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 13:38:29 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P49792/2_msa/P49792_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P49792/3_mltree/P49792.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P49792/4_raxmlng_ancestral/P49792 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803109 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/P49792/2_msa/P49792_nogap_msa.fasta [00:00:00] Loaded alignment with 963 taxa and 3224 sites WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and sp_Q0ZQL0_PPIA_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and sp_Q0ZQL1_PPIA_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and sp_P62937_PPIA_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and sp_P62940_PPIA_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and tr_G7PWP2_G7PWP2_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and sp_P62941_PPIA_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and tr_A0A0D9RT22_A0A0D9RT22_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q0ZQK7_PPIA_NOMLE_61853 and sp_Q0ZQL2_PPIA_PANPA_9597 are exactly identical! WARNING: Sequences tr_B2WMD5_B2WMD5_PYRTR_426418 and tr_A0A2W1F917_A0A2W1F917_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8NM00_B8NM00_ASPFN_332952 and tr_Q2U5W2_Q2U5W2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NM00_B8NM00_ASPFN_332952 and tr_A0A1S9D883_A0A1S9D883_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A2K6HGX5_A0A2K6HGX5_PANTR_9598 and tr_A0A2R9A2X4_A0A2R9A2X4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A088A8D4_A0A088A8D4_APIME_7460 and tr_A0A2A3EAB9_A0A2A3EAB9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NHS7_A0A158NHS7_ATTCE_12957 and tr_F4WCN7_F4WCN7_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A0K0K0J4_A0A0K0K0J4_BRUMA_6279 and tr_A0A0N4T521_A0A0N4T521_BRUPA_6280 are exactly identical! WARNING: Sequences sp_P62936_PPIA_PIG_9823 and sp_P62935_PPIA_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P62936_PPIA_PIG_9823 and tr_A0A2U3WX41_A0A2U3WX41_ODORO_9708 are exactly identical! WARNING: Sequences tr_A8WY38_A8WY38_CAEBR_6238 and tr_A0A2G5TN92_A0A2G5TN92_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B3RVS0_B3RVS0_TRIAD_10228 and tr_A0A369SJS9_A0A369SJS9_9METZ_287889 are exactly identical! WARNING: Sequences tr_M4D2M5_M4D2M5_BRARP_51351 and tr_A0A078DMP0_A0A078DMP0_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4EXN7_M4EXN7_BRARP_51351 and tr_A0A078GAL1_A0A078GAL1_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4F885_M4F885_BRARP_51351 and tr_A0A078IDN6_A0A078IDN6_BRANA_3708 are exactly identical! WARNING: Sequences tr_U3JWP1_U3JWP1_FICAL_59894 and tr_A0A091F797_A0A091F797_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3JWP1_U3JWP1_FICAL_59894 and tr_A0A093QP66_A0A093QP66_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3JWP1_U3JWP1_FICAL_59894 and tr_A0A0A0AHF8_A0A0A0AHF8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A044R7X9_A0A044R7X9_ONCVO_6282 and tr_A0A182EG70_A0A182EG70_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096P4H0_A0A096P4H0_PAPAN_9555 and tr_A0A0D9RAD8_A0A0D9RAD8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P4H0_A0A096P4H0_PAPAN_9555 and tr_A0A2K5NGX0_A0A2K5NGX0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P4H0_A0A096P4H0_PAPAN_9555 and tr_A0A2K6BAX8_A0A2K6BAX8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A078GNF2_A0A078GNF2_BRANA_3708 and tr_A0A0D3E317_A0A0D3E317_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0D2TQ56_A0A0D2TQ56_GOSRA_29730 and tr_A0A1U8IUI3_A0A1U8IUI3_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2TWE2_A0A0D2TWE2_GOSRA_29730 and tr_A0A1U8N910_A0A1U8N910_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F8W8Y4_A0A0F8W8Y4_9EURO_308745 and tr_A0A2T5M0F3_A0A2T5M0F3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A091JF81_A0A091JF81_EGRGA_188379 and tr_A0A091UM35_A0A091UM35_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JF81_A0A091JF81_EGRGA_188379 and tr_A0A087QUL8_A0A087QUL8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0V1CD67_A0A0V1CD67_TRIBR_45882 and tr_A0A0V1NQ80_A0A0V1NQ80_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CD67_A0A0V1CD67_TRIBR_45882 and tr_A0A0V0TIN0_A0A0V0TIN0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A151XAA5_A0A151XAA5_9HYME_64791 and tr_A0A195AUN3_A0A195AUN3_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1S4A196_A0A1S4A196_TOBAC_4097 and tr_A0A1J6L2N8_A0A1J6L2N8_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4A196_A0A1S4A196_TOBAC_4097 and tr_A0A1U7XG51_A0A1U7XG51_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4ABZ9_A0A1S4ABZ9_TOBAC_4097 and tr_A0A1J6KKB4_A0A1J6KKB4_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4ABZ9_A0A1S4ABZ9_TOBAC_4097 and tr_A0A1U7VBP4_A0A1U7VBP4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3NYT1_A0A1S3NYT1_SALSA_8030 and tr_A0A1S3NYW4_A0A1S3NYW4_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MEL2_A0A226MEL2_CALSU_9009 and tr_A0A226P3A0_A0A226P3A0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3V8D9_A0A2U3V8D9_TURTR_9739 and tr_A0A2Y9PUE1_A0A2Y9PUE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V8D9_A0A2U3V8D9_TURTR_9739 and tr_A0A384AK70_A0A384AK70_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 46 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/P49792/4_raxmlng_ancestral/P49792.raxml.reduced.phy Alignment comprises 1 partitions and 3224 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 3224 Gaps: 85.07 % Invariant sites: 2.79 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P49792/4_raxmlng_ancestral/P49792.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/P49792/3_mltree/P49792.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 806 / 64480 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:01] Tree #1, initial LogLikelihood: -325247.303040 [00:00:02 -325247.303040] Initial branch length optimization [00:01:36 -279908.267466] Model parameter optimization (eps = 0.100000) [00:08:39] Tree #1, final logLikelihood: -278339.448338 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.180697,0.418151) (0.159596,0.936054) (0.324102,0.674040) (0.335605,1.658476) 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/P49792/4_raxmlng_ancestral/P49792.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P49792/4_raxmlng_ancestral/P49792.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P49792/4_raxmlng_ancestral/P49792.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P49792/4_raxmlng_ancestral/P49792.raxml.log Analysis started: 04-Jun-2021 13:38:29 / finished: 04-Jun-2021 13:47:37 Elapsed time: 548.138 seconds