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 14:08:19 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q06210/2_msa/Q06210_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q06210/3_mltree/Q06210.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q06210/4_raxmlng_ancestral/Q06210 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622632099 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/Q06210/2_msa/Q06210_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 699 sites WARNING: Sequences tr_J3K9Y7_J3K9Y7_COCIM_246410 and tr_A0A0J6Y3Q9_A0A0J6Y3Q9_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QRG2_B6QRG2_TALMQ_441960 and tr_A0A093V5D5_A0A093V5D5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2YMN4_A0A2I2YMN4_GORGO_9595 and tr_H2R176_H2R176_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YMN4_A0A2I2YMN4_GORGO_9595 and sp_Q06210_GFPT1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G2X1U8_G2X1U8_VERDV_498257 and tr_A0A0G4N348_A0A0G4N348_9PEZI_100787 are exactly identical! WARNING: Sequences tr_C0P131_C0P131_AJECG_447093 and tr_F0UW28_F0UW28_AJEC8_544711 are exactly identical! WARNING: Sequences tr_B8N2M1_B8N2M1_ASPFN_332952 and tr_Q2UMH2_Q2UMH2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N2M1_B8N2M1_ASPFN_332952 and tr_A0A0F0ICL3_A0A0F0ICL3_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8N2M1_B8N2M1_ASPFN_332952 and tr_A0A1S9DP86_A0A1S9DP86_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_E9F4K3_E9F4K3_METRA_655844 and tr_A0A0D9NYV0_A0A0D9NYV0_METAN_1291518 are exactly identical! WARNING: Sequences tr_E9R5E2_E9R5E2_ASPFU_330879 and tr_A1DM30_A1DM30_NEOFI_331117 are exactly identical! WARNING: Sequences tr_E9R5E2_E9R5E2_ASPFU_330879 and tr_A0A0S7DL17_A0A0S7DL17_9EURO_293939 are exactly identical! WARNING: Sequences tr_J5JMH9_J5JMH9_BEAB2_655819 and tr_A0A0A2VAC6_A0A0A2VAC6_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5JMH9_J5JMH9_BEAB2_655819 and tr_A0A2N6NZU1_A0A2N6NZU1_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A180H4E0_A0A180H4E0_PUCT1_630390 and tr_E3LAS8_E3LAS8_PUCGT_418459 are exactly identical! WARNING: Sequences sp_O94808_GFPT2_HUMAN_9606 and tr_A0A2R9A2S2_A0A2R9A2S2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0HZ86_A0A0E0HZ86_ORYNI_4536 and tr_B8BLW8_B8BLW8_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A2RBI3_A2RBI3_ASPNC_425011 and tr_A0A319AY93_A0A319AY93_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XT48_G7XT48_ASPKW_1033177 and tr_A0A100IP85_A0A100IP85_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XT48_G7XT48_ASPKW_1033177 and tr_A0A146F642_A0A146F642_9EURO_1069201 are exactly identical! WARNING: Sequences tr_B8BIX5_B8BIX5_ORYSI_39946 and tr_I1QXD8_I1QXD8_ORYGL_4538 are exactly identical! WARNING: Sequences tr_F4P6E4_F4P6E4_BATDJ_684364 and tr_A0A177WQZ1_A0A177WQZ1_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1R3Q6_I1R3Q6_ORYGL_4538 and tr_A0A0D3HR19_A0A0D3HR19_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_F9XEP0_F9XEP0_ZYMTI_336722 and tr_A0A1X7RXP3_A0A1X7RXP3_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XYV8_G2XYV8_BOTF4_999810 and tr_M7TM13_M7TM13_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A8WTD8_A8WTD8_CAEBR_6238 and tr_A0A2G5V2W5_A0A2G5V2W5_9PELO_1611254 are exactly identical! WARNING: Sequences tr_C4V8B6_C4V8B6_NOSCE_578460 and tr_A0A0F9WPX8_A0A0F9WPX8_9MICR_40302 are exactly identical! WARNING: Sequences tr_A0A0D2X8I1_A0A0D2X8I1_FUSO4_426428 and tr_S0DLU2_S0DLU2_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_A0A0D2X8I1_A0A0D2X8I1_FUSO4_426428 and tr_N4TDZ7_N4TDZ7_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0D2X8I1_A0A0D2X8I1_FUSO4_426428 and tr_X0D3Z9_X0D3Z9_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2X8I1_A0A0D2X8I1_FUSO4_426428 and tr_A0A2H3SU00_A0A2H3SU00_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0D2X8I1_A0A0D2X8I1_FUSO4_426428 and tr_A0A365MT47_A0A365MT47_GIBIN_948311 are exactly identical! WARNING: Sequences tr_L2FVS6_L2FVS6_COLFN_1213859 and tr_T0L964_T0L964_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M7ZTK2_M7ZTK2_TRIUA_4572 and tr_A0A3B6KEE9_A0A3B6KEE9_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M2SIB8_M2SIB8_COCSN_665912 and tr_M2UBI6_M2UBI6_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2SIB8_M2SIB8_COCSN_665912 and tr_W6YMH9_W6YMH9_COCCA_930089 are exactly identical! WARNING: Sequences tr_A0A015MZL6_A0A015MZL6_9GLOM_1432141 and tr_A0A2H5SY08_A0A2H5SY08_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094E509_A0A094E509_9PEZI_1420912 and tr_A0A1B8GS84_A0A1B8GS84_9PEZI_342668 are exactly identical! WARNING: Sequences tr_V4SMH8_V4SMH8_9ROSI_85681 and tr_A0A2H5Q5V3_A0A2H5Q5V3_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A087REZ6_A0A087REZ6_APTFO_9233 and tr_A0A0A0AXN8_A0A0A0AXN8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1DE33_A0A0V1DE33_TRIBR_45882 and tr_A0A0V0X6L6_A0A0V0X6L6_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DE33_A0A0V1DE33_TRIBR_45882 and tr_A0A0V0VVE5_A0A0V0VVE5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DE33_A0A0V1DE33_TRIBR_45882 and tr_A0A0V1LT74_A0A0V1LT74_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DE33_A0A0V1DE33_TRIBR_45882 and tr_A0A0V1AFA3_A0A0V1AFA3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DE33_A0A0V1DE33_TRIBR_45882 and tr_A0A0V0UGA3_A0A0V0UGA3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A164ZZ84_A0A164ZZ84_9HOMO_1314777 and tr_A0A166FFK1_A0A166FFK1_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A194VSA0_A0A194VSA0_9PEZI_105487 and tr_A0A194V1Z4_A0A194V1Z4_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A2G2ZJ46_A0A2G2ZJ46_CAPAN_4072 and tr_A0A2G3DH74_A0A2G3DH74_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U4BYS9_A0A2U4BYS9_TURTR_9739 and tr_A0A2Y9M5F3_A0A2Y9M5F3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A319BUP2_A0A319BUP2_9EURO_1448315 and tr_A0A2V5HTD8_A0A2V5HTD8_9EURO_1450541 are exactly identical! WARNING: Duplicate sequences found: 50 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/Q06210/4_raxmlng_ancestral/Q06210.raxml.reduced.phy Alignment comprises 1 partitions and 699 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 699 Gaps: 5.43 % Invariant sites: 3.72 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q06210/4_raxmlng_ancestral/Q06210.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/Q06210/3_mltree/Q06210.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 175 / 14000 [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: -175689.875281 [00:00:00 -175689.875281] Initial branch length optimization [00:00:01 -174403.652507] Model parameter optimization (eps = 0.100000) [00:00:42] Tree #1, final logLikelihood: -173820.750316 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.275747,0.257754) (0.349617,0.418413) (0.219025,1.156509) (0.155611,3.401664) 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/Q06210/4_raxmlng_ancestral/Q06210.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q06210/4_raxmlng_ancestral/Q06210.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q06210/4_raxmlng_ancestral/Q06210.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q06210/4_raxmlng_ancestral/Q06210.raxml.log Analysis started: 02-Jun-2021 14:08:19 / finished: 02-Jun-2021 14:09:08 Elapsed time: 48.588 seconds