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 17-Jun-2021 23:41:18 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/2_msa/O75503_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/2_msa/O75503_trimmed_msa.fasta
[00:00:00] Loaded alignment with 104 taxa and 291 sites

WARNING: Sequences tr_A0A2R8QDG4_A0A2R8QDG4_DANRE_7955 and tr_E7F6N2_E7F6N2_DANRE_7955 are exactly identical!
WARNING: Sequences sp_A2TJ54_CLN5_SHEEP_9940 and tr_W5Q3A2_W5Q3A2_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_G1LMV2_G1LMV2_AILME_9646 and tr_A0A384BRM8_A0A384BRM8_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A096NRV3_A0A096NRV3_PAPAN_9555 and tr_A0A2K5MA92_A0A2K5MA92_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NRV3_A0A096NRV3_PAPAN_9555 and tr_A0A2K6DZ72_A0A2K6DZ72_MACNE_9545 are exactly identical!
WARNING: Duplicate sequences found: 5

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503.raxml.reduced.phy

Alignment comprises 1 partitions and 282 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 291 / 282
Gaps: 2.08 %
Invariant sites: 13.75 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503.raxml.rba

Parallelization scheme autoconfig: 6 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 104 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 282 / 22560
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -25163.374637] Initial branch length optimization
[00:00:00 -20478.577322] Model parameter optimization (eps = 10.000000)
[00:00:06 -20372.287526] AUTODETECT spr round 1 (radius: 5)
[00:00:10 -14158.035199] AUTODETECT spr round 2 (radius: 10)
[00:00:16 -12603.941876] AUTODETECT spr round 3 (radius: 15)
[00:00:24 -11934.226651] AUTODETECT spr round 4 (radius: 20)
[00:00:29 -11934.203019] SPR radius for FAST iterations: 15 (autodetect)
[00:00:29 -11934.203019] Model parameter optimization (eps = 3.000000)
[00:00:35 -11917.184689] FAST spr round 1 (radius: 15)
[00:00:42 -11217.387562] FAST spr round 2 (radius: 15)
[00:00:47 -11172.058865] FAST spr round 3 (radius: 15)
[00:00:52 -11163.363403] FAST spr round 4 (radius: 15)
[00:00:55 -11163.363359] Model parameter optimization (eps = 1.000000)
[00:00:56 -11162.755974] SLOW spr round 1 (radius: 5)
[00:01:06 -11160.956349] SLOW spr round 2 (radius: 5)
[00:01:16 -11160.953610] SLOW spr round 3 (radius: 10)
[00:01:24 -11160.953304] SLOW spr round 4 (radius: 15)
[00:01:39 -11160.953269] SLOW spr round 5 (radius: 20)
[00:01:54 -11160.953265] SLOW spr round 6 (radius: 25)
[00:01:57] [worker #4] ML tree search #5, logLikelihood: -11163.498051
[00:02:02] [worker #3] ML tree search #4, logLikelihood: -11161.567684
[00:02:07 -11160.953265] Model parameter optimization (eps = 0.100000)

[00:02:10] [worker #0] ML tree search #1, logLikelihood: -11160.829362

[00:02:10 -25659.517121] Initial branch length optimization
[00:02:10 -20396.845866] Model parameter optimization (eps = 10.000000)
[00:02:17 -20315.225288] AUTODETECT spr round 1 (radius: 5)
[00:02:17] [worker #2] ML tree search #3, logLikelihood: -11157.356051
[00:02:18] [worker #1] ML tree search #2, logLikelihood: -11159.901451
[00:02:20] [worker #5] ML tree search #6, logLikelihood: -11158.314314
[00:02:25 -14029.600681] AUTODETECT spr round 2 (radius: 10)
[00:02:33 -12155.153143] AUTODETECT spr round 3 (radius: 15)
[00:02:46 -11815.376508] AUTODETECT spr round 4 (radius: 20)
[00:02:58 -11815.376325] SPR radius for FAST iterations: 15 (autodetect)
[00:02:58 -11815.376325] Model parameter optimization (eps = 3.000000)
[00:03:06 -11802.668653] FAST spr round 1 (radius: 15)
[00:03:15 -11224.460468] FAST spr round 2 (radius: 15)
[00:03:22 -11164.832446] FAST spr round 3 (radius: 15)
[00:03:27 -11161.999479] FAST spr round 4 (radius: 15)
[00:03:34 -11161.999334] Model parameter optimization (eps = 1.000000)
[00:03:37 -11161.255033] SLOW spr round 1 (radius: 5)
[00:03:53 -11161.208369] SLOW spr round 2 (radius: 10)
[00:04:05] [worker #4] ML tree search #11, logLikelihood: -11160.892378
[00:04:07 -11161.208330] SLOW spr round 3 (radius: 15)
[00:04:10] [worker #3] ML tree search #10, logLikelihood: -11161.568144
[00:04:20 -11161.208328] SLOW spr round 4 (radius: 20)
[00:04:31 -11161.208328] SLOW spr round 5 (radius: 25)
[00:04:36] [worker #2] ML tree search #9, logLikelihood: -11157.356272
[00:04:38 -11161.208328] Model parameter optimization (eps = 0.100000)

[00:04:39] [worker #0] ML tree search #7, logLikelihood: -11161.197290

[00:04:39 -25413.194679] Initial branch length optimization
[00:04:40 -20709.498724] Model parameter optimization (eps = 10.000000)
[00:04:45 -20617.463361] AUTODETECT spr round 1 (radius: 5)
[00:04:48] [worker #5] ML tree search #12, logLikelihood: -11160.829470
[00:04:49 -14375.624849] AUTODETECT spr round 2 (radius: 10)
[00:04:51] [worker #1] ML tree search #8, logLikelihood: -11161.067996
[00:04:55 -12690.713210] AUTODETECT spr round 3 (radius: 15)
[00:05:03 -12185.574376] AUTODETECT spr round 4 (radius: 20)
[00:05:10 -12093.928384] AUTODETECT spr round 5 (radius: 25)
[00:05:12 -12093.909209] SPR radius for FAST iterations: 20 (autodetect)
[00:05:12 -12093.909209] Model parameter optimization (eps = 3.000000)
[00:05:17 -12075.908791] FAST spr round 1 (radius: 20)
[00:05:24 -11211.350816] FAST spr round 2 (radius: 20)
[00:05:28 -11165.375854] FAST spr round 3 (radius: 20)
[00:05:32 -11165.374841] Model parameter optimization (eps = 1.000000)
[00:05:36 -11162.718824] SLOW spr round 1 (radius: 5)
[00:05:46 -11161.864885] SLOW spr round 2 (radius: 5)
[00:05:55 -11161.864616] SLOW spr round 3 (radius: 10)
[00:06:02 -11161.864582] SLOW spr round 4 (radius: 15)
[00:06:13 -11161.864578] SLOW spr round 5 (radius: 20)
[00:06:15] [worker #3] ML tree search #16, logLikelihood: -11159.901883
[00:06:24 -11161.864577] SLOW spr round 6 (radius: 25)
[00:06:27] [worker #4] ML tree search #17, logLikelihood: -11160.829342
[00:06:31 -11161.864577] Model parameter optimization (eps = 0.100000)

[00:06:32] [worker #0] ML tree search #13, logLikelihood: -11161.861998

[00:06:32 -25449.351247] Initial branch length optimization
[00:06:32 -20509.856242] Model parameter optimization (eps = 10.000000)
[00:06:36] [worker #2] ML tree search #15, logLikelihood: -11160.892887
[00:06:38 -20433.386507] AUTODETECT spr round 1 (radius: 5)
[00:06:42 -15007.790807] AUTODETECT spr round 2 (radius: 10)
[00:06:48 -12754.057445] AUTODETECT spr round 3 (radius: 15)
[00:06:48] [worker #1] ML tree search #14, logLikelihood: -11158.313306
[00:06:56] [worker #5] ML tree search #18, logLikelihood: -11158.452761
[00:06:56 -11991.979554] AUTODETECT spr round 4 (radius: 20)
[00:07:02 -11991.976679] SPR radius for FAST iterations: 15 (autodetect)
[00:07:02 -11991.976679] Model parameter optimization (eps = 3.000000)
[00:07:06 -11981.629466] FAST spr round 1 (radius: 15)
[00:07:12 -11302.306328] FAST spr round 2 (radius: 15)
[00:07:17 -11172.352640] FAST spr round 3 (radius: 15)
[00:07:22 -11161.695716] FAST spr round 4 (radius: 15)
[00:07:26 -11161.695655] Model parameter optimization (eps = 1.000000)
[00:07:28 -11161.163800] SLOW spr round 1 (radius: 5)
[00:07:38 -11158.342855] SLOW spr round 2 (radius: 5)
[00:07:46 -11158.342791] SLOW spr round 3 (radius: 10)
[00:07:54 -11158.342788] SLOW spr round 4 (radius: 15)
[00:08:05 -11158.342787] SLOW spr round 5 (radius: 20)
[00:08:16 -11158.342787] SLOW spr round 6 (radius: 25)
[00:08:24 -11158.342787] Model parameter optimization (eps = 0.100000)

[00:08:26] [worker #0] ML tree search #19, logLikelihood: -11158.313434

[00:08:57] [worker #1] ML tree search #20, logLikelihood: -11159.019591

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.241122,0.260704) (0.327722,0.468893) (0.310896,1.225804) (0.120261,3.345854) 
   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 


Final LogLikelihood: -11157.356051

AIC score: 22736.712101 / AICc score: 23869.167798 / BIC score: 23511.783311
Free parameters (model + branch lengths): 211

WARNING: Best ML tree contains 14 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75503/3_mltree/O75503.raxml.log

Analysis started: 17-Jun-2021 23:41:18 / finished: 17-Jun-2021 23:50:15

Elapsed time: 537.079 seconds