RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 17-Jul-2021 16:10:32 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/2_msa/Q8TD84_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/2_msa/Q8TD84_trimmed_msa.fasta
[00:00:00] Loaded alignment with 703 taxa and 1326 sites

WARNING: Sequences tr_A0A0N4SUH1_A0A0N4SUH1_CHICK_9031 and sp_F1NY98_DSCAM_CHICK_9031 are exactly identical!
WARNING: Sequences tr_A0A1I7Q400_A0A1I7Q400_CHICK_9031 and sp_E1C8P7_DSCL1_CHICK_9031 are exactly identical!
WARNING: Sequences tr_H2QL16_H2QL16_PANTR_9598 and sp_O60469_DSCAM_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A1D5QAK9_A0A1D5QAK9_MACMU_9544 and tr_A0A2K6C1P6_A0A2K6C1P6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7P0Z0_G7P0Z0_MACFA_9541 and tr_A0A2I3LTD0_A0A2I3LTD0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7P0Z0_G7P0Z0_MACFA_9541 and tr_A0A2K5KWA8_A0A2K5KWA8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3N7T2_A0A2I3N7T2_PAPAN_9555 and tr_A0A0D9S3F9_A0A0D9S3F9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A226MMP7_A0A226MMP7_CALSU_9009 and tr_A0A226PJ38_A0A226PJ38_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2U3ZU65_A0A2U3ZU65_ODORO_9708 and tr_A0A2U3YXM0_A0A2U3YXM0_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 9

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84.raxml.reduced.phy

Alignment comprises 1 partitions and 1326 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1326 / 1326
Gaps: 29.31 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 703 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 166 / 13280
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1260273.474947] Initial branch length optimization
[00:08:54 -1010946.192227] Model parameter optimization (eps = 10.000000)
[00:25:19 -1008700.294117] AUTODETECT spr round 1 (radius: 5)
[01:15:05 -742305.656621] AUTODETECT spr round 2 (radius: 10)
[02:30:24 -581097.417226] AUTODETECT spr round 3 (radius: 15)
[03:55:25 -493601.499798] AUTODETECT spr round 4 (radius: 20)
[05:49:00 -480001.396726] AUTODETECT spr round 5 (radius: 25)
[08:43:17 -448699.996704] SPR radius for FAST iterations: 25 (autodetect)
[08:43:17 -448699.996704] Model parameter optimization (eps = 3.000000)
[08:50:28 -447709.455267] FAST spr round 1 (radius: 25)
[15:20:36 -403923.907909] FAST spr round 2 (radius: 25)
[19:54:47 -401643.167420] FAST spr round 3 (radius: 25)
[21:02:31 -401573.775052] FAST spr round 4 (radius: 25)
[21:25:54 -401545.837056] FAST spr round 5 (radius: 25)
[21:44:53 -401545.387928] FAST spr round 6 (radius: 25)
[21:46:21 -401545.376109] Model parameter optimization (eps = 1.000000)
[21:46:35 -401535.576656] SLOW spr round 1 (radius: 5)
[22:29:51 -401466.337990] SLOW spr round 2 (radius: 5)
[22:38:43 -401461.177209] SLOW spr round 3 (radius: 5)
[22:46:05 -401457.776196] SLOW spr round 4 (radius: 5)
[22:53:42 -401455.397568] SLOW spr round 5 (radius: 5)
[23:02:28 -401454.481327] SLOW spr round 6 (radius: 5)
[23:05:18 -401454.480198] SLOW spr round 7 (radius: 10)
[23:15:33 -401444.038629] SLOW spr round 8 (radius: 5)
[23:19:22 -401443.337795] SLOW spr round 9 (radius: 5)
[23:21:18 -401443.336785] SLOW spr round 10 (radius: 10)
[23:23:29 -401443.336734] SLOW spr round 11 (radius: 15)
[23:27:43 -401443.336723] SLOW spr round 12 (radius: 20)
[23:34:39 -401443.336718] SLOW spr round 13 (radius: 25)
[23:42:51 -401443.336716] Model parameter optimization (eps = 0.100000)

[23:43:04] ML tree search #1, logLikelihood: -401442.757570

[23:43:04 -1253079.731425] Initial branch length optimization
[23:43:09 -1003173.417335] Model parameter optimization (eps = 10.000000)
[23:43:53 -1001145.189263] AUTODETECT spr round 1 (radius: 5)
[23:45:42 -764935.275403] AUTODETECT spr round 2 (radius: 10)
[23:47:27 -582223.125542] AUTODETECT spr round 3 (radius: 15)
[23:49:23 -485996.782267] AUTODETECT spr round 4 (radius: 20)
[23:51:42 -447536.798310] AUTODETECT spr round 5 (radius: 25)
[23:54:07 -443356.282442] SPR radius for FAST iterations: 25 (autodetect)
[23:54:07 -443356.282442] Model parameter optimization (eps = 3.000000)
[23:54:35 -442549.756517] FAST spr round 1 (radius: 25)
[23:57:26 -403313.322950] FAST spr round 2 (radius: 25)
[24:00:02 -401712.314656] FAST spr round 3 (radius: 25)
[24:24:28 -401625.945782] FAST spr round 4 (radius: 25)
[25:09:40 -401607.609388] FAST spr round 5 (radius: 25)
[25:47:49 -401603.600601] FAST spr round 6 (radius: 25)
[26:11:54 -401602.943053] FAST spr round 7 (radius: 25)
[26:42:01 -401602.942350] Model parameter optimization (eps = 1.000000)
[26:42:15 -401593.537214] SLOW spr round 1 (radius: 5)
[28:26:46 -401486.849565] SLOW spr round 2 (radius: 5)
[29:41:24 -401479.721745] SLOW spr round 3 (radius: 5)
[30:49:45 -401479.720872] SLOW spr round 4 (radius: 10)
[31:48:49 -401465.896378] SLOW spr round 5 (radius: 5)
[31:51:01 -401463.517250] SLOW spr round 6 (radius: 5)
[31:52:59 -401463.514866] SLOW spr round 7 (radius: 10)
[31:56:13 -401463.513318] SLOW spr round 8 (radius: 15)
[33:00:34 -401463.441542] SLOW spr round 9 (radius: 20)
[33:09:02 -401461.303721] SLOW spr round 10 (radius: 5)
[33:11:26 -401460.013553] SLOW spr round 11 (radius: 5)
[33:19:56 -401459.892893] SLOW spr round 12 (radius: 5)
[35:13:22 -401459.892637] SLOW spr round 13 (radius: 10)
[38:15:49 -401459.892637] SLOW spr round 14 (radius: 15)
[38:20:14 -401459.868383] SLOW spr round 15 (radius: 20)
[38:36:31 -401458.230252] SLOW spr round 16 (radius: 5)
[38:38:56 -401458.229090] SLOW spr round 17 (radius: 10)
[38:41:51 -401458.229050] SLOW spr round 18 (radius: 15)
[38:46:03 -401458.229047] SLOW spr round 19 (radius: 20)
[38:54:59 -401458.229047] SLOW spr round 20 (radius: 25)
[41:44:16 -401458.229047] Model parameter optimization (eps = 0.100000)

[41:44:23] ML tree search #2, logLikelihood: -401458.126565

[41:44:23 -1247839.341595] Initial branch length optimization
[41:44:28 -996551.760381] Model parameter optimization (eps = 10.000000)
[41:45:23 -994447.422929] AUTODETECT spr round 1 (radius: 5)
[41:51:13 -735926.252664] AUTODETECT spr round 2 (radius: 10)
[42:25:44 -599004.273852] AUTODETECT spr round 3 (radius: 15)
[43:33:06 -496924.649904] AUTODETECT spr round 4 (radius: 20)
[44:48:33 -451926.832879] AUTODETECT spr round 5 (radius: 25)
[45:01:59 -447302.223138] SPR radius for FAST iterations: 25 (autodetect)
[45:01:59 -447302.223138] Model parameter optimization (eps = 3.000000)
[45:02:28 -446398.665642] FAST spr round 1 (radius: 25)
[45:13:22 -403446.589228] FAST spr round 2 (radius: 25)
[45:31:32 -401718.657308] FAST spr round 3 (radius: 25)
[45:35:18 -401545.035998] FAST spr round 4 (radius: 25)
[45:37:45 -401539.860401] FAST spr round 5 (radius: 25)
[45:55:34 -401539.836138] Model parameter optimization (eps = 1.000000)
[45:56:00 -401536.747403] SLOW spr round 1 (radius: 5)
[48:31:13 -401459.659287] SLOW spr round 2 (radius: 5)
[53:48:03 -401454.368339] SLOW spr round 3 (radius: 5)
[60:33:41 -401450.625829] SLOW spr round 4 (radius: 5)
[75:24:41 -401450.624303] SLOW spr round 5 (radius: 10)
[94:39:07 -401444.651850] SLOW spr round 6 (radius: 5)
[122:24:00 -401444.645811] SLOW spr round 7 (radius: 10)
[129:35:18 -401444.644466] SLOW spr round 8 (radius: 15)
[132:32:56 -401444.183972] SLOW spr round 9 (radius: 5)
[134:10:56 -401444.063731] SLOW spr round 10 (radius: 5)
[135:34:10 -401444.062947] SLOW spr round 11 (radius: 10)
[137:23:32 -401444.062214] SLOW spr round 12 (radius: 15)
[144:21:31 -401443.983914] SLOW spr round 13 (radius: 20)
[146:39:49 -401443.911714] SLOW spr round 14 (radius: 25)

RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 24-Jul-2021 21:01:11 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/2_msa/Q8TD84_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

WARNING: The model you specified on the command line (LG4X) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84.raxml.rba
[00:00:00] Alignment comprises 703 taxa, 1 partitions and 1326 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1326 / 1326
Gaps: 29.31 %
Invariant sites: 0.00 %


Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s)

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -401443.91, ML trees: 2, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 166 / 13280
[00:00:00] Data distribution: max. searches per worker: 18

Starting ML tree search with 20 distinct starting trees

[00:00:00 -401443.911714] SPR radius for FAST iterations: 25 (autodetect)
[00:00:00 -401443.911714] SLOW spr round 14 (radius: 25)
[00:07:24 -401443.548287] SLOW spr round 15 (radius: 5)
[00:09:38 -401443.415416] SLOW spr round 16 (radius: 5)
[00:11:34 -401443.415046] SLOW spr round 17 (radius: 10)
[00:13:48 -401443.415045] SLOW spr round 18 (radius: 15)
[00:17:43 -401443.414983] SLOW spr round 19 (radius: 20)
[00:23:58 -401443.414983] SLOW spr round 20 (radius: 25)
[00:31:14 -401443.414983] Model parameter optimization (eps = 0.100000)

[00:31:24] ML tree search #3, logLikelihood: -401442.651650

[00:31:24 -1259670.401097] Initial branch length optimization
[00:31:29 -1011048.229273] Model parameter optimization (eps = 10.000000)
[00:32:19 -1009036.375618] AUTODETECT spr round 1 (radius: 5)
[00:33:45 -740582.303401] AUTODETECT spr round 2 (radius: 10)
[00:35:17 -592428.971061] AUTODETECT spr round 3 (radius: 15)
[00:37:10 -479962.128768] AUTODETECT spr round 4 (radius: 20)
[00:39:27 -443101.680579] AUTODETECT spr round 5 (radius: 25)
[00:42:13 -441105.297189] SPR radius for FAST iterations: 25 (autodetect)
[00:42:13 -441105.297189] Model parameter optimization (eps = 3.000000)
[00:42:37 -440120.926124] FAST spr round 1 (radius: 25)
[00:45:20 -403030.006791] FAST spr round 2 (radius: 25)
[00:47:21 -401779.321881] FAST spr round 3 (radius: 25)
[00:49:01 -401631.453763] FAST spr round 4 (radius: 25)
[00:50:23 -401610.520077] FAST spr round 5 (radius: 25)
[00:51:38 -401576.611462] FAST spr round 6 (radius: 25)
[00:52:49 -401571.902698] FAST spr round 7 (radius: 25)
[00:54:00 -401571.880489] Model parameter optimization (eps = 1.000000)
[00:54:11 -401561.153079] SLOW spr round 1 (radius: 5)
[00:55:45 -401472.091911] SLOW spr round 2 (radius: 5)
[00:57:23 -401470.394926] SLOW spr round 3 (radius: 5)
[00:58:58 -401470.172526] SLOW spr round 4 (radius: 5)
[01:00:33 -401470.169639] SLOW spr round 5 (radius: 10)
[01:02:26 -401469.848159] SLOW spr round 6 (radius: 5)
[01:04:26 -401469.825093] SLOW spr round 7 (radius: 10)
[01:06:41 -401469.824453] SLOW spr round 8 (radius: 15)
[01:10:33 -401469.732224] SLOW spr round 9 (radius: 20)
[01:16:45 -401469.359356] SLOW spr round 10 (radius: 5)
[01:18:55 -401469.173943] SLOW spr round 11 (radius: 5)
[01:20:48 -401469.173778] SLOW spr round 12 (radius: 10)
[01:22:55 -401469.172201] SLOW spr round 13 (radius: 15)
[01:26:50 -401469.172200] SLOW spr round 14 (radius: 20)
[01:33:00 -401469.029346] SLOW spr round 15 (radius: 5)
[01:35:09 -401468.587082] SLOW spr round 16 (radius: 5)
[01:37:02 -401468.559599] SLOW spr round 17 (radius: 10)
[01:39:10 -401468.559588] SLOW spr round 18 (radius: 15)
[01:43:04 -401468.559587] SLOW spr round 19 (radius: 20)
[01:49:14 -401468.559586] SLOW spr round 20 (radius: 25)
[01:56:08 -401468.559585] Model parameter optimization (eps = 0.100000)

[01:56:12] ML tree search #4, logLikelihood: -401468.518784

[01:56:12 -1254357.447556] Initial branch length optimization
[01:56:17 -1000638.739824] Model parameter optimization (eps = 10.000000)
[01:57:00 -998603.965338] AUTODETECT spr round 1 (radius: 5)
[01:58:27 -735757.602293] AUTODETECT spr round 2 (radius: 10)
[01:59:58 -571987.146630] AUTODETECT spr round 3 (radius: 15)
[02:01:47 -470675.375104] AUTODETECT spr round 4 (radius: 20)
[02:04:08 -442155.353225] AUTODETECT spr round 5 (radius: 25)
[02:07:06 -439429.463488] SPR radius for FAST iterations: 25 (autodetect)
[02:07:06 -439429.463488] Model parameter optimization (eps = 3.000000)
[02:07:30 -438262.095203] FAST spr round 1 (radius: 25)
[02:10:37 -403311.964415] FAST spr round 2 (radius: 25)
[02:12:50 -401755.201737] FAST spr round 3 (radius: 25)
[02:14:27 -401564.425582] FAST spr round 4 (radius: 25)
[02:15:48 -401562.072243] FAST spr round 5 (radius: 25)
[02:17:04 -401560.505751] FAST spr round 6 (radius: 25)
[02:18:16 -401559.838178] FAST spr round 7 (radius: 25)
[02:19:28 -401558.019270] FAST spr round 8 (radius: 25)
[02:20:37 -401558.002703] Model parameter optimization (eps = 1.000000)
[02:20:49 -401552.199063] SLOW spr round 1 (radius: 5)
[02:22:29 -401478.043515] SLOW spr round 2 (radius: 5)
[02:24:07 -401474.778278] SLOW spr round 3 (radius: 5)
[02:25:42 -401474.776870] SLOW spr round 4 (radius: 10)
[02:27:34 -401470.526728] SLOW spr round 5 (radius: 5)
[02:29:39 -401466.912835] SLOW spr round 6 (radius: 5)
[02:31:26 -401466.911932] SLOW spr round 7 (radius: 10)
[02:33:25 -401466.716741] SLOW spr round 8 (radius: 5)
[02:35:24 -401466.713519] SLOW spr round 9 (radius: 10)
[02:37:38 -401464.808556] SLOW spr round 10 (radius: 5)
[02:39:35 -401464.807180] SLOW spr round 11 (radius: 10)
[02:41:47 -401464.764257] SLOW spr round 12 (radius: 15)
[02:45:48 -401464.164815] SLOW spr round 13 (radius: 5)
[02:47:52 -401463.739830] SLOW spr round 14 (radius: 5)
[02:49:42 -401463.535110] SLOW spr round 15 (radius: 5)
[02:51:23 -401463.535097] SLOW spr round 16 (radius: 10)
[02:53:20 -401463.533465] SLOW spr round 17 (radius: 15)
[02:57:31 -401463.533465] SLOW spr round 18 (radius: 20)
[03:03:38 -401463.533465] SLOW spr round 19 (radius: 25)
[03:10:42 -401463.533465] Model parameter optimization (eps = 0.100000)

[03:10:48] ML tree search #5, logLikelihood: -401463.401800

[03:10:49 -1259286.237881] Initial branch length optimization
[03:10:54 -1004971.939474] Model parameter optimization (eps = 10.000000)
[03:11:38 -1002933.356522] AUTODETECT spr round 1 (radius: 5)
[03:13:04 -756834.892773] AUTODETECT spr round 2 (radius: 10)
[03:14:37 -583857.666883] AUTODETECT spr round 3 (radius: 15)
[03:16:30 -469750.565150] AUTODETECT spr round 4 (radius: 20)
[03:18:49 -440630.383332] AUTODETECT spr round 5 (radius: 25)
[03:22:01 -438688.347515] SPR radius for FAST iterations: 25 (autodetect)
[03:22:01 -438688.347515] Model parameter optimization (eps = 3.000000)
[03:22:27 -437808.579154] FAST spr round 1 (radius: 25)
[03:25:07 -403438.427572] FAST spr round 2 (radius: 25)
[03:27:04 -401702.318331] FAST spr round 3 (radius: 25)
[03:28:45 -401636.774860] FAST spr round 4 (radius: 25)
[03:30:07 -401631.381138] FAST spr round 5 (radius: 25)
[03:31:21 -401631.369624] Model parameter optimization (eps = 1.000000)
[03:31:34 -401618.941472] SLOW spr round 1 (radius: 5)
[03:33:10 -401455.231562] SLOW spr round 2 (radius: 5)
[03:34:51 -401447.306661] SLOW spr round 3 (radius: 5)
[03:36:26 -401447.305228] SLOW spr round 4 (radius: 10)
[03:38:21 -401445.383190] SLOW spr round 5 (radius: 5)
[03:40:21 -401445.358006] SLOW spr round 6 (radius: 10)
[03:42:39 -401445.356232] SLOW spr round 7 (radius: 15)
[03:46:47 -401443.450894] SLOW spr round 8 (radius: 5)
[03:48:52 -401442.817818] SLOW spr round 9 (radius: 5)
[03:50:43 -401442.699333] SLOW spr round 10 (radius: 5)
[03:52:26 -401442.699332] SLOW spr round 11 (radius: 10)
[03:54:25 -401442.699332] SLOW spr round 12 (radius: 15)
[03:58:46 -401442.699332] SLOW spr round 13 (radius: 20)
[04:05:05 -401442.699332] SLOW spr round 14 (radius: 25)
[04:11:57 -401442.699332] Model parameter optimization (eps = 0.100000)

[04:12:04] ML tree search #6, logLikelihood: -401442.652607

[04:12:04 -1251929.038632] Initial branch length optimization
[04:12:09 -999706.719556] Model parameter optimization (eps = 10.000000)
[04:12:55 -997729.387350] AUTODETECT spr round 1 (radius: 5)
[04:14:20 -745412.409906] AUTODETECT spr round 2 (radius: 10)
[04:15:53 -576839.250380] AUTODETECT spr round 3 (radius: 15)
[04:17:41 -478198.879237] AUTODETECT spr round 4 (radius: 20)
[04:19:45 -449447.011105] AUTODETECT spr round 5 (radius: 25)
[04:22:28 -446016.949343] SPR radius for FAST iterations: 25 (autodetect)
[04:22:28 -446016.949343] Model parameter optimization (eps = 3.000000)
[04:22:54 -445010.798662] FAST spr round 1 (radius: 25)
[04:25:51 -404435.824458] FAST spr round 2 (radius: 25)
[04:28:01 -401824.190697] FAST spr round 3 (radius: 25)
[04:29:50 -401585.966928] FAST spr round 4 (radius: 25)
[04:31:16 -401579.253087] FAST spr round 5 (radius: 25)
[04:32:33 -401572.327038] FAST spr round 6 (radius: 25)
[04:33:47 -401567.553653] FAST spr round 7 (radius: 25)
[04:35:00 -401565.490358] FAST spr round 8 (radius: 25)
[04:36:11 -401563.092583] FAST spr round 9 (radius: 25)
[04:37:21 -401563.091800] Model parameter optimization (eps = 1.000000)
[04:37:35 -401554.027422] SLOW spr round 1 (radius: 5)
[04:39:16 -401464.798019] SLOW spr round 2 (radius: 5)
[04:40:55 -401461.757902] SLOW spr round 3 (radius: 5)
[04:42:31 -401461.756451] SLOW spr round 4 (radius: 10)
[04:44:30 -401455.556085] SLOW spr round 5 (radius: 5)
[04:46:32 -401450.696967] SLOW spr round 6 (radius: 5)
[04:48:20 -401450.695723] SLOW spr round 7 (radius: 10)
[04:50:27 -401450.695060] SLOW spr round 8 (radius: 15)
[04:54:40 -401450.587038] SLOW spr round 9 (radius: 5)
[04:56:45 -401450.266900] SLOW spr round 10 (radius: 5)
[04:58:36 -401450.052543] SLOW spr round 11 (radius: 5)
[05:00:18 -401450.051573] SLOW spr round 12 (radius: 10)
[05:02:21 -401450.051563] SLOW spr round 13 (radius: 15)
[05:06:36 -401450.051563] SLOW spr round 14 (radius: 20)
[05:12:52 -401450.051563] SLOW spr round 15 (radius: 25)
[05:19:55 -401450.051563] Model parameter optimization (eps = 0.100000)

[05:20:03] ML tree search #7, logLikelihood: -401449.906216

[05:20:03 -1257419.222345] Initial branch length optimization
[05:20:08 -1012443.748767] Model parameter optimization (eps = 10.000000)
[05:20:54 -1010429.746034] AUTODETECT spr round 1 (radius: 5)
[05:22:18 -750863.744548] AUTODETECT spr round 2 (radius: 10)
[05:23:51 -556380.925784] AUTODETECT spr round 3 (radius: 15)
[05:25:44 -460556.146676] AUTODETECT spr round 4 (radius: 20)
[05:27:58 -440937.220055] AUTODETECT spr round 5 (radius: 25)
[05:31:00 -438772.425608] SPR radius for FAST iterations: 25 (autodetect)
[05:31:00 -438772.425608] Model parameter optimization (eps = 3.000000)
[05:31:25 -437814.131768] FAST spr round 1 (radius: 25)
[05:34:15 -403202.393428] FAST spr round 2 (radius: 25)
[05:36:23 -401718.286292] FAST spr round 3 (radius: 25)
[05:38:10 -401586.128256] FAST spr round 4 (radius: 25)
[05:39:42 -401559.180408] FAST spr round 5 (radius: 25)
[05:40:58 -401556.779034] FAST spr round 6 (radius: 25)
[05:42:11 -401554.501875] FAST spr round 7 (radius: 25)
[05:43:22 -401554.500412] Model parameter optimization (eps = 1.000000)
[05:43:35 -401545.115684] SLOW spr round 1 (radius: 5)
[05:45:14 -401454.720059] SLOW spr round 2 (radius: 5)
[05:46:53 -401447.850412] SLOW spr round 3 (radius: 5)
[05:48:29 -401447.508846] SLOW spr round 4 (radius: 5)
[05:50:04 -401447.508795] SLOW spr round 5 (radius: 10)
[05:51:58 -401445.446748] SLOW spr round 6 (radius: 5)
[05:54:00 -401442.950410] SLOW spr round 7 (radius: 5)
[05:55:48 -401442.944265] SLOW spr round 8 (radius: 10)
[05:57:50 -401442.310807] SLOW spr round 9 (radius: 5)
[05:59:49 -401442.308671] SLOW spr round 10 (radius: 10)
[06:02:03 -401442.308621] SLOW spr round 11 (radius: 15)
[06:05:59 -401442.308614] SLOW spr round 12 (radius: 20)
[06:12:08 -401442.308613] SLOW spr round 13 (radius: 25)
[06:19:14 -401442.308613] Model parameter optimization (eps = 0.100000)

[06:19:24] ML tree search #8, logLikelihood: -401442.075680

[06:19:24 -1248985.336690] Initial branch length optimization
[06:19:29 -998994.528810] Model parameter optimization (eps = 10.000000)
[06:20:22 -996957.689552] AUTODETECT spr round 1 (radius: 5)
[06:21:48 -759214.073919] AUTODETECT spr round 2 (radius: 10)
[06:23:22 -582888.910149] AUTODETECT spr round 3 (radius: 15)
[06:25:14 -470923.036394] AUTODETECT spr round 4 (radius: 20)
[06:27:27 -438739.000340] AUTODETECT spr round 5 (radius: 25)
[06:30:35 -438284.241439] SPR radius for FAST iterations: 25 (autodetect)
[06:30:35 -438284.241439] Model parameter optimization (eps = 3.000000)
[06:30:59 -437241.325053] FAST spr round 1 (radius: 25)
[06:34:02 -403195.482300] FAST spr round 2 (radius: 25)
[06:36:14 -401641.737967] FAST spr round 3 (radius: 25)
[06:38:02 -401585.773639] FAST spr round 4 (radius: 25)
[06:39:36 -401564.738577] FAST spr round 5 (radius: 25)
[06:40:52 -401563.361413] FAST spr round 6 (radius: 25)
[06:42:05 -401563.335373] Model parameter optimization (eps = 1.000000)
[06:42:18 -401557.085915] SLOW spr round 1 (radius: 5)
[06:43:58 -401488.163674] SLOW spr round 2 (radius: 5)
[06:45:35 -401488.112955] SLOW spr round 3 (radius: 10)
[06:47:31 -401481.128614] SLOW spr round 4 (radius: 5)
[06:49:33 -401481.053672] SLOW spr round 5 (radius: 10)
[06:51:51 -401481.053391] SLOW spr round 6 (radius: 15)
[06:55:39 -401479.100812] SLOW spr round 7 (radius: 5)
[06:57:52 -401472.960763] SLOW spr round 8 (radius: 5)
[06:59:44 -401472.702440] SLOW spr round 9 (radius: 5)
[07:01:27 -401472.657895] SLOW spr round 10 (radius: 10)
[07:03:26 -401472.657859] SLOW spr round 11 (radius: 15)
[07:07:21 -401472.657850] SLOW spr round 12 (radius: 20)
[07:13:28 -401472.358512] SLOW spr round 13 (radius: 5)
[07:15:39 -401472.047233] SLOW spr round 14 (radius: 5)
[07:17:34 -401472.042531] SLOW spr round 15 (radius: 10)
[07:19:43 -401472.042521] SLOW spr round 16 (radius: 15)
[07:23:30 -401472.042512] SLOW spr round 17 (radius: 20)
[07:29:38 -401472.042502] SLOW spr round 18 (radius: 25)
[07:37:06 -401472.042493] Model parameter optimization (eps = 0.100000)

[07:37:17] ML tree search #9, logLikelihood: -401471.659773

[07:37:17 -1251204.513361] Initial branch length optimization
[07:37:22 -994910.140034] Model parameter optimization (eps = 10.000000)
[07:38:04 -992776.887846] AUTODETECT spr round 1 (radius: 5)
[07:39:29 -704912.934702] AUTODETECT spr round 2 (radius: 10)
[07:41:05 -566570.558123] AUTODETECT spr round 3 (radius: 15)
[07:42:58 -466887.917099] AUTODETECT spr round 4 (radius: 20)
[07:45:05 -446376.996231] AUTODETECT spr round 5 (radius: 25)
[07:47:39 -443566.369405] SPR radius for FAST iterations: 25 (autodetect)
[07:47:39 -443566.369405] Model parameter optimization (eps = 3.000000)
[07:48:05 -442792.350504] FAST spr round 1 (radius: 25)
[07:50:52 -404163.065198] FAST spr round 2 (radius: 25)
[07:53:03 -401646.358739] FAST spr round 3 (radius: 25)
[07:54:47 -401566.258848] FAST spr round 4 (radius: 25)
[07:56:11 -401555.434530] FAST spr round 5 (radius: 25)
[07:57:27 -401554.005478] FAST spr round 6 (radius: 25)
[07:58:39 -401554.004920] Model parameter optimization (eps = 1.000000)
[07:58:53 -401545.539919] SLOW spr round 1 (radius: 5)
[08:00:30 -401459.181767] SLOW spr round 2 (radius: 5)
[08:02:11 -401443.691031] SLOW spr round 3 (radius: 5)
[08:03:47 -401443.618275] SLOW spr round 4 (radius: 10)
[08:05:42 -401443.532109] SLOW spr round 5 (radius: 15)
[08:09:52 -401443.412919] SLOW spr round 6 (radius: 5)
[08:11:58 -401443.001886] SLOW spr round 7 (radius: 5)
[08:13:50 -401442.766209] SLOW spr round 8 (radius: 5)
[08:15:33 -401442.752481] SLOW spr round 9 (radius: 10)
[08:17:32 -401442.749758] SLOW spr round 10 (radius: 15)
[08:21:38 -401442.749750] SLOW spr round 11 (radius: 20)
[08:27:52 -401442.749749] SLOW spr round 12 (radius: 25)
[08:35:12 -401442.749747] Model parameter optimization (eps = 0.100000)

[08:35:21] ML tree search #10, logLikelihood: -401441.934699

[08:35:21 -1241092.330138] Initial branch length optimization
[08:35:27 -998274.396135] Model parameter optimization (eps = 10.000000)
[08:36:12 -996112.084719] AUTODETECT spr round 1 (radius: 5)
[08:37:38 -767631.034031] AUTODETECT spr round 2 (radius: 10)
[08:39:12 -594694.926291] AUTODETECT spr round 3 (radius: 15)
[08:41:00 -488019.698121] AUTODETECT spr round 4 (radius: 20)
[08:43:17 -450740.801472] AUTODETECT spr round 5 (radius: 25)
[08:45:48 -446559.093794] SPR radius for FAST iterations: 25 (autodetect)
[08:45:48 -446559.093794] Model parameter optimization (eps = 3.000000)
[08:46:12 -445702.595975] FAST spr round 1 (radius: 25)
[08:48:52 -404535.353334] FAST spr round 2 (radius: 25)
[08:50:56 -401915.268138] FAST spr round 3 (radius: 25)
[08:52:39 -401739.789422] FAST spr round 4 (radius: 25)
[08:54:01 -401731.667181] FAST spr round 5 (radius: 25)
[08:55:16 -401731.440254] FAST spr round 6 (radius: 25)
[08:56:27 -401731.439779] Model parameter optimization (eps = 1.000000)
[08:56:43 -401720.075705] SLOW spr round 1 (radius: 5)
[08:58:19 -401503.686300] SLOW spr round 2 (radius: 5)
[08:59:56 -401495.808036] SLOW spr round 3 (radius: 5)
[09:01:35 -401493.848428] SLOW spr round 4 (radius: 5)
[09:03:11 -401493.846837] SLOW spr round 5 (radius: 10)
[09:05:05 -401493.846480] SLOW spr round 6 (radius: 15)
[09:09:30 -401491.102394] SLOW spr round 7 (radius: 5)
[09:11:35 -401491.086279] SLOW spr round 8 (radius: 10)
[09:14:02 -401490.541169] SLOW spr round 9 (radius: 5)
[09:16:00 -401490.118009] SLOW spr round 10 (radius: 5)
[09:17:47 -401490.010739] SLOW spr round 11 (radius: 5)
[09:19:27 -401490.010308] SLOW spr round 12 (radius: 10)
[09:21:24 -401488.633939] SLOW spr round 13 (radius: 5)
[09:23:24 -401488.471597] SLOW spr round 14 (radius: 5)
[09:25:12 -401488.471005] SLOW spr round 15 (radius: 10)
[09:27:15 -401488.470835] SLOW spr round 16 (radius: 15)
[09:31:27 -401488.014329] SLOW spr round 17 (radius: 5)
[09:33:33 -401487.864273] SLOW spr round 18 (radius: 5)
[09:35:23 -401487.864135] SLOW spr round 19 (radius: 10)
[09:37:30 -401487.862467] SLOW spr round 20 (radius: 15)
[09:41:39 -401487.862452] SLOW spr round 21 (radius: 20)
[09:47:41 -401487.862447] SLOW spr round 22 (radius: 25)
[09:54:27 -401487.862445] Model parameter optimization (eps = 0.100000)

[09:54:36] ML tree search #11, logLikelihood: -401487.659244

[09:54:36 -1258227.316112] Initial branch length optimization
[09:54:41 -1015856.929637] Model parameter optimization (eps = 10.000000)
[09:55:24 -1013660.250273] AUTODETECT spr round 1 (radius: 5)
[09:56:49 -744192.783970] AUTODETECT spr round 2 (radius: 10)
[09:58:24 -569845.361548] AUTODETECT spr round 3 (radius: 15)
[10:00:10 -502586.325231] AUTODETECT spr round 4 (radius: 20)
[10:02:33 -460594.926993] AUTODETECT spr round 5 (radius: 25)
[10:05:07 -453810.035052] SPR radius for FAST iterations: 25 (autodetect)
[10:05:07 -453810.035052] Model parameter optimization (eps = 3.000000)
[10:05:31 -452708.859155] FAST spr round 1 (radius: 25)
[10:08:12 -404087.074674] FAST spr round 2 (radius: 25)
[10:10:17 -401753.501795] FAST spr round 3 (radius: 25)
[10:11:57 -401701.038348] FAST spr round 4 (radius: 25)
[10:13:25 -401676.174011] FAST spr round 5 (radius: 25)
[10:14:41 -401676.151226] Model parameter optimization (eps = 1.000000)
[10:14:58 -401670.239107] SLOW spr round 1 (radius: 5)
[10:16:33 -401464.739999] SLOW spr round 2 (radius: 5)
[10:18:12 -401459.798293] SLOW spr round 3 (radius: 5)
[10:19:49 -401459.574010] SLOW spr round 4 (radius: 5)
[10:21:25 -401459.573702] SLOW spr round 5 (radius: 10)
[10:23:22 -401456.946648] SLOW spr round 6 (radius: 5)
[10:25:22 -401456.944659] SLOW spr round 7 (radius: 10)
[10:27:46 -401456.944238] SLOW spr round 8 (radius: 15)
[10:31:52 -401456.452977] SLOW spr round 9 (radius: 5)
[10:33:57 -401456.382405] SLOW spr round 10 (radius: 10)
[10:36:30 -401456.380715] SLOW spr round 11 (radius: 15)
[10:40:33 -401456.312043] SLOW spr round 12 (radius: 20)
[10:46:57 -401456.016344] SLOW spr round 13 (radius: 5)
[10:49:08 -401455.776440] SLOW spr round 14 (radius: 5)
[10:51:03 -401455.740775] SLOW spr round 15 (radius: 10)
[10:53:18 -401455.739634] SLOW spr round 16 (radius: 15)
[10:57:28 -401455.739631] SLOW spr round 17 (radius: 20)
[11:03:50 -401455.725449] SLOW spr round 18 (radius: 25)
[11:10:52 -401455.725271] Model parameter optimization (eps = 0.100000)

[11:11:06] ML tree search #12, logLikelihood: -401455.236271

[11:11:06 -1248949.817863] Initial branch length optimization
[11:11:12 -1005107.888911] Model parameter optimization (eps = 10.000000)
[11:12:00 -1002932.945934] AUTODETECT spr round 1 (radius: 5)
[11:13:26 -747430.348658] AUTODETECT spr round 2 (radius: 10)
[11:15:02 -554309.761700] AUTODETECT spr round 3 (radius: 15)
[11:16:57 -461793.963623] AUTODETECT spr round 4 (radius: 20)
[11:19:09 -434854.925179] AUTODETECT spr round 5 (radius: 25)
[11:22:00 -432079.701051] SPR radius for FAST iterations: 25 (autodetect)
[11:22:00 -432079.701051] Model parameter optimization (eps = 3.000000)
[11:22:27 -430958.672151] FAST spr round 1 (radius: 25)
[11:25:14 -402529.534251] FAST spr round 2 (radius: 25)
[11:27:20 -401619.572044] FAST spr round 3 (radius: 25)
[11:29:06 -401567.005475] FAST spr round 4 (radius: 25)
[11:30:30 -401552.691893] FAST spr round 5 (radius: 25)
[11:31:45 -401552.691568] Model parameter optimization (eps = 1.000000)
[11:32:00 -401551.373462] SLOW spr round 1 (radius: 5)
[11:33:42 -401453.504339] SLOW spr round 2 (radius: 5)
[11:35:24 -401448.419378] SLOW spr round 3 (radius: 5)
[11:37:05 -401446.401717] SLOW spr round 4 (radius: 5)
[11:38:41 -401446.400935] SLOW spr round 5 (radius: 10)
[11:40:32 -401446.400417] SLOW spr round 6 (radius: 15)
[11:44:41 -401445.151970] SLOW spr round 7 (radius: 5)
[11:46:53 -401439.772684] SLOW spr round 8 (radius: 5)
[11:48:45 -401439.026380] SLOW spr round 9 (radius: 5)
[11:50:28 -401439.025676] SLOW spr round 10 (radius: 10)
[11:52:23 -401439.025530] SLOW spr round 11 (radius: 15)
[11:56:24 -401439.025485] SLOW spr round 12 (radius: 20)
[12:02:29 -401439.025458] SLOW spr round 13 (radius: 25)
[12:09:46 -401439.025435] Model parameter optimization (eps = 0.100000)

[12:09:57] ML tree search #13, logLikelihood: -401438.895318

[12:09:58 -1255105.454689] Initial branch length optimization
[12:10:03 -1005293.968137] Model parameter optimization (eps = 10.000000)
[12:10:49 -1003193.763093] AUTODETECT spr round 1 (radius: 5)
[12:12:14 -761261.574202] AUTODETECT spr round 2 (radius: 10)
[12:13:48 -585986.178975] AUTODETECT spr round 3 (radius: 15)
[12:15:39 -497665.094316] AUTODETECT spr round 4 (radius: 20)
[12:17:46 -446638.992346] AUTODETECT spr round 5 (radius: 25)
[12:20:32 -444210.676485] SPR radius for FAST iterations: 25 (autodetect)
[12:20:32 -444210.676485] Model parameter optimization (eps = 3.000000)
[12:20:57 -443336.098275] FAST spr round 1 (radius: 25)
[12:23:47 -403615.278339] FAST spr round 2 (radius: 25)
[12:25:47 -401677.418665] FAST spr round 3 (radius: 25)
[12:27:32 -401574.934196] FAST spr round 4 (radius: 25)
[12:28:57 -401572.014402] FAST spr round 5 (radius: 25)
[12:30:14 -401571.446409] FAST spr round 6 (radius: 25)
[12:31:27 -401571.243406] FAST spr round 7 (radius: 25)
[12:32:39 -401571.220219] Model parameter optimization (eps = 1.000000)
[12:32:52 -401564.682779] SLOW spr round 1 (radius: 5)
[12:34:29 -401485.864669] SLOW spr round 2 (radius: 5)
[12:36:09 -401479.887944] SLOW spr round 3 (radius: 5)
[12:37:50 -401474.213112] SLOW spr round 4 (radius: 5)
[12:39:29 -401470.131958] SLOW spr round 5 (radius: 5)
[12:41:05 -401470.130354] SLOW spr round 6 (radius: 10)
[12:43:01 -401464.360156] SLOW spr round 7 (radius: 5)
[12:45:01 -401464.343229] SLOW spr round 8 (radius: 10)
[12:47:16 -401464.342998] SLOW spr round 9 (radius: 15)
[12:51:09 -401461.454169] SLOW spr round 10 (radius: 5)
[12:53:18 -401459.264629] SLOW spr round 11 (radius: 5)
[12:55:09 -401459.066757] SLOW spr round 12 (radius: 5)
[12:56:51 -401459.065028] SLOW spr round 13 (radius: 10)
[12:58:49 -401459.065025] SLOW spr round 14 (radius: 15)
[13:02:55 -401459.065025] SLOW spr round 15 (radius: 20)
[13:09:21 -401459.046877] SLOW spr round 16 (radius: 25)
[13:16:58 -401459.046619] Model parameter optimization (eps = 0.100000)

[13:17:03] ML tree search #14, logLikelihood: -401458.982235

[13:17:03 -1251986.761203] Initial branch length optimization
[13:17:08 -1007445.332277] Model parameter optimization (eps = 10.000000)
[13:17:52 -1005479.115916] AUTODETECT spr round 1 (radius: 5)
[13:19:18 -737496.893132] AUTODETECT spr round 2 (radius: 10)
[13:20:52 -595382.162839] AUTODETECT spr round 3 (radius: 15)
[13:22:49 -473945.248016] AUTODETECT spr round 4 (radius: 20)
[13:25:02 -446011.832495] AUTODETECT spr round 5 (radius: 25)
[13:27:57 -443501.808656] SPR radius for FAST iterations: 25 (autodetect)
[13:27:57 -443501.808656] Model parameter optimization (eps = 3.000000)
[13:28:24 -442423.737956] FAST spr round 1 (radius: 25)
[13:31:26 -404784.795445] FAST spr round 2 (radius: 25)
[13:33:42 -402194.900808] FAST spr round 3 (radius: 25)
[13:35:24 -401800.973789] FAST spr round 4 (radius: 25)
[13:36:53 -401607.244319] FAST spr round 5 (radius: 25)
[13:38:21 -401582.181006] FAST spr round 6 (radius: 25)
[13:39:33 -401582.098098] Model parameter optimization (eps = 1.000000)
[13:39:45 -401572.618227] SLOW spr round 1 (radius: 5)
[13:41:25 -401475.262461] SLOW spr round 2 (radius: 5)
[13:43:08 -401466.688072] SLOW spr round 3 (radius: 5)
[13:44:47 -401465.743858] SLOW spr round 4 (radius: 5)
[13:46:24 -401465.743308] SLOW spr round 5 (radius: 10)
[13:48:21 -401463.017807] SLOW spr round 6 (radius: 5)
[13:50:24 -401452.648266] SLOW spr round 7 (radius: 5)
[13:52:13 -401452.646164] SLOW spr round 8 (radius: 10)
[13:54:17 -401452.645485] SLOW spr round 9 (radius: 15)
[13:58:21 -401452.245317] SLOW spr round 10 (radius: 5)
[14:00:27 -401451.945941] SLOW spr round 11 (radius: 5)
[14:02:18 -401451.781857] SLOW spr round 12 (radius: 5)
[14:04:01 -401451.781755] SLOW spr round 13 (radius: 10)
[14:06:02 -401450.712950] SLOW spr round 14 (radius: 5)
[14:08:02 -401450.241842] SLOW spr round 15 (radius: 5)
[14:09:49 -401450.239066] SLOW spr round 16 (radius: 10)
[14:11:53 -401450.238389] SLOW spr round 17 (radius: 15)
[14:15:56 -401450.238262] SLOW spr round 18 (radius: 20)
[14:22:14 -401450.238239] SLOW spr round 19 (radius: 25)
[14:29:31 -401450.238234] Model parameter optimization (eps = 0.100000)

[14:29:41] ML tree search #15, logLikelihood: -401450.058403

[14:29:41 -1250627.343973] Initial branch length optimization
[14:29:46 -997219.158135] Model parameter optimization (eps = 10.000000)
[14:30:32 -995137.507099] AUTODETECT spr round 1 (radius: 5)
[14:31:59 -743923.997938] AUTODETECT spr round 2 (radius: 10)
[14:33:33 -593034.298631] AUTODETECT spr round 3 (radius: 15)
[14:35:23 -485695.045533] AUTODETECT spr round 4 (radius: 20)
[14:37:37 -442301.363759] AUTODETECT spr round 5 (radius: 25)
[14:40:09 -436534.876984] SPR radius for FAST iterations: 25 (autodetect)
[14:40:09 -436534.876984] Model parameter optimization (eps = 3.000000)
[14:40:39 -435622.601134] FAST spr round 1 (radius: 25)
[14:43:22 -403371.829475] FAST spr round 2 (radius: 25)
[14:45:33 -401715.391703] FAST spr round 3 (radius: 25)
[14:47:18 -401565.050869] FAST spr round 4 (radius: 25)
[14:48:40 -401555.296778] FAST spr round 5 (radius: 25)
[14:49:54 -401555.294994] Model parameter optimization (eps = 1.000000)
[14:50:07 -401550.703019] SLOW spr round 1 (radius: 5)
[14:51:48 -401475.551911] SLOW spr round 2 (radius: 5)
[14:53:28 -401453.528955] SLOW spr round 3 (radius: 5)
[14:55:04 -401453.432961] SLOW spr round 4 (radius: 10)
[14:57:00 -401448.800696] SLOW spr round 5 (radius: 5)
[14:59:01 -401448.797905] SLOW spr round 6 (radius: 10)
[15:01:20 -401444.302265] SLOW spr round 7 (radius: 5)
[15:03:21 -401437.272094] SLOW spr round 8 (radius: 5)
[15:05:08 -401437.269641] SLOW spr round 9 (radius: 10)
[15:07:09 -401437.269236] SLOW spr round 10 (radius: 15)
[15:11:12 -401437.269131] SLOW spr round 11 (radius: 20)
[15:17:18 -401437.269089] SLOW spr round 12 (radius: 25)
[15:24:12 -401437.269066] Model parameter optimization (eps = 0.100000)

[15:24:20] ML tree search #16, logLikelihood: -401437.151186

[15:24:21 -1247543.251826] Initial branch length optimization
[15:24:26 -1004843.119282] Model parameter optimization (eps = 10.000000)
[15:25:11 -1002899.738728] AUTODETECT spr round 1 (radius: 5)
[15:26:37 -731296.623113] AUTODETECT spr round 2 (radius: 10)
[15:28:11 -551468.255202] AUTODETECT spr round 3 (radius: 15)
[15:29:54 -484588.611062] AUTODETECT spr round 4 (radius: 20)
[15:32:07 -445816.296855] AUTODETECT spr round 5 (radius: 25)
[15:34:36 -443384.296807] SPR radius for FAST iterations: 25 (autodetect)
[15:34:36 -443384.296807] Model parameter optimization (eps = 3.000000)
[15:35:02 -442335.687351] FAST spr round 1 (radius: 25)
[15:37:57 -403316.288502] FAST spr round 2 (radius: 25)
[15:40:17 -401638.384409] FAST spr round 3 (radius: 25)
[15:42:04 -401562.741723] FAST spr round 4 (radius: 25)
[15:43:24 -401562.689401] Model parameter optimization (eps = 1.000000)
[15:43:38 -401554.777389] SLOW spr round 1 (radius: 5)
[15:45:26 -401496.848316] SLOW spr round 2 (radius: 5)
[15:47:11 -401481.478838] SLOW spr round 3 (radius: 5)
[15:48:49 -401480.493091] SLOW spr round 4 (radius: 5)
[15:50:25 -401480.488517] SLOW spr round 5 (radius: 10)
[15:52:21 -401480.487497] SLOW spr round 6 (radius: 15)
[15:56:35 -401478.349189] SLOW spr round 7 (radius: 5)
[15:58:42 -401477.301800] SLOW spr round 8 (radius: 5)
[16:00:34 -401476.983234] SLOW spr round 9 (radius: 5)
[16:02:16 -401476.982442] SLOW spr round 10 (radius: 10)
[16:04:19 -401476.576367] SLOW spr round 11 (radius: 5)
[16:06:18 -401476.576277] SLOW spr round 12 (radius: 10)
[16:08:37 -401476.100916] SLOW spr round 13 (radius: 5)
[16:10:37 -401473.106503] SLOW spr round 14 (radius: 5)
[16:12:26 -401469.693830] SLOW spr round 15 (radius: 5)
[16:14:06 -401469.693340] SLOW spr round 16 (radius: 10)
[16:16:07 -401469.693261] SLOW spr round 17 (radius: 15)
[16:20:34 -401469.693238] SLOW spr round 18 (radius: 20)
[16:26:59 -401469.693229] SLOW spr round 19 (radius: 25)
[16:34:04 -401469.693225] Model parameter optimization (eps = 0.100000)

[16:34:08] ML tree search #17, logLikelihood: -401469.593458

[16:34:08 -1258702.777587] Initial branch length optimization
[16:34:14 -1005722.321161] Model parameter optimization (eps = 10.000000)
[16:34:53 -1003612.643403] AUTODETECT spr round 1 (radius: 5)
[16:36:20 -741211.481068] AUTODETECT spr round 2 (radius: 10)
[16:37:52 -543361.318341] AUTODETECT spr round 3 (radius: 15)
[16:39:46 -453557.014552] AUTODETECT spr round 4 (radius: 20)
[16:41:58 -442291.095615] AUTODETECT spr round 5 (radius: 25)
[16:44:33 -438183.829827] SPR radius for FAST iterations: 25 (autodetect)
[16:44:33 -438183.829827] Model parameter optimization (eps = 3.000000)
[16:45:06 -437128.477320] FAST spr round 1 (radius: 25)
[16:47:54 -403286.867930] FAST spr round 2 (radius: 25)
[16:49:51 -401742.662111] FAST spr round 3 (radius: 25)
[16:51:28 -401639.114049] FAST spr round 4 (radius: 25)
[16:52:50 -401631.590333] FAST spr round 5 (radius: 25)
[16:54:05 -401628.988620] FAST spr round 6 (radius: 25)
[16:55:17 -401623.260531] FAST spr round 7 (radius: 25)
[16:56:28 -401620.838705] FAST spr round 8 (radius: 25)
[16:57:38 -401620.837265] Model parameter optimization (eps = 1.000000)
[16:57:53 -401613.072925] SLOW spr round 1 (radius: 5)
[16:59:25 -401529.000104] SLOW spr round 2 (radius: 5)
[17:01:02 -401525.500843] SLOW spr round 3 (radius: 5)
[17:02:38 -401523.432777] SLOW spr round 4 (radius: 5)
[17:04:13 -401523.432200] SLOW spr round 5 (radius: 10)
[17:06:06 -401518.988201] SLOW spr round 6 (radius: 5)
[17:08:06 -401518.230495] SLOW spr round 7 (radius: 5)
[17:09:54 -401518.229158] SLOW spr round 8 (radius: 10)
[17:11:54 -401517.826872] SLOW spr round 9 (radius: 5)
[17:13:56 -401516.651853] SLOW spr round 10 (radius: 5)
[17:15:43 -401516.594557] SLOW spr round 11 (radius: 10)
[17:17:44 -401514.820577] SLOW spr round 12 (radius: 5)
[17:19:46 -401513.025265] SLOW spr round 13 (radius: 5)
[17:21:36 -401512.343491] SLOW spr round 14 (radius: 5)
[17:23:16 -401512.342705] SLOW spr round 15 (radius: 10)
[17:25:13 -401512.342637] SLOW spr round 16 (radius: 15)
[17:29:34 -401512.342619] SLOW spr round 17 (radius: 20)
[17:35:51 -401511.100592] SLOW spr round 18 (radius: 5)
[17:38:05 -401510.196976] SLOW spr round 19 (radius: 5)
[17:40:00 -401510.170210] SLOW spr round 20 (radius: 10)
[17:42:10 -401510.170209] SLOW spr round 21 (radius: 15)
[17:46:19 -401510.170209] SLOW spr round 22 (radius: 20)
[17:52:39 -401510.170209] SLOW spr round 23 (radius: 25)
[17:59:50 -401510.170209] Model parameter optimization (eps = 0.100000)

[17:59:59] ML tree search #18, logLikelihood: -401509.962548

[17:59:59 -1248693.948568] Initial branch length optimization
[18:00:04 -999030.856435] Model parameter optimization (eps = 10.000000)
[18:00:45 -997032.552589] AUTODETECT spr round 1 (radius: 5)
[18:02:11 -753632.095688] AUTODETECT spr round 2 (radius: 10)
[18:03:45 -601956.163958] AUTODETECT spr round 3 (radius: 15)
[18:05:39 -519567.905194] AUTODETECT spr round 4 (radius: 20)
[18:07:57 -438842.708609] AUTODETECT spr round 5 (radius: 25)
[18:11:00 -436802.916858] SPR radius for FAST iterations: 25 (autodetect)
[18:11:00 -436802.916858] Model parameter optimization (eps = 3.000000)
[18:11:24 -435901.676633] FAST spr round 1 (radius: 25)
[18:14:25 -403028.220183] FAST spr round 2 (radius: 25)
[18:16:35 -401926.220168] FAST spr round 3 (radius: 25)
[18:18:23 -401669.451271] FAST spr round 4 (radius: 25)
[18:19:48 -401619.880833] FAST spr round 5 (radius: 25)
[18:21:04 -401618.747225] FAST spr round 6 (radius: 25)
[18:22:18 -401617.338505] FAST spr round 7 (radius: 25)
[18:23:30 -401617.337160] Model parameter optimization (eps = 1.000000)
[18:23:48 -401614.317683] SLOW spr round 1 (radius: 5)
[18:25:28 -401535.503117] SLOW spr round 2 (radius: 5)
[18:27:10 -401528.296745] SLOW spr round 3 (radius: 5)
[18:28:50 -401521.303034] SLOW spr round 4 (radius: 5)
[18:30:27 -401518.855493] SLOW spr round 5 (radius: 5)
[18:32:04 -401517.647483] SLOW spr round 6 (radius: 5)
[18:33:40 -401517.646880] SLOW spr round 7 (radius: 10)
[18:35:38 -401508.816768] SLOW spr round 8 (radius: 5)
[18:37:39 -401508.353063] SLOW spr round 9 (radius: 5)
[18:39:26 -401508.136131] SLOW spr round 10 (radius: 5)
[18:41:08 -401508.135812] SLOW spr round 11 (radius: 10)
[18:43:07 -401506.875793] SLOW spr round 12 (radius: 5)
[18:45:08 -401506.045713] SLOW spr round 13 (radius: 5)
[18:46:55 -401506.038210] SLOW spr round 14 (radius: 10)
[18:48:58 -401506.037271] SLOW spr round 15 (radius: 15)
[18:52:49 -401506.037054] SLOW spr round 16 (radius: 20)
[18:58:42 -401505.997802] SLOW spr round 17 (radius: 25)
[19:05:36 -401505.997409] Model parameter optimization (eps = 0.100000)

[19:05:44] ML tree search #19, logLikelihood: -401505.779384

[19:05:44 -1255315.463918] Initial branch length optimization
[19:05:49 -1000122.493685] Model parameter optimization (eps = 10.000000)
[19:06:41 -998110.951780] AUTODETECT spr round 1 (radius: 5)
[19:08:07 -742282.223393] AUTODETECT spr round 2 (radius: 10)
[19:09:41 -555944.028737] AUTODETECT spr round 3 (radius: 15)
[19:11:32 -500638.568557] AUTODETECT spr round 4 (radius: 20)
[19:13:40 -448119.841164] AUTODETECT spr round 5 (radius: 25)
[19:16:09 -444176.947027] SPR radius for FAST iterations: 25 (autodetect)
[19:16:09 -444176.947027] Model parameter optimization (eps = 3.000000)
[19:16:48 -443129.240406] FAST spr round 1 (radius: 25)
[19:19:32 -403095.113210] FAST spr round 2 (radius: 25)
[19:21:33 -401607.975606] FAST spr round 3 (radius: 25)
[19:23:10 -401557.523853] FAST spr round 4 (radius: 25)
[19:24:31 -401556.664418] FAST spr round 5 (radius: 25)
[19:25:46 -401556.605807] Model parameter optimization (eps = 1.000000)
[19:25:56 -401550.456397] SLOW spr round 1 (radius: 5)
[19:27:33 -401461.176072] SLOW spr round 2 (radius: 5)
[19:29:14 -401451.753102] SLOW spr round 3 (radius: 5)
[19:30:51 -401451.604429] SLOW spr round 4 (radius: 5)
[19:32:27 -401451.603280] SLOW spr round 5 (radius: 10)
[19:34:26 -401451.603278] SLOW spr round 6 (radius: 15)
[19:38:57 -401451.603276] SLOW spr round 7 (radius: 20)
[19:45:26 -401451.603276] SLOW spr round 8 (radius: 25)
[19:52:24 -401451.603276] Model parameter optimization (eps = 0.100000)

[19:52:29] ML tree search #20, logLikelihood: -401451.572660


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.161280,0.537642) (0.158777,0.596044) (0.425997,0.969533) (0.253946,1.597319) 
   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: -401437.151186

AIC score: 805692.302372 / AICc score: 4779072.302372 / BIC score: 813004.902711
Free parameters (model + branch lengths): 1409

WARNING: Number of free parameters (K=1409) is larger than alignment size (n=1326).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD84/3_mltree/Q8TD84.raxml.log

Analysis started: 24-Jul-2021 21:01:11 / finished: 25-Jul-2021 16:53:40

Elapsed time: 71549.217 seconds (this run) / 599539.145 seconds (total with restarts)