_A0A165Z273_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S4AHD4_A0A1S4AHD4_TOBAC_4097 and tr_A0A1U7V4M4_A0A1U7V4M4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2S7QJ57_A0A2S7QJ57_9HELO_2070414 and tr_A0A2S7P0N4_A0A2S7P0N4_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2V5IUR2_A0A2V5IUR2_9EURO_1450541 and tr_A0A2V5HJI1_A0A2V5HJI1_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 31 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/P34949/4_raxmlng_ancestral/P34949.raxml.reduced.phy Alignment comprises 1 partitions and 423 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 423 Gaps: 6.85 % Invariant sites: 1.18 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34949/4_raxmlng_ancestral/P34949.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/P34949/3_mltree/P34949.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 106 / 8480 [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: -241438.783521 [00:00:00 -241438.783521] Initial branch length optimization [00:00:01 -240837.933531] Model parameter optimization (eps = 0.100000) [00:00:11] Tree #1, final logLikelihood: -240829.823214 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.182733,0.118623) (0.243506,0.412942) (0.256624,0.866156) (0.317138,2.066904) 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/P34949/4_raxmlng_ancestral/P34949.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34949/4_raxmlng_ancestral/P34949.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34949/4_raxmlng_ancestral/P34949.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34949/4_raxmlng_ancestral/P34949.raxml.log Analysis started: 02-Jun-2021 14:08:33 / finished: 02-Jun-2021 14:08:48 Elapsed time: 14.978 seconds