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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jun-2021 18:05:03 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/2_msa/Q99814_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/3_mltree/Q99814.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/4_raxmlng_ancestral/Q99814 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646303 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/2_msa/Q99814_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 870 sites WARNING: Sequences tr_A0A2I3HUF1_A0A2I3HUF1_NOMLE_61853 and tr_A0A2I2Z8X7_A0A2I2Z8X7_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I2Y3I5_A0A2I2Y3I5_GORGO_9595 and tr_A0A2I3TNB0_A0A2I3TNB0_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2QGN8_H2QGN8_PANTR_9598 and sp_Q99742_NPAS1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QGN8_H2QGN8_PANTR_9598 and tr_A0A2R9C067_A0A2R9C067_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_G3WDB7_G3WDB7_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_H0ZNU4_H0ZNU4_TAEGU_59729 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_H2ZV55_H2ZV55_LATCH_7897 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_D2I5J7_D2I5J7_AILME_9646 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_R0LC48_R0LC48_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A0Q3MTJ2_A0A0Q3MTJ2_AMAAE_12930 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A091FR19_A0A091FR19_CORBR_85066 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A091JND8_A0A091JND8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A093SGR4_A0A093SGR4_9PASS_328815 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A091UYV6_A0A091UYV6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A087QMG3_A0A087QMG3_APTFO_9233 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A093H840_A0A093H840_STRCA_441894 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A091VFX3_A0A091VFX3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A099ZBJ2_A0A099ZBJ2_TINGU_94827 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A091GAI8_A0A091GAI8_9AVES_55661 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A0A0AK50_A0A0A0AK50_CHAVO_50402 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A093GR39_A0A093GR39_DRYPU_118200 are exactly identical! WARNING: Sequences tr_F6PGN4_F6PGN4_ORNAN_9258 and tr_A0A091I4T1_A0A091I4T1_CALAN_9244 are exactly identical! WARNING: Sequences tr_F6X815_F6X815_MACMU_9544 and tr_G7P440_G7P440_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6X815_F6X815_MACMU_9544 and tr_A0A2K6C1R3_A0A2K6C1R3_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZNU6_H0ZNU6_TAEGU_59729 and tr_A0A091W300_A0A091W300_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZNU6_H0ZNU6_TAEGU_59729 and tr_A0A091G735_A0A091G735_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZNU6_H0ZNU6_TAEGU_59729 and tr_A0A0A0APA3_A0A0A0APA3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_D2HIC6_D2HIC6_AILME_9646 and tr_A0A2U3X445_A0A2U3X445_ODORO_9708 are exactly identical! WARNING: Sequences tr_G7PM49_G7PM49_MACFA_9541 and tr_A0A2K6ASG9_A0A2K6ASG9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0JND0_A0JND0_BOVIN_9913 and sp_Q9XTA5_HIF1A_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I3MH29_A0A2I3MH29_PAPAN_9555 and tr_A0A2K5NIC2_A0A2K5NIC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MH29_A0A2I3MH29_PAPAN_9555 and tr_A0A2K5ZID3_A0A2K5ZID3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RNL7_A0A0D9RNL7_CHLSB_60711 and tr_A0A2K6DZ30_A0A2K6DZ30_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151NTB9_A0A151NTB9_ALLMI_8496 and tr_A0A1U7RM06_A0A1U7RM06_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A093Q0K7_A0A093Q0K7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A091UWP6_A0A091UWP6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A087QGR6_A0A087QGR6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A091XRF8_A0A091XRF8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A099ZFM7_A0A099ZFM7_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A091GBQ6_A0A091GBQ6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A0A0AYJ1_A0A0A0AYJ1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091EZX7_A0A091EZX7_CORBR_85066 and tr_A0A093I575_A0A093I575_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091F365_A0A091F365_CORBR_85066 and tr_A0A091JPF3_A0A091JPF3_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F365_A0A091F365_CORBR_85066 and tr_A0A087QMG4_A0A087QMG4_APTFO_9233 are exactly identical! WARNING: Sequences tr_R7VVI1_R7VVI1_COLLI_8932 and tr_A0A1V4JM20_A0A1V4JM20_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3JV10_A0A1S3JV10_LINUN_7574 and tr_A0A1S3JVT4_A0A1S3JVT4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A226N195_A0A226N195_CALSU_9009 and tr_A0A226PUL3_A0A226PUL3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5KJ51_A0A2K5KJ51_CERAT_9531 and tr_A0A2K5YV69_A0A2K5YV69_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4ACD6_A0A2U4ACD6_TURTR_9739 and tr_A0A2Y9MZ41_A0A2Y9MZ41_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AVC1_A0A2U4AVC1_TURTR_9739 and tr_A0A2Y9MM05_A0A2Y9MM05_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AVC1_A0A2U4AVC1_TURTR_9739 and tr_A0A2Y9F9Q3_A0A2Y9F9Q3_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 51 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/4_raxmlng_ancestral/Q99814.raxml.reduced.phy Alignment comprises 1 partitions and 870 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 870 Gaps: 44.42 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/4_raxmlng_ancestral/Q99814.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/3_mltree/Q99814.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 218 / 17440 [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: -267377.906636 [00:00:00 -267377.906636] Initial branch length optimization [00:00:02 -260928.460595] Model parameter optimization (eps = 0.100000) [00:01:27] Tree #1, final logLikelihood: -259654.866244 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.120956,0.418100) (0.071782,0.339269) (0.235398,0.478394) (0.571864,1.420725) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/4_raxmlng_ancestral/Q99814.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/4_raxmlng_ancestral/Q99814.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/4_raxmlng_ancestral/Q99814.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q99814/4_raxmlng_ancestral/Q99814.raxml.log Analysis started: 02-Jun-2021 18:05:03 / finished: 02-Jun-2021 18:06:39 Elapsed time: 96.237 seconds Consumed energy: 8.232 Wh