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 13:35:55 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00558/2_msa/P00558_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00558/3_mltree/P00558.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00558/4_raxmlng_ancestral/P00558 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802955 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/P00558/2_msa/P00558_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 417 sites WARNING: Sequences tr_B6QS27_B6QS27_TALMQ_441960 and tr_A0A093VCW0_A0A093VCW0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2VTC1_B2VTC1_PYRTR_426418 and tr_A0A2W1HK85_A0A2W1HK85_9PLEO_45151 are exactly identical! WARNING: Sequences sp_Q5NVB5_PGK1_PONAB_9601 and tr_G7Q337_G7Q337_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q5NVB5_PGK1_PONAB_9601 and tr_A0A096NZ57_A0A096NZ57_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G2XCC3_G2XCC3_VERDV_498257 and tr_C9S883_C9S883_VERA1_526221 are exactly identical! WARNING: Sequences sp_P38667_PGK_NEUCR_367110 and tr_G4UM01_G4UM01_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q29KW9_Q29KW9_DROPS_46245 and tr_B4GSP3_B4GSP3_DROPE_7234 are exactly identical! WARNING: Sequences sp_A5A6K4_PGK1_PANTR_9598 and sp_P00558_PGK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A158NNB5_A0A158NNB5_ATTCE_12957 and tr_A0A195AV49_A0A195AV49_9HYME_520822 are exactly identical! WARNING: Sequences sp_P41756_PGK_ASPOR_510516 and tr_A0A1S9DJA1_A0A1S9DJA1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0GWR2_A0A0E0GWR2_ORYNI_4536 and tr_A2YG06_A2YG06_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GWR2_A0A0E0GWR2_ORYNI_4536 and tr_A0A0E0E560_A0A0E0E560_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GWR2_A0A0E0GWR2_ORYNI_4536 and tr_A0A0E0Q1D7_A0A0E0Q1D7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GWR2_A0A0E0GWR2_ORYNI_4536 and tr_Q655T1_Q655T1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QQE6_A2QQE6_ASPNC_425011 and tr_G3YG88_G3YG88_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7XRH4_G7XRH4_ASPKW_1033177 and tr_A0A146FVG0_A0A146FVG0_9EURO_1069201 are exactly identical! WARNING: Sequences tr_I1NXN0_I1NXN0_ORYGL_4538 and tr_A0A0E0CGA5_A0A0E0CGA5_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1NXN0_I1NXN0_ORYGL_4538 and tr_A0A0D9YMV6_A0A0D9YMV6_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F9X1L7_F9X1L7_ZYMTI_336722 and tr_A0A1X7RHU5_A0A1X7RHU5_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YFB4_G2YFB4_BOTF4_999810 and tr_M7TL22_M7TL22_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A8XEQ5_A8XEQ5_CAEBR_6238 and tr_A0A2G5VHM3_A0A2G5VHM3_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SRN7_F2SRN7_TRIRC_559305 and tr_A0A178EXT5_A0A178EXT5_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F2PS97_F2PS97_TRIEC_559882 and tr_A0A059JC36_A0A059JC36_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L2FNX9_L2FNX9_COLFN_1213859 and tr_T0M7C1_T0M7C1_COLGC_1237896 are exactly identical! WARNING: Sequences tr_S0EFJ9_S0EFJ9_GIBF5_1279085 and tr_N4U2Z2_N4U2Z2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_S0EFJ9_S0EFJ9_GIBF5_1279085 and tr_X0CFE7_X0CFE7_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_S0EFJ9_S0EFJ9_GIBF5_1279085 and tr_A0A2H3TQ98_A0A2H3TQ98_FUSOX_5507 are exactly identical! WARNING: Sequences tr_S0EFJ9_S0EFJ9_GIBF5_1279085 and tr_A0A2H3GV36_A0A2H3GV36_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W2R7Y3_W2R7Y3_PHYPN_761204 and tr_A0A0W8C1M5_A0A0W8C1M5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R7Y3_W2R7Y3_PHYPN_761204 and tr_W2GFK5_W2GFK5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015NGL4_A0A015NGL4_9GLOM_1432141 and tr_U9SVR8_U9SVR8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044SSE1_A0A044SSE1_ONCVO_6282 and tr_A0A182E8G5_A0A182E8G5_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A094GR12_A0A094GR12_9PEZI_1420912 and tr_A0A2P2SWX4_A0A2P2SWX4_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A151NNS5_A0A151NNS5_ALLMI_8496 and tr_A0A1U7S573_A0A1U7S573_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A117DZT2_A0A117DZT2_ASPNG_5061 and tr_A0A1L9NN92_A0A1L9NN92_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A165AN94_A0A165AN94_9HOMO_1314777 and tr_A0A166C2D4_A0A166C2D4_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3Z828_A0A1S3Z828_TOBAC_4097 and tr_A0A1J6INF9_A0A1J6INF9_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3Z828_A0A1S3Z828_TOBAC_4097 and tr_A0A1U7XH34_A0A1U7XH34_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CGR1_A0A1S4CGR1_TOBAC_4097 and tr_A0A1U7WUE6_A0A1U7WUE6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U8HDS2_A0A1U8HDS2_CAPAN_4072 and tr_A0A2G3C3B1_A0A2G3C3B1_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U3V9F2_A0A2U3V9F2_TURTR_9739 and tr_A0A2Y9P333_A0A2Y9P333_DELLE_9749 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/P00558/4_raxmlng_ancestral/P00558.raxml.reduced.phy Alignment comprises 1 partitions and 417 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 417 Gaps: 1.84 % Invariant sites: 3.12 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00558/4_raxmlng_ancestral/P00558.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/P00558/3_mltree/P00558.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 105 / 8400 [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: -141228.057361 [00:00:00 -141228.057361] Initial branch length optimization [00:00:01 -140874.028975] Model parameter optimization (eps = 0.100000) [00:00:25] Tree #1, final logLikelihood: -140649.087395 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.258027,0.251205) (0.329968,0.487100) (0.207807,1.012590) (0.204198,2.762177) 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/P00558/4_raxmlng_ancestral/P00558.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00558/4_raxmlng_ancestral/P00558.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00558/4_raxmlng_ancestral/P00558.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00558/4_raxmlng_ancestral/P00558.raxml.log Analysis started: 04-Jun-2021 13:35:55 / finished: 04-Jun-2021 13:36:23 Elapsed time: 28.774 seconds