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 12-Jul-2021 17:45:40 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/2_msa/Q00975_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/3_mltree/Q00975 --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/Q00975/2_msa/Q00975_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1311 sites

WARNING: Sequences sp_O73700_CAC1D_CHICK_9031 and tr_G1N2R9_G1N2R9_MELGA_9103 are exactly identical!
WARNING: Sequences tr_M3YZF3_M3YZF3_MUSPF_9669 and tr_A0A2Y9IXI9_A0A2Y9IXI9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QJV7_G3QJV7_GORGO_9595 and tr_H2Q573_H2Q573_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QJV7_G3QJV7_GORGO_9595 and tr_A0A2R9AG85_A0A2R9AG85_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R686_G3R686_GORGO_9595 and tr_A0A2J8N6N1_A0A2J8N6N1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R686_G3R686_GORGO_9595 and sp_Q15878_CAC1E_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R686_G3R686_GORGO_9595 and tr_A0A2R8ZZU9_A0A2R8ZZU9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5PFM3_W5PFM3_SHEEP_9940 and tr_F1N1E0_F1N1E0_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_I3MDF0_I3MDF0_ICTTR_43179 and tr_M3WMM1_M3WMM1_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A1D5Q7C3_A0A1D5Q7C3_MACMU_9544 and tr_A0A096N1R0_A0A096N1R0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_E3M7B8_E3M7B8_CAERE_31234 and tr_A0A261ATP3_A0A261ATP3_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8X1H0_A8X1H0_CAEBR_6238 and tr_A0A2G5U3C7_A0A2G5U3C7_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_G7NZU3_G7NZU3_MACFA_9541 and tr_A0A2I3MXE9_A0A2I3MXE9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7NZU3_G7NZU3_MACFA_9541 and tr_A0A2K5LA59_A0A2K5LA59_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7NZU3_G7NZU3_MACFA_9541 and tr_A0A2K5YVZ2_A0A2K5YVZ2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NWL7_A0A096NWL7_PAPAN_9555 and tr_A0A0D9RWC5_A0A0D9RWC5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3LLL6_A0A2I3LLL6_PAPAN_9555 and tr_A0A2K5P0X4_A0A2K5P0X4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3LLL6_A0A2I3LLL6_PAPAN_9555 and tr_A0A2K5ZFV4_A0A2K5ZFV4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091E6I9_A0A091E6I9_FUKDA_885580 and tr_A0A1S3F576_A0A1S3F576_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_A0A0K0F0E8_A0A0K0F0E8_STRVS_75913 and tr_A0A0N5BCI2_A0A0N5BCI2_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A151MF56_A0A151MF56_ALLMI_8496 and tr_A0A3Q0H4I5_A0A3Q0H4I5_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091VM10_A0A091VM10_NIPNI_128390 and tr_A0A091WME9_A0A091WME9_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091VM10_A0A091VM10_NIPNI_128390 and tr_A0A099ZY36_A0A099ZY36_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V0SF48_A0A0V0SF48_9BILA_6336 and tr_A0A0V1A803_A0A0V1A803_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0SF48_A0A0V0SF48_9BILA_6336 and tr_A0A0V1P1C0_A0A0V1P1C0_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0SF48_A0A0V0SF48_9BILA_6336 and tr_A0A0V0TY51_A0A0V0TY51_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1D2F4_A0A0V1D2F4_TRIBR_45882 and tr_A0A0V0XAU9_A0A0V0XAU9_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1D2F4_A0A0V1D2F4_TRIBR_45882 and tr_A0A0V0V3B6_A0A0V0V3B6_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1L1M4_A0A0V1L1M4_9BILA_6335 and tr_A0A0V0TSN8_A0A0V0TSN8_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1MW10_A0A0V1MW10_9BILA_268474 and tr_A0A0V1I4J4_A0A0V1I4J4_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1I7V0H2_A0A1I7V0H2_9PELO_1561998 and tr_A0A1I7V0H3_A0A1I7V0H3_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1D1V1T7_A0A1D1V1T7_RAMVA_947166 and tr_A0A1D1V6K9_A0A1D1V6K9_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A2K5L595_A0A2K5L595_CERAT_9531 and tr_A0A2K5Z1P9_A0A2K5Z1P9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5MI80_A0A2K5MI80_CERAT_9531 and tr_A0A2K5YZ45_A0A2K5YZ45_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U3VUG2_A0A2U3VUG2_ODORO_9708 and tr_A0A2Y9LBZ8_A0A2Y9LBZ8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2U3WEB7_A0A2U3WEB7_ODORO_9708 and tr_A0A2Y9KW23_A0A2Y9KW23_ENHLU_391180 are exactly identical!
WARNING: Duplicate sequences found: 36

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/Q00975/3_mltree/Q00975.raxml.reduced.phy

Alignment comprises 1 partitions and 1311 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1311 / 1311
Gaps: 12.20 %
Invariant sites: 0.08 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/3_mltree/Q00975.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 164 / 13120
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1381610.439367] Initial branch length optimization
[00:00:09 -1158187.674175] Model parameter optimization (eps = 10.000000)
[00:00:50 -1156919.935538] AUTODETECT spr round 1 (radius: 5)
[00:03:51 -662968.368809] AUTODETECT spr round 2 (radius: 10)
[00:07:01 -450711.670004] AUTODETECT spr round 3 (radius: 15)
[00:10:01 -357722.608714] AUTODETECT spr round 4 (radius: 20)
[00:13:18 -314551.869611] AUTODETECT spr round 5 (radius: 25)
[00:17:13 -305533.396299] SPR radius for FAST iterations: 25 (autodetect)
[00:17:13 -305533.396299] Model parameter optimization (eps = 3.000000)
[00:17:23 -305528.921185] FAST spr round 1 (radius: 25)
[00:20:31 -267014.423902] FAST spr round 2 (radius: 25)
[00:23:03 -264443.740195] FAST spr round 3 (radius: 25)
[00:25:10 -264312.505670] FAST spr round 4 (radius: 25)
[00:27:09 -264305.571273] FAST spr round 5 (radius: 25)
[00:29:03 -264300.107564] FAST spr round 6 (radius: 25)
[00:30:53 -264300.107470] Model parameter optimization (eps = 1.000000)
[00:31:24 -263210.637344] SLOW spr round 1 (radius: 5)
[00:33:54 -263144.060582] SLOW spr round 2 (radius: 5)
[00:36:21 -263131.291237] SLOW spr round 3 (radius: 5)
[00:38:45 -263126.261703] SLOW spr round 4 (radius: 5)
[00:41:05 -263126.260603] SLOW spr round 5 (radius: 10)
[00:43:31 -263122.523275] SLOW spr round 6 (radius: 5)
[00:46:36 -263078.996900] SLOW spr round 7 (radius: 5)
[00:49:16 -263077.831826] SLOW spr round 8 (radius: 5)
[00:51:42 -263077.831738] SLOW spr round 9 (radius: 10)
[00:54:09 -263077.831659] SLOW spr round 10 (radius: 15)
[00:57:52 -263077.831586] SLOW spr round 11 (radius: 20)
[01:03:20 -263077.831516] SLOW spr round 12 (radius: 25)
[01:10:18 -263077.831447] Model parameter optimization (eps = 0.100000)

[01:10:48] ML tree search #1, logLikelihood: -263018.363418

[01:10:48 -1375494.751461] Initial branch length optimization
[01:10:58 -1151920.674905] Model parameter optimization (eps = 10.000000)
[01:11:40 -1150433.039176] AUTODETECT spr round 1 (radius: 5)
[01:14:44 -687702.075353] AUTODETECT spr round 2 (radius: 10)
[01:18:07 -475992.432857] AUTODETECT spr round 3 (radius: 15)
[01:21:18 -353370.374339] AUTODETECT spr round 4 (radius: 20)
[01:24:42 -314160.498421] AUTODETECT spr round 5 (radius: 25)
[01:28:17 -305296.615364] SPR radius for FAST iterations: 25 (autodetect)
[01:28:17 -305296.615364] Model parameter optimization (eps = 3.000000)
[01:28:53 -304441.404493] FAST spr round 1 (radius: 25)
[01:31:56 -264544.111937] FAST spr round 2 (radius: 25)
[01:34:16 -263323.533941] FAST spr round 3 (radius: 25)
[01:36:22 -263268.078136] FAST spr round 4 (radius: 25)
[01:38:19 -263266.364731] FAST spr round 5 (radius: 25)
[01:40:12 -263266.352870] Model parameter optimization (eps = 1.000000)
[01:40:40 -263191.167921] SLOW spr round 1 (radius: 5)
[01:43:19 -263101.802004] SLOW spr round 2 (radius: 5)
[01:45:46 -263084.810412] SLOW spr round 3 (radius: 5)
[01:48:11 -263084.489229] SLOW spr round 4 (radius: 5)
[01:50:32 -263084.488440] SLOW spr round 5 (radius: 10)
[01:52:58 -263084.085083] SLOW spr round 6 (radius: 5)
[01:55:56 -263084.085022] SLOW spr round 7 (radius: 10)
[01:58:41 -263083.586598] SLOW spr round 8 (radius: 5)
[02:01:35 -263083.586580] SLOW spr round 9 (radius: 10)
[02:04:15 -263083.586569] SLOW spr round 10 (radius: 15)
[02:07:51 -263083.382260] SLOW spr round 11 (radius: 5)
[02:10:58 -263083.382252] SLOW spr round 12 (radius: 10)
[02:13:53 -263083.382245] SLOW spr round 13 (radius: 15)
[02:17:25 -263083.382239] SLOW spr round 14 (radius: 20)
[02:23:03 -263083.382233] SLOW spr round 15 (radius: 25)
[02:30:12 -263083.382227] Model parameter optimization (eps = 0.100000)

[02:30:25] ML tree search #2, logLikelihood: -263082.406926

[02:30:26 -1378736.378116] Initial branch length optimization
[02:30:34 -1153338.971692] Model parameter optimization (eps = 10.000000)
[02:31:15 -1151919.513216] AUTODETECT spr round 1 (radius: 5)
[02:34:18 -669643.478285] AUTODETECT spr round 2 (radius: 10)
[02:37:32 -463091.471267] AUTODETECT spr round 3 (radius: 15)
[02:40:30 -368328.815710] AUTODETECT spr round 4 (radius: 20)
[02:43:35 -314513.351502] AUTODETECT spr round 5 (radius: 25)
[02:47:26 -299515.300876] SPR radius for FAST iterations: 25 (autodetect)
[02:47:26 -299515.300876] Model parameter optimization (eps = 3.000000)
[02:47:52 -298584.312036] FAST spr round 1 (radius: 25)
[02:50:53 -265175.200497] FAST spr round 2 (radius: 25)
[02:53:16 -263336.201970] FAST spr round 3 (radius: 25)
[02:55:24 -263276.644215] FAST spr round 4 (radius: 25)
[02:57:19 -263276.642945] Model parameter optimization (eps = 1.000000)
[02:57:48 -263154.033714] SLOW spr round 1 (radius: 5)
[03:00:21 -263076.941823] SLOW spr round 2 (radius: 5)
[03:02:52 -263069.881039] SLOW spr round 3 (radius: 5)
[03:05:15 -263069.515658] SLOW spr round 4 (radius: 5)
[03:07:39 -263067.212588] SLOW spr round 5 (radius: 5)
[03:10:01 -263067.210890] SLOW spr round 6 (radius: 10)
[03:12:30 -263066.653017] SLOW spr round 7 (radius: 5)
[03:15:32 -263066.652370] SLOW spr round 8 (radius: 10)
[03:18:18 -263066.245653] SLOW spr round 9 (radius: 5)
[03:21:14 -263066.245519] SLOW spr round 10 (radius: 10)
[03:23:55 -263066.245462] SLOW spr round 11 (radius: 15)
[03:27:35 -263065.963998] SLOW spr round 12 (radius: 5)
[03:30:43 -263065.963939] SLOW spr round 13 (radius: 10)
[03:33:39 -263065.963887] SLOW spr round 14 (radius: 15)
[03:37:15 -263065.963837] SLOW spr round 15 (radius: 20)
[03:42:53 -263065.963786] SLOW spr round 16 (radius: 25)
[03:49:43 -263065.963735] Model parameter optimization (eps = 0.100000)

[03:49:54] ML tree search #3, logLikelihood: -263065.804923

[03:49:54 -1366726.484820] Initial branch length optimization
[03:50:03 -1150676.414918] Model parameter optimization (eps = 10.000000)
[03:50:56 -1149404.663873] AUTODETECT spr round 1 (radius: 5)
[03:53:51 -644082.825510] AUTODETECT spr round 2 (radius: 10)
[03:56:55 -448612.744631] AUTODETECT spr round 3 (radius: 15)
[03:59:49 -363134.465187] AUTODETECT spr round 4 (radius: 20)
[04:03:18 -318418.166539] AUTODETECT spr round 5 (radius: 25)
[04:07:15 -308217.748390] SPR radius for FAST iterations: 25 (autodetect)
[04:07:15 -308217.748390] Model parameter optimization (eps = 3.000000)
[04:07:46 -307323.406592] FAST spr round 1 (radius: 25)
[04:10:54 -265771.540841] FAST spr round 2 (radius: 25)
[04:13:21 -263406.245517] FAST spr round 3 (radius: 25)
[04:15:30 -263284.268269] FAST spr round 4 (radius: 25)
[04:17:34 -263258.120194] FAST spr round 5 (radius: 25)
[04:19:29 -263245.729260] FAST spr round 6 (radius: 25)
[04:21:21 -263245.717851] Model parameter optimization (eps = 1.000000)
[04:21:53 -263131.833889] SLOW spr round 1 (radius: 5)
[04:24:26 -263047.133466] SLOW spr round 2 (radius: 5)
[04:26:56 -263041.818292] SLOW spr round 3 (radius: 5)
[04:29:20 -263040.072919] SLOW spr round 4 (radius: 5)
[04:31:43 -263038.998919] SLOW spr round 5 (radius: 5)
[04:34:05 -263038.998560] SLOW spr round 6 (radius: 10)
[04:36:35 -263029.903576] SLOW spr round 7 (radius: 5)
[04:39:39 -263025.192325] SLOW spr round 8 (radius: 5)
[04:42:19 -263024.615808] SLOW spr round 9 (radius: 5)
[04:44:48 -263024.473705] SLOW spr round 10 (radius: 5)
[04:47:11 -263024.473634] SLOW spr round 11 (radius: 10)
[04:49:38 -263024.303890] SLOW spr round 12 (radius: 5)
[04:52:37 -263024.303809] SLOW spr round 13 (radius: 10)
[04:55:22 -263024.303743] SLOW spr round 14 (radius: 15)
[04:58:56 -263021.697057] SLOW spr round 15 (radius: 5)
[05:02:05 -263021.396277] SLOW spr round 16 (radius: 5)
[05:04:50 -263019.495511] SLOW spr round 17 (radius: 5)
[05:07:20 -263019.495242] SLOW spr round 18 (radius: 10)
[05:09:49 -263019.495206] SLOW spr round 19 (radius: 15)
[05:13:32 -263019.495199] SLOW spr round 20 (radius: 20)
[05:18:51 -263019.495193] SLOW spr round 21 (radius: 25)
[05:25:50 -263019.495186] Model parameter optimization (eps = 0.100000)

[05:26:01] ML tree search #4, logLikelihood: -263019.233174

[05:26:01 -1368365.451637] Initial branch length optimization
[05:26:08 -1144098.006315] Model parameter optimization (eps = 10.000000)
[05:26:56 -1142661.240315] AUTODETECT spr round 1 (radius: 5)
[05:29:49 -666242.506151] AUTODETECT spr round 2 (radius: 10)
[05:33:08 -477050.446037] AUTODETECT spr round 3 (radius: 15)
[05:36:20 -390839.038879] AUTODETECT spr round 4 (radius: 20)
[05:39:38 -350448.758724] AUTODETECT spr round 5 (radius: 25)
[05:44:05 -316574.618169] SPR radius for FAST iterations: 25 (autodetect)
[05:44:05 -316574.618169] Model parameter optimization (eps = 3.000000)
[05:44:36 -315765.899575] FAST spr round 1 (radius: 25)
[05:47:46 -266249.699894] FAST spr round 2 (radius: 25)
[05:50:16 -263473.531891] FAST spr round 3 (radius: 25)
[05:52:36 -263288.218349] FAST spr round 4 (radius: 25)
[05:54:35 -263278.466338] FAST spr round 5 (radius: 25)
[05:56:28 -263278.466194] Model parameter optimization (eps = 1.000000)
[05:56:58 -263122.661286] SLOW spr round 1 (radius: 5)
[05:59:38 -263047.626812] SLOW spr round 2 (radius: 5)
[06:02:08 -263031.206094] SLOW spr round 3 (radius: 5)
[06:04:30 -263031.183681] SLOW spr round 4 (radius: 10)
[06:06:57 -263031.183392] SLOW spr round 5 (radius: 15)
[06:10:46 -263030.876429] SLOW spr round 6 (radius: 5)
[06:13:57 -263026.610619] SLOW spr round 7 (radius: 5)
[06:16:44 -263024.764799] SLOW spr round 8 (radius: 5)
[06:19:14 -263024.764533] SLOW spr round 9 (radius: 10)
[06:21:43 -263024.764465] SLOW spr round 10 (radius: 15)
[06:25:27 -263024.764402] SLOW spr round 11 (radius: 20)
[06:30:54 -263019.920784] SLOW spr round 12 (radius: 5)
[06:34:06 -263019.621320] SLOW spr round 13 (radius: 5)
[06:36:54 -263019.621256] SLOW spr round 14 (radius: 10)
[06:39:31 -263019.621193] SLOW spr round 15 (radius: 15)
[06:43:10 -263019.621129] SLOW spr round 16 (radius: 20)
[06:48:39 -263019.621064] SLOW spr round 17 (radius: 25)
[06:55:37 -263019.621000] Model parameter optimization (eps = 0.100000)

[06:55:53] ML tree search #5, logLikelihood: -263019.144689

[06:55:53 -1361386.799758] Initial branch length optimization
[06:56:04 -1132022.549102] Model parameter optimization (eps = 10.000000)
[06:56:47 -1130659.231365] AUTODETECT spr round 1 (radius: 5)
[06:59:54 -675526.801479] AUTODETECT spr round 2 (radius: 10)
[07:03:07 -455938.102380] AUTODETECT spr round 3 (radius: 15)
[07:06:07 -368900.558604] AUTODETECT spr round 4 (radius: 20)
[07:09:42 -339383.733220] AUTODETECT spr round 5 (radius: 25)
[07:13:46 -328430.787235] SPR radius for FAST iterations: 25 (autodetect)
[07:13:46 -328430.787235] Model parameter optimization (eps = 3.000000)
[07:14:11 -327689.000851] FAST spr round 1 (radius: 25)
[07:17:23 -269671.647687] FAST spr round 2 (radius: 25)
[07:19:57 -263668.345860] FAST spr round 3 (radius: 25)
[07:22:11 -263362.332072] FAST spr round 4 (radius: 25)
[07:24:16 -263315.272851] FAST spr round 5 (radius: 25)
[07:26:09 -263314.811409] FAST spr round 6 (radius: 25)
[07:27:59 -263314.808662] Model parameter optimization (eps = 1.000000)
[07:28:28 -263153.213773] SLOW spr round 1 (radius: 5)
[07:31:04 -263086.230642] SLOW spr round 2 (radius: 5)
[07:33:34 -263053.134007] SLOW spr round 3 (radius: 5)
[07:35:57 -263052.427986] SLOW spr round 4 (radius: 5)
[07:38:19 -263051.197179] SLOW spr round 5 (radius: 5)
[07:40:38 -263051.196464] SLOW spr round 6 (radius: 10)
[07:43:05 -263037.877115] SLOW spr round 7 (radius: 5)
[07:46:08 -263034.952120] SLOW spr round 8 (radius: 5)
[07:48:47 -263034.951619] SLOW spr round 9 (radius: 10)
[07:51:17 -263034.951466] SLOW spr round 10 (radius: 15)
[07:55:00 -263031.850687] SLOW spr round 11 (radius: 5)
[07:58:07 -263025.583557] SLOW spr round 12 (radius: 5)
[08:00:50 -263025.580559] SLOW spr round 13 (radius: 10)
[08:03:23 -263025.579824] SLOW spr round 14 (radius: 15)
[08:07:02 -263025.225254] SLOW spr round 15 (radius: 5)
[08:10:10 -263023.765063] SLOW spr round 16 (radius: 5)
[08:12:53 -263023.764718] SLOW spr round 17 (radius: 10)
[08:15:27 -263021.807749] SLOW spr round 18 (radius: 5)
[08:18:24 -263021.758839] SLOW spr round 19 (radius: 10)
[08:21:06 -263021.756224] SLOW spr round 20 (radius: 15)
[08:24:38 -263021.756218] SLOW spr round 21 (radius: 20)
[08:29:57 -263021.756211] SLOW spr round 22 (radius: 25)
[08:36:42 -263021.756205] Model parameter optimization (eps = 0.100000)

[08:36:54] ML tree search #6, logLikelihood: -263021.392926

[08:36:55 -1363344.804155] Initial branch length optimization
[08:37:04 -1141283.515988] Model parameter optimization (eps = 10.000000)
[08:37:43 -1139759.873461] AUTODETECT spr round 1 (radius: 5)
[08:40:38 -669790.974201] AUTODETECT spr round 2 (radius: 10)
[08:43:58 -490015.008976] AUTODETECT spr round 3 (radius: 15)
[08:47:07 -357769.904855] AUTODETECT spr round 4 (radius: 20)
[08:50:32 -309238.222024] AUTODETECT spr round 5 (radius: 25)
[08:54:26 -305102.111062] SPR radius for FAST iterations: 25 (autodetect)
[08:54:26 -305102.111062] Model parameter optimization (eps = 3.000000)
[08:54:55 -304179.050010] FAST spr round 1 (radius: 25)
[08:57:55 -266622.264715] FAST spr round 2 (radius: 25)
[09:00:21 -263412.628547] FAST spr round 3 (radius: 25)
[09:02:29 -263216.307337] FAST spr round 4 (radius: 25)
[09:04:29 -263204.280294] FAST spr round 5 (radius: 25)
[09:06:23 -263198.166871] FAST spr round 6 (radius: 25)
[09:08:14 -263197.037207] FAST spr round 7 (radius: 25)
[09:10:03 -263197.036971] Model parameter optimization (eps = 1.000000)
[09:10:33 -263092.765279] SLOW spr round 1 (radius: 5)
[09:13:02 -263006.694292] SLOW spr round 2 (radius: 5)
[09:15:33 -262990.775984] SLOW spr round 3 (radius: 5)
[09:17:55 -262990.505146] SLOW spr round 4 (radius: 5)
[09:20:15 -262990.505033] SLOW spr round 5 (radius: 10)
[09:22:42 -262989.607016] SLOW spr round 6 (radius: 5)
[09:25:42 -262989.521368] SLOW spr round 7 (radius: 10)
[09:28:27 -262989.521298] SLOW spr round 8 (radius: 15)
[09:32:05 -262989.521250] SLOW spr round 9 (radius: 20)
[09:37:43 -262989.521202] SLOW spr round 10 (radius: 25)
[09:44:43 -262989.521154] Model parameter optimization (eps = 0.100000)

[09:44:52] ML tree search #7, logLikelihood: -262989.488899

[09:44:52 -1369940.197214] Initial branch length optimization
[09:44:59 -1143475.186939] Model parameter optimization (eps = 10.000000)
[09:45:45 -1142264.257977] AUTODETECT spr round 1 (radius: 5)
[09:48:47 -669417.591581] AUTODETECT spr round 2 (radius: 10)
[09:52:04 -452895.375880] AUTODETECT spr round 3 (radius: 15)
[09:55:05 -371387.902387] AUTODETECT spr round 4 (radius: 20)
[09:58:38 -313516.921436] AUTODETECT spr round 5 (radius: 25)
[10:03:00 -306562.083175] SPR radius for FAST iterations: 25 (autodetect)
[10:03:00 -306562.083175] Model parameter optimization (eps = 3.000000)
[10:03:37 -305656.277267] FAST spr round 1 (radius: 25)
[10:06:50 -264933.260141] FAST spr round 2 (radius: 25)
[10:09:24 -263430.020205] FAST spr round 3 (radius: 25)
[10:11:39 -263318.338039] FAST spr round 4 (radius: 25)
[10:13:41 -263294.257818] FAST spr round 5 (radius: 25)
[10:15:36 -263294.216456] Model parameter optimization (eps = 1.000000)
[10:16:17 -263169.833516] SLOW spr round 1 (radius: 5)
[10:18:54 -263052.934371] SLOW spr round 2 (radius: 5)
[10:21:24 -263037.977083] SLOW spr round 3 (radius: 5)
[10:23:46 -263037.976609] SLOW spr round 4 (radius: 10)
[10:26:14 -263037.246221] SLOW spr round 5 (radius: 5)
[10:29:20 -263023.814209] SLOW spr round 6 (radius: 5)
[10:32:03 -263021.362338] SLOW spr round 7 (radius: 5)
[10:34:31 -263021.362084] SLOW spr round 8 (radius: 10)
[10:36:59 -263021.188163] SLOW spr round 9 (radius: 5)
[10:39:58 -263021.187111] SLOW spr round 10 (radius: 10)
[10:42:42 -263021.187047] SLOW spr round 11 (radius: 15)
[10:46:19 -263020.999705] SLOW spr round 12 (radius: 5)
[10:49:27 -263020.822041] SLOW spr round 13 (radius: 5)
[10:52:12 -263020.821948] SLOW spr round 14 (radius: 10)
[10:54:46 -263020.821884] SLOW spr round 15 (radius: 15)
[10:58:28 -263020.821821] SLOW spr round 16 (radius: 20)
[11:03:52 -263020.821757] SLOW spr round 17 (radius: 25)
[11:10:49 -263020.821693] Model parameter optimization (eps = 0.100000)

[11:11:02] ML tree search #8, logLikelihood: -263020.436886

[11:11:02 -1360594.037230] Initial branch length optimization
[11:11:12 -1132598.993778] Model parameter optimization (eps = 10.000000)
[11:11:54 -1131090.353558] AUTODETECT spr round 1 (radius: 5)
[11:14:55 -648659.702960] AUTODETECT spr round 2 (radius: 10)
[11:18:03 -455889.742594] AUTODETECT spr round 3 (radius: 15)
[11:21:06 -372836.925717] AUTODETECT spr round 4 (radius: 20)
[11:24:25 -313745.393540] AUTODETECT spr round 5 (radius: 25)
[11:28:28 -304656.951405] SPR radius for FAST iterations: 25 (autodetect)
[11:28:28 -304656.951405] Model parameter optimization (eps = 3.000000)
[11:28:56 -303770.589328] FAST spr round 1 (radius: 25)
[11:32:05 -265485.485047] FAST spr round 2 (radius: 25)
[11:34:33 -263402.424732] FAST spr round 3 (radius: 25)
[11:36:40 -263305.839553] FAST spr round 4 (radius: 25)
[11:38:41 -263290.859858] FAST spr round 5 (radius: 25)
[11:40:37 -263284.438610] FAST spr round 6 (radius: 25)
[11:42:28 -263282.741717] FAST spr round 7 (radius: 25)
[11:44:19 -263282.729106] Model parameter optimization (eps = 1.000000)
[11:44:26 -263281.274045] SLOW spr round 1 (radius: 5)
[11:46:57 -263214.845211] SLOW spr round 2 (radius: 5)
[11:49:26 -263202.379462] SLOW spr round 3 (radius: 5)
[11:51:50 -263202.156781] SLOW spr round 4 (radius: 5)
[11:54:13 -263202.155572] SLOW spr round 5 (radius: 10)
[11:56:39 -263202.154534] SLOW spr round 6 (radius: 15)
[12:00:30 -263202.153501] SLOW spr round 7 (radius: 20)
[12:06:03 -263202.152468] SLOW spr round 8 (radius: 25)
[12:12:58 -263202.151434] Model parameter optimization (eps = 0.100000)

[12:13:02] ML tree search #9, logLikelihood: -263202.144480

[12:13:02 -1383597.042367] Initial branch length optimization
[12:13:10 -1159002.951001] Model parameter optimization (eps = 10.000000)
[12:14:03 -1157690.219261] AUTODETECT spr round 1 (radius: 5)
[12:17:07 -677237.878014] AUTODETECT spr round 2 (radius: 10)
[12:20:25 -471574.110079] AUTODETECT spr round 3 (radius: 15)
[12:23:27 -371302.214748] AUTODETECT spr round 4 (radius: 20)
[12:26:55 -314297.241329] AUTODETECT spr round 5 (radius: 25)
[12:31:01 -310303.710088] SPR radius for FAST iterations: 25 (autodetect)
[12:31:01 -310303.710088] Model parameter optimization (eps = 3.000000)
[12:31:27 -309441.139497] FAST spr round 1 (radius: 25)
[12:34:27 -265323.458326] FAST spr round 2 (radius: 25)
[12:36:51 -263398.926069] FAST spr round 3 (radius: 25)
[12:39:00 -263300.212212] FAST spr round 4 (radius: 25)
[12:41:02 -263277.881877] FAST spr round 5 (radius: 25)
[12:42:55 -263277.879041] Model parameter optimization (eps = 1.000000)
[12:43:20 -263211.813319] SLOW spr round 1 (radius: 5)
[12:45:55 -263143.044477] SLOW spr round 2 (radius: 5)
[12:48:24 -263136.932195] SLOW spr round 3 (radius: 5)
[12:50:46 -263136.931163] SLOW spr round 4 (radius: 10)
[12:53:14 -263136.900211] SLOW spr round 5 (radius: 15)
[12:56:58 -263136.898812] SLOW spr round 6 (radius: 20)
[13:02:28 -263136.897912] SLOW spr round 7 (radius: 25)
[13:09:17 -263136.897080] Model parameter optimization (eps = 0.100000)

[13:09:28] ML tree search #10, logLikelihood: -263136.782593

[13:09:28 -1368878.055214] Initial branch length optimization
[13:09:37 -1148526.936970] Model parameter optimization (eps = 10.000000)
[13:10:21 -1147079.407605] AUTODETECT spr round 1 (radius: 5)
[13:13:27 -668223.228621] AUTODETECT spr round 2 (radius: 10)
[13:16:48 -466967.631205] AUTODETECT spr round 3 (radius: 15)
[13:19:46 -354633.847706] AUTODETECT spr round 4 (radius: 20)
[13:23:14 -313581.308927] AUTODETECT spr round 5 (radius: 25)
[13:26:56 -306916.740482] SPR radius for FAST iterations: 25 (autodetect)
[13:26:56 -306916.740482] Model parameter optimization (eps = 3.000000)
[13:27:29 -306053.545954] FAST spr round 1 (radius: 25)
[13:30:32 -264882.807393] FAST spr round 2 (radius: 25)
[13:32:58 -263349.480833] FAST spr round 3 (radius: 25)
[13:35:05 -263207.027687] FAST spr round 4 (radius: 25)
[13:37:07 -263194.586119] FAST spr round 5 (radius: 25)
[13:39:01 -263194.584787] Model parameter optimization (eps = 1.000000)
[13:39:49 -263093.861264] SLOW spr round 1 (radius: 5)
[13:42:28 -263001.049387] SLOW spr round 2 (radius: 5)
[13:45:00 -262977.985216] SLOW spr round 3 (radius: 5)
[13:47:24 -262977.841574] SLOW spr round 4 (radius: 5)
[13:49:46 -262977.841358] SLOW spr round 5 (radius: 10)
[13:52:14 -262977.499809] SLOW spr round 6 (radius: 5)
[13:55:14 -262977.495634] SLOW spr round 7 (radius: 10)
[13:57:59 -262977.494749] SLOW spr round 8 (radius: 15)
[14:01:33 -262977.494506] SLOW spr round 9 (radius: 20)
[14:07:10 -262977.494404] SLOW spr round 10 (radius: 25)
[14:14:12 -262977.494333] Model parameter optimization (eps = 0.100000)

[14:14:18] ML tree search #11, logLikelihood: -262977.462759

[14:14:18 -1356574.589190] Initial branch length optimization
[14:14:26 -1136475.834334] Model parameter optimization (eps = 10.000000)
[14:15:16 -1134965.245240] AUTODETECT spr round 1 (radius: 5)
[14:18:16 -676843.226034] AUTODETECT spr round 2 (radius: 10)
[14:21:38 -453488.091756] AUTODETECT spr round 3 (radius: 15)
[14:24:36 -356107.572138] AUTODETECT spr round 4 (radius: 20)
[14:27:57 -303222.383611] AUTODETECT spr round 5 (radius: 25)
[14:31:45 -299813.156847] SPR radius for FAST iterations: 25 (autodetect)
[14:31:45 -299813.156847] Model parameter optimization (eps = 3.000000)
[14:32:18 -298804.306868] FAST spr round 1 (radius: 25)
[14:35:14 -265453.915553] FAST spr round 2 (radius: 25)
[14:37:30 -263603.850572] FAST spr round 3 (radius: 25)
[14:39:38 -263260.995590] FAST spr round 4 (radius: 25)
[14:41:35 -263242.099261] FAST spr round 5 (radius: 25)
[14:43:26 -263242.098350] Model parameter optimization (eps = 1.000000)
[14:43:45 -263193.339279] SLOW spr round 1 (radius: 5)
[14:46:19 -263125.171461] SLOW spr round 2 (radius: 5)
[14:48:48 -263108.231469] SLOW spr round 3 (radius: 5)
[14:51:13 -263107.542440] SLOW spr round 4 (radius: 5)
[14:53:33 -263107.542086] SLOW spr round 5 (radius: 10)
[14:55:59 -263107.042370] SLOW spr round 6 (radius: 5)
[14:58:58 -263107.042347] SLOW spr round 7 (radius: 10)
[15:01:43 -263107.042332] SLOW spr round 8 (radius: 15)
[15:05:15 -263107.042321] SLOW spr round 9 (radius: 20)
[15:10:49 -263107.042311] SLOW spr round 10 (radius: 25)
[15:17:49 -263107.042303] Model parameter optimization (eps = 0.100000)

[15:18:00] ML tree search #12, logLikelihood: -263106.931766

[15:18:00 -1368859.912250] Initial branch length optimization
[15:18:07 -1137370.486373] Model parameter optimization (eps = 10.000000)
[15:18:49 -1135844.182679] AUTODETECT spr round 1 (radius: 5)
[15:21:54 -669660.301120] AUTODETECT spr round 2 (radius: 10)
[15:25:16 -441637.344225] AUTODETECT spr round 3 (radius: 15)
[15:28:20 -367198.973200] AUTODETECT spr round 4 (radius: 20)
[15:31:39 -340010.353670] AUTODETECT spr round 5 (radius: 25)
[15:35:32 -314526.418925] SPR radius for FAST iterations: 25 (autodetect)
[15:35:32 -314526.418925] Model parameter optimization (eps = 3.000000)
[15:36:06 -313737.847125] FAST spr round 1 (radius: 25)
[15:39:16 -268561.368406] FAST spr round 2 (radius: 25)
[15:41:41 -263590.811290] FAST spr round 3 (radius: 25)
[15:43:53 -263332.671939] FAST spr round 4 (radius: 25)
[15:45:57 -263294.232275] FAST spr round 5 (radius: 25)
[15:47:52 -263288.281284] FAST spr round 6 (radius: 25)
[15:49:43 -263288.280913] Model parameter optimization (eps = 1.000000)
[15:50:13 -263115.312895] SLOW spr round 1 (radius: 5)
[15:52:43 -263042.002966] SLOW spr round 2 (radius: 5)
[15:55:10 -263038.207134] SLOW spr round 3 (radius: 5)
[15:57:36 -263032.277508] SLOW spr round 4 (radius: 5)
[15:59:58 -263032.276039] SLOW spr round 5 (radius: 10)
[16:02:25 -263023.680520] SLOW spr round 6 (radius: 5)
[16:05:30 -263019.068609] SLOW spr round 7 (radius: 5)
[16:08:13 -263018.498418] SLOW spr round 8 (radius: 5)
[16:10:42 -263018.356998] SLOW spr round 9 (radius: 5)
[16:13:06 -263018.356943] SLOW spr round 10 (radius: 10)
[16:15:33 -263018.356891] SLOW spr round 11 (radius: 15)
[16:19:20 -263018.356838] SLOW spr round 12 (radius: 20)
[16:24:42 -263018.356786] SLOW spr round 13 (radius: 25)
[16:31:32 -263018.356734] Model parameter optimization (eps = 0.100000)

[16:31:44] ML tree search #13, logLikelihood: -263018.026697

[16:31:44 -1370341.235850] Initial branch length optimization
[16:31:53 -1142108.869706] Model parameter optimization (eps = 10.000000)
[16:32:36 -1140698.040098] AUTODETECT spr round 1 (radius: 5)
[16:35:42 -668683.133328] AUTODETECT spr round 2 (radius: 10)
[16:39:05 -464999.431636] AUTODETECT spr round 3 (radius: 15)
[16:42:03 -368076.102883] AUTODETECT spr round 4 (radius: 20)
[16:45:36 -318301.873390] AUTODETECT spr round 5 (radius: 25)
[16:49:41 -312715.189594] SPR radius for FAST iterations: 25 (autodetect)
[16:49:41 -312715.189594] Model parameter optimization (eps = 3.000000)
[16:50:14 -311811.206173] FAST spr round 1 (radius: 25)
[16:53:20 -265052.032594] FAST spr round 2 (radius: 25)
[16:55:38 -263272.391468] FAST spr round 3 (radius: 25)
[16:57:44 -263222.012853] FAST spr round 4 (radius: 25)
[16:59:42 -263217.259701] FAST spr round 5 (radius: 25)
[17:01:35 -263216.637124] FAST spr round 6 (radius: 25)
[17:03:26 -263216.634479] Model parameter optimization (eps = 1.000000)
[17:03:55 -263146.025048] SLOW spr round 1 (radius: 5)
[17:06:24 -263085.296029] SLOW spr round 2 (radius: 5)
[17:08:52 -263076.927806] SLOW spr round 3 (radius: 5)
[17:11:18 -263075.702946] SLOW spr round 4 (radius: 5)
[17:13:41 -263075.702550] SLOW spr round 5 (radius: 10)
[17:16:07 -263074.508864] SLOW spr round 6 (radius: 5)
[17:19:07 -263074.095620] SLOW spr round 7 (radius: 5)
[17:21:46 -263074.093717] SLOW spr round 8 (radius: 10)
[17:24:17 -263074.093269] SLOW spr round 9 (radius: 15)
[17:28:04 -263074.093156] SLOW spr round 10 (radius: 20)
[17:33:43 -263074.093125] SLOW spr round 11 (radius: 25)
[17:40:50 -263074.093112] Model parameter optimization (eps = 0.100000)

[17:41:16] ML tree search #14, logLikelihood: -263014.033294

[17:41:16 -1372635.543089] Initial branch length optimization
[17:41:26 -1156783.236034] Model parameter optimization (eps = 10.000000)
[17:42:08 -1155410.067085] AUTODETECT spr round 1 (radius: 5)
[17:45:10 -652902.475675] AUTODETECT spr round 2 (radius: 10)
[17:48:25 -449586.438156] AUTODETECT spr round 3 (radius: 15)
[17:51:33 -328886.138569] AUTODETECT spr round 4 (radius: 20)
[17:55:08 -306601.789709] AUTODETECT spr round 5 (radius: 25)
[17:59:47 -301808.777877] SPR radius for FAST iterations: 25 (autodetect)
[17:59:47 -301808.777877] Model parameter optimization (eps = 3.000000)
[17:59:57 -301803.048460] FAST spr round 1 (radius: 25)
[18:03:05 -265665.777054] FAST spr round 2 (radius: 25)
[18:05:38 -264404.601463] FAST spr round 3 (radius: 25)
[18:07:53 -264298.194436] FAST spr round 4 (radius: 25)
[18:09:52 -264286.796791] FAST spr round 5 (radius: 25)
[18:11:45 -264286.794185] Model parameter optimization (eps = 1.000000)
[18:12:21 -263224.731352] SLOW spr round 1 (radius: 5)
[18:14:57 -263119.601813] SLOW spr round 2 (radius: 5)
[18:17:28 -263115.714952] SLOW spr round 3 (radius: 5)
[18:19:54 -263111.842799] SLOW spr round 4 (radius: 5)
[18:22:15 -263111.831724] SLOW spr round 5 (radius: 10)
[18:24:43 -263107.762911] SLOW spr round 6 (radius: 5)
[18:27:43 -263107.255381] SLOW spr round 7 (radius: 5)
[18:30:23 -263107.254369] SLOW spr round 8 (radius: 10)
[18:32:53 -263107.253356] SLOW spr round 9 (radius: 15)
[18:36:42 -263107.252342] SLOW spr round 10 (radius: 20)
[18:42:19 -263104.923276] SLOW spr round 11 (radius: 5)
[18:45:31 -263103.773809] SLOW spr round 12 (radius: 5)
[18:48:19 -263103.773770] SLOW spr round 13 (radius: 10)
[18:50:54 -263103.773733] SLOW spr round 14 (radius: 15)
[18:54:37 -263103.726185] SLOW spr round 15 (radius: 20)
[19:00:16 -263103.722622] SLOW spr round 16 (radius: 25)
[19:07:23 -263103.719061] Model parameter optimization (eps = 0.100000)

[19:07:51] ML tree search #15, logLikelihood: -263026.634845

[19:07:51 -1371959.637211] Initial branch length optimization
[19:08:00 -1154162.115445] Model parameter optimization (eps = 10.000000)
[19:08:49 -1152784.513138] AUTODETECT spr round 1 (radius: 5)
[19:11:53 -663468.821173] AUTODETECT spr round 2 (radius: 10)
[19:14:57 -477664.225654] AUTODETECT spr round 3 (radius: 15)
[19:18:03 -370090.461870] AUTODETECT spr round 4 (radius: 20)
[19:21:31 -338414.787814] AUTODETECT spr round 5 (radius: 25)
[19:25:51 -318429.201369] SPR radius for FAST iterations: 25 (autodetect)
[19:25:51 -318429.201369] Model parameter optimization (eps = 3.000000)
[19:26:23 -317694.863682] FAST spr round 1 (radius: 25)
[19:29:34 -266057.271750] FAST spr round 2 (radius: 25)
[19:32:10 -263451.283170] FAST spr round 3 (radius: 25)
[19:34:25 -263293.296211] FAST spr round 4 (radius: 25)
[19:36:23 -263286.459767] FAST spr round 5 (radius: 25)
[19:38:17 -263286.447673] Model parameter optimization (eps = 1.000000)
[19:38:46 -263162.847097] SLOW spr round 1 (radius: 5)
[19:41:22 -263100.916300] SLOW spr round 2 (radius: 5)
[19:43:51 -263091.813808] SLOW spr round 3 (radius: 5)
[19:46:14 -263091.802619] SLOW spr round 4 (radius: 10)
[19:48:45 -263075.261895] SLOW spr round 5 (radius: 5)
[19:51:47 -263075.249902] SLOW spr round 6 (radius: 10)
[19:54:33 -263075.248887] SLOW spr round 7 (radius: 15)
[19:58:14 -263074.980441] SLOW spr round 8 (radius: 5)
[20:01:23 -263074.969187] SLOW spr round 9 (radius: 10)
[20:04:20 -263074.968162] SLOW spr round 10 (radius: 15)
[20:07:59 -263074.967465] SLOW spr round 11 (radius: 20)
[20:13:48 -263074.967365] SLOW spr round 12 (radius: 25)
[20:20:53 -263074.967297] Model parameter optimization (eps = 0.100000)

[20:21:02] ML tree search #16, logLikelihood: -263074.836617

[20:21:02 -1362634.086463] Initial branch length optimization
[20:21:12 -1143474.507036] Model parameter optimization (eps = 10.000000)
[20:21:52 -1141975.492644] AUTODETECT spr round 1 (radius: 5)
[20:24:52 -656618.919655] AUTODETECT spr round 2 (radius: 10)
[20:28:05 -469301.812746] AUTODETECT spr round 3 (radius: 15)
[20:31:04 -394326.820779] AUTODETECT spr round 4 (radius: 20)
[20:34:35 -346147.236927] AUTODETECT spr round 5 (radius: 25)
[20:38:26 -313291.883436] SPR radius for FAST iterations: 25 (autodetect)
[20:38:26 -313291.883436] Model parameter optimization (eps = 3.000000)
[20:38:35 -313287.905983] FAST spr round 1 (radius: 25)
[20:41:46 -266995.296220] FAST spr round 2 (radius: 25)
[20:44:12 -264421.871263] FAST spr round 3 (radius: 25)
[20:46:20 -264332.679146] FAST spr round 4 (radius: 25)
[20:48:21 -264312.902930] FAST spr round 5 (radius: 25)
[20:50:16 -264309.883046] FAST spr round 6 (radius: 25)
[20:52:07 -264309.882696] Model parameter optimization (eps = 1.000000)
[20:52:37 -263212.269879] SLOW spr round 1 (radius: 5)
[20:55:08 -263119.489085] SLOW spr round 2 (radius: 5)
[20:57:36 -263111.417079] SLOW spr round 3 (radius: 5)
[21:00:01 -263111.341448] SLOW spr round 4 (radius: 10)
[21:02:27 -263111.340651] SLOW spr round 5 (radius: 15)
[21:06:17 -263111.340104] SLOW spr round 6 (radius: 20)
[21:11:48 -263111.339723] SLOW spr round 7 (radius: 25)
[21:18:58 -263111.339452] Model parameter optimization (eps = 0.100000)

[21:19:09] ML tree search #17, logLikelihood: -263111.059287

[21:19:09 -1358759.188945] Initial branch length optimization
[21:19:17 -1135164.154690] Model parameter optimization (eps = 10.000000)
[21:20:05 -1133600.107392] AUTODETECT spr round 1 (radius: 5)
[21:23:03 -663467.047349] AUTODETECT spr round 2 (radius: 10)
[21:26:21 -475707.384714] AUTODETECT spr round 3 (radius: 15)
[21:29:26 -365924.081282] AUTODETECT spr round 4 (radius: 20)
[21:32:37 -335379.535899] AUTODETECT spr round 5 (radius: 25)
[21:36:28 -315486.037138] SPR radius for FAST iterations: 25 (autodetect)
[21:36:28 -315486.037138] Model parameter optimization (eps = 3.000000)
[21:36:39 -315480.263257] FAST spr round 1 (radius: 25)
[21:39:46 -268516.003575] FAST spr round 2 (radius: 25)
[21:42:19 -264576.500494] FAST spr round 3 (radius: 25)
[21:44:28 -264317.364949] FAST spr round 4 (radius: 25)
[21:46:30 -264309.269356] FAST spr round 5 (radius: 25)
[21:48:23 -264309.195827] Model parameter optimization (eps = 1.000000)
[21:48:53 -263214.844460] SLOW spr round 1 (radius: 5)
[21:51:28 -263122.739456] SLOW spr round 2 (radius: 5)
[21:53:56 -263119.586595] SLOW spr round 3 (radius: 5)
[21:56:21 -263119.315067] SLOW spr round 4 (radius: 5)
[21:58:43 -263119.314910] SLOW spr round 5 (radius: 10)
[22:01:08 -263118.858302] SLOW spr round 6 (radius: 5)
[22:04:11 -263074.070589] SLOW spr round 7 (radius: 5)
[22:06:52 -263073.710441] SLOW spr round 8 (radius: 5)
[22:09:20 -263073.710239] SLOW spr round 9 (radius: 10)
[22:11:47 -263073.269901] SLOW spr round 10 (radius: 5)
[22:14:46 -263073.269703] SLOW spr round 11 (radius: 10)
[22:17:30 -263073.269682] SLOW spr round 12 (radius: 15)
[22:21:05 -263073.269662] SLOW spr round 13 (radius: 20)
[22:26:50 -263073.269644] SLOW spr round 14 (radius: 25)
[22:34:03 -263073.269627] Model parameter optimization (eps = 0.100000)

[22:34:36] ML tree search #18, logLikelihood: -263016.226688

[22:34:36 -1364186.745047] Initial branch length optimization
[22:34:44 -1133715.715656] Model parameter optimization (eps = 10.000000)
[22:35:28 -1132283.132329] AUTODETECT spr round 1 (radius: 5)
[22:38:32 -661007.815629] AUTODETECT spr round 2 (radius: 10)
[22:41:35 -457473.282464] AUTODETECT spr round 3 (radius: 15)
[22:44:33 -364836.746550] AUTODETECT spr round 4 (radius: 20)
[22:48:04 -331163.274901] AUTODETECT spr round 5 (radius: 25)
[22:51:45 -308430.675091] SPR radius for FAST iterations: 25 (autodetect)
[22:51:45 -308430.675091] Model parameter optimization (eps = 3.000000)
[22:52:09 -307633.822066] FAST spr round 1 (radius: 25)
[22:55:23 -264749.106271] FAST spr round 2 (radius: 25)
[22:57:55 -263369.307009] FAST spr round 3 (radius: 25)
[23:00:00 -263324.398961] FAST spr round 4 (radius: 25)
[23:01:59 -263283.810503] FAST spr round 5 (radius: 25)
[23:03:50 -263283.809365] Model parameter optimization (eps = 1.000000)
[23:04:21 -263118.072604] SLOW spr round 1 (radius: 5)
[23:06:54 -263019.973125] SLOW spr round 2 (radius: 5)
[23:09:24 -263003.936534] SLOW spr round 3 (radius: 5)
[23:11:47 -263003.613676] SLOW spr round 4 (radius: 5)
[23:14:08 -263003.613613] SLOW spr round 5 (radius: 10)
[23:16:34 -263003.613561] SLOW spr round 6 (radius: 15)
[23:20:21 -263003.272738] SLOW spr round 7 (radius: 5)
[23:23:34 -262994.831545] SLOW spr round 8 (radius: 5)
[23:26:20 -262994.831438] SLOW spr round 9 (radius: 10)
[23:28:53 -262994.831388] SLOW spr round 10 (radius: 15)
[23:32:34 -262994.831340] SLOW spr round 11 (radius: 20)
[23:38:04 -262994.831291] SLOW spr round 12 (radius: 25)
[23:45:05 -262994.831242] Model parameter optimization (eps = 0.100000)

[23:45:14] ML tree search #19, logLikelihood: -262994.777485

[23:45:14 -1358168.137783] Initial branch length optimization
[23:45:25 -1130050.476090] Model parameter optimization (eps = 10.000000)
[23:46:13 -1128529.080558] AUTODETECT spr round 1 (radius: 5)
[23:49:14 -678460.470619] AUTODETECT spr round 2 (radius: 10)
[23:52:37 -463571.767621] AUTODETECT spr round 3 (radius: 15)
[23:55:33 -360964.368021] AUTODETECT spr round 4 (radius: 20)
[23:58:54 -315308.303237] AUTODETECT spr round 5 (radius: 25)
[24:03:01 -307034.354164] SPR radius for FAST iterations: 25 (autodetect)
[24:03:01 -307034.354164] Model parameter optimization (eps = 3.000000)
[24:03:32 -305980.595957] FAST spr round 1 (radius: 25)
[24:06:27 -266031.571670] FAST spr round 2 (radius: 25)
[24:08:42 -263490.287719] FAST spr round 3 (radius: 25)
[24:10:51 -263318.024910] FAST spr round 4 (radius: 25)
[24:12:52 -263303.688022] FAST spr round 5 (radius: 25)
[24:14:46 -263301.208791] FAST spr round 6 (radius: 25)
[24:16:38 -263301.207884] Model parameter optimization (eps = 1.000000)
[24:17:05 -263190.162811] SLOW spr round 1 (radius: 5)
[24:19:38 -263100.730499] SLOW spr round 2 (radius: 5)
[24:22:08 -263092.750362] SLOW spr round 3 (radius: 5)
[24:24:33 -263092.749685] SLOW spr round 4 (radius: 10)
[24:27:01 -263092.749639] SLOW spr round 5 (radius: 15)
[24:30:52 -263090.248628] SLOW spr round 6 (radius: 5)
[24:34:04 -263088.959428] SLOW spr round 7 (radius: 5)
[24:36:50 -263088.945130] SLOW spr round 8 (radius: 10)
[24:39:26 -263088.944149] SLOW spr round 9 (radius: 15)
[24:43:07 -263088.944137] SLOW spr round 10 (radius: 20)
[24:48:40 -263088.944124] SLOW spr round 11 (radius: 25)
[24:55:32 -263088.944112] Model parameter optimization (eps = 0.100000)

[24:55:47] ML tree search #20, logLikelihood: -263088.172934


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.331120,0.453071) (0.215252,0.958972) (0.311283,0.806723) (0.142344,2.756974) 
   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: -262977.462759

AIC score: 529964.925519 / AICc score: 8574024.925519 / BIC score: 540347.909214
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1311).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 136 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/3_mltree/Q00975.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/3_mltree/Q00975.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/3_mltree/Q00975.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/3_mltree/Q00975.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q00975/3_mltree/Q00975.raxml.log

Analysis started: 12-Jul-2021 17:45:40 / finished: 13-Jul-2021 18:41:27

Elapsed time: 89747.362 seconds