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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 12-Jul-2021 17:34:11 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/2_msa/P51610_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/4_raxmlng_ancestral/P51610 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626100451
  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/300621_run/phylogeny-snakemake/results/P51610/2_msa/P51610_nogap_msa.fasta
[00:00:00] Loaded alignment with 895 taxa and 2035 sites

WARNING: Sequences tr_E1BSD7_E1BSD7_CHICK_9031 and tr_A0A091G886_A0A091G886_9AVES_55661 are exactly identical!
WARNING: Sequences tr_G3HR72_G3HR72_CRIGR_10029 and sp_Q6AYI2_KLDC3_RAT_10116 are exactly identical!
WARNING: Sequences tr_G3HR72_G3HR72_CRIGR_10029 and tr_A0A1U7QES9_A0A1U7QES9_MESAU_10036 are exactly identical!
WARNING: Sequences tr_B6QQV5_B6QQV5_TALMQ_441960 and tr_A0A093XE30_A0A093XE30_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_H2PJ37_H2PJ37_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_G2HIN0_G2HIN0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A096NI88_A0A096NI88_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A0D9RGK8_A0A0D9RGK8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A2K5MK54_A0A2K5MK54_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A2K6B6Q7_A0A2K6B6Q7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A2R9BC63_A0A2R9BC63_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A179U7M8_A0A179U7M8_BLAGS_559298 and tr_C5GX79_C5GX79_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2QZT7_H2QZT7_PANTR_9598 and tr_A0A2R9CM34_A0A2R9CM34_PANPA_9597 are exactly identical!
WARNING: Sequences tr_I1QMA2_I1QMA2_ORYGL_4538 and tr_Q6ZXK6_Q6ZXK6_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0MV54_A0A0E0MV54_ORYRU_4529 and tr_Q94D04_Q94D04_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F2SEM9_F2SEM9_TRIRC_559305 and tr_A0A178ETG7_A0A178ETG7_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A093PRB6_A0A093PRB6_9PASS_328815 are exactly identical!
WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A0A0A320_A0A0A0A320_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A2I0LV87_A0A2I0LV87_COLLI_8932 are exactly identical!
WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A1V4KBD3_A0A1V4KBD3_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A015JNQ8_A0A015JNQ8_9GLOM_1432141 and tr_A0A2H5RP79_A0A2H5RP79_RHIID_747089 are exactly identical!
WARNING: Sequences tr_X0CZA5_X0CZA5_FUSOX_1089458 and tr_A0A2H3T0C9_A0A2H3T0C9_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_X0CZA5_X0CZA5_FUSOX_1089458 and tr_A0A2H3HV43_A0A2H3HV43_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0A1MML8_A0A0A1MML8_9FUNG_58291 and tr_A0A367JJD2_A0A367JJD2_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A1S3UXI3_A0A1S3UXI3_VIGRR_3916 and tr_A0A3Q0F611_A0A3Q0F611_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1U7Q220_A0A1U7Q220_MESAU_10036 and sp_P51611_HCFC1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A2D0T4I9_A0A2D0T4I9_ICTPU_7998 and tr_A0A2D0T549_A0A2D0T549_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2U4CRD6_A0A2U4CRD6_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2U4CRE2_A0A2U4CRE2_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2Y9QKG9_A0A2Y9QKG9_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 30

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/4_raxmlng_ancestral/P51610.raxml.reduced.phy

Alignment comprises 1 partitions and 2035 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 2035
Gaps: 68.65 %
Invariant sites: 0.15 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/4_raxmlng_ancestral/P51610.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/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 509 / 40720
[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: -474014.248184

[00:00:00 -474014.248184] Initial branch length optimization
[00:00:04 -429933.240925] Model parameter optimization (eps = 0.100000)

[00:04:11] Tree #1, final logLikelihood: -426933.665233


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.222041,2.425056) (0.052888,0.183798) (0.246789,0.324141) (0.478282,0.777413) 
   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/300621_run/phylogeny-snakemake/results/P51610/4_raxmlng_ancestral/P51610.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/4_raxmlng_ancestral/P51610.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/4_raxmlng_ancestral/P51610.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/4_raxmlng_ancestral/P51610.raxml.log

Analysis started: 12-Jul-2021 17:34:11 / finished: 12-Jul-2021 17:38:40

Elapsed time: 268.876 seconds

Consumed energy: 16.744 Wh