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 15:02:07 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8IXZ2/2_msa/Q8IXZ2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8IXZ2/3_mltree/Q8IXZ2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8IXZ2/4_raxmlng_ancestral/Q8IXZ2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635327 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/Q8IXZ2/2_msa/Q8IXZ2_nogap_msa.fasta [00:00:00] Loaded alignment with 998 taxa and 948 sites WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_F7DCT2_F7DCT2_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_A0A287D9Y7_A0A287D9Y7_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_G1LI40_G1LI40_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_L5KIZ1_L5KIZ1_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_A0A337RX23_A0A337RX23_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_A0A1U7R2Y8_A0A1U7R2Y8_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_A0A2U3VHH8_A0A2U3VHH8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_A0A2U3YX64_A0A2U3YX64_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YYJ5_M3YYJ5_MUSPF_9669 and tr_A0A384CQ25_A0A384CQ25_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1QL67_G1QL67_NOMLE_61853 and tr_G3SJG1_G3SJG1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_H2QV04_H2QV04_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and sp_O95639_CPSF4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_F7BI49_F7BI49_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_U3BK11_U3BK11_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_G7P0A7_G7P0A7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_A0A096N5S3_A0A096N5S3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_A0A0D9RYX9_A0A0D9RYX9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_A0A2K5MZ68_A0A2K5MZ68_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_A0A2K6BYW5_A0A2K6BYW5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_A0A2K5YZY5_A0A2K5YZY5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RGL8_G3RGL8_GORGO_9595 and tr_A0A2R9CR90_A0A2R9CR90_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A179UMF7_A0A179UMF7_BLAGS_559298 and tr_C5GTX6_C5GTX6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QDS1_H2QDS1_PANTR_9598 and sp_A6NMK7_CPS4L_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7FVV8_F7FVV8_MONDO_13616 and tr_G3WDI8_G3WDI8_SARHA_9305 are exactly identical! WARNING: Sequences sp_Q5FVR7_CPSF4_RAT_10116 and tr_A0A286XUE3_A0A286XUE3_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A3B5R4T8_A0A3B5R4T8_XIPMA_8083 and tr_A0A087YAD5_A0A087YAD5_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NJE9_A0A158NJE9_ATTCE_12957 and tr_F4WCG2_F4WCG2_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NJE9_A0A158NJE9_ATTCE_12957 and tr_A0A151XK19_A0A151XK19_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NJE9_A0A158NJE9_ATTCE_12957 and tr_A0A195FQN0_A0A195FQN0_9HYME_34720 are exactly identical! WARNING: Sequences tr_F7CXF4_F7CXF4_MACMU_9544 and tr_G7PVA9_G7PVA9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7CXF4_F7CXF4_MACMU_9544 and tr_A0A096NU57_A0A096NU57_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7CXF4_F7CXF4_MACMU_9544 and tr_A0A2K5P359_A0A2K5P359_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7CXF4_F7CXF4_MACMU_9544 and tr_A0A2K6ECJ3_A0A2K6ECJ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7CXF4_F7CXF4_MACMU_9544 and tr_A0A2K5ZL98_A0A2K5ZL98_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7XQN5_G7XQN5_ASPKW_1033177 and tr_A0A146FT70_A0A146FT70_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G2YNL5_G2YNL5_BOTF4_999810 and tr_M7U130_M7U130_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3MSW9_E3MSW9_CAERE_31234 and tr_A0A261CEK9_A0A261CEK9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_U3KH95_U3KH95_FICAL_59894 and tr_A0A093QDG0_A0A093QDG0_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3KH95_U3KH95_FICAL_59894 and tr_A0A218UW32_A0A218UW32_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3IH73_U3IH73_ANAPL_8839 and tr_A0A093K838_A0A093K838_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3IH73_U3IH73_ANAPL_8839 and tr_A0A099YTU0_A0A099YTU0_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3IH73_U3IH73_ANAPL_8839 and tr_A0A091G959_A0A091G959_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3IH73_U3IH73_ANAPL_8839 and tr_A0A091IBF7_A0A091IBF7_CALAN_9244 are exactly identical! WARNING: Sequences tr_N4TTU8_N4TTU8_FUSC1_1229664 and tr_A0A2H3I2H6_A0A2H3I2H6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_V2XZ78_V2XZ78_MONRO_1381753 and tr_A0A0W0G8J7_A0A0W0G8J7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015JLN6_A0A015JLN6_9GLOM_1432141 and tr_A0A2H5RHQ5_A0A2H5RHQ5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015MS36_A0A015MS36_9GLOM_1432141 and tr_A0A2H5R1G9_A0A2H5R1G9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015NA98_A0A015NA98_9GLOM_1432141 and tr_A0A2H5S2I0_A0A2H5S2I0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094EY37_A0A094EY37_9PEZI_1420912 and tr_A0A1B8GAL9_A0A1B8GAL9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_X0C2F9_X0C2F9_FUSOX_1089458 and tr_A0A2H3T4I7_A0A2H3T4I7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0F8XQN5_A0A0F8XQN5_9EURO_308745 and tr_A0A2T5M5Y2_A0A2T5M5Y2_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V1DBM1_A0A0V1DBM1_TRIBR_45882 and tr_A0A0V0TWD8_A0A0V0TWD8_9BILA_144512 are exactly identical! WARNING: Duplicate sequences found: 52 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/Q8IXZ2/4_raxmlng_ancestral/Q8IXZ2.raxml.reduced.phy Alignment comprises 1 partitions and 948 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 948 Gaps: 63.62 % Invariant sites: 0.32 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8IXZ2/4_raxmlng_ancestral/Q8IXZ2.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/Q8IXZ2/3_mltree/Q8IXZ2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 237 / 18960 [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: -397038.123522 [00:00:00 -397038.123522] Initial branch length optimization [00:00:02 -330476.509948] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -329867.982067 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.063886,0.096364) (0.028547,0.227644) (0.268705,0.606344) (0.638862,1.290447) 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/Q8IXZ2/4_raxmlng_ancestral/Q8IXZ2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8IXZ2/4_raxmlng_ancestral/Q8IXZ2.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8IXZ2/4_raxmlng_ancestral/Q8IXZ2.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8IXZ2/4_raxmlng_ancestral/Q8IXZ2.raxml.log Analysis started: 02-Jun-2021 15:02:07 / finished: 02-Jun-2021 15:02:57 Elapsed time: 50.416 seconds