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 15:01:54 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P28799/2_msa/P28799_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P28799/3_mltree/P28799.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P28799/4_raxmlng_ancestral/P28799 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635314 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/P28799/2_msa/P28799_nogap_msa.fasta [00:00:00] Loaded alignment with 598 taxa and 593 sites WARNING: Sequences tr_A0A0E0H6P6_A0A0E0H6P6_ORYNI_4536 and tr_B8AVK3_B8AVK3_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H6P6_A0A0E0H6P6_ORYNI_4536 and tr_I1PQB7_I1PQB7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0H6P6_A0A0E0H6P6_ORYNI_4536 and tr_A0A0E0PEY1_A0A0E0PEY1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H6P6_A0A0E0H6P6_ORYNI_4536 and tr_A0A0D3G0Z7_A0A0D3G0Z7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0H6P6_A0A0E0H6P6_ORYNI_4536 and tr_A0A0D9ZRN4_A0A0D9ZRN4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0H6P6_A0A0E0H6P6_ORYNI_4536 and sp_P25776_ORYA_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0HGL1_A0A0E0HGL1_ORYNI_4536 and tr_A2Y6C6_A2Y6C6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HGL1_A0A0E0HGL1_ORYNI_4536 and tr_A0A0E0PPR3_A0A0E0PPR3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HGL1_A0A0E0HGL1_ORYNI_4536 and tr_Q6L4X7_Q6L4X7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2XYT1_A2XYT1_ORYSI_39946 and tr_I1PQR8_I1PQR8_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2XYT1_A2XYT1_ORYSI_39946 and tr_A0A0E0PFH1_A0A0E0PFH1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2XYT1_A2XYT1_ORYSI_39946 and tr_A0A0D3G1H2_A0A0D3G1H2_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2XYT1_A2XYT1_ORYSI_39946 and sp_P25777_ORYB_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A3Q0KSR3_A0A3Q0KSR3_SCHMA_6183 and tr_A0A3Q0KSR6_A0A3Q0KSR6_SCHMA_6183 are exactly identical! WARNING: Sequences tr_B3RQV7_B3RQV7_TRIAD_10228 and tr_A0A369S146_A0A369S146_9METZ_287889 are exactly identical! WARNING: Sequences tr_M8A017_M8A017_TRIUA_4572 and tr_Q0WXG7_Q0WXG7_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A078GKV6_A0A078GKV6_BRANA_3708 and tr_A0A0D3ATN6_A0A0D3ATN6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0V0X746_A0A0V0X746_9BILA_92179 and tr_A0A0V0VJI9_A0A0V0VJI9_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0X746_A0A0V0X746_9BILA_92179 and tr_A0A0V1L717_A0A0V1L717_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A1S3YIC8_A0A1S3YIC8_TOBAC_4097 and tr_A0A1U7WE69_A0A1U7WE69_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AAW5_A0A1S4AAW5_TOBAC_4097 and tr_A0A1U7W549_A0A1U7W549_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4B1Z6_A0A1S4B1Z6_TOBAC_4097 and tr_A0A1U7W4Z0_A0A1U7W4Z0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4C9J7_A0A1S4C9J7_TOBAC_4097 and tr_A0A1U7VY41_A0A1U7VY41_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CTT1_A0A1S4CTT1_TOBAC_4097 and tr_A0A1U7XZN2_A0A1U7XZN2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3RAE7_A0A1S3RAE7_SALSA_8030 and tr_C0HA53_C0HA53_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2D0PVP5_A0A2D0PVP5_ICTPU_7998 and tr_A0A2D0PX31_A0A2D0PX31_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SMB3_A0A2D0SMB3_ICTPU_7998 and tr_A0A2D0SMC1_A0A2D0SMC1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8E6T4_A0A1U8E6T4_CAPAN_4072 and tr_A0A2G3BVF2_A0A2G3BVF2_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 28 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/P28799/4_raxmlng_ancestral/P28799.raxml.reduced.phy Alignment comprises 1 partitions and 593 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 593 Gaps: 52.02 % Invariant sites: 0.51 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P28799/4_raxmlng_ancestral/P28799.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/P28799/3_mltree/P28799.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 149 / 11920 [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: -137211.558834 [00:00:00 -137211.558834] Initial branch length optimization [00:00:01 -134673.336289] Model parameter optimization (eps = 0.100000) [00:04:52] Tree #1, final logLikelihood: -134321.073810 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.175831,0.208530) (0.035757,0.375471) (0.419065,0.852703) (0.369347,1.604372) 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/P28799/4_raxmlng_ancestral/P28799.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P28799/4_raxmlng_ancestral/P28799.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P28799/4_raxmlng_ancestral/P28799.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P28799/4_raxmlng_ancestral/P28799.raxml.log Analysis started: 02-Jun-2021 15:01:54 / finished: 02-Jun-2021 15:07:03 Elapsed time: 308.495 seconds