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 13:34:12 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99714/2_msa/Q99714_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99714/3_mltree/Q99714.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99714/4_raxmlng_ancestral/Q99714 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802852 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/Q99714/2_msa/Q99714_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 261 sites WARNING: Sequences tr_M3Y8E7_M3Y8E7_MUSPF_9669 and tr_A0A2Y9KFB7_A0A2Y9KFB7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B2W4Z9_B2W4Z9_PYRTR_426418 and tr_A0A2W1DH66_A0A2W1DH66_9PLEO_45151 are exactly identical! WARNING: Sequences tr_Q29H71_Q29H71_DROPS_46245 and tr_B4H078_B4H078_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QSS7_H2QSS7_PANTR_9598 and sp_Q92506_DHB8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QSS7_H2QSS7_PANTR_9598 and tr_A0A2R9ALS4_A0A2R9ALS4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QYN3_H2QYN3_PANTR_9598 and sp_Q99714_HCD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QYN3_H2QYN3_PANTR_9598 and tr_A0A2R9ANQ0_A0A2R9ANQ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R3K8_H2R3K8_PANTR_9598 and tr_A0A2R9BGS9_A0A2R9BGS9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FUP9_F9FUP9_FUSOF_660025 and tr_A0A0D2XB82_A0A0D2XB82_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FUP9_F9FUP9_FUSOF_660025 and tr_N4TVK1_N4TVK1_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FUP9_F9FUP9_FUSOF_660025 and tr_A0A2H3SRB6_A0A2H3SRB6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_C6HFH5_C6HFH5_AJECH_544712 and tr_F0UPC9_F0UPC9_AJEC8_544711 are exactly identical! WARNING: Sequences tr_K3XYD1_K3XYD1_SETIT_4555 and tr_K3YIQ0_K3YIQ0_SETIT_4555 are exactly identical! WARNING: Sequences tr_A2QZI1_A2QZI1_ASPNC_425011 and tr_G3XVL9_G3XVL9_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QZI1_A2QZI1_ASPNC_425011 and tr_A0A319A9D5_A0A319A9D5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7H1H7_F7H1H7_MACMU_9544 and tr_Q4JK74_Q4JK74_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H1H7_F7H1H7_MACMU_9544 and tr_A0A0D9RJE2_A0A0D9RJE2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7MSA6_G7MSA6_MACMU_9544 and tr_G8F422_G8F422_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MSA6_G7MSA6_MACMU_9544 and tr_A0A0D9S226_A0A0D9S226_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7MSA6_G7MSA6_MACMU_9544 and tr_A0A2K5P344_A0A2K5P344_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MSA6_G7MSA6_MACMU_9544 and tr_A0A2K5Y394_A0A2K5Y394_MANLE_9568 are exactly identical! WARNING: Sequences tr_B8BP22_B8BP22_ORYSI_39946 and tr_I1R576_I1R576_ORYGL_4538 are exactly identical! WARNING: Sequences tr_G2YP32_G2YP32_BOTF4_999810 and tr_M7TGJ4_M7TGJ4_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_B3RSU4_B3RSU4_TRIAD_10228 and tr_A0A369SFX6_A0A369SFX6_9METZ_287889 are exactly identical! WARNING: Sequences tr_V2XL34_V2XL34_MONRO_1381753 and tr_A0A0W0G1K2_A0A0W0G1K2_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2REK3_W2REK3_PHYPN_761204 and tr_A0A0W8BXV2_A0A0W8BXV2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2REK3_W2REK3_PHYPN_761204 and tr_W2H2V5_W2H2V5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015J437_A0A015J437_9GLOM_1432141 and tr_A0A2H5SE01_A0A2H5SE01_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015KW66_A0A015KW66_9GLOM_1432141 and tr_A0A2H5SE07_A0A2H5SE07_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015MBS6_A0A015MBS6_9GLOM_1432141 and tr_A0A2I1H618_A0A2I1H618_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015MBS6_A0A015MBS6_9GLOM_1432141 and tr_A0A2H5SE53_A0A2H5SE53_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096NBK4_A0A096NBK4_PAPAN_9555 and tr_A0A2K5MB01_A0A2K5MB01_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NBK4_A0A096NBK4_PAPAN_9555 and tr_A0A2K5ZGZ9_A0A2K5ZGZ9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094EHM4_A0A094EHM4_9PEZI_1420912 and tr_A0A2P2SXW7_A0A2P2SXW7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094GYQ8_A0A094GYQ8_9PEZI_1420912 and tr_A0A1B8GQA6_A0A1B8GQA6_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A2VPW7_A0A0A2VPW7_BEABA_1245745 and tr_A0A2N6NU05_A0A2N6NU05_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0D2PUF3_A0A0D2PUF3_GOSRA_29730 and tr_A0A1U8JW26_A0A1U8JW26_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F8TY08_A0A0F8TY08_9EURO_308745 and tr_A0A2T5LXV3_A0A2T5LXV3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A164VQU5_A0A164VQU5_9HOMO_1314777 and tr_A0A166CYK1_A0A166CYK1_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3XFF8_A0A1S3XFF8_TOBAC_4097 and tr_A0A1U7XIY3_A0A1U7XIY3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZI83_A0A1S3ZI83_TOBAC_4097 and tr_A0A1U7V1U8_A0A1U7V1U8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1Y2F616_A0A1Y2F616_9BASI_106004 and tr_A0A1Y2F6M8_A0A1Y2F6M8_9BASI_106004 are exactly identical! WARNING: Sequences tr_A0A226MBQ5_A0A226MBQ5_CALSU_9009 and tr_A0A226PAR7_A0A226PAR7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3B4Y4_A0A2H3B4Y4_9AGAR_1076256 and tr_A0A284R3S2_A0A284R3S2_9AGAR_47428 are exactly identical! WARNING: Duplicate sequences found: 44 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/Q99714/4_raxmlng_ancestral/Q99714.raxml.reduced.phy Alignment comprises 1 partitions and 261 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 261 Gaps: 10.13 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99714/4_raxmlng_ancestral/Q99714.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/Q99714/3_mltree/Q99714.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 66 / 5280 [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: -152499.433040 [00:00:00 -152499.433040] Initial branch length optimization [00:00:00 -151388.291768] Model parameter optimization (eps = 0.100000) [00:00:29] Tree #1, final logLikelihood: -150805.778288 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.175989,0.375698) (0.306839,0.456110) (0.287438,1.025063) (0.229734,2.173328) 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/Q99714/4_raxmlng_ancestral/Q99714.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99714/4_raxmlng_ancestral/Q99714.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99714/4_raxmlng_ancestral/Q99714.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99714/4_raxmlng_ancestral/Q99714.raxml.log Analysis started: 04-Jun-2021 13:34:12 / finished: 04-Jun-2021 13:34:44 Elapsed time: 31.557 seconds