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 18:50:16 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75155/2_msa/O75155_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75155/3_mltree/O75155.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75155/4_raxmlng_ancestral/O75155 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622649016
  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/O75155/2_msa/O75155_nogap_msa.fasta
[00:00:00] Loaded alignment with 709 taxa and 1236 sites

WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_H2NHZ1_H2NHZ1_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and sp_Q86VP6_CAND1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_F6XT20_F6XT20_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_G1LQ96_G1LQ96_AILME_9646 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_G7PHZ3_G7PHZ3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and sp_A7MBJ5_CAND1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_L5JW20_L5JW20_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_M3X6G0_M3X6G0_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A0D9QWF7_A0A0D9QWF7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2K5KZY4_A0A2K5KZY4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2K6E382_A0A2K6E382_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2K6AD74_A0A2K6AD74_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2U3ZYS2_A0A2U3ZYS2_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2U3X3K3_A0A2U3X3K3_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2Y9IQ35_A0A2Y9IQ35_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2Y9N2I3_A0A2Y9N2I3_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A2Y9FWI3_A0A2Y9FWI3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A384BK33_A0A384BK33_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G3QF05_G3QF05_GORGO_9595 and tr_A0A384B6F6_A0A384B6F6_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G1SN14_G1SN14_RABIT_9986 and tr_A0A2U3ZYS8_A0A2U3ZYS8_TURTR_9739 are exactly identical!
WARNING: Sequences tr_Q29CJ5_Q29CJ5_DROPS_46245 and tr_B4G795_B4G795_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A088ARY2_A0A088ARY2_APIME_7460 and tr_A0A2A3EF13_A0A2A3EF13_APICC_94128 are exactly identical!
WARNING: Sequences tr_B8AIH4_B8AIH4_ORYSI_39946 and tr_Q6H4V4_Q6H4V4_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_M4ECS6_M4ECS6_BRARP_51351 and tr_A0A078F8K3_A0A078F8K3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A067DKI4_A0A067DKI4_CITSI_2711 and tr_V4T576_V4T576_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A091JNL7_A0A091JNL7_EGRGA_188379 and tr_A0A091UZW5_A0A091UZW5_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JNL7_A0A091JNL7_EGRGA_188379 and tr_A0A087QQC7_A0A087QQC7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JNL7_A0A091JNL7_EGRGA_188379 and tr_A0A091VUZ4_A0A091VUZ4_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A093Q3G5_A0A093Q3G5_9PASS_328815 and tr_A0A093GXR1_A0A093GXR1_DRYPU_118200 are exactly identical!
WARNING: Duplicate sequences found: 29

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/O75155/4_raxmlng_ancestral/O75155.raxml.reduced.phy

Alignment comprises 1 partitions and 1236 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 1236
Gaps: 18.68 %
Invariant sites: 0.08 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75155/4_raxmlng_ancestral/O75155.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/O75155/3_mltree/O75155.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 309 / 24720
[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: -379490.808041

[00:00:00 -379490.808041] Initial branch length optimization
[00:00:02 -378965.460136] Model parameter optimization (eps = 0.100000)

[00:01:08] Tree #1, final logLikelihood: -377643.690928


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.208817,0.555236) (0.242443,0.536237) (0.296302,0.835941) (0.252438,2.005874) 
   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/O75155/4_raxmlng_ancestral/O75155.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75155/4_raxmlng_ancestral/O75155.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75155/4_raxmlng_ancestral/O75155.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75155/4_raxmlng_ancestral/O75155.raxml.log

Analysis started: 02-Jun-2021 18:50:16 / finished: 02-Jun-2021 18:51:33

Elapsed time: 77.136 seconds

Consumed energy: 6.409 Wh