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

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 14-Jul-2021 00:29:59 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/2_msa/O14841_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841 --seed 2 --threads 9 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (9 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/2_msa/O14841_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1232 sites

WARNING: Sequences tr_J3KI44_J3KI44_COCIM_246410 and tr_A0A0J6XXC9_A0A0J6XXC9_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6Q8T2_B6Q8T2_TALMQ_441960 and tr_A0A093V4Q6_A0A093V4Q6_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WN62_B2WN62_PYRTR_426418 and tr_A0A2W1GZN8_A0A2W1GZN8_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_F9F7T4_F9F7T4_FUSOF_660025 and tr_N4TG92_N4TG92_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9F7T4_F9F7T4_FUSOF_660025 and tr_X0CH99_X0CH99_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A2QQ54_A2QQ54_ASPNC_425011 and tr_G3YFS2_G3YFS2_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R1Q7_A2R1Q7_ASPNC_425011 and tr_A0A319AIN1_A0A319AIN1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XKJ0_G7XKJ0_ASPKW_1033177 and tr_A0A146FVQ6_A0A146FVQ6_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9XDC4_F9XDC4_ZYMTI_336722 and tr_A0A1X7RW95_A0A1X7RW95_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_F2SCT1_F2SCT1_TRIRC_559305 and tr_A0A178ETF5_A0A178ETF5_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_W2QVT6_W2QVT6_PHYPN_761204 and tr_A0A0W8C6L4_A0A0W8C6L4_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QVT6_W2QVT6_PHYPN_761204 and tr_W2MEP6_W2MEP6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A100IPT1_A0A100IPT1_ASPNG_5061 and tr_A0A1L9NQL0_A0A1L9NQL0_ASPTU_767770 are exactly identical!
WARNING: Duplicate sequences found: 13

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841.raxml.reduced.phy

Alignment comprises 1 partitions and 1228 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1232 / 1228
Gaps: 1.89 %
Invariant sites: 3.57 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841.raxml.rba

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

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 137 / 10960
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1539414.150704] Initial branch length optimization
[00:00:07 -1351464.616067] Model parameter optimization (eps = 10.000000)
[00:00:43 -1348731.063374] AUTODETECT spr round 1 (radius: 5)
[00:03:14 -1007831.816824] AUTODETECT spr round 2 (radius: 10)
[00:07:15 -706885.056492] AUTODETECT spr round 3 (radius: 15)
[00:11:42 -595290.098523] AUTODETECT spr round 4 (radius: 20)
[00:15:33 -574225.231523] AUTODETECT spr round 5 (radius: 25)
[00:19:50 -573357.222036] SPR radius for FAST iterations: 25 (autodetect)
[00:19:50 -573357.222036] Model parameter optimization (eps = 3.000000)
[00:20:16 -573066.114287] FAST spr round 1 (radius: 25)
[00:23:37 -508714.993491] FAST spr round 2 (radius: 25)
[00:26:06 -506604.323725] FAST spr round 3 (radius: 25)
[00:28:13 -506464.799010] FAST spr round 4 (radius: 25)
[00:30:06 -506442.194019] FAST spr round 5 (radius: 25)
[00:31:50 -506439.106983] FAST spr round 6 (radius: 25)
[00:33:32 -506438.094383] FAST spr round 7 (radius: 25)
[00:35:13 -506436.696606] FAST spr round 8 (radius: 25)
[00:36:57 -506429.125946] FAST spr round 9 (radius: 25)
[00:38:38 -506428.278258] FAST spr round 10 (radius: 25)
[00:40:19 -506426.119592] FAST spr round 11 (radius: 25)
[00:42:01 -506426.119554] Model parameter optimization (eps = 1.000000)
[00:42:15 -506415.942528] SLOW spr round 1 (radius: 5)
[00:44:57 -506328.087330] SLOW spr round 2 (radius: 5)
[00:47:24 -506324.389074] SLOW spr round 3 (radius: 5)
[00:49:46 -506322.555890] SLOW spr round 4 (radius: 5)
[00:52:06 -506322.555887] SLOW spr round 5 (radius: 10)
[00:54:40 -506322.555887] SLOW spr round 6 (radius: 15)
[00:59:37 -506322.555887] SLOW spr round 7 (radius: 20)
[01:08:24 -506322.555887] SLOW spr round 8 (radius: 25)
[01:19:40 -506322.555887] Model parameter optimization (eps = 0.100000)

[01:19:49] ML tree search #1, logLikelihood: -506322.416176

[01:19:50 -1556113.927435] Initial branch length optimization
[01:19:55 -1363732.756739] Model parameter optimization (eps = 10.000000)
[01:20:29 -1360978.596020] AUTODETECT spr round 1 (radius: 5)
[01:23:02 -991446.954362] AUTODETECT spr round 2 (radius: 10)
[01:27:19 -692447.530934] AUTODETECT spr round 3 (radius: 15)
[01:31:26 -606560.990967] AUTODETECT spr round 4 (radius: 20)
[01:35:10 -572539.361878] AUTODETECT spr round 5 (radius: 25)
[01:39:54 -570216.107299] SPR radius for FAST iterations: 25 (autodetect)
[01:39:54 -570216.107299] Model parameter optimization (eps = 3.000000)
[01:40:18 -569947.871664] FAST spr round 1 (radius: 25)
[01:43:31 -509023.663201] FAST spr round 2 (radius: 25)
[01:45:54 -506464.643495] FAST spr round 3 (radius: 25)
[01:47:56 -506391.505011] FAST spr round 4 (radius: 25)
[01:49:40 -506390.020964] FAST spr round 5 (radius: 25)
[01:51:21 -506388.772589] FAST spr round 6 (radius: 25)
[01:53:01 -506387.837848] FAST spr round 7 (radius: 25)
[01:54:40 -506386.635718] FAST spr round 8 (radius: 25)
[01:56:19 -506384.738147] FAST spr round 9 (radius: 25)
[01:57:57 -506383.986877] FAST spr round 10 (radius: 25)
[01:59:34 -506379.696957] FAST spr round 11 (radius: 25)
[02:01:12 -506379.204253] FAST spr round 12 (radius: 25)
[02:02:49 -506377.251732] FAST spr round 13 (radius: 25)
[02:04:27 -506376.984979] FAST spr round 14 (radius: 25)
[02:06:04 -506376.928039] Model parameter optimization (eps = 1.000000)
[02:06:18 -506369.596286] SLOW spr round 1 (radius: 5)
[02:08:56 -506317.260962] SLOW spr round 2 (radius: 5)
[02:11:15 -506317.260622] SLOW spr round 3 (radius: 10)
[02:13:46 -506317.260609] SLOW spr round 4 (radius: 15)
[02:18:37 -506317.260608] SLOW spr round 5 (radius: 20)
[02:27:26 -506317.260608] SLOW spr round 6 (radius: 25)
[02:38:39 -506317.260608] Model parameter optimization (eps = 0.100000)

[02:38:46] ML tree search #2, logLikelihood: -506316.994436

[02:38:47 -1559868.451017] Initial branch length optimization
[02:38:51 -1364722.362390] Model parameter optimization (eps = 10.000000)
[02:39:23 -1361961.551098] AUTODETECT spr round 1 (radius: 5)
[02:41:53 -1005821.894086] AUTODETECT spr round 2 (radius: 10)
[02:45:51 -694543.800804] AUTODETECT spr round 3 (radius: 15)
[02:49:33 -592844.731089] AUTODETECT spr round 4 (radius: 20)
[02:53:06 -571884.141827] AUTODETECT spr round 5 (radius: 25)
[02:57:42 -570586.194696] SPR radius for FAST iterations: 25 (autodetect)
[02:57:42 -570586.194696] Model parameter optimization (eps = 3.000000)
[02:58:03 -570280.632338] FAST spr round 1 (radius: 25)
[03:01:09 -508385.347993] FAST spr round 2 (radius: 25)
[03:03:29 -506529.329162] FAST spr round 3 (radius: 25)
[03:05:35 -506397.579466] FAST spr round 4 (radius: 25)
[03:07:20 -506394.511650] FAST spr round 5 (radius: 25)
[03:09:00 -506388.899478] FAST spr round 6 (radius: 25)
[03:10:38 -506387.290005] FAST spr round 7 (radius: 25)
[03:12:16 -506386.371985] FAST spr round 8 (radius: 25)
[03:13:53 -506379.021506] FAST spr round 9 (radius: 25)
[03:15:30 -506378.471413] FAST spr round 10 (radius: 25)
[03:17:08 -506378.251567] FAST spr round 11 (radius: 25)
[03:18:45 -506378.187040] Model parameter optimization (eps = 1.000000)
[03:18:59 -506373.349603] SLOW spr round 1 (radius: 5)
[03:21:36 -506314.739301] SLOW spr round 2 (radius: 5)
[03:23:56 -506306.588780] SLOW spr round 3 (radius: 5)
[03:26:13 -506306.588700] SLOW spr round 4 (radius: 10)
[03:28:42 -506306.588699] SLOW spr round 5 (radius: 15)
[03:33:20 -506306.588699] SLOW spr round 6 (radius: 20)
[03:41:20 -506306.588699] SLOW spr round 7 (radius: 25)
[03:51:56 -506306.588699] Model parameter optimization (eps = 0.100000)

[03:52:01] ML tree search #3, logLikelihood: -506306.565414

[03:52:01 -1555134.448880] Initial branch length optimization
[03:52:06 -1363025.294049] Model parameter optimization (eps = 10.000000)
[03:52:37 -1360389.923582] AUTODETECT spr round 1 (radius: 5)
[03:55:07 -1017892.087936] AUTODETECT spr round 2 (radius: 10)
[03:59:17 -719848.095085] AUTODETECT spr round 3 (radius: 15)
[04:03:34 -600364.561335] AUTODETECT spr round 4 (radius: 20)
[04:07:21 -576195.882449] AUTODETECT spr round 5 (radius: 25)
[04:11:33 -574890.245590] SPR radius for FAST iterations: 25 (autodetect)
[04:11:33 -574890.245590] Model parameter optimization (eps = 3.000000)
[04:11:55 -574535.009726] FAST spr round 1 (radius: 25)
[04:15:07 -508784.707232] FAST spr round 2 (radius: 25)
[04:17:28 -506576.555771] FAST spr round 3 (radius: 25)
[04:19:33 -506461.181724] FAST spr round 4 (radius: 25)
[04:21:21 -506434.270028] FAST spr round 5 (radius: 25)
[04:23:00 -506433.387163] FAST spr round 6 (radius: 25)
[04:24:38 -506432.472625] FAST spr round 7 (radius: 25)
[04:26:15 -506431.777747] FAST spr round 8 (radius: 25)
[04:27:53 -506429.475186] FAST spr round 9 (radius: 25)
[04:29:30 -506425.817686] FAST spr round 10 (radius: 25)
[04:31:06 -506425.409875] FAST spr round 11 (radius: 25)
[04:32:42 -506425.348640] Model parameter optimization (eps = 1.000000)
[04:32:50 -506424.486241] SLOW spr round 1 (radius: 5)
[04:35:25 -506351.226585] SLOW spr round 2 (radius: 5)
[04:37:44 -506348.173658] SLOW spr round 3 (radius: 5)
[04:40:06 -506342.627308] SLOW spr round 4 (radius: 5)
[04:42:21 -506342.627226] SLOW spr round 5 (radius: 10)
[04:44:50 -506342.627225] SLOW spr round 6 (radius: 15)
[04:49:35 -506342.627225] SLOW spr round 7 (radius: 20)
[04:58:03 -506342.627225] SLOW spr round 8 (radius: 25)
[05:08:59 -506342.627225] Model parameter optimization (eps = 0.100000)

[05:09:09] ML tree search #4, logLikelihood: -506341.885749

[05:09:09 -1550001.651890] Initial branch length optimization
[05:09:14 -1356887.629329] Model parameter optimization (eps = 10.000000)
[05:09:45 -1354125.676739] AUTODETECT spr round 1 (radius: 5)
[05:12:16 -1008090.272698] AUTODETECT spr round 2 (radius: 10)
[05:16:39 -699135.915129] AUTODETECT spr round 3 (radius: 15)
[05:20:56 -588403.696524] AUTODETECT spr round 4 (radius: 20)
[05:25:12 -572336.015372] AUTODETECT spr round 5 (radius: 25)
[05:30:06 -572087.936078] SPR radius for FAST iterations: 25 (autodetect)
[05:30:06 -572087.936078] Model parameter optimization (eps = 3.000000)
[05:30:11 -572086.980599] FAST spr round 1 (radius: 25)
[05:33:28 -509073.180066] FAST spr round 2 (radius: 25)
[05:35:52 -506789.821719] FAST spr round 3 (radius: 25)
[05:38:02 -506696.616095] FAST spr round 4 (radius: 25)
[05:39:47 -506684.922456] FAST spr round 5 (radius: 25)
[05:41:31 -506677.386296] FAST spr round 6 (radius: 25)
[05:43:10 -506676.361369] FAST spr round 7 (radius: 25)
[05:44:48 -506675.496774] FAST spr round 8 (radius: 25)
[05:46:26 -506674.621737] FAST spr round 9 (radius: 25)
[05:48:03 -506673.902508] FAST spr round 10 (radius: 25)
[05:49:41 -506670.093456] FAST spr round 11 (radius: 25)
[05:51:20 -506667.330117] FAST spr round 12 (radius: 25)
[05:52:58 -506664.860891] FAST spr round 13 (radius: 25)
[05:54:35 -506664.860890] Model parameter optimization (eps = 1.000000)
[05:54:54 -506405.262314] SLOW spr round 1 (radius: 5)
[05:57:34 -506325.330415] SLOW spr round 2 (radius: 5)
[05:59:55 -506316.926822] SLOW spr round 3 (radius: 5)
[06:02:13 -506315.706039] SLOW spr round 4 (radius: 5)
[06:04:29 -506315.706037] SLOW spr round 5 (radius: 10)
[06:06:57 -506315.706037] SLOW spr round 6 (radius: 15)
[06:11:34 -506315.706037] SLOW spr round 7 (radius: 20)
[06:19:12 -506315.706037] SLOW spr round 8 (radius: 25)
[06:29:22 -506315.706037] Model parameter optimization (eps = 0.100000)

[06:29:24] ML tree search #5, logLikelihood: -506315.705910

[06:29:24 -1547204.983710] Initial branch length optimization
[06:29:29 -1353870.235539] Model parameter optimization (eps = 10.000000)
[06:29:59 -1351254.330180] AUTODETECT spr round 1 (radius: 5)
[06:32:29 -1017054.520561] AUTODETECT spr round 2 (radius: 10)
[06:36:56 -691798.026873] AUTODETECT spr round 3 (radius: 15)
[06:41:01 -598887.031370] AUTODETECT spr round 4 (radius: 20)
[06:45:02 -570041.936830] AUTODETECT spr round 5 (radius: 25)
[06:50:01 -566857.533218] SPR radius for FAST iterations: 25 (autodetect)
[06:50:01 -566857.533218] Model parameter optimization (eps = 3.000000)
[06:50:24 -566498.827530] FAST spr round 1 (radius: 25)
[06:53:36 -508406.352739] FAST spr round 2 (radius: 25)
[06:55:58 -506531.320584] FAST spr round 3 (radius: 25)
[06:58:00 -506445.179837] FAST spr round 4 (radius: 25)
[06:59:45 -506442.626792] FAST spr round 5 (radius: 25)
[07:01:26 -506440.800274] FAST spr round 6 (radius: 25)
[07:03:06 -506439.566384] FAST spr round 7 (radius: 25)
[07:04:44 -506438.925991] FAST spr round 8 (radius: 25)
[07:06:24 -506438.172492] FAST spr round 9 (radius: 25)
[07:08:02 -506437.755749] FAST spr round 10 (radius: 25)
[07:09:41 -506437.728307] Model parameter optimization (eps = 1.000000)
[07:09:55 -506434.428999] SLOW spr round 1 (radius: 5)
[07:12:34 -506321.521702] SLOW spr round 2 (radius: 5)
[07:15:06 -506303.872701] SLOW spr round 3 (radius: 5)
[07:17:27 -506301.294586] SLOW spr round 4 (radius: 5)
[07:19:45 -506301.294571] SLOW spr round 5 (radius: 10)
[07:22:15 -506301.294571] SLOW spr round 6 (radius: 15)
[07:26:52 -506301.294571] SLOW spr round 7 (radius: 20)
[07:34:38 -506301.294571] SLOW spr round 8 (radius: 25)
[07:44:58 -506301.294571] Model parameter optimization (eps = 0.100000)

[07:45:03] ML tree search #6, logLikelihood: -506301.220062

[07:45:04 -1553769.560436] Initial branch length optimization
[07:45:09 -1360032.682068] Model parameter optimization (eps = 10.000000)
[07:45:37 -1357336.300719] AUTODETECT spr round 1 (radius: 5)
[07:48:06 -1019699.378453] AUTODETECT spr round 2 (radius: 10)
[07:52:10 -716190.785429] AUTODETECT spr round 3 (radius: 15)
[07:56:35 -603301.011025] AUTODETECT spr round 4 (radius: 20)
[07:59:59 -575855.599235] AUTODETECT spr round 5 (radius: 25)
[08:05:10 -570482.507402] SPR radius for FAST iterations: 25 (autodetect)
[08:05:10 -570482.507402] Model parameter optimization (eps = 3.000000)
[08:05:30 -570181.920753] FAST spr round 1 (radius: 25)
[08:08:43 -508792.553286] FAST spr round 2 (radius: 25)
[08:11:07 -506525.407705] FAST spr round 3 (radius: 25)
[08:13:10 -506440.971511] FAST spr round 4 (radius: 25)
[08:14:57 -506424.006152] FAST spr round 5 (radius: 25)
[08:16:40 -506415.355937] FAST spr round 6 (radius: 25)
[08:18:19 -506413.077675] FAST spr round 7 (radius: 25)
[08:19:58 -506412.650463] FAST spr round 8 (radius: 25)
[08:21:36 -506412.056765] FAST spr round 9 (radius: 25)
[08:23:14 -506411.864765] FAST spr round 10 (radius: 25)
[08:24:51 -506411.864727] Model parameter optimization (eps = 1.000000)
[08:25:05 -506407.437684] SLOW spr round 1 (radius: 5)
[08:27:43 -506342.865327] SLOW spr round 2 (radius: 5)
[08:30:06 -506333.926175] SLOW spr round 3 (radius: 5)
[08:32:23 -506333.926105] SLOW spr round 4 (radius: 10)
[08:34:53 -506333.926103] SLOW spr round 5 (radius: 15)
[08:39:42 -506333.926103] SLOW spr round 6 (radius: 20)
[08:47:59 -506333.926103] SLOW spr round 7 (radius: 25)
[08:58:54 -506333.926103] Model parameter optimization (eps = 0.100000)

[08:59:09] ML tree search #7, logLikelihood: -506333.584329

[08:59:09 -1553087.092667] Initial branch length optimization
[08:59:16 -1359003.403665] Model parameter optimization (eps = 10.000000)
[08:59:43 -1356240.532158] AUTODETECT spr round 1 (radius: 5)
[09:02:13 -1015216.027144] AUTODETECT spr round 2 (radius: 10)
[09:06:35 -691977.584993] AUTODETECT spr round 3 (radius: 15)
[09:10:50 -593005.756520] AUTODETECT spr round 4 (radius: 20)
[09:14:27 -577221.227621] AUTODETECT spr round 5 (radius: 25)
[09:19:19 -575841.027774] SPR radius for FAST iterations: 25 (autodetect)
[09:19:19 -575841.027774] Model parameter optimization (eps = 3.000000)
[09:19:38 -575507.898704] FAST spr round 1 (radius: 25)
[09:23:00 -510421.849033] FAST spr round 2 (radius: 25)
[09:25:29 -506588.194430] FAST spr round 3 (radius: 25)
[09:27:38 -506465.663493] FAST spr round 4 (radius: 25)
[09:29:31 -506444.524499] FAST spr round 5 (radius: 25)
[09:31:16 -506440.344712] FAST spr round 6 (radius: 25)
[09:32:56 -506439.266486] FAST spr round 7 (radius: 25)
[09:34:34 -506438.787224] FAST spr round 8 (radius: 25)
[09:36:13 -506437.847658] FAST spr round 9 (radius: 25)
[09:37:51 -506436.910827] FAST spr round 10 (radius: 25)
[09:39:31 -506432.499640] FAST spr round 11 (radius: 25)
[09:41:10 -506431.651130] FAST spr round 12 (radius: 25)
[09:42:49 -506429.051548] FAST spr round 13 (radius: 25)
[09:44:28 -506427.781594] FAST spr round 14 (radius: 25)
[09:46:07 -506426.992344] FAST spr round 15 (radius: 25)
[09:47:45 -506426.992337] Model parameter optimization (eps = 1.000000)
[09:48:04 -506419.973504] SLOW spr round 1 (radius: 5)
[09:50:45 -506331.017855] SLOW spr round 2 (radius: 5)
[09:53:05 -506330.524936] SLOW spr round 3 (radius: 5)
[09:55:23 -506330.524777] SLOW spr round 4 (radius: 10)
[09:57:54 -506330.524772] SLOW spr round 5 (radius: 15)
[10:02:41 -506330.524772] SLOW spr round 6 (radius: 20)
[10:11:05 -506330.524772] SLOW spr round 7 (radius: 25)
[10:22:00 -506330.524772] Model parameter optimization (eps = 0.100000)

[10:22:06] ML tree search #8, logLikelihood: -506330.485879

[10:22:06 -1553740.077263] Initial branch length optimization
[10:22:11 -1361502.081686] Model parameter optimization (eps = 10.000000)
[10:22:42 -1358769.096234] AUTODETECT spr round 1 (radius: 5)
[10:25:12 -986762.508211] AUTODETECT spr round 2 (radius: 10)
[10:29:27 -696512.826841] AUTODETECT spr round 3 (radius: 15)
[10:33:28 -606221.715027] AUTODETECT spr round 4 (radius: 20)
[10:37:43 -578606.135120] AUTODETECT spr round 5 (radius: 25)
[10:43:18 -576804.028487] SPR radius for FAST iterations: 25 (autodetect)
[10:43:18 -576804.028487] Model parameter optimization (eps = 3.000000)
[10:43:35 -576490.321191] FAST spr round 1 (radius: 25)
[10:46:50 -508775.159830] FAST spr round 2 (radius: 25)
[10:49:19 -506662.309404] FAST spr round 3 (radius: 25)
[10:51:24 -506446.805811] FAST spr round 4 (radius: 25)
[10:53:11 -506416.960759] FAST spr round 5 (radius: 25)
[10:54:52 -506414.953176] FAST spr round 6 (radius: 25)
[10:56:31 -506413.756139] FAST spr round 7 (radius: 25)
[10:58:09 -506412.870355] FAST spr round 8 (radius: 25)
[10:59:46 -506412.140242] FAST spr round 9 (radius: 25)
[11:01:23 -506411.402173] FAST spr round 10 (radius: 25)
[11:03:01 -506407.111014] FAST spr round 11 (radius: 25)
[11:04:38 -506399.860595] FAST spr round 12 (radius: 25)
[11:06:16 -506399.157616] FAST spr round 13 (radius: 25)
[11:07:54 -506397.705325] FAST spr round 14 (radius: 25)
[11:09:31 -506397.135684] FAST spr round 15 (radius: 25)
[11:11:09 -506397.135671] Model parameter optimization (eps = 1.000000)
[11:11:21 -506391.679305] SLOW spr round 1 (radius: 5)
[11:13:59 -506322.571247] SLOW spr round 2 (radius: 5)
[11:16:24 -506316.192277] SLOW spr round 3 (radius: 5)
[11:18:43 -506315.590266] SLOW spr round 4 (radius: 5)
[11:20:59 -506315.590262] SLOW spr round 5 (radius: 10)
[11:23:28 -506315.590262] SLOW spr round 6 (radius: 15)
[11:28:16 -506315.590262] SLOW spr round 7 (radius: 20)
[11:36:35 -506315.590262] SLOW spr round 8 (radius: 25)
[11:47:25 -506315.590262] Model parameter optimization (eps = 0.100000)

[11:47:32] ML tree search #9, logLikelihood: -506315.401584

[11:47:32 -1553530.209177] Initial branch length optimization
[11:47:37 -1360191.536729] Model parameter optimization (eps = 10.000000)
[11:48:17 -1357470.969566] AUTODETECT spr round 1 (radius: 5)
[11:50:46 -1023693.297824] AUTODETECT spr round 2 (radius: 10)
[11:54:50 -720470.992060] AUTODETECT spr round 3 (radius: 15)
[11:59:01 -600657.383982] AUTODETECT spr round 4 (radius: 20)
[12:03:01 -576449.459122] AUTODETECT spr round 5 (radius: 25)
[12:08:06 -571181.138755] SPR radius for FAST iterations: 25 (autodetect)
[12:08:06 -571181.138755] Model parameter optimization (eps = 3.000000)
[12:08:11 -571180.022143] FAST spr round 1 (radius: 25)
[12:11:25 -508525.973543] FAST spr round 2 (radius: 25)
[12:13:46 -506822.835572] FAST spr round 3 (radius: 25)
[12:15:58 -506697.244828] FAST spr round 4 (radius: 25)
[12:17:53 -506682.926687] FAST spr round 5 (radius: 25)
[12:19:38 -506680.780905] FAST spr round 6 (radius: 25)
[12:21:23 -506680.422766] FAST spr round 7 (radius: 25)
[12:23:01 -506679.208621] FAST spr round 8 (radius: 25)
[12:24:40 -506678.892661] FAST spr round 9 (radius: 25)
[12:26:14 -506678.598587] FAST spr round 10 (radius: 25)
[12:27:47 -506675.425435] FAST spr round 11 (radius: 25)
[12:29:21 -506670.920164] FAST spr round 12 (radius: 25)
[12:30:52 -506670.920164] Model parameter optimization (eps = 1.000000)
[12:31:14 -506393.963188] SLOW spr round 1 (radius: 5)
[12:33:43 -506302.754470] SLOW spr round 2 (radius: 5)
[12:35:56 -506302.163155] SLOW spr round 3 (radius: 5)
[12:38:02 -506302.162990] SLOW spr round 4 (radius: 10)
[12:40:18 -506302.162985] SLOW spr round 5 (radius: 15)
[12:44:27 -506302.162984] SLOW spr round 6 (radius: 20)
[12:51:29 -506302.162984] SLOW spr round 7 (radius: 25)
[13:00:45 -506302.162984] Model parameter optimization (eps = 0.100000)

[13:00:55] ML tree search #10, logLikelihood: -506301.583492

[13:00:55 -1556792.173992] Initial branch length optimization
[13:01:00 -1363578.796482] Model parameter optimization (eps = 10.000000)
[13:01:31 -1360852.970739] AUTODETECT spr round 1 (radius: 5)
[13:03:50 -1012127.601466] AUTODETECT spr round 2 (radius: 10)
[13:07:34 -729085.654112] AUTODETECT spr round 3 (radius: 15)
[13:11:09 -601745.960115] AUTODETECT spr round 4 (radius: 20)
[13:14:26 -575946.715704] AUTODETECT spr round 5 (radius: 25)
[13:19:03 -574123.545315] SPR radius for FAST iterations: 25 (autodetect)
[13:19:03 -574123.545315] Model parameter optimization (eps = 3.000000)
[13:19:31 -573806.786887] FAST spr round 1 (radius: 25)
[13:22:25 -509007.209163] FAST spr round 2 (radius: 25)
[13:24:39 -506573.554266] FAST spr round 3 (radius: 25)
[13:26:37 -506472.684396] FAST spr round 4 (radius: 25)
[13:28:23 -506439.906803] FAST spr round 5 (radius: 25)
[13:30:02 -506426.587122] FAST spr round 6 (radius: 25)
[13:31:36 -506423.072050] FAST spr round 7 (radius: 25)
[13:33:08 -506421.909195] FAST spr round 8 (radius: 25)
[13:34:40 -506417.149377] FAST spr round 9 (radius: 25)
[13:36:11 -506416.287268] FAST spr round 10 (radius: 25)
[13:37:43 -506415.351406] FAST spr round 11 (radius: 25)
[13:39:14 -506414.535091] FAST spr round 12 (radius: 25)
[13:40:45 -506414.312016] FAST spr round 13 (radius: 25)
[13:42:21 -506406.621451] FAST spr round 14 (radius: 25)
[13:43:52 -506405.186988] FAST spr round 15 (radius: 25)
[13:45:24 -506403.765853] FAST spr round 16 (radius: 25)
[13:46:55 -506403.765823] Model parameter optimization (eps = 1.000000)
[13:47:09 -506402.074320] SLOW spr round 1 (radius: 5)
[13:49:37 -506307.932889] SLOW spr round 2 (radius: 5)
[13:51:45 -506305.671435] SLOW spr round 3 (radius: 5)
[13:53:55 -506305.671255] SLOW spr round 4 (radius: 10)
[13:56:15 -506305.671251] SLOW spr round 5 (radius: 15)
[14:00:46 -506305.671250] SLOW spr round 6 (radius: 20)
[14:08:51 -506305.671250] SLOW spr round 7 (radius: 25)
[14:18:56 -506305.671250] Model parameter optimization (eps = 0.100000)

[14:19:06] ML tree search #11, logLikelihood: -506305.523960

[14:19:06 -1558219.010226] Initial branch length optimization
[14:19:12 -1362948.464598] Model parameter optimization (eps = 10.000000)
[14:19:40 -1360232.426253] AUTODETECT spr round 1 (radius: 5)
[14:21:57 -1015308.549979] AUTODETECT spr round 2 (radius: 10)
[14:25:51 -745910.907964] AUTODETECT spr round 3 (radius: 15)
[14:29:23 -674152.206280] AUTODETECT spr round 4 (radius: 20)
[14:33:42 -613159.741210] AUTODETECT spr round 5 (radius: 25)
[14:38:06 -601987.707062] SPR radius for FAST iterations: 25 (autodetect)
[14:38:06 -601987.707062] Model parameter optimization (eps = 3.000000)
[14:38:26 -601676.481500] FAST spr round 1 (radius: 25)
[14:41:39 -509058.585666] FAST spr round 2 (radius: 25)
[14:43:50 -506615.660950] FAST spr round 3 (radius: 25)
[14:45:55 -506447.562266] FAST spr round 4 (radius: 25)
[14:47:42 -506430.773584] FAST spr round 5 (radius: 25)
[14:49:20 -506414.673618] FAST spr round 6 (radius: 25)
[14:50:55 -506411.992236] FAST spr round 7 (radius: 25)
[14:52:28 -506410.002349] FAST spr round 8 (radius: 25)
[14:54:02 -506408.930458] FAST spr round 9 (radius: 25)
[14:55:36 -506402.377057] FAST spr round 10 (radius: 25)
[14:57:12 -506396.738760] FAST spr round 11 (radius: 25)
[14:58:46 -506395.895590] FAST spr round 12 (radius: 25)
[15:00:26 -506394.966613] FAST spr round 13 (radius: 25)
[15:02:11 -506394.966613] Model parameter optimization (eps = 1.000000)
[15:02:25 -506385.045026] SLOW spr round 1 (radius: 5)
[15:05:05 -506327.016363] SLOW spr round 2 (radius: 5)
[15:07:34 -506325.051334] SLOW spr round 3 (radius: 5)
[15:09:56 -506325.050916] SLOW spr round 4 (radius: 10)
[15:12:31 -506325.050884] SLOW spr round 5 (radius: 15)
[15:17:24 -506325.050881] SLOW spr round 6 (radius: 20)
[15:25:51 -506325.050881] SLOW spr round 7 (radius: 25)
[15:36:49 -506325.050881] Model parameter optimization (eps = 0.100000)

[15:36:58] ML tree search #12, logLikelihood: -506324.943600

[15:36:58 -1555273.126600] Initial branch length optimization
[15:37:04 -1361661.399667] Model parameter optimization (eps = 10.000000)
[15:37:41 -1358934.338185] AUTODETECT spr round 1 (radius: 5)
[15:40:14 -999462.610646] AUTODETECT spr round 2 (radius: 10)
[15:44:32 -686887.058119] AUTODETECT spr round 3 (radius: 15)
[15:48:22 -597523.391782] AUTODETECT spr round 4 (radius: 20)
[15:51:52 -568038.845277] AUTODETECT spr round 5 (radius: 25)
[15:56:28 -566484.924282] SPR radius for FAST iterations: 25 (autodetect)
[15:56:28 -566484.924282] Model parameter optimization (eps = 3.000000)
[15:56:34 -566483.886225] FAST spr round 1 (radius: 25)
[15:59:54 -508656.775472] FAST spr round 2 (radius: 25)
[16:02:26 -506773.475832] FAST spr round 3 (radius: 25)
[16:04:32 -506683.083995] FAST spr round 4 (radius: 25)
[16:06:25 -506679.585703] FAST spr round 5 (radius: 25)
[16:08:09 -506676.274410] FAST spr round 6 (radius: 25)
[16:09:50 -506664.265485] FAST spr round 7 (radius: 25)
[16:11:38 -506662.680536] FAST spr round 8 (radius: 25)
[16:13:19 -506661.734343] FAST spr round 9 (radius: 25)
[16:15:00 -506660.991542] FAST spr round 10 (radius: 25)
[16:16:46 -506660.359490] FAST spr round 11 (radius: 25)
[16:18:26 -506660.019771] FAST spr round 12 (radius: 25)
[16:19:59 -506659.126856] FAST spr round 13 (radius: 25)
[16:21:34 -506654.865341] FAST spr round 14 (radius: 25)
[16:23:14 -506650.548593] FAST spr round 15 (radius: 25)
[16:24:48 -506650.487203] Model parameter optimization (eps = 1.000000)
[16:24:52 -506650.002220] SLOW spr round 1 (radius: 5)
[16:27:24 -506582.247587] SLOW spr round 2 (radius: 5)
[16:30:20 -506576.885633] SLOW spr round 3 (radius: 5)
[16:32:25 -506576.885617] SLOW spr round 4 (radius: 10)
[16:34:38 -506576.885617] SLOW spr round 5 (radius: 15)
[16:38:52 -506576.885617] SLOW spr round 6 (radius: 20)
[16:46:25 -506576.885617] SLOW spr round 7 (radius: 25)
[16:56:22 -506576.885616] Model parameter optimization (eps = 0.100000)

[16:56:26] ML tree search #13, logLikelihood: -506576.880918

[16:56:26 -1554372.234008] Initial branch length optimization
[16:56:31 -1361059.086623] Model parameter optimization (eps = 10.000000)
[16:57:01 -1358495.728587] AUTODETECT spr round 1 (radius: 5)
[16:59:24 -1007900.343063] AUTODETECT spr round 2 (radius: 10)
[17:02:55 -747389.169719] AUTODETECT spr round 3 (radius: 15)
[17:06:26 -606404.658737] AUTODETECT spr round 4 (radius: 20)
[17:09:49 -577202.521953] AUTODETECT spr round 5 (radius: 25)
[17:14:09 -576181.564522] SPR radius for FAST iterations: 25 (autodetect)
[17:14:09 -576181.564522] Model parameter optimization (eps = 3.000000)
[17:14:29 -575775.104244] FAST spr round 1 (radius: 25)
[17:17:29 -508635.535489] FAST spr round 2 (radius: 25)
[17:19:45 -506540.860891] FAST spr round 3 (radius: 25)
[17:21:44 -506427.217032] FAST spr round 4 (radius: 25)
[17:23:21 -506424.987095] FAST spr round 5 (radius: 25)
[17:24:55 -506419.244019] FAST spr round 6 (radius: 25)
[17:26:29 -506418.790735] FAST spr round 7 (radius: 25)
[17:28:02 -506418.160764] FAST spr round 8 (radius: 25)
[17:29:35 -506417.880407] FAST spr round 9 (radius: 25)
[17:31:11 -506417.373476] FAST spr round 10 (radius: 25)
[17:32:44 -506416.413127] FAST spr round 11 (radius: 25)
[17:34:16 -506416.157060] FAST spr round 12 (radius: 25)
[17:35:49 -506416.014639] FAST spr round 13 (radius: 25)
[17:37:22 -506414.700296] FAST spr round 14 (radius: 25)
[17:38:56 -506414.612444] Model parameter optimization (eps = 1.000000)
[17:39:09 -506411.608640] SLOW spr round 1 (radius: 5)
[17:41:34 -506341.635222] SLOW spr round 2 (radius: 5)
[17:43:45 -506340.780388] SLOW spr round 3 (radius: 5)
[17:45:56 -506340.780355] SLOW spr round 4 (radius: 10)
[17:48:17 -506340.780352] SLOW spr round 5 (radius: 15)
[17:52:43 -506340.780351] SLOW spr round 6 (radius: 20)
[18:01:00 -506340.780351] SLOW spr round 7 (radius: 25)
[18:11:28 -506340.780351] Model parameter optimization (eps = 0.100000)

[18:11:39] ML tree search #14, logLikelihood: -506340.590912

[18:11:39 -1558878.822960] Initial branch length optimization
[18:11:44 -1367727.793957] Model parameter optimization (eps = 10.000000)
[18:12:22 -1364961.175434] AUTODETECT spr round 1 (radius: 5)
[18:14:44 -1009834.602998] AUTODETECT spr round 2 (radius: 10)
[18:18:34 -743638.071943] AUTODETECT spr round 3 (radius: 15)
[18:22:26 -660995.937225] AUTODETECT spr round 4 (radius: 20)
[18:26:20 -595483.963618] AUTODETECT spr round 5 (radius: 25)
[18:30:11 -584463.701055] SPR radius for FAST iterations: 25 (autodetect)
[18:30:11 -584463.701055] Model parameter optimization (eps = 3.000000)
[18:30:30 -584072.010077] FAST spr round 1 (radius: 25)
[18:33:41 -508990.508768] FAST spr round 2 (radius: 25)
[18:35:52 -506664.727771] FAST spr round 3 (radius: 25)
[18:37:50 -506450.334511] FAST spr round 4 (radius: 25)
[18:39:26 -506446.459309] FAST spr round 5 (radius: 25)
[18:40:59 -506445.445513] FAST spr round 6 (radius: 25)
[18:42:30 -506444.503939] FAST spr round 7 (radius: 25)
[18:44:00 -506443.685989] FAST spr round 8 (radius: 25)
[18:45:30 -506442.153253] FAST spr round 9 (radius: 25)
[18:47:07 -506434.842936] FAST spr round 10 (radius: 25)
[18:48:45 -506434.215533] FAST spr round 11 (radius: 25)
[18:50:24 -506430.804179] FAST spr round 12 (radius: 25)
[18:52:02 -506428.874711] FAST spr round 13 (radius: 25)
[18:53:40 -506428.642293] FAST spr round 14 (radius: 25)
[18:55:19 -506428.642284] Model parameter optimization (eps = 1.000000)
[18:55:31 -506426.438206] SLOW spr round 1 (radius: 5)
[18:58:13 -506333.509982] SLOW spr round 2 (radius: 5)
[19:00:40 -506326.952317] SLOW spr round 3 (radius: 5)
[19:02:58 -506326.951999] SLOW spr round 4 (radius: 10)
[19:05:28 -506326.951992] SLOW spr round 5 (radius: 15)
[19:10:11 -506326.951991] SLOW spr round 6 (radius: 20)
[19:18:29 -506326.951991] SLOW spr round 7 (radius: 25)
[19:29:15 -506326.951991] Model parameter optimization (eps = 0.100000)

[19:29:25] ML tree search #15, logLikelihood: -506326.768746

[19:29:25 -1546183.741077] Initial branch length optimization
[19:29:31 -1358410.806939] Model parameter optimization (eps = 10.000000)
[19:29:59 -1355731.088623] AUTODETECT spr round 1 (radius: 5)
[19:32:30 -989576.238023] AUTODETECT spr round 2 (radius: 10)
[19:36:36 -751742.740533] AUTODETECT spr round 3 (radius: 15)
[19:40:29 -609234.977120] AUTODETECT spr round 4 (radius: 20)
[19:44:24 -582012.127943] AUTODETECT spr round 5 (radius: 25)
[19:48:37 -577701.234162] SPR radius for FAST iterations: 25 (autodetect)
[19:48:37 -577701.234162] Model parameter optimization (eps = 3.000000)
[19:49:00 -577362.574983] FAST spr round 1 (radius: 25)
[19:52:12 -509392.804101] FAST spr round 2 (radius: 25)
[19:54:31 -506696.606850] FAST spr round 3 (radius: 25)
[19:56:37 -506454.541987] FAST spr round 4 (radius: 25)
[19:58:24 -506446.691974] FAST spr round 5 (radius: 25)
[20:00:05 -506444.701649] FAST spr round 6 (radius: 25)
[20:01:44 -506444.135636] FAST spr round 7 (radius: 25)
[20:03:23 -506443.904021] FAST spr round 8 (radius: 25)
[20:05:03 -506443.904020] Model parameter optimization (eps = 1.000000)
[20:05:17 -506438.632942] SLOW spr round 1 (radius: 5)
[20:07:56 -506329.308430] SLOW spr round 2 (radius: 5)
[20:10:19 -506320.966019] SLOW spr round 3 (radius: 5)
[20:12:39 -506320.965764] SLOW spr round 4 (radius: 10)
[20:15:09 -506320.965758] SLOW spr round 5 (radius: 15)
[20:20:01 -506320.965758] SLOW spr round 6 (radius: 20)
[20:28:44 -506320.965758] SLOW spr round 7 (radius: 25)
[20:40:11 -506320.965758] Model parameter optimization (eps = 0.100000)

[20:40:23] ML tree search #16, logLikelihood: -506320.290779

[20:40:23 -1553882.626546] Initial branch length optimization
[20:40:28 -1361387.534761] Model parameter optimization (eps = 10.000000)
[20:41:07 -1358727.291228] AUTODETECT spr round 1 (radius: 5)
[20:43:38 -1023074.042014] AUTODETECT spr round 2 (radius: 10)
[20:47:31 -750142.305416] AUTODETECT spr round 3 (radius: 15)
[20:51:31 -645936.886465] AUTODETECT spr round 4 (radius: 20)
[20:56:43 -591628.776207] AUTODETECT spr round 5 (radius: 25)
[21:01:59 -587987.627913] SPR radius for FAST iterations: 25 (autodetect)
[21:01:59 -587987.627913] Model parameter optimization (eps = 3.000000)
[21:02:21 -587701.820616] FAST spr round 1 (radius: 25)
[21:05:50 -509095.813948] FAST spr round 2 (radius: 25)
[21:08:20 -506708.371157] FAST spr round 3 (radius: 25)
[21:10:32 -506416.256711] FAST spr round 4 (radius: 25)
[21:12:21 -506408.465357] FAST spr round 5 (radius: 25)
[21:14:02 -506407.657133] FAST spr round 6 (radius: 25)
[21:15:42 -506403.192169] FAST spr round 7 (radius: 25)
[21:17:22 -506401.830946] FAST spr round 8 (radius: 25)
[21:19:02 -506401.547333] FAST spr round 9 (radius: 25)
[21:20:42 -506398.664954] FAST spr round 10 (radius: 25)
[21:22:29 -506397.299138] FAST spr round 11 (radius: 25)
[21:24:13 -506397.126112] FAST spr round 12 (radius: 25)
[21:25:52 -506396.250540] FAST spr round 13 (radius: 25)
[21:27:33 -506394.871370] FAST spr round 14 (radius: 25)
[21:29:13 -506394.871313] Model parameter optimization (eps = 1.000000)
[21:29:17 -506394.610582] SLOW spr round 1 (radius: 5)
[21:31:58 -506318.712234] SLOW spr round 2 (radius: 5)
[21:34:26 -506310.433153] SLOW spr round 3 (radius: 5)
[21:36:46 -506310.433151] SLOW spr round 4 (radius: 10)
[21:39:19 -506310.433151] SLOW spr round 5 (radius: 15)
[21:44:01 -506310.433151] SLOW spr round 6 (radius: 20)
[21:52:05 -506310.433151] SLOW spr round 7 (radius: 25)
[22:02:52 -506310.433151] Model parameter optimization (eps = 0.100000)

[22:03:08] ML tree search #17, logLikelihood: -506307.580590

[22:03:08 -1551504.229283] Initial branch length optimization
[22:03:13 -1360079.405338] Model parameter optimization (eps = 10.000000)
[22:03:41 -1357375.689754] AUTODETECT spr round 1 (radius: 5)
[22:06:09 -1007901.930792] AUTODETECT spr round 2 (radius: 10)
[22:10:18 -692755.473163] AUTODETECT spr round 3 (radius: 15)
[22:14:00 -589278.797394] AUTODETECT spr round 4 (radius: 20)
[22:17:52 -576973.420402] AUTODETECT spr round 5 (radius: 25)
[22:22:24 -570699.607537] SPR radius for FAST iterations: 25 (autodetect)
[22:22:24 -570699.607537] Model parameter optimization (eps = 3.000000)
[22:22:30 -570698.669395] FAST spr round 1 (radius: 25)
[22:25:52 -508733.117599] FAST spr round 2 (radius: 25)
[22:28:16 -506787.199523] FAST spr round 3 (radius: 25)
[22:30:18 -506690.519058] FAST spr round 4 (radius: 25)
[22:32:06 -506678.562460] FAST spr round 5 (radius: 25)
[22:33:49 -506670.612513] FAST spr round 6 (radius: 25)
[22:35:31 -506664.178613] FAST spr round 7 (radius: 25)
[22:37:12 -506661.228651] FAST spr round 8 (radius: 25)
[22:38:51 -506660.433959] FAST spr round 9 (radius: 25)
[22:40:29 -506660.101859] FAST spr round 10 (radius: 25)
[22:42:08 -506659.236258] FAST spr round 11 (radius: 25)
[22:43:46 -506657.893507] FAST spr round 12 (radius: 25)
[22:45:24 -506657.893497] Model parameter optimization (eps = 1.000000)
[22:45:43 -506413.536057] SLOW spr round 1 (radius: 5)
[22:48:24 -506332.935146] SLOW spr round 2 (radius: 5)
[22:50:53 -506327.205444] SLOW spr round 3 (radius: 5)
[22:53:14 -506326.828107] SLOW spr round 4 (radius: 5)
[22:55:32 -506326.828102] SLOW spr round 5 (radius: 10)
[22:58:03 -506326.828102] SLOW spr round 6 (radius: 15)
[23:02:49 -506326.828102] SLOW spr round 7 (radius: 20)
[23:10:51 -506326.828102] SLOW spr round 8 (radius: 25)
[23:21:29 -506326.828101] Model parameter optimization (eps = 0.100000)

[23:21:41] ML tree search #18, logLikelihood: -506326.527431

[23:21:41 -1558198.277831] Initial branch length optimization
[23:21:47 -1363660.157939] Model parameter optimization (eps = 10.000000)
[23:22:17 -1360975.734072] AUTODETECT spr round 1 (radius: 5)
[23:24:51 -1013214.428192] AUTODETECT spr round 2 (radius: 10)
[23:29:13 -741135.594545] AUTODETECT spr round 3 (radius: 15)
[23:33:23 -605721.236518] AUTODETECT spr round 4 (radius: 20)
[23:37:20 -580635.140979] AUTODETECT spr round 5 (radius: 25)
[23:41:50 -580036.458934] SPR radius for FAST iterations: 25 (autodetect)
[23:41:50 -580036.458934] Model parameter optimization (eps = 3.000000)
[23:41:56 -580035.804335] FAST spr round 1 (radius: 25)
[23:45:21 -509161.110911] FAST spr round 2 (radius: 25)
[23:47:48 -506854.547760] FAST spr round 3 (radius: 25)
[23:49:58 -506712.391956] FAST spr round 4 (radius: 25)
[23:51:50 -506700.577623] FAST spr round 5 (radius: 25)
[23:53:44 -506664.281291] FAST spr round 6 (radius: 25)
[23:55:26 -506660.365237] FAST spr round 7 (radius: 25)
[23:57:07 -506658.925850] FAST spr round 8 (radius: 25)
[23:58:47 -506658.008544] FAST spr round 9 (radius: 25)
[24:00:26 -506657.729684] FAST spr round 10 (radius: 25)
[24:02:04 -506656.164654] FAST spr round 11 (radius: 25)
[24:03:43 -506655.898349] FAST spr round 12 (radius: 25)
[24:05:21 -506655.894939] Model parameter optimization (eps = 1.000000)
[24:05:46 -506413.644243] SLOW spr round 1 (radius: 5)
[24:08:26 -506317.945731] SLOW spr round 2 (radius: 5)
[24:10:48 -506314.757676] SLOW spr round 3 (radius: 5)
[24:13:06 -506311.485068] SLOW spr round 4 (radius: 5)
[24:15:23 -506311.485003] SLOW spr round 5 (radius: 10)
[24:17:51 -506311.485002] SLOW spr round 6 (radius: 15)
[24:22:27 -506311.485002] SLOW spr round 7 (radius: 20)
[24:30:12 -506311.485001] SLOW spr round 8 (radius: 25)
[24:40:29 -506311.485001] Model parameter optimization (eps = 0.100000)

[24:40:39] ML tree search #19, logLikelihood: -506311.337986

[24:40:39 -1557991.357627] Initial branch length optimization
[24:40:44 -1360468.828249] Model parameter optimization (eps = 10.000000)
[24:41:19 -1357826.008539] AUTODETECT spr round 1 (radius: 5)
[24:43:47 -997588.579938] AUTODETECT spr round 2 (radius: 10)
[24:47:39 -691295.987782] AUTODETECT spr round 3 (radius: 15)
[24:51:37 -601466.161180] AUTODETECT spr round 4 (radius: 20)
[24:55:26 -580474.659725] AUTODETECT spr round 5 (radius: 25)
[24:59:57 -577753.341890] SPR radius for FAST iterations: 25 (autodetect)
[24:59:57 -577753.341890] Model parameter optimization (eps = 3.000000)
[25:00:02 -577752.900774] FAST spr round 1 (radius: 25)
[25:03:19 -509459.448416] FAST spr round 2 (radius: 25)
[25:05:45 -506839.190450] FAST spr round 3 (radius: 25)
[25:07:52 -506723.811439] FAST spr round 4 (radius: 25)
[25:09:41 -506709.554752] FAST spr round 5 (radius: 25)
[25:11:24 -506705.819982] FAST spr round 6 (radius: 25)
[25:13:04 -506703.320317] FAST spr round 7 (radius: 25)
[25:14:44 -506701.167184] FAST spr round 8 (radius: 25)
[25:16:27 -506693.855736] FAST spr round 9 (radius: 25)
[25:18:10 -506692.717397] FAST spr round 10 (radius: 25)
[25:19:51 -506692.280796] FAST spr round 11 (radius: 25)
[25:21:37 -506691.642766] FAST spr round 12 (radius: 25)
[25:23:19 -506690.782400] FAST spr round 13 (radius: 25)
[25:25:07 -506686.229540] FAST spr round 14 (radius: 25)
[25:26:57 -506682.218185] FAST spr round 15 (radius: 25)
[25:28:44 -506678.337418] FAST spr round 16 (radius: 25)
[25:30:37 -506672.966958] FAST spr round 17 (radius: 25)
[25:32:23 -506669.702825] FAST spr round 18 (radius: 25)
[25:34:06 -506669.439378] FAST spr round 19 (radius: 25)
[25:35:56 -506669.439350] Model parameter optimization (eps = 1.000000)
[25:36:18 -506427.198768] SLOW spr round 1 (radius: 5)
[25:39:09 -506333.689979] SLOW spr round 2 (radius: 5)
[25:41:45 -506308.747422] SLOW spr round 3 (radius: 5)
[25:44:14 -506303.008880] SLOW spr round 4 (radius: 5)
[25:46:38 -506303.008880] SLOW spr round 5 (radius: 10)
[25:49:11 -506303.008880] SLOW spr round 6 (radius: 15)
[25:53:57 -506303.008880] SLOW spr round 7 (radius: 20)
[26:01:57 -506303.008880] SLOW spr round 8 (radius: 25)
[26:12:48 -506303.008880] Model parameter optimization (eps = 0.100000)

[26:13:02] ML tree search #20, logLikelihood: -506302.545829


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.260540,0.207736) (0.331072,0.356621) (0.220315,1.103443) (0.188073,3.108926) 
   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: -506301.220062

AIC score: 1016612.440123 / AICc score: 9060672.440123 / BIC score: 1026870.810382
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1232).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 9 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O14841/3_mltree/O14841.raxml.log

Analysis started: 14-Jul-2021 00:29:59 / finished: 15-Jul-2021 02:43:01

Elapsed time: 94382.387 seconds

Consumed energy: 8559.155 Wh (= 43 km in an electric car, or 214 km with an e-scooter!)