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 04-Jul-2021 17:41:59 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/2_msa/Q8TDP1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/3_mltree/Q8TDP1 --seed 2 --threads 1 --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), NONE/sequential

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/2_msa/Q8TDP1_trimmed_msa.fasta
[00:00:00] Loaded alignment with 177 taxa and 65 sites

WARNING: Sequences tr_A0A2I3GNK3_A0A2I3GNK3_NOMLE_61853 and tr_A0A2I3SZU0_A0A2I3SZU0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GNK3_A0A2I3GNK3_NOMLE_61853 and tr_A0A2R9CD26_A0A2R9CD26_PANPA_9597 are exactly identical!
WARNING: Sequences tr_B8NNS1_B8NNS1_ASPFN_332952 and tr_Q2UMQ1_Q2UMQ1_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NNS1_B8NNS1_ASPFN_332952 and tr_A0A1S9D6B1_A0A1S9D6B1_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_F9FD36_F9FD36_FUSOF_660025 and tr_A0A0D2Y520_A0A0D2Y520_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FD36_F9FD36_FUSOF_660025 and tr_N4UHH5_N4UHH5_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FD36_F9FD36_FUSOF_660025 and tr_X0C8I6_X0C8I6_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FD36_F9FD36_FUSOF_660025 and tr_A0A2H3TLK0_A0A2H3TLK0_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_H9H3U9_H9H3U9_MACMU_9544 and tr_G7PPH4_G7PPH4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H9H3U9_H9H3U9_MACMU_9544 and tr_A0A0D9R6K7_A0A0D9R6K7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9H3U9_H9H3U9_MACMU_9544 and tr_A0A2K6DI20_A0A2K6DI20_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K1YCG9_A0A2K1YCG9_POPTR_3694 and tr_A9P9L9_A9P9L9_POPTR_3694 are exactly identical!
WARNING: Sequences tr_A0A2D0RFX2_A0A2D0RFX2_ICTPU_7998 and tr_E3TGI1_E3TGI1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2G2XYT6_A0A2G2XYT6_CAPAN_4072 and tr_A0A2G3D417_A0A2G3D417_CAPCH_80379 are exactly identical!
WARNING: Duplicate sequences found: 14

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/Q8TDP1/3_mltree/Q8TDP1.raxml.reduced.phy

Alignment comprises 1 partitions and 65 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 65 / 65
Gaps: 2.84 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/3_mltree/Q8TDP1.raxml.rba

Parallelization scheme autoconfig: 1 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 177 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 65 / 5200
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -21345.662408] Initial branch length optimization
[00:00:00 -17191.697428] Model parameter optimization (eps = 10.000000)
[00:00:05 -17152.238345] AUTODETECT spr round 1 (radius: 5)
[00:00:09 -12373.042489] AUTODETECT spr round 2 (radius: 10)
[00:00:13 -10439.289077] AUTODETECT spr round 3 (radius: 15)
[00:00:19 -9959.310484] AUTODETECT spr round 4 (radius: 20)
[00:00:24 -9465.400744] AUTODETECT spr round 5 (radius: 25)
[00:00:30 -9429.921865] SPR radius for FAST iterations: 25 (autodetect)
[00:00:30 -9429.921865] Model parameter optimization (eps = 3.000000)
[00:00:32 -9422.672344] FAST spr round 1 (radius: 25)
[00:00:38 -8527.673210] FAST spr round 2 (radius: 25)
[00:00:43 -8444.666121] FAST spr round 3 (radius: 25)
[00:00:46 -8431.880877] FAST spr round 4 (radius: 25)
[00:00:50 -8427.510976] FAST spr round 5 (radius: 25)
[00:00:53 -8424.239042] FAST spr round 6 (radius: 25)
[00:00:57 -8424.238504] Model parameter optimization (eps = 1.000000)
[00:00:58 -8423.216836] SLOW spr round 1 (radius: 5)
[00:01:04 -8421.580997] SLOW spr round 2 (radius: 5)
[00:01:10 -8421.028265] SLOW spr round 3 (radius: 5)
[00:01:15 -8419.341522] SLOW spr round 4 (radius: 5)
[00:01:20 -8419.325082] SLOW spr round 5 (radius: 10)
[00:01:25 -8419.017561] SLOW spr round 6 (radius: 5)
[00:01:34 -8419.015902] SLOW spr round 7 (radius: 10)
[00:01:40 -8417.573744] SLOW spr round 8 (radius: 5)
[00:01:48 -8417.573730] SLOW spr round 9 (radius: 10)
[00:01:55 -8417.573729] SLOW spr round 10 (radius: 15)
[00:02:02 -8417.521749] SLOW spr round 11 (radius: 20)
[00:02:09 -8417.521749] SLOW spr round 12 (radius: 25)
[00:02:18 -8417.521749] Model parameter optimization (eps = 0.100000)

[00:02:19] ML tree search #1, logLikelihood: -8417.506737

[00:02:19 -21524.286662] Initial branch length optimization
[00:02:19 -17365.472499] Model parameter optimization (eps = 10.000000)
[00:02:23 -17332.836664] AUTODETECT spr round 1 (radius: 5)
[00:02:26 -12721.638760] AUTODETECT spr round 2 (radius: 10)
[00:02:31 -10614.878851] AUTODETECT spr round 3 (radius: 15)
[00:02:36 -9593.043289] AUTODETECT spr round 4 (radius: 20)
[00:02:42 -9276.417216] AUTODETECT spr round 5 (radius: 25)
[00:02:47 -9276.361400] SPR radius for FAST iterations: 20 (autodetect)
[00:02:47 -9276.361400] Model parameter optimization (eps = 3.000000)
[00:02:49 -9266.172765] FAST spr round 1 (radius: 20)
[00:02:54 -8440.622599] FAST spr round 2 (radius: 20)
[00:02:57 -8424.841404] FAST spr round 3 (radius: 20)
[00:03:01 -8423.369006] FAST spr round 4 (radius: 20)
[00:03:04 -8423.368089] Model parameter optimization (eps = 1.000000)
[00:03:06 -8418.897502] SLOW spr round 1 (radius: 5)
[00:03:13 -8416.650062] SLOW spr round 2 (radius: 5)
[00:03:19 -8416.647892] SLOW spr round 3 (radius: 10)
[00:03:25 -8412.740471] SLOW spr round 4 (radius: 5)
[00:03:33 -8412.358143] SLOW spr round 5 (radius: 5)
[00:03:40 -8412.340520] SLOW spr round 6 (radius: 10)
[00:03:46 -8412.340369] SLOW spr round 7 (radius: 15)
[00:03:53 -8412.340245] SLOW spr round 8 (radius: 20)
[00:04:01 -8412.340152] SLOW spr round 9 (radius: 25)
[00:04:10 -8412.340152] Model parameter optimization (eps = 0.100000)

[00:04:11] ML tree search #2, logLikelihood: -8412.186408

[00:04:11 -20901.338037] Initial branch length optimization
[00:04:11 -16937.217998] Model parameter optimization (eps = 10.000000)
[00:04:14 -16912.355039] AUTODETECT spr round 1 (radius: 5)
[00:04:18 -12189.142191] AUTODETECT spr round 2 (radius: 10)
[00:04:22 -10483.886193] AUTODETECT spr round 3 (radius: 15)
[00:04:27 -9675.885806] AUTODETECT spr round 4 (radius: 20)
[00:04:34 -9466.073078] AUTODETECT spr round 5 (radius: 25)
[00:04:39 -9444.058440] SPR radius for FAST iterations: 25 (autodetect)
[00:04:39 -9444.058440] Model parameter optimization (eps = 3.000000)
[00:04:42 -9412.899074] FAST spr round 1 (radius: 25)
[00:04:47 -8495.411291] FAST spr round 2 (radius: 25)
[00:04:52 -8445.934518] FAST spr round 3 (radius: 25)
[00:04:55 -8442.031749] FAST spr round 4 (radius: 25)
[00:04:59 -8440.480851] FAST spr round 5 (radius: 25)
[00:05:03 -8436.852129] FAST spr round 6 (radius: 25)
[00:05:06 -8436.318455] FAST spr round 7 (radius: 25)
[00:05:10 -8436.318445] Model parameter optimization (eps = 1.000000)
[00:05:12 -8434.380513] SLOW spr round 1 (radius: 5)
[00:05:18 -8434.235420] SLOW spr round 2 (radius: 5)
[00:05:24 -8434.235148] SLOW spr round 3 (radius: 10)
[00:05:30 -8434.235134] SLOW spr round 4 (radius: 15)
[00:05:36 -8434.235132] SLOW spr round 5 (radius: 20)
[00:05:44 -8434.235132] SLOW spr round 6 (radius: 25)
[00:05:53 -8434.235132] Model parameter optimization (eps = 0.100000)

[00:05:54] ML tree search #3, logLikelihood: -8434.230915

[00:05:54 -21293.692886] Initial branch length optimization
[00:05:54 -17109.346679] Model parameter optimization (eps = 10.000000)
[00:05:57 -17076.097157] AUTODETECT spr round 1 (radius: 5)
[00:06:01 -12722.388466] AUTODETECT spr round 2 (radius: 10)
[00:06:05 -10057.862936] AUTODETECT spr round 3 (radius: 15)
[00:06:11 -9122.529463] AUTODETECT spr round 4 (radius: 20)
[00:06:16 -9088.274757] AUTODETECT spr round 5 (radius: 25)
[00:06:21 -9078.636988] SPR radius for FAST iterations: 25 (autodetect)
[00:06:21 -9078.636988] Model parameter optimization (eps = 3.000000)
[00:06:24 -9061.432284] FAST spr round 1 (radius: 25)
[00:06:29 -8453.521805] FAST spr round 2 (radius: 25)
[00:06:33 -8428.889015] FAST spr round 3 (radius: 25)
[00:06:37 -8428.428070] FAST spr round 4 (radius: 25)
[00:06:40 -8428.427273] Model parameter optimization (eps = 1.000000)
[00:06:43 -8426.306910] SLOW spr round 1 (radius: 5)
[00:06:50 -8423.738114] SLOW spr round 2 (radius: 5)
[00:06:56 -8423.601865] SLOW spr round 3 (radius: 5)
[00:07:03 -8423.600945] SLOW spr round 4 (radius: 10)
[00:07:08 -8422.096759] SLOW spr round 5 (radius: 5)
[00:07:17 -8420.437034] SLOW spr round 6 (radius: 5)
[00:07:24 -8420.436354] SLOW spr round 7 (radius: 10)
[00:07:30 -8419.081643] SLOW spr round 8 (radius: 5)
[00:07:38 -8419.050459] SLOW spr round 9 (radius: 10)
[00:07:43 -8419.048863] SLOW spr round 10 (radius: 15)
[00:07:48 -8418.515555] SLOW spr round 11 (radius: 5)
[00:07:56 -8418.515473] SLOW spr round 12 (radius: 10)
[00:08:03 -8418.515469] SLOW spr round 13 (radius: 15)
[00:08:10 -8418.515468] SLOW spr round 14 (radius: 20)
[00:08:17 -8418.515468] SLOW spr round 15 (radius: 25)
[00:08:25 -8418.361638] SLOW spr round 16 (radius: 5)
[00:08:35 -8418.360091] SLOW spr round 17 (radius: 10)
[00:08:41 -8418.096422] SLOW spr round 18 (radius: 5)
[00:08:49 -8415.919720] SLOW spr round 19 (radius: 5)
[00:08:56 -8412.259142] SLOW spr round 20 (radius: 5)
[00:09:01 -8412.259119] SLOW spr round 21 (radius: 10)
[00:09:06 -8412.259119] SLOW spr round 22 (radius: 15)
[00:09:12 -8412.259118] SLOW spr round 23 (radius: 20)
[00:09:18 -8412.259118] SLOW spr round 24 (radius: 25)
[00:09:24 -8412.259118] Model parameter optimization (eps = 0.100000)

[00:09:26] ML tree search #4, logLikelihood: -8411.562513

[00:09:26 -20867.223698] Initial branch length optimization
[00:09:26 -16813.116305] Model parameter optimization (eps = 10.000000)
[00:09:28 -16795.792041] AUTODETECT spr round 1 (radius: 5)
[00:09:31 -12563.405396] AUTODETECT spr round 2 (radius: 10)
[00:09:35 -10453.712190] AUTODETECT spr round 3 (radius: 15)
[00:09:41 -9485.519917] AUTODETECT spr round 4 (radius: 20)
[00:09:47 -9354.099610] AUTODETECT spr round 5 (radius: 25)
[00:09:53 -9344.944223] SPR radius for FAST iterations: 25 (autodetect)
[00:09:53 -9344.944223] Model parameter optimization (eps = 3.000000)
[00:09:57 -9312.094827] FAST spr round 1 (radius: 25)
[00:10:03 -8480.517776] FAST spr round 2 (radius: 25)
[00:10:08 -8445.098283] FAST spr round 3 (radius: 25)
[00:10:13 -8440.918870] FAST spr round 4 (radius: 25)
[00:10:16 -8440.834797] Model parameter optimization (eps = 1.000000)
[00:10:19 -8439.433892] SLOW spr round 1 (radius: 5)
[00:10:26 -8437.558317] SLOW spr round 2 (radius: 5)
[00:10:32 -8437.552353] SLOW spr round 3 (radius: 10)
[00:10:38 -8416.141397] SLOW spr round 4 (radius: 5)
[00:10:47 -8416.138056] SLOW spr round 5 (radius: 10)
[00:10:54 -8416.136187] SLOW spr round 6 (radius: 15)
[00:11:01 -8415.644360] SLOW spr round 7 (radius: 5)
[00:11:10 -8415.644173] SLOW spr round 8 (radius: 10)
[00:11:17 -8415.644071] SLOW spr round 9 (radius: 15)
[00:11:24 -8415.643986] SLOW spr round 10 (radius: 20)
[00:11:33 -8415.643905] SLOW spr round 11 (radius: 25)
[00:11:41 -8415.643825] Model parameter optimization (eps = 0.100000)

[00:11:44] ML tree search #5, logLikelihood: -8415.462723

[00:11:44 -21249.510771] Initial branch length optimization
[00:11:44 -16986.789520] Model parameter optimization (eps = 10.000000)
[00:11:46 -16963.872407] AUTODETECT spr round 1 (radius: 5)
[00:11:49 -12563.055293] AUTODETECT spr round 2 (radius: 10)
[00:11:53 -10546.900225] AUTODETECT spr round 3 (radius: 15)
[00:11:57 -9982.979647] AUTODETECT spr round 4 (radius: 20)
[00:12:02 -9974.350355] AUTODETECT spr round 5 (radius: 25)
[00:12:07 -9867.482227] SPR radius for FAST iterations: 25 (autodetect)
[00:12:07 -9867.482227] Model parameter optimization (eps = 3.000000)
[00:12:11 -9834.161615] FAST spr round 1 (radius: 25)
[00:12:16 -9103.874804] FAST spr round 2 (radius: 25)
[00:12:21 -9039.381350] FAST spr round 3 (radius: 25)
[00:12:25 -9037.613211] FAST spr round 4 (radius: 25)
[00:12:28 -9037.611515] Model parameter optimization (eps = 1.000000)
[00:12:31 -9035.745991] SLOW spr round 1 (radius: 5)
[00:12:38 -9030.886621] SLOW spr round 2 (radius: 5)
[00:12:44 -9029.940301] SLOW spr round 3 (radius: 5)
[00:12:49 -9029.940250] SLOW spr round 4 (radius: 10)
[00:12:54 -9029.940204] SLOW spr round 5 (radius: 15)
[00:13:00 -9029.922507] SLOW spr round 6 (radius: 20)
[00:13:06 -9029.920875] SLOW spr round 7 (radius: 25)
[00:13:13 -8999.267357] SLOW spr round 8 (radius: 5)
[00:13:22 -8790.747632] SLOW spr round 9 (radius: 5)
[00:13:31 -8571.935098] SLOW spr round 10 (radius: 5)
[00:13:38 -8555.867811] SLOW spr round 11 (radius: 5)
[00:13:45 -8553.816632] SLOW spr round 12 (radius: 5)
[00:13:52 -8553.816297] SLOW spr round 13 (radius: 10)
[00:13:58 -8444.534233] SLOW spr round 14 (radius: 5)
[00:14:07 -8436.003147] SLOW spr round 15 (radius: 5)
[00:14:14 -8436.000545] SLOW spr round 16 (radius: 10)
[00:14:20 -8431.840449] SLOW spr round 17 (radius: 5)
[00:14:27 -8429.188189] SLOW spr round 18 (radius: 5)
[00:14:33 -8429.188094] SLOW spr round 19 (radius: 10)
[00:14:40 -8429.188090] SLOW spr round 20 (radius: 15)
[00:14:47 -8429.188090] SLOW spr round 21 (radius: 20)
[00:14:55 -8425.947102] SLOW spr round 22 (radius: 5)
[00:15:03 -8423.044599] SLOW spr round 23 (radius: 5)
[00:15:10 -8420.499042] SLOW spr round 24 (radius: 5)
[00:15:16 -8420.478361] SLOW spr round 25 (radius: 10)
[00:15:21 -8420.159389] SLOW spr round 26 (radius: 5)
[00:15:30 -8417.171244] SLOW spr round 27 (radius: 5)
[00:15:37 -8417.170723] SLOW spr round 28 (radius: 10)
[00:15:43 -8417.170651] SLOW spr round 29 (radius: 15)
[00:15:50 -8417.170640] SLOW spr round 30 (radius: 20)
[00:15:58 -8417.170639] SLOW spr round 31 (radius: 25)
[00:16:08 -8417.170639] Model parameter optimization (eps = 0.100000)

[00:16:08] ML tree search #6, logLikelihood: -8417.093760

[00:16:08 -21357.688324] Initial branch length optimization
[00:16:08 -17189.611591] Model parameter optimization (eps = 10.000000)
[00:16:12 -17144.357709] AUTODETECT spr round 1 (radius: 5)
[00:16:16 -11993.426427] AUTODETECT spr round 2 (radius: 10)
[00:16:20 -9670.327680] AUTODETECT spr round 3 (radius: 15)
[00:16:26 -9097.651481] AUTODETECT spr round 4 (radius: 20)
[00:16:31 -9061.676772] AUTODETECT spr round 5 (radius: 25)
[00:16:35 -9034.190493] SPR radius for FAST iterations: 25 (autodetect)
[00:16:35 -9034.190493] Model parameter optimization (eps = 3.000000)
[00:16:38 -9021.548432] FAST spr round 1 (radius: 25)
[00:16:42 -8452.394996] FAST spr round 2 (radius: 25)
[00:16:46 -8422.578288] FAST spr round 3 (radius: 25)
[00:16:49 -8420.454590] FAST spr round 4 (radius: 25)
[00:16:53 -8420.454544] Model parameter optimization (eps = 1.000000)
[00:16:54 -8419.970316] SLOW spr round 1 (radius: 5)
[00:17:01 -8419.488435] SLOW spr round 2 (radius: 5)
[00:17:07 -8419.487897] SLOW spr round 3 (radius: 10)
[00:17:13 -8416.835602] SLOW spr round 4 (radius: 5)
[00:17:21 -8416.168051] SLOW spr round 5 (radius: 5)
[00:17:28 -8416.167886] SLOW spr round 6 (radius: 10)
[00:17:34 -8416.167765] SLOW spr round 7 (radius: 15)
[00:17:42 -8415.925129] SLOW spr round 8 (radius: 5)
[00:17:50 -8413.318911] SLOW spr round 9 (radius: 5)
[00:17:58 -8412.824436] SLOW spr round 10 (radius: 5)
[00:18:04 -8412.823616] SLOW spr round 11 (radius: 10)
[00:18:10 -8411.957984] SLOW spr round 12 (radius: 5)
[00:18:18 -8411.957636] SLOW spr round 13 (radius: 10)
[00:18:24 -8411.957495] SLOW spr round 14 (radius: 15)
[00:18:31 -8411.827192] SLOW spr round 15 (radius: 5)
[00:18:40 -8411.825747] SLOW spr round 16 (radius: 10)
[00:18:47 -8411.825740] SLOW spr round 17 (radius: 15)
[00:18:54 -8411.722411] SLOW spr round 18 (radius: 5)
[00:19:03 -8411.686993] SLOW spr round 19 (radius: 10)
[00:19:09 -8411.686957] SLOW spr round 20 (radius: 15)
[00:19:16 -8411.686956] SLOW spr round 21 (radius: 20)
[00:19:23 -8411.686956] SLOW spr round 22 (radius: 25)
[00:19:31 -8411.686956] Model parameter optimization (eps = 0.100000)

[00:19:33] ML tree search #7, logLikelihood: -8411.366242

[00:19:33 -21542.863673] Initial branch length optimization
[00:19:33 -17377.309456] Model parameter optimization (eps = 10.000000)
[00:19:36 -17352.189212] AUTODETECT spr round 1 (radius: 5)
[00:19:40 -11580.996413] AUTODETECT spr round 2 (radius: 10)
[00:19:44 -9777.816975] AUTODETECT spr round 3 (radius: 15)
[00:19:50 -9651.890991] AUTODETECT spr round 4 (radius: 20)
[00:19:55 -9103.274991] AUTODETECT spr round 5 (radius: 25)
[00:20:00 -9080.960044] SPR radius for FAST iterations: 25 (autodetect)
[00:20:00 -9080.960044] Model parameter optimization (eps = 3.000000)
[00:20:02 -9060.975861] FAST spr round 1 (radius: 25)
[00:20:07 -8482.159874] FAST spr round 2 (radius: 25)
[00:20:12 -8429.228892] FAST spr round 3 (radius: 25)
[00:20:16 -8427.180513] FAST spr round 4 (radius: 25)
[00:20:20 -8425.826968] FAST spr round 5 (radius: 25)
[00:20:22 -8425.825989] Model parameter optimization (eps = 1.000000)
[00:20:24 -8422.528151] SLOW spr round 1 (radius: 5)
[00:20:31 -8418.763694] SLOW spr round 2 (radius: 5)
[00:20:38 -8418.459064] SLOW spr round 3 (radius: 5)
[00:20:44 -8418.458309] SLOW spr round 4 (radius: 10)
[00:20:50 -8418.458122] SLOW spr round 5 (radius: 15)
[00:20:58 -8418.018252] SLOW spr round 6 (radius: 5)
[00:21:07 -8418.005487] SLOW spr round 7 (radius: 10)
[00:21:14 -8417.765366] SLOW spr round 8 (radius: 5)
[00:21:21 -8417.765179] SLOW spr round 9 (radius: 10)
[00:21:28 -8417.765049] SLOW spr round 10 (radius: 15)
[00:21:34 -8417.764921] SLOW spr round 11 (radius: 20)
[00:21:42 -8417.764792] SLOW spr round 12 (radius: 25)
[00:21:51 -8417.764662] Model parameter optimization (eps = 0.100000)

[00:21:53] ML tree search #8, logLikelihood: -8415.903065

[00:21:53 -21333.797910] Initial branch length optimization
[00:21:54 -17325.736140] Model parameter optimization (eps = 10.000000)
[00:21:57 -17304.560189] AUTODETECT spr round 1 (radius: 5)
[00:22:00 -12519.958271] AUTODETECT spr round 2 (radius: 10)
[00:22:05 -11113.176229] AUTODETECT spr round 3 (radius: 15)
[00:22:10 -9947.572546] AUTODETECT spr round 4 (radius: 20)
[00:22:16 -9453.737786] AUTODETECT spr round 5 (radius: 25)
[00:22:21 -9451.819374] SPR radius for FAST iterations: 25 (autodetect)
[00:22:21 -9451.819374] Model parameter optimization (eps = 3.000000)
[00:22:25 -9415.404181] FAST spr round 1 (radius: 25)
[00:22:30 -8581.751608] FAST spr round 2 (radius: 25)
[00:22:35 -8437.308364] FAST spr round 3 (radius: 25)
[00:22:39 -8430.010886] FAST spr round 4 (radius: 25)
[00:22:43 -8428.160438] FAST spr round 5 (radius: 25)
[00:22:46 -8428.160048] Model parameter optimization (eps = 1.000000)
[00:22:47 -8427.432025] SLOW spr round 1 (radius: 5)
[00:22:54 -8422.744102] SLOW spr round 2 (radius: 5)
[00:23:01 -8422.252963] SLOW spr round 3 (radius: 5)
[00:23:07 -8422.252217] SLOW spr round 4 (radius: 10)
[00:23:13 -8415.252749] SLOW spr round 5 (radius: 5)
[00:23:21 -8415.144134] SLOW spr round 6 (radius: 5)
[00:23:29 -8415.038612] SLOW spr round 7 (radius: 5)
[00:23:35 -8415.038597] SLOW spr round 8 (radius: 10)
[00:23:41 -8415.038596] SLOW spr round 9 (radius: 15)
[00:23:48 -8414.602754] SLOW spr round 10 (radius: 5)
[00:23:56 -8414.594107] SLOW spr round 11 (radius: 10)
[00:24:03 -8414.593922] SLOW spr round 12 (radius: 15)
[00:24:10 -8414.593885] SLOW spr round 13 (radius: 20)
[00:24:19 -8414.593877] SLOW spr round 14 (radius: 25)
[00:24:28 -8414.593875] Model parameter optimization (eps = 0.100000)

[00:24:30] ML tree search #9, logLikelihood: -8414.153089

[00:24:30 -20508.068470] Initial branch length optimization
[00:24:30 -16822.503581] Model parameter optimization (eps = 10.000000)
[00:24:33 -16794.979972] AUTODETECT spr round 1 (radius: 5)
[00:24:36 -12530.315887] AUTODETECT spr round 2 (radius: 10)
[00:24:40 -9312.700746] AUTODETECT spr round 3 (radius: 15)
[00:24:44 -9114.357748] AUTODETECT spr round 4 (radius: 20)
[00:24:49 -9108.398967] AUTODETECT spr round 5 (radius: 25)
[00:24:53 -9108.329255] SPR radius for FAST iterations: 20 (autodetect)
[00:24:53 -9108.329255] Model parameter optimization (eps = 3.000000)
[00:24:56 -9084.193926] FAST spr round 1 (radius: 20)
[00:25:01 -8508.034475] FAST spr round 2 (radius: 20)
[00:25:06 -8435.042073] FAST spr round 3 (radius: 20)
[00:25:10 -8428.392175] FAST spr round 4 (radius: 20)
[00:25:13 -8428.389185] Model parameter optimization (eps = 1.000000)
[00:25:15 -8425.145421] SLOW spr round 1 (radius: 5)
[00:25:22 -8422.735716] SLOW spr round 2 (radius: 5)
[00:25:28 -8422.733326] SLOW spr round 3 (radius: 10)
[00:25:34 -8422.661408] SLOW spr round 4 (radius: 15)
[00:25:41 -8422.522403] SLOW spr round 5 (radius: 5)
[00:25:50 -8422.518689] SLOW spr round 6 (radius: 10)
[00:25:56 -8421.932446] SLOW spr round 7 (radius: 5)
[00:26:04 -8421.932040] SLOW spr round 8 (radius: 10)
[00:26:09 -8421.931993] SLOW spr round 9 (radius: 15)
[00:26:16 -8421.931985] SLOW spr round 10 (radius: 20)
[00:26:23 -8421.931984] SLOW spr round 11 (radius: 25)
[00:26:30 -8421.931983] Model parameter optimization (eps = 0.100000)

[00:26:33] ML tree search #10, logLikelihood: -8421.574144

[00:26:33 -20666.782301] Initial branch length optimization
[00:26:33 -16688.044418] Model parameter optimization (eps = 10.000000)
[00:26:35 -16669.638717] AUTODETECT spr round 1 (radius: 5)
[00:26:38 -11814.673446] AUTODETECT spr round 2 (radius: 10)
[00:26:43 -9903.958204] AUTODETECT spr round 3 (radius: 15)
[00:26:49 -9394.998814] AUTODETECT spr round 4 (radius: 20)
[00:26:54 -9229.001388] AUTODETECT spr round 5 (radius: 25)
[00:26:59 -9177.559434] SPR radius for FAST iterations: 25 (autodetect)
[00:26:59 -9177.559434] Model parameter optimization (eps = 3.000000)
[00:27:03 -9162.550873] FAST spr round 1 (radius: 25)
[00:27:09 -8534.577123] FAST spr round 2 (radius: 25)
[00:27:14 -8427.084018] FAST spr round 3 (radius: 25)
[00:27:18 -8422.282309] FAST spr round 4 (radius: 25)
[00:27:21 -8419.303704] FAST spr round 5 (radius: 25)
[00:27:25 -8418.152518] FAST spr round 6 (radius: 25)
[00:27:28 -8418.152356] Model parameter optimization (eps = 1.000000)
[00:27:30 -8415.725164] SLOW spr round 1 (radius: 5)
[00:27:37 -8413.812559] SLOW spr round 2 (radius: 5)
[00:27:43 -8413.811542] SLOW spr round 3 (radius: 10)
[00:27:49 -8413.685007] SLOW spr round 4 (radius: 5)
[00:27:57 -8413.320179] SLOW spr round 5 (radius: 5)
[00:28:04 -8413.319695] SLOW spr round 6 (radius: 10)
[00:28:10 -8413.319443] SLOW spr round 7 (radius: 15)
[00:28:16 -8413.319298] SLOW spr round 8 (radius: 20)
[00:28:22 -8413.319207] SLOW spr round 9 (radius: 25)
[00:28:29 -8413.319142] Model parameter optimization (eps = 0.100000)

[00:28:30] ML tree search #11, logLikelihood: -8413.209958

[00:28:30 -21061.111065] Initial branch length optimization
[00:28:30 -16896.459697] Model parameter optimization (eps = 10.000000)
[00:28:33 -16883.909054] AUTODETECT spr round 1 (radius: 5)
[00:28:36 -13070.685220] AUTODETECT spr round 2 (radius: 10)
[00:28:41 -10158.503183] AUTODETECT spr round 3 (radius: 15)
[00:28:47 -9228.196328] AUTODETECT spr round 4 (radius: 20)
[00:28:52 -9205.735734] AUTODETECT spr round 5 (radius: 25)
[00:28:56 -9205.702746] SPR radius for FAST iterations: 20 (autodetect)
[00:28:56 -9205.702746] Model parameter optimization (eps = 3.000000)
[00:28:59 -9166.948891] FAST spr round 1 (radius: 20)
[00:29:05 -8467.234172] FAST spr round 2 (radius: 20)
[00:29:10 -8429.889823] FAST spr round 3 (radius: 20)
[00:29:13 -8419.523233] FAST spr round 4 (radius: 20)
[00:29:17 -8419.522892] Model parameter optimization (eps = 1.000000)
[00:29:18 -8419.048955] SLOW spr round 1 (radius: 5)
[00:29:25 -8418.464513] SLOW spr round 2 (radius: 5)
[00:29:31 -8418.462112] SLOW spr round 3 (radius: 10)
[00:29:36 -8418.461857] SLOW spr round 4 (radius: 15)
[00:29:44 -8418.389752] SLOW spr round 5 (radius: 20)
[00:29:52 -8418.388739] SLOW spr round 6 (radius: 25)
[00:30:02 -8418.388621] Model parameter optimization (eps = 0.100000)

[00:30:02] ML tree search #12, logLikelihood: -8418.386051

[00:30:02 -21220.136884] Initial branch length optimization
[00:30:02 -17001.805693] Model parameter optimization (eps = 10.000000)
[00:30:06 -16980.872206] AUTODETECT spr round 1 (radius: 5)
[00:30:10 -12606.668326] AUTODETECT spr round 2 (radius: 10)
[00:30:14 -10802.200085] AUTODETECT spr round 3 (radius: 15)
[00:30:19 -10243.331314] AUTODETECT spr round 4 (radius: 20)
[00:30:24 -10116.017302] AUTODETECT spr round 5 (radius: 25)
[00:30:30 -9707.477346] SPR radius for FAST iterations: 25 (autodetect)
[00:30:30 -9707.477346] Model parameter optimization (eps = 3.000000)
[00:30:32 -9675.231705] FAST spr round 1 (radius: 25)
[00:30:37 -8974.069071] FAST spr round 2 (radius: 25)
[00:30:41 -8906.533510] FAST spr round 3 (radius: 25)
[00:30:46 -8900.156907] FAST spr round 4 (radius: 25)
[00:30:49 -8900.156594] Model parameter optimization (eps = 1.000000)
[00:30:51 -8898.759060] SLOW spr round 1 (radius: 5)
[00:30:58 -8895.821418] SLOW spr round 2 (radius: 5)
[00:31:05 -8895.494279] SLOW spr round 3 (radius: 5)
[00:31:11 -8895.493086] SLOW spr round 4 (radius: 10)
[00:31:16 -8895.223144] SLOW spr round 5 (radius: 5)
[00:31:24 -8895.222993] SLOW spr round 6 (radius: 10)
[00:31:30 -8895.222969] SLOW spr round 7 (radius: 15)
[00:31:37 -8895.222954] SLOW spr round 8 (radius: 20)
[00:31:46 -8767.241227] SLOW spr round 9 (radius: 5)
[00:31:57 -8530.874317] SLOW spr round 10 (radius: 5)
[00:32:06 -8414.778303] SLOW spr round 11 (radius: 5)
[00:32:13 -8413.608587] SLOW spr round 12 (radius: 5)
[00:32:19 -8413.608403] SLOW spr round 13 (radius: 10)
[00:32:25 -8413.608367] SLOW spr round 14 (radius: 15)
[00:32:32 -8413.608356] SLOW spr round 15 (radius: 20)
[00:32:40 -8413.498043] SLOW spr round 16 (radius: 5)
[00:32:47 -8413.493474] SLOW spr round 17 (radius: 10)
[00:32:53 -8413.493351] SLOW spr round 18 (radius: 15)
[00:32:59 -8413.493317] SLOW spr round 19 (radius: 20)
[00:33:06 -8413.493307] SLOW spr round 20 (radius: 25)
[00:33:14 -8413.493304] Model parameter optimization (eps = 0.100000)

[00:33:17] ML tree search #13, logLikelihood: -8409.905508

[00:33:17 -21130.766143] Initial branch length optimization
[00:33:17 -16974.264177] Model parameter optimization (eps = 10.000000)
[00:33:20 -16947.162730] AUTODETECT spr round 1 (radius: 5)
[00:33:23 -12176.620571] AUTODETECT spr round 2 (radius: 10)
[00:33:28 -10419.674508] AUTODETECT spr round 3 (radius: 15)
[00:33:33 -9474.096229] AUTODETECT spr round 4 (radius: 20)
[00:33:39 -9314.178198] AUTODETECT spr round 5 (radius: 25)
[00:33:45 -9311.687838] SPR radius for FAST iterations: 25 (autodetect)
[00:33:45 -9311.687838] Model parameter optimization (eps = 3.000000)
[00:33:48 -9295.079008] FAST spr round 1 (radius: 25)
[00:33:52 -8456.270504] FAST spr round 2 (radius: 25)
[00:33:56 -8423.019634] FAST spr round 3 (radius: 25)
[00:33:59 -8416.635798] FAST spr round 4 (radius: 25)
[00:34:02 -8416.633859] Model parameter optimization (eps = 1.000000)
[00:34:04 -8413.163966] SLOW spr round 1 (radius: 5)
[00:34:10 -8412.483485] SLOW spr round 2 (radius: 5)
[00:34:15 -8412.463619] SLOW spr round 3 (radius: 10)
[00:34:19 -8411.453888] SLOW spr round 4 (radius: 5)
[00:34:26 -8411.449042] SLOW spr round 5 (radius: 10)
[00:34:31 -8411.448075] SLOW spr round 6 (radius: 15)
[00:34:38 -8411.317392] SLOW spr round 7 (radius: 5)
[00:34:47 -8411.316088] SLOW spr round 8 (radius: 10)
[00:34:54 -8411.316079] SLOW spr round 9 (radius: 15)
[00:35:01 -8411.316077] SLOW spr round 10 (radius: 20)
[00:35:09 -8410.238974] SLOW spr round 11 (radius: 5)
[00:35:18 -8410.236360] SLOW spr round 12 (radius: 10)
[00:35:26 -8410.235710] SLOW spr round 13 (radius: 15)
[00:35:33 -8409.713244] SLOW spr round 14 (radius: 5)
[00:35:42 -8409.712338] SLOW spr round 15 (radius: 10)
[00:35:49 -8409.654985] SLOW spr round 16 (radius: 15)
[00:35:56 -8409.608713] SLOW spr round 17 (radius: 20)
[00:36:04 -8409.608670] SLOW spr round 18 (radius: 25)
[00:36:11 -8409.608668] Model parameter optimization (eps = 0.100000)

[00:36:13] ML tree search #14, logLikelihood: -8408.781693

[00:36:13 -20995.038448] Initial branch length optimization
[00:36:13 -16917.618004] Model parameter optimization (eps = 10.000000)
[00:36:15 -16907.980780] AUTODETECT spr round 1 (radius: 5)
[00:36:18 -11964.932453] AUTODETECT spr round 2 (radius: 10)
[00:36:23 -10077.784135] AUTODETECT spr round 3 (radius: 15)
[00:36:29 -9413.808804] AUTODETECT spr round 4 (radius: 20)
[00:36:35 -9344.678655] AUTODETECT spr round 5 (radius: 25)
[00:36:41 -9339.561885] SPR radius for FAST iterations: 25 (autodetect)
[00:36:41 -9339.561885] Model parameter optimization (eps = 3.000000)
[00:36:44 -9304.881829] FAST spr round 1 (radius: 25)
[00:36:49 -8559.796395] FAST spr round 2 (radius: 25)
[00:36:53 -8430.934707] FAST spr round 3 (radius: 25)
[00:36:57 -8421.701992] FAST spr round 4 (radius: 25)
[00:37:00 -8421.695768] Model parameter optimization (eps = 1.000000)
[00:37:01 -8420.091194] SLOW spr round 1 (radius: 5)
[00:37:08 -8418.344722] SLOW spr round 2 (radius: 5)
[00:37:15 -8417.779761] SLOW spr round 3 (radius: 5)
[00:37:22 -8417.779291] SLOW spr round 4 (radius: 10)
[00:37:27 -8417.779140] SLOW spr round 5 (radius: 15)
[00:37:35 -8417.710540] SLOW spr round 6 (radius: 20)
[00:37:42 -8416.433700] SLOW spr round 7 (radius: 5)
[00:37:50 -8416.433310] SLOW spr round 8 (radius: 10)
[00:37:56 -8416.433182] SLOW spr round 9 (radius: 15)
[00:38:01 -8416.433061] SLOW spr round 10 (radius: 20)
[00:38:07 -8415.730465] SLOW spr round 11 (radius: 5)
[00:38:15 -8415.486775] SLOW spr round 12 (radius: 5)
[00:38:23 -8414.464592] SLOW spr round 13 (radius: 5)
[00:38:29 -8414.463871] SLOW spr round 14 (radius: 10)
[00:38:35 -8414.463649] SLOW spr round 15 (radius: 15)
[00:38:42 -8414.463451] SLOW spr round 16 (radius: 20)
[00:38:51 -8414.463434] SLOW spr round 17 (radius: 25)
[00:39:00 -8414.463434] Model parameter optimization (eps = 0.100000)

[00:39:02] ML tree search #15, logLikelihood: -8414.162015

[00:39:02 -21414.787792] Initial branch length optimization
[00:39:02 -17354.258164] Model parameter optimization (eps = 10.000000)
[00:39:06 -17315.602401] AUTODETECT spr round 1 (radius: 5)
[00:39:10 -12515.034590] AUTODETECT spr round 2 (radius: 10)
[00:39:14 -10107.189266] AUTODETECT spr round 3 (radius: 15)
[00:39:20 -9230.853820] AUTODETECT spr round 4 (radius: 20)
[00:39:24 -9202.653867] AUTODETECT spr round 5 (radius: 25)
[00:39:28 -9200.407103] SPR radius for FAST iterations: 25 (autodetect)
[00:39:28 -9200.407103] Model parameter optimization (eps = 3.000000)
[00:39:32 -9191.475233] FAST spr round 1 (radius: 25)
[00:39:37 -8476.582832] FAST spr round 2 (radius: 25)
[00:39:42 -8429.496705] FAST spr round 3 (radius: 25)
[00:39:46 -8424.767768] FAST spr round 4 (radius: 25)
[00:39:49 -8421.567687] FAST spr round 5 (radius: 25)
[00:39:52 -8419.454193] FAST spr round 6 (radius: 25)
[00:39:55 -8419.453049] Model parameter optimization (eps = 1.000000)
[00:39:59 -8417.258980] SLOW spr round 1 (radius: 5)
[00:40:04 -8413.770240] SLOW spr round 2 (radius: 5)
[00:40:10 -8412.316308] SLOW spr round 3 (radius: 5)
[00:40:16 -8412.072867] SLOW spr round 4 (radius: 5)
[00:40:22 -8412.071422] SLOW spr round 5 (radius: 10)
[00:40:27 -8412.071245] SLOW spr round 6 (radius: 15)
[00:40:35 -8411.713340] SLOW spr round 7 (radius: 5)
[00:40:44 -8411.694504] SLOW spr round 8 (radius: 10)
[00:40:50 -8411.694372] SLOW spr round 9 (radius: 15)
[00:40:57 -8411.694256] SLOW spr round 10 (radius: 20)
[00:41:05 -8411.694154] SLOW spr round 11 (radius: 25)
[00:41:13 -8411.694064] Model parameter optimization (eps = 0.100000)

[00:41:14] ML tree search #16, logLikelihood: -8411.571869

[00:41:14 -21214.105851] Initial branch length optimization
[00:41:15 -17084.135919] Model parameter optimization (eps = 10.000000)
[00:41:17 -17072.099714] AUTODETECT spr round 1 (radius: 5)
[00:41:21 -12623.372191] AUTODETECT spr round 2 (radius: 10)
[00:41:25 -10319.045148] AUTODETECT spr round 3 (radius: 15)
[00:41:29 -9244.108076] AUTODETECT spr round 4 (radius: 20)
[00:41:34 -9217.724091] AUTODETECT spr round 5 (radius: 25)
[00:41:38 -9217.714223] SPR radius for FAST iterations: 20 (autodetect)
[00:41:38 -9217.714223] Model parameter optimization (eps = 3.000000)
[00:41:41 -9179.540995] FAST spr round 1 (radius: 20)
[00:41:46 -8465.239779] FAST spr round 2 (radius: 20)
[00:41:50 -8435.200510] FAST spr round 3 (radius: 20)
[00:41:54 -8427.610039] FAST spr round 4 (radius: 20)
[00:41:57 -8427.609910] Model parameter optimization (eps = 1.000000)
[00:41:59 -8425.954040] SLOW spr round 1 (radius: 5)
[00:42:06 -8424.297472] SLOW spr round 2 (radius: 5)
[00:42:12 -8424.297016] SLOW spr round 3 (radius: 10)
[00:42:17 -8423.062722] SLOW spr round 4 (radius: 5)
[00:42:26 -8422.506917] SLOW spr round 5 (radius: 5)
[00:42:33 -8422.506759] SLOW spr round 6 (radius: 10)
[00:42:39 -8422.154258] SLOW spr round 7 (radius: 5)
[00:42:46 -8421.812787] SLOW spr round 8 (radius: 5)
[00:42:53 -8421.811010] SLOW spr round 9 (radius: 10)
[00:42:59 -8421.658737] SLOW spr round 10 (radius: 5)
[00:43:07 -8418.313813] SLOW spr round 11 (radius: 5)
[00:43:14 -8417.885728] SLOW spr round 12 (radius: 5)
[00:43:20 -8417.884687] SLOW spr round 13 (radius: 10)
[00:43:25 -8417.884633] SLOW spr round 14 (radius: 15)
[00:43:33 -8417.884630] SLOW spr round 15 (radius: 20)
[00:43:41 -8416.887778] SLOW spr round 16 (radius: 5)
[00:43:50 -8416.271784] SLOW spr round 17 (radius: 5)
[00:43:58 -8415.745877] SLOW spr round 18 (radius: 5)
[00:44:05 -8415.745284] SLOW spr round 19 (radius: 10)
[00:44:11 -8415.720113] SLOW spr round 20 (radius: 15)
[00:44:19 -8415.720047] SLOW spr round 21 (radius: 20)
[00:44:27 -8415.611601] SLOW spr round 22 (radius: 5)
[00:44:36 -8415.610357] SLOW spr round 23 (radius: 10)
[00:44:44 -8415.610276] SLOW spr round 24 (radius: 15)
[00:44:51 -8415.610270] SLOW spr round 25 (radius: 20)
[00:44:59 -8415.610270] SLOW spr round 26 (radius: 25)
[00:45:07 -8415.610270] Model parameter optimization (eps = 0.100000)

[00:45:09] ML tree search #17, logLikelihood: -8415.531559

[00:45:09 -21326.865237] Initial branch length optimization
[00:45:09 -17076.125323] Model parameter optimization (eps = 10.000000)
[00:45:11 -17056.343018] AUTODETECT spr round 1 (radius: 5)
[00:45:15 -12560.250488] AUTODETECT spr round 2 (radius: 10)
[00:45:20 -10666.641423] AUTODETECT spr round 3 (radius: 15)
[00:45:24 -9721.465371] AUTODETECT spr round 4 (radius: 20)
[00:45:30 -9600.558418] AUTODETECT spr round 5 (radius: 25)
[00:45:36 -9591.530800] SPR radius for FAST iterations: 25 (autodetect)
[00:45:36 -9591.530800] Model parameter optimization (eps = 3.000000)
[00:45:40 -9535.512361] FAST spr round 1 (radius: 25)
[00:45:45 -8782.232711] FAST spr round 2 (radius: 25)
[00:45:51 -8607.121000] FAST spr round 3 (radius: 25)
[00:45:55 -8600.155906] FAST spr round 4 (radius: 25)
[00:45:58 -8600.153967] Model parameter optimization (eps = 1.000000)
[00:46:01 -8595.490659] SLOW spr round 1 (radius: 5)
[00:46:08 -8592.907230] SLOW spr round 2 (radius: 5)
[00:46:14 -8592.904656] SLOW spr round 3 (radius: 10)
[00:46:19 -8592.904122] SLOW spr round 4 (radius: 15)
[00:46:27 -8592.903942] SLOW spr round 5 (radius: 20)
[00:46:35 -8592.903829] SLOW spr round 6 (radius: 25)
[00:46:45 -8524.516983] SLOW spr round 7 (radius: 5)
[00:46:55 -8462.166579] SLOW spr round 8 (radius: 5)
[00:47:03 -8420.988316] SLOW spr round 9 (radius: 5)
[00:47:10 -8420.984725] SLOW spr round 10 (radius: 10)
[00:47:16 -8420.183424] SLOW spr round 11 (radius: 5)
[00:47:25 -8419.597969] SLOW spr round 12 (radius: 5)
[00:47:32 -8419.493190] SLOW spr round 13 (radius: 5)
[00:47:38 -8419.493178] SLOW spr round 14 (radius: 10)
[00:47:44 -8419.493178] SLOW spr round 15 (radius: 15)
[00:47:51 -8416.653032] SLOW spr round 16 (radius: 5)
[00:48:00 -8416.644415] SLOW spr round 17 (radius: 10)
[00:48:07 -8416.642083] SLOW spr round 18 (radius: 15)
[00:48:14 -8416.641380] SLOW spr round 19 (radius: 20)
[00:48:21 -8416.250923] SLOW spr round 20 (radius: 5)
[00:48:30 -8416.249794] SLOW spr round 21 (radius: 10)
[00:48:37 -8416.249763] SLOW spr round 22 (radius: 15)
[00:48:44 -8416.249758] SLOW spr round 23 (radius: 20)
[00:48:50 -8416.249756] SLOW spr round 24 (radius: 25)
[00:48:57 -8416.249756] Model parameter optimization (eps = 0.100000)

[00:49:00] ML tree search #18, logLikelihood: -8413.580613

[00:49:00 -21484.304757] Initial branch length optimization
[00:49:01 -17320.352305] Model parameter optimization (eps = 10.000000)
[00:49:04 -17305.511564] AUTODETECT spr round 1 (radius: 5)
[00:49:08 -12123.202448] AUTODETECT spr round 2 (radius: 10)
[00:49:13 -9973.048423] AUTODETECT spr round 3 (radius: 15)
[00:49:19 -9283.113791] AUTODETECT spr round 4 (radius: 20)
[00:49:26 -9085.184683] AUTODETECT spr round 5 (radius: 25)
[00:49:32 -9085.163934] SPR radius for FAST iterations: 20 (autodetect)
[00:49:32 -9085.163934] Model parameter optimization (eps = 3.000000)
[00:49:34 -9053.544585] FAST spr round 1 (radius: 20)
[00:49:38 -8520.557422] FAST spr round 2 (radius: 20)
[00:49:43 -8427.201333] FAST spr round 3 (radius: 20)
[00:49:46 -8425.705465] FAST spr round 4 (radius: 20)
[00:49:49 -8425.705360] Model parameter optimization (eps = 1.000000)
[00:49:50 -8425.116642] SLOW spr round 1 (radius: 5)
[00:49:56 -8420.023496] SLOW spr round 2 (radius: 5)
[00:50:03 -8419.858411] SLOW spr round 3 (radius: 5)
[00:50:09 -8419.856495] SLOW spr round 4 (radius: 10)
[00:50:14 -8419.855884] SLOW spr round 5 (radius: 15)
[00:50:22 -8419.758365] SLOW spr round 6 (radius: 20)
[00:50:31 -8419.758305] SLOW spr round 7 (radius: 25)
[00:50:40 -8419.758285] Model parameter optimization (eps = 0.100000)

[00:50:41] ML tree search #19, logLikelihood: -8419.705899

[00:50:41 -20878.659488] Initial branch length optimization
[00:50:41 -17087.603054] Model parameter optimization (eps = 10.000000)
[00:50:44 -17001.507650] AUTODETECT spr round 1 (radius: 5)
[00:50:48 -12038.833262] AUTODETECT spr round 2 (radius: 10)
[00:50:52 -10254.113976] AUTODETECT spr round 3 (radius: 15)
[00:50:57 -9269.869893] AUTODETECT spr round 4 (radius: 20)
[00:51:03 -9195.564389] AUTODETECT spr round 5 (radius: 25)
[00:51:08 -9187.061950] SPR radius for FAST iterations: 25 (autodetect)
[00:51:08 -9187.061950] Model parameter optimization (eps = 3.000000)
[00:51:11 -9164.045691] FAST spr round 1 (radius: 25)
[00:51:15 -8480.384888] FAST spr round 2 (radius: 25)
[00:51:19 -8436.012104] FAST spr round 3 (radius: 25)
[00:51:23 -8431.940226] FAST spr round 4 (radius: 25)
[00:51:25 -8431.938979] Model parameter optimization (eps = 1.000000)
[00:51:30 -8430.180897] SLOW spr round 1 (radius: 5)
[00:51:36 -8424.167554] SLOW spr round 2 (radius: 5)
[00:51:41 -8424.060035] SLOW spr round 3 (radius: 5)
[00:51:46 -8424.059081] SLOW spr round 4 (radius: 10)
[00:51:52 -8423.591805] SLOW spr round 5 (radius: 5)
[00:52:00 -8423.591414] SLOW spr round 6 (radius: 10)
[00:52:06 -8423.591402] SLOW spr round 7 (radius: 15)
[00:52:13 -8422.875555] SLOW spr round 8 (radius: 5)
[00:52:22 -8420.229907] SLOW spr round 9 (radius: 5)
[00:52:30 -8420.229457] SLOW spr round 10 (radius: 10)
[00:52:36 -8420.055401] SLOW spr round 11 (radius: 5)
[00:52:44 -8419.995557] SLOW spr round 12 (radius: 10)
[00:52:50 -8419.994454] SLOW spr round 13 (radius: 15)
[00:52:57 -8419.993647] SLOW spr round 14 (radius: 20)
[00:53:04 -8419.993050] SLOW spr round 15 (radius: 25)
[00:53:12 -8419.992605] Model parameter optimization (eps = 0.100000)

[00:53:13] ML tree search #20, logLikelihood: -8419.477095


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.092854,0.276213) (0.350479,0.699836) (0.331636,0.998134) (0.225031,1.768903) 
   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: -8408.781693

AIC score: 17531.563386 / AICc score: 273143.563386 / BIC score: 18307.819641
Free parameters (model + branch lengths): 357

WARNING: Number of free parameters (K=357) is larger than alignment size (n=65).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 29 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/3_mltree/Q8TDP1.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/3_mltree/Q8TDP1.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/3_mltree/Q8TDP1.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/3_mltree/Q8TDP1.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDP1/3_mltree/Q8TDP1.raxml.log

Analysis started: 04-Jul-2021 17:41:59 / finished: 04-Jul-2021 18:35:12

Elapsed time: 3193.672 seconds

Consumed energy: 263.602 Wh (= 1 km in an electric car, or 7 km with an e-scooter!)