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 14-Jul-2021 04:53:41 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/2_msa/P53621_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/3_mltree/P53621 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/2_msa/P53621_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1239 sites

WARNING: Sequences tr_A0A179UCS1_A0A179UCS1_BLAGS_559298 and tr_C5GH54_C5GH54_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2Q0E3_H2Q0E3_PANTR_9598 and tr_A0A2R9A2F0_A0A2R9A2F0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158N931_A0A158N931_ATTCE_12957 and tr_A0A195BVP9_A0A195BVP9_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A2XLA1_A2XLA1_ORYSI_39946 and sp_Q9AUR7_COPA2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0QN31_A0A0E0QN31_ORYRU_4529 and sp_Q0J3D9_COPA3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G3Y5L7_G3Y5L7_ASPNA_380704 and tr_A0A319ABA2_A0A319ABA2_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7NWD0_G7NWD0_MACFA_9541 and tr_A0A2K6B6Y4_A0A2K6B6Y4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_L0PCR2_L0PCR2_PNEJ8_1209962 and tr_A0A0W4ZL29_A0A0W4ZL29_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_A0A0D9S3P5_A0A0D9S3P5_CHLSB_60711 and tr_A0A2K5KVE1_A0A2K5KVE1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9S3P5_A0A0D9S3P5_CHLSB_60711 and tr_A0A2K5YJ63_A0A2K5YJ63_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0W8D507_A0A0W8D507_PHYNI_4790 and tr_W2L5D3_W2L5D3_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A100ISJ8_A0A100ISJ8_ASPNG_5061 and tr_A0A1L9N316_A0A1L9N316_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S3LZ47_A0A1S3LZ47_SALSA_8030 and tr_B5X3T4_B5X3T4_SALSA_8030 are exactly identical!
WARNING: Duplicate sequences found: 13

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/P53621/3_mltree/P53621.raxml.reduced.phy

Alignment comprises 1 partitions and 1239 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1239 / 1239
Gaps: 6.03 %
Invariant sites: 0.97 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/3_mltree/P53621.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 9 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 138 / 11040
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1585233.321790] Initial branch length optimization
[00:00:06 -1357515.187181] Model parameter optimization (eps = 10.000000)
[00:00:33 -1352819.927926] AUTODETECT spr round 1 (radius: 5)
[00:02:40 -870361.508088] AUTODETECT spr round 2 (radius: 10)
[00:04:59 -666062.541320] AUTODETECT spr round 3 (radius: 15)
[00:07:21 -547948.575696] AUTODETECT spr round 4 (radius: 20)
[00:10:04 -486448.956608] AUTODETECT spr round 5 (radius: 25)
[00:13:11 -482607.539670] SPR radius for FAST iterations: 25 (autodetect)
[00:13:11 -482607.539670] Model parameter optimization (eps = 3.000000)
[00:13:18 -482603.785762] FAST spr round 1 (radius: 25)
[00:15:50 -411319.085552] FAST spr round 2 (radius: 25)
[00:17:43 -409362.453756] FAST spr round 3 (radius: 25)
[00:19:26 -409250.900806] FAST spr round 4 (radius: 25)
[00:20:53 -409234.091388] FAST spr round 5 (radius: 25)
[00:22:17 -409234.090492] Model parameter optimization (eps = 1.000000)
[00:22:29 -409105.726639] SLOW spr round 1 (radius: 5)
[00:24:35 -409000.607440] SLOW spr round 2 (radius: 5)
[00:26:31 -408996.331233] SLOW spr round 3 (radius: 5)
[00:28:23 -408996.330186] SLOW spr round 4 (radius: 10)
[00:30:18 -408996.329197] SLOW spr round 5 (radius: 15)
[00:33:25 -408996.328203] SLOW spr round 6 (radius: 20)
[00:37:38 -408996.327205] SLOW spr round 7 (radius: 25)
[00:43:08 -408996.326202] Model parameter optimization (eps = 0.100000)

[00:43:17] ML tree search #1, logLikelihood: -408995.002728

[00:43:17 -1591410.670907] Initial branch length optimization
[00:43:22 -1362403.999919] Model parameter optimization (eps = 10.000000)
[00:43:51 -1357932.209846] AUTODETECT spr round 1 (radius: 5)
[00:46:01 -896566.220892] AUTODETECT spr round 2 (radius: 10)
[00:48:21 -659550.556422] AUTODETECT spr round 3 (radius: 15)
[00:50:47 -524564.511504] AUTODETECT spr round 4 (radius: 20)
[00:53:28 -486380.930664] AUTODETECT spr round 5 (radius: 25)
[00:56:40 -475305.520270] SPR radius for FAST iterations: 25 (autodetect)
[00:56:40 -475305.520270] Model parameter optimization (eps = 3.000000)
[00:56:54 -475082.090158] FAST spr round 1 (radius: 25)
[00:59:23 -411310.034549] FAST spr round 2 (radius: 25)
[01:01:19 -409253.826478] FAST spr round 3 (radius: 25)
[01:02:58 -409195.858627] FAST spr round 4 (radius: 25)
[01:04:28 -409177.394027] FAST spr round 5 (radius: 25)
[01:05:53 -409177.393923] Model parameter optimization (eps = 1.000000)
[01:06:03 -409174.530695] SLOW spr round 1 (radius: 5)
[01:08:05 -409026.552643] SLOW spr round 2 (radius: 5)
[01:10:04 -409002.786339] SLOW spr round 3 (radius: 5)
[01:11:59 -409002.307576] SLOW spr round 4 (radius: 5)
[01:13:57 -409000.002668] SLOW spr round 5 (radius: 5)
[01:15:50 -409000.002644] SLOW spr round 6 (radius: 10)
[01:17:48 -408994.970654] SLOW spr round 7 (radius: 5)
[01:20:15 -408993.501218] SLOW spr round 8 (radius: 5)
[01:22:23 -408993.501217] SLOW spr round 9 (radius: 10)
[01:24:24 -408993.501217] SLOW spr round 10 (radius: 15)
[01:27:26 -408993.501217] SLOW spr round 11 (radius: 20)
[01:31:35 -408993.501217] SLOW spr round 12 (radius: 25)
[01:36:55 -408993.501217] Model parameter optimization (eps = 0.100000)

[01:37:02] ML tree search #2, logLikelihood: -408993.180958

[01:37:02 -1591065.763097] Initial branch length optimization
[01:37:07 -1364119.900996] Model parameter optimization (eps = 10.000000)
[01:37:36 -1359470.076451] AUTODETECT spr round 1 (radius: 5)
[01:39:44 -890107.903939] AUTODETECT spr round 2 (radius: 10)
[01:42:08 -634611.576492] AUTODETECT spr round 3 (radius: 15)
[01:44:32 -519337.583809] AUTODETECT spr round 4 (radius: 20)
[01:47:26 -486599.651655] AUTODETECT spr round 5 (radius: 25)
[01:50:45 -486238.837750] SPR radius for FAST iterations: 25 (autodetect)
[01:50:45 -486238.837750] Model parameter optimization (eps = 3.000000)
[01:50:49 -486236.948886] FAST spr round 1 (radius: 25)
[01:53:17 -410933.273090] FAST spr round 2 (radius: 25)
[01:55:13 -409410.890256] FAST spr round 3 (radius: 25)
[01:56:54 -409269.928285] FAST spr round 4 (radius: 25)
[01:58:22 -409256.139656] FAST spr round 5 (radius: 25)
[01:59:48 -409256.138761] Model parameter optimization (eps = 1.000000)
[02:00:01 -409114.433316] SLOW spr round 1 (radius: 5)
[02:02:11 -408998.932189] SLOW spr round 2 (radius: 5)
[02:04:08 -408990.752876] SLOW spr round 3 (radius: 5)
[02:06:02 -408987.484084] SLOW spr round 4 (radius: 5)
[02:07:54 -408987.484083] SLOW spr round 5 (radius: 10)
[02:09:51 -408987.484083] SLOW spr round 6 (radius: 15)
[02:12:58 -408987.484083] SLOW spr round 7 (radius: 20)
[02:17:09 -408987.484083] SLOW spr round 8 (radius: 25)
[02:22:43 -408987.484083] Model parameter optimization (eps = 0.100000)

[02:22:54] ML tree search #3, logLikelihood: -408986.138183

[02:22:54 -1598907.612143] Initial branch length optimization
[02:23:02 -1372385.964472] Model parameter optimization (eps = 10.000000)
[02:23:33 -1367846.370657] AUTODETECT spr round 1 (radius: 5)
[02:25:39 -883495.610244] AUTODETECT spr round 2 (radius: 10)
[02:28:01 -658621.508897] AUTODETECT spr round 3 (radius: 15)
[02:30:23 -550163.258701] AUTODETECT spr round 4 (radius: 20)
[02:33:13 -502820.074109] AUTODETECT spr round 5 (radius: 25)
[02:36:35 -487843.664618] SPR radius for FAST iterations: 25 (autodetect)
[02:36:35 -487843.664618] Model parameter optimization (eps = 3.000000)
[02:36:50 -487646.257396] FAST spr round 1 (radius: 25)
[02:39:18 -412130.601321] FAST spr round 2 (radius: 25)
[02:41:09 -409220.149499] FAST spr round 3 (radius: 25)
[02:42:51 -409100.422361] FAST spr round 4 (radius: 25)
[02:44:19 -409097.640772] FAST spr round 5 (radius: 25)
[02:45:44 -409097.640608] Model parameter optimization (eps = 1.000000)
[02:45:55 -409092.330292] SLOW spr round 1 (radius: 5)
[02:48:02 -408997.239021] SLOW spr round 2 (radius: 5)
[02:50:00 -408990.996414] SLOW spr round 3 (radius: 5)
[02:51:52 -408990.996378] SLOW spr round 4 (radius: 10)
[02:53:48 -408990.996378] SLOW spr round 5 (radius: 15)
[02:56:56 -408990.996378] SLOW spr round 6 (radius: 20)
[03:01:12 -408990.996378] SLOW spr round 7 (radius: 25)
[03:06:44 -408990.996378] Model parameter optimization (eps = 0.100000)

[03:06:51] ML tree search #4, logLikelihood: -408990.626186

[03:06:51 -1596767.659099] Initial branch length optimization
[03:06:57 -1366604.666218] Model parameter optimization (eps = 10.000000)
[03:07:23 -1362114.040758] AUTODETECT spr round 1 (radius: 5)
[03:09:30 -891786.507777] AUTODETECT spr round 2 (radius: 10)
[03:11:49 -687199.255002] AUTODETECT spr round 3 (radius: 15)
[03:14:09 -574873.792101] AUTODETECT spr round 4 (radius: 20)
[03:16:37 -499272.263607] AUTODETECT spr round 5 (radius: 25)
[03:19:22 -481400.135136] SPR radius for FAST iterations: 25 (autodetect)
[03:19:22 -481400.135136] Model parameter optimization (eps = 3.000000)
[03:19:36 -481218.984393] FAST spr round 1 (radius: 25)
[03:22:04 -411601.554028] FAST spr round 2 (radius: 25)
[03:23:59 -409407.086327] FAST spr round 3 (radius: 25)
[03:25:45 -409143.646541] FAST spr round 4 (radius: 25)
[03:27:16 -409102.687056] FAST spr round 5 (radius: 25)
[03:28:40 -409102.686193] Model parameter optimization (eps = 1.000000)
[03:28:56 -409099.515958] SLOW spr round 1 (radius: 5)
[03:31:04 -409024.905789] SLOW spr round 2 (radius: 5)
[03:33:00 -409021.381836] SLOW spr round 3 (radius: 5)
[03:34:52 -409021.380909] SLOW spr round 4 (radius: 10)
[03:36:48 -409021.379991] SLOW spr round 5 (radius: 15)
[03:39:55 -409021.379069] SLOW spr round 6 (radius: 20)
[03:44:02 -409021.378143] SLOW spr round 7 (radius: 25)
[03:49:24 -409021.377212] Model parameter optimization (eps = 0.100000)

[03:49:30] ML tree search #5, logLikelihood: -409021.175396

[03:49:31 -1582723.061669] Initial branch length optimization
[03:49:36 -1360070.367965] Model parameter optimization (eps = 10.000000)
[03:50:12 -1355378.528980] AUTODETECT spr round 1 (radius: 5)
[03:52:19 -885417.439733] AUTODETECT spr round 2 (radius: 10)
[03:54:39 -648283.932484] AUTODETECT spr round 3 (radius: 15)
[03:57:01 -570035.469022] AUTODETECT spr round 4 (radius: 20)
[04:00:04 -505687.511583] AUTODETECT spr round 5 (radius: 25)
[04:03:22 -490179.096630] SPR radius for FAST iterations: 25 (autodetect)
[04:03:22 -490179.096630] Model parameter optimization (eps = 3.000000)
[04:03:40 -490023.352120] FAST spr round 1 (radius: 25)
[04:06:10 -412770.279935] FAST spr round 2 (radius: 25)
[04:08:03 -409205.977621] FAST spr round 3 (radius: 25)
[04:09:45 -409132.568022] FAST spr round 4 (radius: 25)
[04:11:13 -409124.593240] FAST spr round 5 (radius: 25)
[04:12:38 -409124.593237] Model parameter optimization (eps = 1.000000)
[04:12:51 -409123.206653] SLOW spr round 1 (radius: 5)
[04:14:56 -409011.251932] SLOW spr round 2 (radius: 5)
[04:16:54 -409003.004769] SLOW spr round 3 (radius: 5)
[04:18:47 -409003.004672] SLOW spr round 4 (radius: 10)
[04:20:44 -409003.004672] SLOW spr round 5 (radius: 15)
[04:23:53 -409003.004672] SLOW spr round 6 (radius: 20)
[04:28:12 -409003.004672] SLOW spr round 7 (radius: 25)
[04:33:49 -409003.004672] Model parameter optimization (eps = 0.100000)

[04:33:57] ML tree search #6, logLikelihood: -409002.885108

[04:33:57 -1591379.276086] Initial branch length optimization
[04:34:02 -1363890.330093] Model parameter optimization (eps = 10.000000)
[04:34:40 -1359229.720520] AUTODETECT spr round 1 (radius: 5)
[04:36:47 -898835.814103] AUTODETECT spr round 2 (radius: 10)
[04:39:06 -649356.355763] AUTODETECT spr round 3 (radius: 15)
[04:41:40 -532909.803473] AUTODETECT spr round 4 (radius: 20)
[04:44:47 -481866.923300] AUTODETECT spr round 5 (radius: 25)
[04:48:30 -479590.845103] SPR radius for FAST iterations: 25 (autodetect)
[04:48:30 -479590.845103] Model parameter optimization (eps = 3.000000)
[04:48:42 -479380.393715] FAST spr round 1 (radius: 25)
[04:51:08 -410824.993896] FAST spr round 2 (radius: 25)
[04:53:02 -409264.986113] FAST spr round 3 (radius: 25)
[04:54:40 -409123.755796] FAST spr round 4 (radius: 25)
[04:56:09 -409111.026538] FAST spr round 5 (radius: 25)
[04:57:34 -409111.026497] Model parameter optimization (eps = 1.000000)
[04:57:40 -409110.150606] SLOW spr round 1 (radius: 5)
[04:59:47 -409015.417750] SLOW spr round 2 (radius: 5)
[05:01:44 -409009.181967] SLOW spr round 3 (radius: 5)
[05:03:37 -409009.181944] SLOW spr round 4 (radius: 10)
[05:05:34 -409009.181944] SLOW spr round 5 (radius: 15)
[05:08:44 -409009.181944] SLOW spr round 6 (radius: 20)
[05:13:01 -409009.181944] SLOW spr round 7 (radius: 25)
[05:18:32 -409009.181944] Model parameter optimization (eps = 0.100000)

[05:18:36] ML tree search #7, logLikelihood: -409009.154288

[05:18:36 -1597356.473934] Initial branch length optimization
[05:18:42 -1367485.102823] Model parameter optimization (eps = 10.000000)
[05:19:21 -1362970.711957] AUTODETECT spr round 1 (radius: 5)
[05:21:28 -879780.189142] AUTODETECT spr round 2 (radius: 10)
[05:23:46 -638925.005087] AUTODETECT spr round 3 (radius: 15)
[05:26:11 -541175.092428] AUTODETECT spr round 4 (radius: 20)
[05:28:53 -507381.974795] AUTODETECT spr round 5 (radius: 25)
[05:31:44 -479276.058353] SPR radius for FAST iterations: 25 (autodetect)
[05:31:44 -479276.058353] Model parameter optimization (eps = 3.000000)
[05:32:00 -479111.469953] FAST spr round 1 (radius: 25)
[05:34:28 -411089.597887] FAST spr round 2 (radius: 25)
[05:36:22 -409225.139247] FAST spr round 3 (radius: 25)
[05:38:05 -409122.356166] FAST spr round 4 (radius: 25)
[05:39:33 -409122.345045] Model parameter optimization (eps = 1.000000)
[05:39:37 -409122.191694] SLOW spr round 1 (radius: 5)
[05:41:50 -409008.099941] SLOW spr round 2 (radius: 5)
[05:43:47 -409004.784781] SLOW spr round 3 (radius: 5)
[05:45:42 -409004.783727] SLOW spr round 4 (radius: 10)
[05:47:39 -409004.783678] SLOW spr round 5 (radius: 15)
[05:50:48 -409004.783678] SLOW spr round 6 (radius: 20)
[05:55:05 -409004.783678] SLOW spr round 7 (radius: 25)
[06:00:45 -409004.783678] Model parameter optimization (eps = 0.100000)

[06:00:56] ML tree search #8, logLikelihood: -409000.374088

[06:00:56 -1589633.712783] Initial branch length optimization
[06:01:02 -1362557.920687] Model parameter optimization (eps = 10.000000)
[06:01:36 -1357826.742113] AUTODETECT spr round 1 (radius: 5)
[06:03:43 -897044.006134] AUTODETECT spr round 2 (radius: 10)
[06:06:06 -633971.660956] AUTODETECT spr round 3 (radius: 15)
[06:08:29 -525585.288771] AUTODETECT spr round 4 (radius: 20)
[06:11:11 -499703.054331] AUTODETECT spr round 5 (radius: 25)
[06:14:40 -482083.642763] SPR radius for FAST iterations: 25 (autodetect)
[06:14:40 -482083.642763] Model parameter optimization (eps = 3.000000)
[06:14:47 -482080.483372] FAST spr round 1 (radius: 25)
[06:17:15 -411970.437808] FAST spr round 2 (radius: 25)
[06:19:01 -409366.689380] FAST spr round 3 (radius: 25)
[06:20:40 -409263.168675] FAST spr round 4 (radius: 25)
[06:22:11 -409234.163765] FAST spr round 5 (radius: 25)
[06:23:48 -409234.162913] Model parameter optimization (eps = 1.000000)
[06:24:03 -409104.199861] SLOW spr round 1 (radius: 5)
[06:26:26 -409003.943185] SLOW spr round 2 (radius: 5)
[06:28:49 -408997.897543] SLOW spr round 3 (radius: 5)
[06:31:05 -408997.389647] SLOW spr round 4 (radius: 5)
[06:33:20 -408997.389643] SLOW spr round 5 (radius: 10)
[06:35:39 -408997.389643] SLOW spr round 6 (radius: 15)
[06:39:26 -408997.389643] SLOW spr round 7 (radius: 20)
[06:44:33 -408997.389643] SLOW spr round 8 (radius: 25)
[06:51:12 -408997.389643] Model parameter optimization (eps = 0.100000)

[06:51:26] ML tree search #9, logLikelihood: -408995.629811

[06:51:26 -1606899.879301] Initial branch length optimization
[06:51:32 -1375029.174660] Model parameter optimization (eps = 10.000000)
[06:52:18 -1370491.574696] AUTODETECT spr round 1 (radius: 5)
[06:54:51 -899175.416604] AUTODETECT spr round 2 (radius: 10)
[06:57:36 -649160.451097] AUTODETECT spr round 3 (radius: 15)
[07:00:36 -523194.522642] AUTODETECT spr round 4 (radius: 20)
[07:04:09 -476064.896133] AUTODETECT spr round 5 (radius: 25)
[07:07:26 -473722.385547] SPR radius for FAST iterations: 25 (autodetect)
[07:07:26 -473722.385547] Model parameter optimization (eps = 3.000000)
[07:07:48 -473551.934177] FAST spr round 1 (radius: 25)
[07:10:44 -411149.089505] FAST spr round 2 (radius: 25)
[07:13:04 -409198.201289] FAST spr round 3 (radius: 25)
[07:15:04 -409146.590408] FAST spr round 4 (radius: 25)
[07:16:53 -409145.963452] FAST spr round 5 (radius: 25)
[07:18:38 -409145.963388] Model parameter optimization (eps = 1.000000)
[07:18:53 -409141.458111] SLOW spr round 1 (radius: 5)
[07:21:30 -409002.806406] SLOW spr round 2 (radius: 5)
[07:23:54 -408987.009252] SLOW spr round 3 (radius: 5)
[07:26:13 -408987.009088] SLOW spr round 4 (radius: 10)
[07:28:36 -408987.009087] SLOW spr round 5 (radius: 15)
[07:32:30 -408987.009087] SLOW spr round 6 (radius: 20)
[07:37:50 -408987.009087] SLOW spr round 7 (radius: 25)
[07:44:43 -408987.009087] Model parameter optimization (eps = 0.100000)

[07:44:56] ML tree search #10, logLikelihood: -408986.554303

[07:44:56 -1584638.965538] Initial branch length optimization
[07:45:06 -1363454.132810] Model parameter optimization (eps = 10.000000)
[07:45:42 -1358864.025774] AUTODETECT spr round 1 (radius: 5)
[07:48:16 -897229.736972] AUTODETECT spr round 2 (radius: 10)
[07:51:09 -649562.142600] AUTODETECT spr round 3 (radius: 15)
[07:54:05 -555754.166199] AUTODETECT spr round 4 (radius: 20)
[07:57:29 -509660.699419] AUTODETECT spr round 5 (radius: 25)
[08:01:13 -485803.977456] SPR radius for FAST iterations: 25 (autodetect)
[08:01:13 -485803.977456] Model parameter optimization (eps = 3.000000)
[08:01:18 -485802.184863] FAST spr round 1 (radius: 25)
[08:04:22 -412057.811277] FAST spr round 2 (radius: 25)
[08:06:41 -409357.448402] FAST spr round 3 (radius: 25)
[08:08:48 -409226.539703] FAST spr round 4 (radius: 25)
[08:10:41 -409209.199398] FAST spr round 5 (radius: 25)
[08:12:24 -409209.188143] Model parameter optimization (eps = 1.000000)
[08:12:41 -409096.737493] SLOW spr round 1 (radius: 5)
[08:15:13 -409002.558195] SLOW spr round 2 (radius: 5)
[08:17:33 -408995.090371] SLOW spr round 3 (radius: 5)
[08:19:51 -408995.089193] SLOW spr round 4 (radius: 10)
[08:22:14 -408995.088039] SLOW spr round 5 (radius: 15)
[08:26:05 -408995.087549] SLOW spr round 6 (radius: 20)
[08:31:15 -408995.087548] SLOW spr round 7 (radius: 25)
[08:38:11 -408995.087548] Model parameter optimization (eps = 0.100000)

[08:38:20] ML tree search #11, logLikelihood: -408994.625820

[08:38:20 -1581870.748498] Initial branch length optimization
[08:38:27 -1359154.244615] Model parameter optimization (eps = 10.000000)
[08:39:02 -1354481.854974] AUTODETECT spr round 1 (radius: 5)
[08:41:37 -887973.176161] AUTODETECT spr round 2 (radius: 10)
[08:44:26 -666550.256242] AUTODETECT spr round 3 (radius: 15)
[08:47:26 -550260.274317] AUTODETECT spr round 4 (radius: 20)
[08:51:14 -513640.301738] AUTODETECT spr round 5 (radius: 25)
[08:55:51 -495415.702366] SPR radius for FAST iterations: 25 (autodetect)
[08:55:51 -495415.702366] Model parameter optimization (eps = 3.000000)
[08:56:11 -495254.319499] FAST spr round 1 (radius: 25)
[08:59:15 -411945.537044] FAST spr round 2 (radius: 25)
[09:01:33 -409196.238573] FAST spr round 3 (radius: 25)
[09:03:39 -409113.840533] FAST spr round 4 (radius: 25)
[09:05:28 -409104.535705] FAST spr round 5 (radius: 25)
[09:07:12 -409104.055233] FAST spr round 6 (radius: 25)
[09:08:53 -409104.054287] Model parameter optimization (eps = 1.000000)
[09:09:04 -409100.313222] SLOW spr round 1 (radius: 5)
[09:11:38 -408996.736869] SLOW spr round 2 (radius: 5)
[09:13:57 -408992.512121] SLOW spr round 3 (radius: 5)
[09:16:13 -408992.511121] SLOW spr round 4 (radius: 10)
[09:18:34 -408992.510129] SLOW spr round 5 (radius: 15)
[09:22:20 -408992.509369] SLOW spr round 6 (radius: 20)
[09:27:24 -408992.509359] SLOW spr round 7 (radius: 25)
[09:33:57 -408992.509359] Model parameter optimization (eps = 0.100000)

[09:34:05] ML tree search #12, logLikelihood: -408992.285137

[09:34:05 -1597852.950976] Initial branch length optimization
[09:34:12 -1371043.511280] Model parameter optimization (eps = 10.000000)
[09:34:54 -1366341.280764] AUTODETECT spr round 1 (radius: 5)
[09:37:26 -878843.772110] AUTODETECT spr round 2 (radius: 10)
[09:40:18 -631664.849167] AUTODETECT spr round 3 (radius: 15)
[09:43:06 -552493.056874] AUTODETECT spr round 4 (radius: 20)
[09:46:04 -518921.538155] AUTODETECT spr round 5 (radius: 25)
[09:49:30 -489324.020444] SPR radius for FAST iterations: 25 (autodetect)
[09:49:30 -489324.020444] Model parameter optimization (eps = 3.000000)
[09:49:51 -489147.686019] FAST spr round 1 (radius: 25)
[09:52:59 -411400.796957] FAST spr round 2 (radius: 25)
[09:55:20 -409181.600052] FAST spr round 3 (radius: 25)
[09:57:25 -409107.016455] FAST spr round 4 (radius: 25)
[09:59:10 -409107.015334] Model parameter optimization (eps = 1.000000)
[09:59:25 -409098.878019] SLOW spr round 1 (radius: 5)
[10:02:03 -408994.012011] SLOW spr round 2 (radius: 5)
[10:04:23 -408992.827202] SLOW spr round 3 (radius: 5)
[10:06:38 -408992.826829] SLOW spr round 4 (radius: 10)
[10:08:57 -408992.826829] SLOW spr round 5 (radius: 15)
[10:12:46 -408992.826829] SLOW spr round 6 (radius: 20)
[10:17:57 -408992.826829] SLOW spr round 7 (radius: 25)
[10:24:42 -408992.826829] Model parameter optimization (eps = 0.100000)

[10:24:47] ML tree search #13, logLikelihood: -408992.743456

[10:24:48 -1586683.739220] Initial branch length optimization
[10:24:55 -1366849.474647] Model parameter optimization (eps = 10.000000)
[10:25:37 -1362107.950287] AUTODETECT spr round 1 (radius: 5)
[10:28:14 -893040.650213] AUTODETECT spr round 2 (radius: 10)
[10:31:05 -681810.826789] AUTODETECT spr round 3 (radius: 15)
[10:33:53 -562964.561624] AUTODETECT spr round 4 (radius: 20)
[10:37:06 -502298.771872] AUTODETECT spr round 5 (radius: 25)
[10:40:36 -494665.319426] SPR radius for FAST iterations: 25 (autodetect)
[10:40:36 -494665.319426] Model parameter optimization (eps = 3.000000)
[10:40:45 -494594.523246] FAST spr round 1 (radius: 25)
[10:43:48 -410804.396156] FAST spr round 2 (radius: 25)
[10:46:05 -409376.120297] FAST spr round 3 (radius: 25)
[10:48:06 -409263.750474] FAST spr round 4 (radius: 25)
[10:49:51 -409253.741486] FAST spr round 5 (radius: 25)
[10:51:31 -409250.936740] FAST spr round 6 (radius: 25)
[10:53:11 -409250.935892] Model parameter optimization (eps = 1.000000)
[10:53:28 -409140.785324] SLOW spr round 1 (radius: 5)
[10:55:58 -409004.633231] SLOW spr round 2 (radius: 5)
[10:58:18 -408987.087389] SLOW spr round 3 (radius: 5)
[11:00:33 -408985.767115] SLOW spr round 4 (radius: 5)
[11:02:46 -408985.767085] SLOW spr round 5 (radius: 10)
[11:05:02 -408985.767085] SLOW spr round 6 (radius: 15)
[11:08:50 -408985.767085] SLOW spr round 7 (radius: 20)
[11:13:56 -408985.767085] SLOW spr round 8 (radius: 25)
[11:20:47 -408985.767085] Model parameter optimization (eps = 0.100000)

[11:20:55] ML tree search #14, logLikelihood: -408985.485263

[11:20:55 -1589716.154651] Initial branch length optimization
[11:21:04 -1365166.526111] Model parameter optimization (eps = 10.000000)
[11:21:43 -1360389.099213] AUTODETECT spr round 1 (radius: 5)
[11:24:19 -890070.754313] AUTODETECT spr round 2 (radius: 10)
[11:27:16 -646222.581741] AUTODETECT spr round 3 (radius: 15)
[11:30:12 -525504.507532] AUTODETECT spr round 4 (radius: 20)
[11:33:45 -473984.748281] AUTODETECT spr round 5 (radius: 25)
[11:37:43 -467732.868732] SPR radius for FAST iterations: 25 (autodetect)
[11:37:43 -467732.868732] Model parameter optimization (eps = 3.000000)
[11:38:01 -467599.656007] FAST spr round 1 (radius: 25)
[11:41:03 -410913.082830] FAST spr round 2 (radius: 25)
[11:43:24 -409299.439354] FAST spr round 3 (radius: 25)
[11:45:34 -409135.512940] FAST spr round 4 (radius: 25)
[11:47:31 -409122.665535] FAST spr round 5 (radius: 25)
[11:49:17 -409122.665534] Model parameter optimization (eps = 1.000000)
[11:49:33 -409114.928052] SLOW spr round 1 (radius: 5)
[11:52:09 -409009.755728] SLOW spr round 2 (radius: 5)
[11:54:28 -409004.835329] SLOW spr round 3 (radius: 5)
[11:56:45 -409004.835241] SLOW spr round 4 (radius: 10)
[11:59:05 -409004.835241] SLOW spr round 5 (radius: 15)
[12:02:47 -409004.835241] SLOW spr round 6 (radius: 20)
[12:07:49 -409004.835241] SLOW spr round 7 (radius: 25)
[12:14:25 -409004.835241] Model parameter optimization (eps = 0.100000)

[12:14:34] ML tree search #15, logLikelihood: -409004.618263

[12:14:34 -1582514.085552] Initial branch length optimization
[12:14:40 -1360369.060975] Model parameter optimization (eps = 10.000000)
[12:15:17 -1355646.068187] AUTODETECT spr round 1 (radius: 5)
[12:17:52 -874800.128936] AUTODETECT spr round 2 (radius: 10)
[12:20:41 -660485.835698] AUTODETECT spr round 3 (radius: 15)
[12:23:43 -553559.859407] AUTODETECT spr round 4 (radius: 20)
[12:27:19 -487051.129805] AUTODETECT spr round 5 (radius: 25)
[12:31:08 -478147.122655] SPR radius for FAST iterations: 25 (autodetect)
[12:31:08 -478147.122655] Model parameter optimization (eps = 3.000000)
[12:31:27 -477996.035045] FAST spr round 1 (radius: 25)
[12:34:26 -411033.844995] FAST spr round 2 (radius: 25)
[12:36:44 -409222.039697] FAST spr round 3 (radius: 25)
[12:38:50 -409111.570181] FAST spr round 4 (radius: 25)
[12:40:37 -409108.556700] FAST spr round 5 (radius: 25)
[12:42:22 -409104.185614] FAST spr round 6 (radius: 25)
[12:44:07 -409104.185611] Model parameter optimization (eps = 1.000000)
[12:44:20 -409097.488657] SLOW spr round 1 (radius: 5)
[12:46:54 -409004.199888] SLOW spr round 2 (radius: 5)
[12:49:19 -408994.658365] SLOW spr round 3 (radius: 5)
[12:51:38 -408993.475201] SLOW spr round 4 (radius: 5)
[12:53:55 -408993.475197] SLOW spr round 5 (radius: 10)
[12:56:17 -408993.475197] SLOW spr round 6 (radius: 15)
[13:00:07 -408993.475197] SLOW spr round 7 (radius: 20)
[13:05:13 -408993.475197] SLOW spr round 8 (radius: 25)
[13:11:45 -408993.475197] Model parameter optimization (eps = 0.100000)

[13:11:54] ML tree search #16, logLikelihood: -408993.265353

[13:11:54 -1582376.103777] Initial branch length optimization
[13:12:06 -1356115.619841] Model parameter optimization (eps = 10.000000)
[13:12:49 -1351465.682971] AUTODETECT spr round 1 (radius: 5)
[13:15:24 -896085.917291] AUTODETECT spr round 2 (radius: 10)
[13:18:14 -656601.137320] AUTODETECT spr round 3 (radius: 15)
[13:21:12 -503020.893181] AUTODETECT spr round 4 (radius: 20)
[13:24:56 -473232.916882] AUTODETECT spr round 5 (radius: 25)
[13:28:51 -470702.001182] SPR radius for FAST iterations: 25 (autodetect)
[13:28:51 -470702.001182] Model parameter optimization (eps = 3.000000)
[13:29:11 -470535.809527] FAST spr round 1 (radius: 25)
[13:32:06 -410592.143019] FAST spr round 2 (radius: 25)
[13:34:18 -409225.712182] FAST spr round 3 (radius: 25)
[13:36:17 -409174.640385] FAST spr round 4 (radius: 25)
[13:38:03 -409171.101129] FAST spr round 5 (radius: 25)
[13:39:51 -409130.587615] FAST spr round 6 (radius: 25)
[13:41:32 -409130.587603] Model parameter optimization (eps = 1.000000)
[13:41:47 -409124.658141] SLOW spr round 1 (radius: 5)
[13:44:17 -409016.060193] SLOW spr round 2 (radius: 5)
[13:46:33 -408999.753771] SLOW spr round 3 (radius: 5)
[13:48:48 -408996.983914] SLOW spr round 4 (radius: 5)
[13:51:02 -408996.983914] SLOW spr round 5 (radius: 10)
[13:53:20 -408996.983914] SLOW spr round 6 (radius: 15)
[13:57:11 -408996.983914] SLOW spr round 7 (radius: 20)
[14:02:26 -408996.983914] SLOW spr round 8 (radius: 25)
[14:09:16 -408996.983914] Model parameter optimization (eps = 0.100000)

[14:09:23] ML tree search #17, logLikelihood: -408996.674168

[14:09:24 -1593891.006020] Initial branch length optimization
[14:09:31 -1367219.147971] Model parameter optimization (eps = 10.000000)
[14:10:07 -1362738.101933] AUTODETECT spr round 1 (radius: 5)
[14:12:35 -887583.506792] AUTODETECT spr round 2 (radius: 10)
[14:15:19 -626741.982237] AUTODETECT spr round 3 (radius: 15)
[14:18:08 -504843.126186] AUTODETECT spr round 4 (radius: 20)
[14:21:16 -477152.018704] AUTODETECT spr round 5 (radius: 25)
[14:24:46 -475888.265655] SPR radius for FAST iterations: 25 (autodetect)
[14:24:46 -475888.265655] Model parameter optimization (eps = 3.000000)
[14:25:02 -475698.341051] FAST spr round 1 (radius: 25)
[14:27:58 -412154.186186] FAST spr round 2 (radius: 25)
[14:30:12 -409228.357380] FAST spr round 3 (radius: 25)
[14:32:13 -409110.063665] FAST spr round 4 (radius: 25)
[14:34:00 -409104.557401] FAST spr round 5 (radius: 25)
[14:35:40 -409104.557396] Model parameter optimization (eps = 1.000000)
[14:35:54 -409100.527596] SLOW spr round 1 (radius: 5)
[14:38:25 -409012.489974] SLOW spr round 2 (radius: 5)
[14:40:38 -409008.876284] SLOW spr round 3 (radius: 5)
[14:42:54 -409004.036001] SLOW spr round 4 (radius: 5)
[14:45:08 -409004.035914] SLOW spr round 5 (radius: 10)
[14:47:27 -409004.035914] SLOW spr round 6 (radius: 15)
[14:51:14 -409004.035914] SLOW spr round 7 (radius: 20)
[14:56:25 -409004.035914] SLOW spr round 8 (radius: 25)
[15:03:13 -409004.035914] Model parameter optimization (eps = 0.100000)

[15:03:18] ML tree search #18, logLikelihood: -409004.030015

[15:03:18 -1593850.265803] Initial branch length optimization
[15:03:25 -1365426.225684] Model parameter optimization (eps = 10.000000)
[15:04:01 -1360801.573267] AUTODETECT spr round 1 (radius: 5)
[15:06:33 -860315.906316] AUTODETECT spr round 2 (radius: 10)
[15:09:18 -628320.002416] AUTODETECT spr round 3 (radius: 15)
[15:12:02 -506159.104108] AUTODETECT spr round 4 (radius: 20)
[15:15:07 -479486.371213] AUTODETECT spr round 5 (radius: 25)
[15:18:55 -474307.285272] SPR radius for FAST iterations: 25 (autodetect)
[15:18:55 -474307.285272] Model parameter optimization (eps = 3.000000)
[15:19:03 -474304.172322] FAST spr round 1 (radius: 25)
[15:22:07 -411936.533630] FAST spr round 2 (radius: 25)
[15:24:27 -409366.509710] FAST spr round 3 (radius: 25)
[15:26:29 -409307.427454] FAST spr round 4 (radius: 25)
[15:28:17 -409305.433959] FAST spr round 5 (radius: 25)
[15:30:02 -409305.422877] Model parameter optimization (eps = 1.000000)
[15:30:20 -409166.899537] SLOW spr round 1 (radius: 5)
[15:33:01 -409022.972510] SLOW spr round 2 (radius: 5)
[15:35:31 -408994.964561] SLOW spr round 3 (radius: 5)
[15:37:55 -408987.236717] SLOW spr round 4 (radius: 5)
[15:40:13 -408987.236665] SLOW spr round 5 (radius: 10)
[15:42:36 -408987.236665] SLOW spr round 6 (radius: 15)
[15:46:30 -408987.236665] SLOW spr round 7 (radius: 20)
[15:51:51 -408987.236665] SLOW spr round 8 (radius: 25)
[15:58:46 -408987.236665] Model parameter optimization (eps = 0.100000)

[15:58:55] ML tree search #19, logLikelihood: -408986.927840

[15:58:55 -1586979.950950] Initial branch length optimization
[15:59:02 -1364000.380410] Model parameter optimization (eps = 10.000000)
[15:59:50 -1359556.220639] AUTODETECT spr round 1 (radius: 5)
[16:02:23 -867105.138061] AUTODETECT spr round 2 (radius: 10)
[16:05:09 -643837.235480] AUTODETECT spr round 3 (radius: 15)
[16:08:02 -547436.847391] AUTODETECT spr round 4 (radius: 20)
[16:11:22 -510607.522277] AUTODETECT spr round 5 (radius: 25)
[16:14:53 -492281.150736] SPR radius for FAST iterations: 25 (autodetect)
[16:14:53 -492281.150736] Model parameter optimization (eps = 3.000000)
[16:15:03 -492277.809605] FAST spr round 1 (radius: 25)
[16:18:08 -412827.494793] FAST spr round 2 (radius: 25)
[16:20:29 -409365.813391] FAST spr round 3 (radius: 25)
[16:22:33 -409244.159942] FAST spr round 4 (radius: 25)
[16:24:19 -409236.061401] FAST spr round 5 (radius: 25)
[16:26:01 -409236.061399] Model parameter optimization (eps = 1.000000)
[16:26:16 -409118.763552] SLOW spr round 1 (radius: 5)
[16:28:50 -408988.499673] SLOW spr round 2 (radius: 5)
[16:31:08 -408986.579886] SLOW spr round 3 (radius: 5)
[16:33:21 -408986.579852] SLOW spr round 4 (radius: 10)
[16:35:42 -408986.579852] SLOW spr round 5 (radius: 15)
[16:39:28 -408986.579852] SLOW spr round 6 (radius: 20)
[16:44:33 -408986.579852] SLOW spr round 7 (radius: 25)
[16:51:23 -408986.579852] Model parameter optimization (eps = 0.100000)

[16:51:33] ML tree search #20, logLikelihood: -408985.754278


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.257154,0.362432) (0.308782,0.522773) (0.257021,1.121616) (0.177043,2.581842) 
   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: -408985.485263

AIC score: 821980.970527 / AICc score: 8866040.970527 / BIC score: 832250.700590
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1239).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 50 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/3_mltree/P53621.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/3_mltree/P53621.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/3_mltree/P53621.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/3_mltree/P53621.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53621/3_mltree/P53621.raxml.log

Analysis started: 14-Jul-2021 04:53:41 / finished: 14-Jul-2021 21:45:15

Elapsed time: 60693.636 seconds

Consumed energy: 5563.119 Wh (= 28 km in an electric car, or 139 km with an e-scooter!)