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 03-Jun-2021 14:59:09 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75792/2_msa/O75792_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75792/3_mltree/O75792.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75792/4_raxmlng_ancestral/O75792 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622721549
  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/O75792/2_msa/O75792_nogap_msa.fasta
[00:00:00] Loaded alignment with 937 taxa and 299 sites

WARNING: Sequences tr_B2W2E2_B2W2E2_PYRTR_426418 and tr_A0A2W1H8T8_A0A2W1H8T8_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3QSS9_G3QSS9_GORGO_9595 and tr_A0A2R9A386_A0A2R9A386_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A179UXD3_A0A179UXD3_BLAGS_559298 and tr_C5GNN0_C5GNN0_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FPQ9_F9FPQ9_FUSOF_660025 and tr_A0A0D2XA76_A0A0D2XA76_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FPQ9_F9FPQ9_FUSOF_660025 and tr_X0CNQ4_X0CNQ4_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_C6HQM6_C6HQM6_AJECH_544712 and tr_F0UML1_F0UML1_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A158NPN1_A0A158NPN1_ATTCE_12957 and tr_A0A195AT70_A0A195AT70_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0IYG1_A0A0E0IYG1_ORYNI_4536 and tr_A2ZBK3_A2ZBK3_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_G7XEN9_G7XEN9_ASPKW_1033177 and tr_A0A146F1Y2_A0A146F1Y2_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_I1QXT2_I1QXT2_ORYGL_4538 and tr_A0A0D3HID4_A0A0D3HID4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1QXT2_I1QXT2_ORYGL_4538 and tr_A0A0E0BFG3_A0A0E0BFG3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0R4D8_A0A0E0R4D8_ORYRU_4529 and tr_Q53QG3_Q53QG3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F9X3H9_F9X3H9_ZYMTI_336722 and tr_A0A1X7RJ26_A0A1X7RJ26_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_F2SU13_F2SU13_TRIRC_559305 and tr_A0A178F756_A0A178F756_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G3XZU9_G3XZU9_ASPNA_380704 and tr_A0A319AMC0_A0A319AMC0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_N4TFI9_N4TFI9_FUSC1_1229664 and tr_A0A2H3TC75_A0A2H3TC75_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_N4TFI9_N4TFI9_FUSC1_1229664 and tr_A0A2H3I3A9_A0A2H3I3A9_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A015N2F0_A0A015N2F0_9GLOM_1432141 and tr_A0A2H5R1N7_A0A2H5R1N7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2I3N0D3_A0A2I3N0D3_PAPAN_9555 and tr_A0A2K5LCI4_A0A2K5LCI4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A078J1G4_A0A078J1G4_BRANA_3708 and tr_A0A0D3C1Z9_A0A0D3C1Z9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_V4TF10_V4TF10_9ROSI_85681 and tr_A0A2H5PNS5_A0A2H5PNS5_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0W8DDQ6_A0A0W8DDQ6_PHYNI_4790 and tr_W2I702_W2I702_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A117DZM3_A0A117DZM3_ASPNG_5061 and tr_A0A1L9MZI7_A0A1L9MZI7_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S3Y3T9_A0A1S3Y3T9_TOBAC_4097 and tr_A0A1U7YHY1_A0A1U7YHY1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1R1XYY9_A0A1R1XYY9_9FUNG_133412 and tr_A0A1R1YBL8_A0A1R1YBL8_9FUNG_133412 are exactly identical!
WARNING: Sequences tr_A0A2G2Y6A8_A0A2G2Y6A8_CAPAN_4072 and tr_A0A2G3B103_A0A2G3B103_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2N5RVR2_A0A2N5RVR2_9BASI_200324 and tr_A0A2N5S3E8_A0A2N5S3E8_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 27

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/O75792/4_raxmlng_ancestral/O75792.raxml.reduced.phy

Alignment comprises 1 partitions and 299 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 299
Gaps: 12.77 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75792/4_raxmlng_ancestral/O75792.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/O75792/3_mltree/O75792.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 75 / 6000
[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: -154501.842901

[00:00:00 -154501.842901] Initial branch length optimization
[00:00:01 -154121.769501] Model parameter optimization (eps = 0.100000)

[00:00:19] Tree #1, final logLikelihood: -153886.432116


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.165697,0.194974) (0.197628,0.314290) (0.281885,0.786153) (0.354790,1.927832) 
   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/O75792/4_raxmlng_ancestral/O75792.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75792/4_raxmlng_ancestral/O75792.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75792/4_raxmlng_ancestral/O75792.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O75792/4_raxmlng_ancestral/O75792.raxml.log

Analysis started: 03-Jun-2021 14:59:09 / finished: 03-Jun-2021 14:59:32

Elapsed time: 22.608 seconds

Consumed energy: 1.820 Wh