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 02-Jul-2021 09:23:08 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/2_msa/P51798_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/3_mltree/P51798 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/2_msa/P51798_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 550 sites

WARNING: Sequences tr_A0A1D5PS57_A0A1D5PS57_CHICK_9031 and tr_A0A226P450_A0A226P450_COLVI_9014 are exactly identical!
WARNING: Sequences tr_E1BZI1_E1BZI1_CHICK_9031 and tr_U3IRK6_U3IRK6_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_E1BZI1_E1BZI1_CHICK_9031 and tr_A0A087QL31_A0A087QL31_APTFO_9233 are exactly identical!
WARNING: Sequences tr_M3YW13_M3YW13_MUSPF_9669 and tr_G1LN61_G1LN61_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YW13_M3YW13_MUSPF_9669 and tr_A0A2U3YE72_A0A2U3YE72_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YW13_M3YW13_MUSPF_9669 and tr_A0A2Y9KL93_A0A2Y9KL93_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3I099_G3I099_CRIGR_10029 and tr_A0A287CUE6_A0A287CUE6_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G3I099_G3I099_CRIGR_10029 and tr_A0A286XWH8_A0A286XWH8_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_G3I099_G3I099_CRIGR_10029 and tr_A0A1U8BXA1_A0A1U8BXA1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_H2PUW4_H2PUW4_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_K7BMC0_K7BMC0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and sp_P51793_CLCN4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_F7BX81_F7BX81_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_G7Q273_G7Q273_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A096NQK3_A0A096NQK3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A0D9RRY3_A0A0D9RRY3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A2K5P7H8_A0A2K5P7H8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A2K6DC20_A0A2K6DC20_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A2K5XN49_A0A2K5XN49_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A2R8Z8M5_A0A2R8Z8M5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q2M106_Q2M106_DROPS_46245 and tr_B4GQU3_B4GQU3_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2QAA1_H2QAA1_PANTR_9598 and tr_F7HXG0_F7HXG0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A0E0GSA0_A0A0E0GSA0_ORYNI_4536 and tr_B8APZ1_B8APZ1_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0H199_A0A0E0H199_ORYNI_4536 and tr_A2XTU8_A2XTU8_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0H199_A0A0E0H199_ORYNI_4536 and tr_I1PLK5_I1PLK5_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0H199_A0A0E0H199_ORYNI_4536 and tr_A0A0E0DEP6_A0A0E0DEP6_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0H199_A0A0E0H199_ORYNI_4536 and tr_A0A0E0P9L1_A0A0E0P9L1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0H199_A0A0E0H199_ORYNI_4536 and tr_A0A0D3FW78_A0A0D3FW78_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0H199_A0A0E0H199_ORYNI_4536 and tr_A0A0D9ZL68_A0A0D9ZL68_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0H6G9_A0A0E0H6G9_ORYNI_4536 and tr_I1PQ81_I1PQ81_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0H6G9_A0A0E0H6G9_ORYNI_4536 and tr_A0A0E0DJ32_A0A0E0DJ32_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0H6G9_A0A0E0H6G9_ORYNI_4536 and tr_A0A0E0PEU0_A0A0E0PEU0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0H6G9_A0A0E0H6G9_ORYNI_4536 and tr_A0A0D3G0V6_A0A0D3G0V6_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0H6G9_A0A0E0H6G9_ORYNI_4536 and tr_A0A0D9ZRJ9_A0A0D9ZRJ9_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0I9Y9_A0A0E0I9Y9_ORYNI_4536 and tr_A2YTR4_A2YTR4_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0I9Y9_A0A0E0I9Y9_ORYNI_4536 and tr_A0A0E0QH35_A0A0E0QH35_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0I9Y9_A0A0E0I9Y9_ORYNI_4536 and tr_Q6ZDC2_Q6ZDC2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B8A715_B8A715_ORYSI_39946 and tr_I1NTV9_I1NTV9_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_B8A715_B8A715_ORYSI_39946 and tr_A0A0D3EWW8_A0A0D3EWW8_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_B8A715_B8A715_ORYSI_39946 and tr_A0A0D9YI50_A0A0D9YI50_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_B8A715_B8A715_ORYSI_39946 and tr_A0A0P0VB46_A0A0P0VB46_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1QHE7_I1QHE7_ORYGL_4538 and tr_A0A0D3GYP5_A0A0D3GYP5_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0D4X5_A0A0E0D4X5_9ORYZ_40149 and tr_A0A0E0NZX7_A0A0E0NZX7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0RGS4_A0A0E0RGS4_ORYRU_4529 and tr_A0A0D3HU12_A0A0D3HU12_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_E3LPY0_E3LPY0_CAERE_31234 and tr_A0A261BPL2_A0A261BPL2_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8Y435_A8Y435_CAEBR_6238 and tr_A0A2G5TGK1_A0A2G5TGK1_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_M4E159_M4E159_BRARP_51351 and tr_A0A078FTJ8_A0A078FTJ8_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4E8Z7_M4E8Z7_BRARP_51351 and tr_A0A078FGY4_A0A078FGY4_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4ENF8_M4ENF8_BRARP_51351 and tr_A0A078FNA3_A0A078FNA3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4FCX8_M4FCX8_BRARP_51351 and tr_A0A078IDX1_A0A078IDX1_BRANA_3708 are exactly identical!
WARNING: Sequences tr_U3JNL4_U3JNL4_FICAL_59894 and tr_A0A218U9B4_A0A218U9B4_9PASE_299123 are exactly identical!
WARNING: Sequences tr_W2PZX9_W2PZX9_PHYPN_761204 and tr_A0A0W8CGX6_A0A0W8CGX6_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PZX9_W2PZX9_PHYPN_761204 and tr_W2GHP2_W2GHP2_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QT73_W2QT73_PHYPN_761204 and tr_A0A0W8BUZ7_A0A0W8BUZ7_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QT73_W2QT73_PHYPN_761204 and tr_W2K189_W2K189_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A3B6AZ64_A0A3B6AZ64_WHEAT_4565 and tr_A0A3B6C7R3_A0A3B6C7R3_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B6AZ64_A0A3B6AZ64_WHEAT_4565 and tr_A0A3B6DEA5_A0A3B6DEA5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A067G542_A0A067G542_CITSI_2711 and tr_V4RGT8_V4RGT8_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A078IUE5_A0A078IUE5_BRANA_3708 and tr_A0A0D3DCN7_A0A0D3DCN7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0D2S8B3_A0A0D2S8B3_GOSRA_29730 and tr_A0A1U8K3A1_A0A1U8K3A1_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A151N3R6_A0A151N3R6_ALLMI_8496 and tr_A0A1U7R2I6_A0A1U7R2I6_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091UT94_A0A091UT94_NIPNI_128390 and tr_A0A1V4KTG5_A0A1V4KTG5_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3YKN5_A0A1S3YKN5_TOBAC_4097 and tr_A0A1U7V924_A0A1U7V924_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4B7U8_A0A1S4B7U8_TOBAC_4097 and tr_A0A1U7VKK4_A0A1U7VKK4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_Q40485_Q40485_TOBAC_4097 and tr_A0A1J6ISC1_A0A1J6ISC1_NICAT_49451 are exactly identical!
WARNING: Sequences tr_Q40485_Q40485_TOBAC_4097 and tr_A0A1U7XQR9_A0A1U7XQR9_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3VSF5_A0A1S3VSF5_VIGRR_3916 and tr_A0A3Q0FHF8_A0A3Q0FHF8_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A2D0Q752_A0A2D0Q752_ICTPU_7998 and tr_W5U6A4_W5U6A4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QVZ8_A0A2D0QVZ8_ICTPU_7998 and tr_A0A2D0QW01_A0A2D0QW01_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R9D5_A0A2D0R9D5_ICTPU_7998 and tr_A0A2D0R9D9_A0A2D0R9D9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R9D5_A0A2D0R9D5_ICTPU_7998 and tr_A0A2D0RAQ2_A0A2D0RAQ2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R9D5_A0A2D0R9D5_ICTPU_7998 and tr_A0A2D0RBE7_A0A2D0RBE7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R9E3_A0A2D0R9E3_ICTPU_7998 and tr_A0A2D0RAR1_A0A2D0RAR1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A1U8G3F4_A0A1U8G3F4_CAPAN_4072 and tr_A0A2G3CT64_A0A2G3CT64_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2U3WKA5_A0A2U3WKA5_ODORO_9708 and tr_A0A2U3Z0U9_A0A2U3Z0U9_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 75

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/P51798/3_mltree/P51798.raxml.reduced.phy

Alignment comprises 1 partitions and 550 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 550 / 550
Gaps: 2.94 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/3_mltree/P51798.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 7 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 / 79 / 6320
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -922847.643540] Initial branch length optimization
[00:00:03 -762555.848607] Model parameter optimization (eps = 10.000000)
[00:00:37 -759213.936557] AUTODETECT spr round 1 (radius: 5)
[00:02:20 -477143.959871] AUTODETECT spr round 2 (radius: 10)
[00:04:35 -339514.361910] AUTODETECT spr round 3 (radius: 15)
[00:06:31 -278550.309280] AUTODETECT spr round 4 (radius: 20)
[00:08:42 -239888.373620] AUTODETECT spr round 5 (radius: 25)
[00:11:13 -235446.370280] SPR radius for FAST iterations: 25 (autodetect)
[00:11:13 -235446.370280] Model parameter optimization (eps = 3.000000)
[00:11:37 -235200.310191] FAST spr round 1 (radius: 25)
[00:13:33 -204675.448746] FAST spr round 2 (radius: 25)
[00:15:09 -203710.307375] FAST spr round 3 (radius: 25)
[00:16:36 -203608.515973] FAST spr round 4 (radius: 25)
[00:17:55 -203605.885702] FAST spr round 5 (radius: 25)
[00:19:12 -203605.885688] Model parameter optimization (eps = 1.000000)
[00:19:24 -203594.466084] SLOW spr round 1 (radius: 5)
[00:21:09 -203554.552422] SLOW spr round 2 (radius: 5)
[00:22:49 -203554.309957] SLOW spr round 3 (radius: 5)
[00:24:27 -203554.308690] SLOW spr round 4 (radius: 10)
[00:26:05 -203552.400467] SLOW spr round 5 (radius: 5)
[00:28:03 -203549.557197] SLOW spr round 6 (radius: 5)
[00:29:48 -203549.557166] SLOW spr round 7 (radius: 10)
[00:31:28 -203549.557166] SLOW spr round 8 (radius: 15)
[00:33:47 -203549.557166] SLOW spr round 9 (radius: 20)
[00:37:07 -203549.557166] SLOW spr round 10 (radius: 25)
[00:41:20 -203549.557166] Model parameter optimization (eps = 0.100000)

[00:41:24] ML tree search #1, logLikelihood: -203549.518343

[00:41:24 -924353.986881] Initial branch length optimization
[00:41:27 -768948.636090] Model parameter optimization (eps = 10.000000)
[00:41:54 -765609.353900] AUTODETECT spr round 1 (radius: 5)
[00:43:37 -476358.780658] AUTODETECT spr round 2 (radius: 10)
[00:45:46 -337642.234482] AUTODETECT spr round 3 (radius: 15)
[00:47:48 -265300.476452] AUTODETECT spr round 4 (radius: 20)
[00:50:05 -239830.295500] AUTODETECT spr round 5 (radius: 25)
[00:52:19 -235298.249512] SPR radius for FAST iterations: 25 (autodetect)
[00:52:19 -235298.249512] Model parameter optimization (eps = 3.000000)
[00:52:39 -235052.196373] FAST spr round 1 (radius: 25)
[00:54:34 -204809.056476] FAST spr round 2 (radius: 25)
[00:56:10 -203685.312918] FAST spr round 3 (radius: 25)
[00:57:39 -203619.783759] FAST spr round 4 (radius: 25)
[00:59:00 -203618.501539] FAST spr round 5 (radius: 25)
[01:00:19 -203618.501537] Model parameter optimization (eps = 1.000000)
[01:00:34 -203607.452529] SLOW spr round 1 (radius: 5)
[01:02:19 -203569.334302] SLOW spr round 2 (radius: 5)
[01:04:01 -203563.755936] SLOW spr round 3 (radius: 5)
[01:05:42 -203563.755864] SLOW spr round 4 (radius: 10)
[01:07:23 -203555.688703] SLOW spr round 5 (radius: 5)
[01:09:25 -203547.405597] SLOW spr round 6 (radius: 5)
[01:11:15 -203540.821934] SLOW spr round 7 (radius: 5)
[01:12:56 -203539.030016] SLOW spr round 8 (radius: 5)
[01:14:35 -203538.371219] SLOW spr round 9 (radius: 5)
[01:16:12 -203538.371196] SLOW spr round 10 (radius: 10)
[01:17:50 -203538.371195] SLOW spr round 11 (radius: 15)
[01:20:13 -203538.371195] SLOW spr round 12 (radius: 20)
[01:23:38 -203538.371195] SLOW spr round 13 (radius: 25)
[01:27:52 -203538.371195] Model parameter optimization (eps = 0.100000)

[01:27:57] ML tree search #2, logLikelihood: -203538.320814

[01:27:57 -925656.694198] Initial branch length optimization
[01:28:01 -767179.654921] Model parameter optimization (eps = 10.000000)
[01:28:26 -763765.134770] AUTODETECT spr round 1 (radius: 5)
[01:30:11 -481662.172651] AUTODETECT spr round 2 (radius: 10)
[01:32:10 -353736.496023] AUTODETECT spr round 3 (radius: 15)
[01:34:09 -289015.101518] AUTODETECT spr round 4 (radius: 20)
[01:36:23 -256339.985850] AUTODETECT spr round 5 (radius: 25)
[01:38:48 -246830.761745] SPR radius for FAST iterations: 25 (autodetect)
[01:38:48 -246830.761745] Model parameter optimization (eps = 3.000000)
[01:38:55 -246821.117932] FAST spr round 1 (radius: 25)
[01:41:01 -205875.690530] FAST spr round 2 (radius: 25)
[01:42:37 -203878.298635] FAST spr round 3 (radius: 25)
[01:44:05 -203785.330843] FAST spr round 4 (radius: 25)
[01:45:26 -203775.523325] FAST spr round 5 (radius: 25)
[01:46:44 -203775.523294] Model parameter optimization (eps = 1.000000)
[01:46:55 -203580.473303] SLOW spr round 1 (radius: 5)
[01:48:39 -203527.544334] SLOW spr round 2 (radius: 5)
[01:50:20 -203523.685549] SLOW spr round 3 (radius: 5)
[01:51:57 -203523.685481] SLOW spr round 4 (radius: 10)
[01:53:36 -203523.685480] SLOW spr round 5 (radius: 15)
[01:56:01 -203523.685480] SLOW spr round 6 (radius: 20)
[01:59:31 -203523.685479] SLOW spr round 7 (radius: 25)
[02:03:54 -203523.685479] Model parameter optimization (eps = 0.100000)

[02:04:08] ML tree search #3, logLikelihood: -203520.653267

[02:04:08 -926275.221645] Initial branch length optimization
[02:04:11 -770005.046272] Model parameter optimization (eps = 10.000000)
[02:04:43 -766741.940020] AUTODETECT spr round 1 (radius: 5)
[02:06:28 -495337.155993] AUTODETECT spr round 2 (radius: 10)
[02:08:25 -356398.253276] AUTODETECT spr round 3 (radius: 15)
[02:10:22 -286064.408914] AUTODETECT spr round 4 (radius: 20)
[02:12:33 -263560.659935] AUTODETECT spr round 5 (radius: 25)
[02:15:18 -244557.116775] SPR radius for FAST iterations: 25 (autodetect)
[02:15:18 -244557.116775] Model parameter optimization (eps = 3.000000)
[02:15:41 -244326.803621] FAST spr round 1 (radius: 25)
[02:17:39 -205510.133445] FAST spr round 2 (radius: 25)
[02:19:16 -203715.338048] FAST spr round 3 (radius: 25)
[02:20:44 -203626.797184] FAST spr round 4 (radius: 25)
[02:22:06 -203620.775646] FAST spr round 5 (radius: 25)
[02:23:25 -203613.949716] FAST spr round 6 (radius: 25)
[02:24:42 -203613.949712] Model parameter optimization (eps = 1.000000)
[02:24:55 -203590.691215] SLOW spr round 1 (radius: 5)
[02:26:38 -203536.954063] SLOW spr round 2 (radius: 5)
[02:28:18 -203531.090321] SLOW spr round 3 (radius: 5)
[02:29:54 -203531.090059] SLOW spr round 4 (radius: 10)
[02:31:33 -203531.090057] SLOW spr round 5 (radius: 15)
[02:33:59 -203531.090057] SLOW spr round 6 (radius: 20)
[02:37:19 -203531.090057] SLOW spr round 7 (radius: 25)
[02:41:27 -203531.090057] Model parameter optimization (eps = 0.100000)

[02:41:35] ML tree search #4, logLikelihood: -203530.883987

[02:41:35 -928431.938191] Initial branch length optimization
[02:41:38 -772108.664494] Model parameter optimization (eps = 10.000000)
[02:42:06 -768788.612009] AUTODETECT spr round 1 (radius: 5)
[02:43:49 -479903.108135] AUTODETECT spr round 2 (radius: 10)
[02:45:45 -349460.661768] AUTODETECT spr round 3 (radius: 15)
[02:47:46 -290812.744554] AUTODETECT spr round 4 (radius: 20)
[02:50:10 -255911.798287] AUTODETECT spr round 5 (radius: 25)
[02:52:57 -246209.634287] SPR radius for FAST iterations: 25 (autodetect)
[02:52:57 -246209.634287] Model parameter optimization (eps = 3.000000)
[02:53:14 -246011.462559] FAST spr round 1 (radius: 25)
[02:55:06 -205488.608192] FAST spr round 2 (radius: 25)
[02:56:43 -203799.092447] FAST spr round 3 (radius: 25)
[02:58:10 -203636.243614] FAST spr round 4 (radius: 25)
[02:59:30 -203625.689597] FAST spr round 5 (radius: 25)
[03:00:47 -203625.689491] Model parameter optimization (eps = 1.000000)
[03:01:02 -203604.133652] SLOW spr round 1 (radius: 5)
[03:02:45 -203549.843061] SLOW spr round 2 (radius: 5)
[03:04:23 -203549.371231] SLOW spr round 3 (radius: 5)
[03:05:59 -203549.371162] SLOW spr round 4 (radius: 10)
[03:07:36 -203549.371161] SLOW spr round 5 (radius: 15)
[03:10:00 -203549.371161] SLOW spr round 6 (radius: 20)
[03:13:23 -203549.371161] SLOW spr round 7 (radius: 25)
[03:17:35 -203549.371161] Model parameter optimization (eps = 0.100000)

[03:17:40] ML tree search #5, logLikelihood: -203549.294313

[03:17:40 -921018.864342] Initial branch length optimization
[03:17:44 -765538.668848] Model parameter optimization (eps = 10.000000)
[03:18:11 -762133.177022] AUTODETECT spr round 1 (radius: 5)
[03:19:55 -479529.319704] AUTODETECT spr round 2 (radius: 10)
[03:21:52 -339683.131250] AUTODETECT spr round 3 (radius: 15)
[03:23:49 -271470.651866] AUTODETECT spr round 4 (radius: 20)
[03:25:55 -240466.106376] AUTODETECT spr round 5 (radius: 25)
[03:28:13 -236431.434600] SPR radius for FAST iterations: 25 (autodetect)
[03:28:13 -236431.434600] Model parameter optimization (eps = 3.000000)
[03:28:32 -236245.184331] FAST spr round 1 (radius: 25)
[03:30:32 -205098.718723] FAST spr round 2 (radius: 25)
[03:32:12 -203654.722471] FAST spr round 3 (radius: 25)
[03:33:42 -203581.923848] FAST spr round 4 (radius: 25)
[03:35:01 -203581.923025] Model parameter optimization (eps = 1.000000)
[03:35:15 -203572.602414] SLOW spr round 1 (radius: 5)
[03:37:05 -203553.775846] SLOW spr round 2 (radius: 5)
[03:38:45 -203545.223211] SLOW spr round 3 (radius: 5)
[03:40:25 -203544.206590] SLOW spr round 4 (radius: 5)
[03:42:02 -203544.206523] SLOW spr round 5 (radius: 10)
[03:43:40 -203541.187332] SLOW spr round 6 (radius: 5)
[03:45:38 -203537.524862] SLOW spr round 7 (radius: 5)
[03:47:23 -203537.524846] SLOW spr round 8 (radius: 10)
[03:49:03 -203537.481406] SLOW spr round 9 (radius: 15)
[03:51:23 -203537.481401] SLOW spr round 10 (radius: 20)
[03:54:51 -203537.481401] SLOW spr round 11 (radius: 25)
[03:59:08 -203537.481401] Model parameter optimization (eps = 0.100000)

[03:59:19] ML tree search #6, logLikelihood: -203536.907300

[03:59:19 -925190.432503] Initial branch length optimization
[03:59:22 -766669.261252] Model parameter optimization (eps = 10.000000)
[03:59:53 -763275.038821] AUTODETECT spr round 1 (radius: 5)
[04:01:38 -487544.449839] AUTODETECT spr round 2 (radius: 10)
[04:03:34 -363608.983534] AUTODETECT spr round 3 (radius: 15)
[04:05:40 -290684.321985] AUTODETECT spr round 4 (radius: 20)
[04:07:48 -248664.060800] AUTODETECT spr round 5 (radius: 25)
[04:10:21 -245311.256492] SPR radius for FAST iterations: 25 (autodetect)
[04:10:21 -245311.256492] Model parameter optimization (eps = 3.000000)
[04:10:38 -245083.834365] FAST spr round 1 (radius: 25)
[04:12:36 -205914.571055] FAST spr round 2 (radius: 25)
[04:14:10 -203750.627432] FAST spr round 3 (radius: 25)
[04:15:35 -203606.235449] FAST spr round 4 (radius: 25)
[04:16:55 -203589.374819] FAST spr round 5 (radius: 25)
[04:18:12 -203589.374635] Model parameter optimization (eps = 1.000000)
[04:18:26 -203584.095904] SLOW spr round 1 (radius: 5)
[04:20:08 -203544.084845] SLOW spr round 2 (radius: 5)
[04:21:48 -203538.279938] SLOW spr round 3 (radius: 5)
[04:23:24 -203537.487940] SLOW spr round 4 (radius: 5)
[04:25:00 -203537.487900] SLOW spr round 5 (radius: 10)
[04:26:37 -203537.487900] SLOW spr round 6 (radius: 15)
[04:29:01 -203537.487899] SLOW spr round 7 (radius: 20)
[04:32:20 -203537.487899] SLOW spr round 8 (radius: 25)
[04:36:42 -203537.487899] Model parameter optimization (eps = 0.100000)

[04:36:49] ML tree search #7, logLikelihood: -203537.379681

[04:36:49 -929462.219104] Initial branch length optimization
[04:36:52 -768662.913550] Model parameter optimization (eps = 10.000000)
[04:37:25 -765235.175464] AUTODETECT spr round 1 (radius: 5)
[04:39:06 -484163.296374] AUTODETECT spr round 2 (radius: 10)
[04:41:03 -341017.960109] AUTODETECT spr round 3 (radius: 15)
[04:43:02 -298534.508323] AUTODETECT spr round 4 (radius: 20)
[04:45:28 -262452.382269] AUTODETECT spr round 5 (radius: 25)
[04:47:51 -247864.139529] SPR radius for FAST iterations: 25 (autodetect)
[04:47:51 -247864.139529] Model parameter optimization (eps = 3.000000)
[04:48:13 -247618.899665] FAST spr round 1 (radius: 25)
[04:50:16 -205152.043514] FAST spr round 2 (radius: 25)
[04:51:48 -203722.348051] FAST spr round 3 (radius: 25)
[04:53:12 -203667.611371] FAST spr round 4 (radius: 25)
[04:54:32 -203647.831495] FAST spr round 5 (radius: 25)
[04:55:49 -203613.355880] FAST spr round 6 (radius: 25)
[04:57:05 -203613.355870] Model parameter optimization (eps = 1.000000)
[04:57:19 -203577.791053] SLOW spr round 1 (radius: 5)
[04:59:01 -203542.264187] SLOW spr round 2 (radius: 5)
[05:00:36 -203542.264117] SLOW spr round 3 (radius: 10)
[05:02:13 -203542.264116] SLOW spr round 4 (radius: 15)
[05:04:36 -203542.264116] SLOW spr round 5 (radius: 20)
[05:07:59 -203542.264116] SLOW spr round 6 (radius: 25)
[05:12:05 -203542.264116] Model parameter optimization (eps = 0.100000)

[05:12:09] ML tree search #8, logLikelihood: -203542.257015

[05:12:09 -923217.862092] Initial branch length optimization
[05:12:13 -764972.764033] Model parameter optimization (eps = 10.000000)
[05:12:40 -761626.878071] AUTODETECT spr round 1 (radius: 5)
[05:14:19 -480158.710977] AUTODETECT spr round 2 (radius: 10)
[05:16:14 -356299.210004] AUTODETECT spr round 3 (radius: 15)
[05:18:18 -286943.354326] AUTODETECT spr round 4 (radius: 20)
[05:20:27 -254355.840186] AUTODETECT spr round 5 (radius: 25)
[05:22:57 -242211.244130] SPR radius for FAST iterations: 25 (autodetect)
[05:22:57 -242211.244130] Model parameter optimization (eps = 3.000000)
[05:23:22 -241984.305051] FAST spr round 1 (radius: 25)
[05:25:18 -205865.423242] FAST spr round 2 (radius: 25)
[05:26:55 -203854.168346] FAST spr round 3 (radius: 25)
[05:28:20 -203672.351212] FAST spr round 4 (radius: 25)
[05:29:41 -203581.973192] FAST spr round 5 (radius: 25)
[05:30:59 -203581.444530] FAST spr round 6 (radius: 25)
[05:32:15 -203581.336334] FAST spr round 7 (radius: 25)
[05:33:30 -203581.336155] Model parameter optimization (eps = 1.000000)
[05:33:43 -203567.413567] SLOW spr round 1 (radius: 5)
[05:35:23 -203538.556786] SLOW spr round 2 (radius: 5)
[05:37:01 -203535.690084] SLOW spr round 3 (radius: 5)
[05:38:35 -203535.690004] SLOW spr round 4 (radius: 10)
[05:40:12 -203535.301384] SLOW spr round 5 (radius: 5)
[05:42:06 -203535.301367] SLOW spr round 6 (radius: 10)
[05:43:52 -203535.301367] SLOW spr round 7 (radius: 15)
[05:46:07 -203535.301367] SLOW spr round 8 (radius: 20)
[05:49:32 -203535.301367] SLOW spr round 9 (radius: 25)
[05:53:45 -203535.301367] Model parameter optimization (eps = 0.100000)

[05:53:50] ML tree search #9, logLikelihood: -203535.261839

[05:53:50 -926025.617155] Initial branch length optimization
[05:53:54 -770194.908096] Model parameter optimization (eps = 10.000000)
[05:54:20 -766862.154612] AUTODETECT spr round 1 (radius: 5)
[05:56:01 -477430.319224] AUTODETECT spr round 2 (radius: 10)
[05:57:56 -351637.046553] AUTODETECT spr round 3 (radius: 15)
[05:59:53 -299776.894246] AUTODETECT spr round 4 (radius: 20)
[06:02:03 -261157.227259] AUTODETECT spr round 5 (radius: 25)
[06:04:57 -248309.014205] SPR radius for FAST iterations: 25 (autodetect)
[06:04:57 -248309.014205] Model parameter optimization (eps = 3.000000)
[06:05:15 -248059.818048] FAST spr round 1 (radius: 25)
[06:07:14 -204815.224097] FAST spr round 2 (radius: 25)
[06:08:50 -203764.693717] FAST spr round 3 (radius: 25)
[06:10:17 -203637.590548] FAST spr round 4 (radius: 25)
[06:11:37 -203624.474615] FAST spr round 5 (radius: 25)
[06:12:54 -203624.474569] Model parameter optimization (eps = 1.000000)
[06:13:07 -203605.328704] SLOW spr round 1 (radius: 5)
[06:14:52 -203556.429606] SLOW spr round 2 (radius: 5)
[06:16:33 -203543.473257] SLOW spr round 3 (radius: 5)
[06:18:10 -203543.472699] SLOW spr round 4 (radius: 10)
[06:19:47 -203543.472688] SLOW spr round 5 (radius: 15)
[06:22:16 -203543.472687] SLOW spr round 6 (radius: 20)
[06:25:46 -203543.472687] SLOW spr round 7 (radius: 25)
[06:30:08 -203543.472686] Model parameter optimization (eps = 0.100000)

[06:30:15] ML tree search #10, logLikelihood: -203543.346344

[06:30:16 -926718.875392] Initial branch length optimization
[06:30:19 -764936.480882] Model parameter optimization (eps = 10.000000)
[06:30:55 -761480.538071] AUTODETECT spr round 1 (radius: 5)
[06:32:38 -486671.348031] AUTODETECT spr round 2 (radius: 10)
[06:34:37 -348988.240141] AUTODETECT spr round 3 (radius: 15)
[06:36:39 -292920.696596] AUTODETECT spr round 4 (radius: 20)
[06:38:53 -266245.870690] AUTODETECT spr round 5 (radius: 25)
[06:41:36 -254271.865641] SPR radius for FAST iterations: 25 (autodetect)
[06:41:36 -254271.865641] Model parameter optimization (eps = 3.000000)
[06:41:43 -254260.412237] FAST spr round 1 (radius: 25)
[06:43:42 -205675.506520] FAST spr round 2 (radius: 25)
[06:45:19 -203979.990839] FAST spr round 3 (radius: 25)
[06:46:46 -203892.441450] FAST spr round 4 (radius: 25)
[06:48:06 -203880.114245] FAST spr round 5 (radius: 25)
[06:49:23 -203880.114000] Model parameter optimization (eps = 1.000000)
[06:49:36 -203630.505878] SLOW spr round 1 (radius: 5)
[06:51:19 -203553.743495] SLOW spr round 2 (radius: 5)
[06:52:59 -203549.863307] SLOW spr round 3 (radius: 5)
[06:54:35 -203549.364773] SLOW spr round 4 (radius: 5)
[06:56:10 -203549.364771] SLOW spr round 5 (radius: 10)
[06:57:46 -203549.364770] SLOW spr round 6 (radius: 15)
[07:00:07 -203549.364770] SLOW spr round 7 (radius: 20)
[07:03:23 -203549.364769] SLOW spr round 8 (radius: 25)
[07:07:26 -203549.364769] Model parameter optimization (eps = 0.100000)

[07:07:37] ML tree search #11, logLikelihood: -203548.098246

[07:07:37 -930796.067212] Initial branch length optimization
[07:07:40 -771278.544519] Model parameter optimization (eps = 10.000000)
[07:08:05 -767767.148357] AUTODETECT spr round 1 (radius: 5)
[07:09:50 -479256.383812] AUTODETECT spr round 2 (radius: 10)
[07:11:49 -344307.381173] AUTODETECT spr round 3 (radius: 15)
[07:13:57 -267229.021443] AUTODETECT spr round 4 (radius: 20)
[07:16:08 -248033.790706] AUTODETECT spr round 5 (radius: 25)
[07:18:44 -238159.497787] SPR radius for FAST iterations: 25 (autodetect)
[07:18:44 -238159.497787] Model parameter optimization (eps = 3.000000)
[07:19:00 -237924.468709] FAST spr round 1 (radius: 25)
[07:21:01 -204920.420102] FAST spr round 2 (radius: 25)
[07:22:38 -203694.850600] FAST spr round 3 (radius: 25)
[07:24:07 -203613.332180] FAST spr round 4 (radius: 25)
[07:25:28 -203607.209773] FAST spr round 5 (radius: 25)
[07:26:50 -203595.962220] FAST spr round 6 (radius: 25)
[07:28:06 -203595.962211] Model parameter optimization (eps = 1.000000)
[07:28:18 -203585.379963] SLOW spr round 1 (radius: 5)
[07:30:01 -203546.155984] SLOW spr round 2 (radius: 5)
[07:31:44 -203536.052466] SLOW spr round 3 (radius: 5)
[07:33:22 -203536.040435] SLOW spr round 4 (radius: 10)
[07:35:00 -203536.040190] SLOW spr round 5 (radius: 15)
[07:37:27 -203536.040184] SLOW spr round 6 (radius: 20)
[07:40:54 -203536.040183] SLOW spr round 7 (radius: 25)
[07:45:17 -203536.040183] Model parameter optimization (eps = 0.100000)

[07:45:26] ML tree search #12, logLikelihood: -203535.712482

[07:45:26 -929687.348438] Initial branch length optimization
[07:45:29 -774346.984071] Model parameter optimization (eps = 10.000000)
[07:45:58 -770859.758756] AUTODETECT spr round 1 (radius: 5)
[07:47:41 -474622.939928] AUTODETECT spr round 2 (radius: 10)
[07:49:38 -350397.642732] AUTODETECT spr round 3 (radius: 15)
[07:51:39 -290366.794645] AUTODETECT spr round 4 (radius: 20)
[07:54:02 -245911.164266] AUTODETECT spr round 5 (radius: 25)
[07:56:59 -239126.553116] SPR radius for FAST iterations: 25 (autodetect)
[07:56:59 -239126.553116] Model parameter optimization (eps = 3.000000)
[07:57:17 -238867.210404] FAST spr round 1 (radius: 25)
[07:59:18 -204992.899985] FAST spr round 2 (radius: 25)
[08:00:55 -203642.406428] FAST spr round 3 (radius: 25)
[08:02:26 -203593.579540] FAST spr round 4 (radius: 25)
[08:03:46 -203582.465635] FAST spr round 5 (radius: 25)
[08:05:03 -203582.465570] Model parameter optimization (eps = 1.000000)
[08:05:17 -203574.593337] SLOW spr round 1 (radius: 5)
[08:07:02 -203543.606409] SLOW spr round 2 (radius: 5)
[08:08:42 -203541.687303] SLOW spr round 3 (radius: 5)
[08:10:18 -203541.687199] SLOW spr round 4 (radius: 10)
[08:11:55 -203539.033174] SLOW spr round 5 (radius: 5)
[08:13:51 -203536.955409] SLOW spr round 6 (radius: 5)
[08:15:36 -203536.955370] SLOW spr round 7 (radius: 10)
[08:17:17 -203534.353147] SLOW spr round 8 (radius: 5)
[08:19:13 -203532.514523] SLOW spr round 9 (radius: 5)
[08:20:58 -203532.514480] SLOW spr round 10 (radius: 10)
[08:22:37 -203532.514480] SLOW spr round 11 (radius: 15)
[08:24:57 -203532.514480] SLOW spr round 12 (radius: 20)
[08:28:23 -203532.514480] SLOW spr round 13 (radius: 25)
[08:32:35 -203532.514480] Model parameter optimization (eps = 0.100000)

[08:32:40] ML tree search #13, logLikelihood: -203532.446105

[08:32:41 -922075.451087] Initial branch length optimization
[08:32:44 -762405.333617] Model parameter optimization (eps = 10.000000)
[08:33:09 -758868.641159] AUTODETECT spr round 1 (radius: 5)
[08:34:50 -471853.407893] AUTODETECT spr round 2 (radius: 10)
[08:36:48 -336616.142117] AUTODETECT spr round 3 (radius: 15)
[08:38:42 -271438.398428] AUTODETECT spr round 4 (radius: 20)
[08:40:50 -244383.378676] AUTODETECT spr round 5 (radius: 25)
[08:43:06 -240988.189195] SPR radius for FAST iterations: 25 (autodetect)
[08:43:06 -240988.189195] Model parameter optimization (eps = 3.000000)
[08:43:14 -240974.331998] FAST spr round 1 (radius: 25)
[08:45:10 -205576.134545] FAST spr round 2 (radius: 25)
[08:46:44 -203896.067203] FAST spr round 3 (radius: 25)
[08:48:10 -203846.144662] FAST spr round 4 (radius: 25)
[08:49:28 -203843.730907] FAST spr round 5 (radius: 25)
[08:50:44 -203843.730876] Model parameter optimization (eps = 1.000000)
[08:50:57 -203638.915513] SLOW spr round 1 (radius: 5)
[08:52:40 -203541.024906] SLOW spr round 2 (radius: 5)
[08:54:18 -203536.997199] SLOW spr round 3 (radius: 5)
[08:55:53 -203536.997142] SLOW spr round 4 (radius: 10)
[08:57:29 -203536.997141] SLOW spr round 5 (radius: 15)
[08:59:51 -203536.997140] SLOW spr round 6 (radius: 20)
[09:03:09 -203536.997140] SLOW spr round 7 (radius: 25)
[09:07:21 -203536.997139] Model parameter optimization (eps = 0.100000)

[09:07:30] ML tree search #14, logLikelihood: -203535.508581

[09:07:30 -930348.843903] Initial branch length optimization
[09:07:34 -771535.952674] Model parameter optimization (eps = 10.000000)
[09:08:03 -768174.346844] AUTODETECT spr round 1 (radius: 5)
[09:09:45 -490449.713097] AUTODETECT spr round 2 (radius: 10)
[09:11:42 -344191.756490] AUTODETECT spr round 3 (radius: 15)
[09:13:40 -279298.146039] AUTODETECT spr round 4 (radius: 20)
[09:15:44 -265897.948390] AUTODETECT spr round 5 (radius: 25)
[09:17:56 -246461.596093] SPR radius for FAST iterations: 25 (autodetect)
[09:17:56 -246461.596093] Model parameter optimization (eps = 3.000000)
[09:18:20 -246227.295427] FAST spr round 1 (radius: 25)
[09:20:20 -206773.559687] FAST spr round 2 (radius: 25)
[09:21:56 -203851.517104] FAST spr round 3 (radius: 25)
[09:23:26 -203654.475829] FAST spr round 4 (radius: 25)
[09:24:50 -203607.600084] FAST spr round 5 (radius: 25)
[09:26:08 -203603.419975] FAST spr round 6 (radius: 25)
[09:27:25 -203603.419929] Model parameter optimization (eps = 1.000000)
[09:27:40 -203592.971333] SLOW spr round 1 (radius: 5)
[09:29:25 -203554.960767] SLOW spr round 2 (radius: 5)
[09:31:02 -203550.717915] SLOW spr round 3 (radius: 5)
[09:32:37 -203550.717837] SLOW spr round 4 (radius: 10)
[09:34:15 -203548.510549] SLOW spr round 5 (radius: 5)
[09:36:11 -203547.149859] SLOW spr round 6 (radius: 5)
[09:37:56 -203545.664236] SLOW spr round 7 (radius: 5)
[09:39:35 -203545.664143] SLOW spr round 8 (radius: 10)
[09:41:13 -203545.664143] SLOW spr round 9 (radius: 15)
[09:43:36 -203545.664143] SLOW spr round 10 (radius: 20)
[09:46:56 -203545.664143] SLOW spr round 11 (radius: 25)
[09:51:05 -203545.664143] Model parameter optimization (eps = 0.100000)

[09:51:13] ML tree search #15, logLikelihood: -203545.344914

[09:51:13 -927199.526944] Initial branch length optimization
[09:51:17 -769033.935162] Model parameter optimization (eps = 10.000000)
[09:51:45 -765756.510834] AUTODETECT spr round 1 (radius: 5)
[09:53:26 -498364.575349] AUTODETECT spr round 2 (radius: 10)
[09:55:24 -343761.279524] AUTODETECT spr round 3 (radius: 15)
[09:57:19 -286896.209913] AUTODETECT spr round 4 (radius: 20)
[09:59:31 -252557.821204] AUTODETECT spr round 5 (radius: 25)
[10:01:59 -247282.450800] SPR radius for FAST iterations: 25 (autodetect)
[10:01:59 -247282.450800] Model parameter optimization (eps = 3.000000)
[10:02:23 -247008.264747] FAST spr round 1 (radius: 25)
[10:04:20 -205591.895370] FAST spr round 2 (radius: 25)
[10:05:55 -203721.499115] FAST spr round 3 (radius: 25)
[10:07:25 -203604.362839] FAST spr round 4 (radius: 25)
[10:08:47 -203584.907240] FAST spr round 5 (radius: 25)
[10:10:05 -203583.436869] FAST spr round 6 (radius: 25)
[10:11:22 -203583.436843] Model parameter optimization (eps = 1.000000)
[10:11:35 -203563.938267] SLOW spr round 1 (radius: 5)
[10:13:17 -203518.571534] SLOW spr round 2 (radius: 5)
[10:14:57 -203514.747022] SLOW spr round 3 (radius: 5)
[10:16:32 -203514.746943] SLOW spr round 4 (radius: 10)
[10:18:10 -203514.746941] SLOW spr round 5 (radius: 15)
[10:20:37 -203514.746941] SLOW spr round 6 (radius: 20)
[10:24:04 -203514.746941] SLOW spr round 7 (radius: 25)
[10:28:30 -203514.746940] Model parameter optimization (eps = 0.100000)

[10:28:34] ML tree search #16, logLikelihood: -203514.733542

[10:28:34 -928032.292157] Initial branch length optimization
[10:28:37 -770464.054722] Model parameter optimization (eps = 10.000000)
[10:29:02 -767158.166071] AUTODETECT spr round 1 (radius: 5)
[10:30:45 -480692.703241] AUTODETECT spr round 2 (radius: 10)
[10:32:42 -345977.493606] AUTODETECT spr round 3 (radius: 15)
[10:34:39 -290108.000574] AUTODETECT spr round 4 (radius: 20)
[10:36:57 -252779.775060] AUTODETECT spr round 5 (radius: 25)
[10:39:30 -247621.992182] SPR radius for FAST iterations: 25 (autodetect)
[10:39:30 -247621.992182] Model parameter optimization (eps = 3.000000)
[10:39:50 -247412.285456] FAST spr round 1 (radius: 25)
[10:41:49 -205568.948195] FAST spr round 2 (radius: 25)
[10:43:28 -203690.101247] FAST spr round 3 (radius: 25)
[10:44:59 -203588.860548] FAST spr round 4 (radius: 25)
[10:46:18 -203584.888262] FAST spr round 5 (radius: 25)
[10:47:37 -203577.211838] FAST spr round 6 (radius: 25)
[10:48:54 -203577.211708] Model parameter optimization (eps = 1.000000)
[10:49:10 -203567.891951] SLOW spr round 1 (radius: 5)
[10:50:47 -203536.220854] SLOW spr round 2 (radius: 5)
[10:52:27 -203533.394145] SLOW spr round 3 (radius: 5)
[10:54:04 -203531.449737] SLOW spr round 4 (radius: 5)
[10:55:41 -203531.449736] SLOW spr round 5 (radius: 10)
[10:57:20 -203531.449736] SLOW spr round 6 (radius: 15)
[10:59:26 -203531.449736] SLOW spr round 7 (radius: 20)
[11:02:19 -203531.449736] SLOW spr round 8 (radius: 25)
[11:06:37 -203531.449736] Model parameter optimization (eps = 0.100000)

[11:06:45] ML tree search #17, logLikelihood: -203531.253042

[11:06:45 -924153.701989] Initial branch length optimization
[11:06:48 -767254.685511] Model parameter optimization (eps = 10.000000)
[11:07:20 -763855.762684] AUTODETECT spr round 1 (radius: 5)
[11:09:05 -481284.765590] AUTODETECT spr round 2 (radius: 10)
[11:11:04 -345303.637818] AUTODETECT spr round 3 (radius: 15)
[11:13:03 -280190.214715] AUTODETECT spr round 4 (radius: 20)
[11:15:14 -245070.055768] AUTODETECT spr round 5 (radius: 25)
[11:17:41 -239954.846105] SPR radius for FAST iterations: 25 (autodetect)
[11:17:41 -239954.846105] Model parameter optimization (eps = 3.000000)
[11:18:04 -239726.776473] FAST spr round 1 (radius: 25)
[11:19:58 -204861.442409] FAST spr round 2 (radius: 25)
[11:21:29 -203650.610270] FAST spr round 3 (radius: 25)
[11:22:57 -203604.705901] FAST spr round 4 (radius: 25)
[11:24:18 -203601.726245] FAST spr round 5 (radius: 25)
[11:25:37 -203601.726232] Model parameter optimization (eps = 1.000000)
[11:25:50 -203587.212512] SLOW spr round 1 (radius: 5)
[11:27:35 -203529.057606] SLOW spr round 2 (radius: 5)
[11:29:17 -203520.863655] SLOW spr round 3 (radius: 5)
[11:30:56 -203518.831274] SLOW spr round 4 (radius: 5)
[11:32:34 -203518.831260] SLOW spr round 5 (radius: 10)
[11:34:13 -203517.622741] SLOW spr round 6 (radius: 5)
[11:36:09 -203517.622738] SLOW spr round 7 (radius: 10)
[11:37:57 -203517.622738] SLOW spr round 8 (radius: 15)
[11:40:14 -203517.622738] SLOW spr round 9 (radius: 20)
[11:43:44 -203517.622738] SLOW spr round 10 (radius: 25)
[11:48:04 -203517.622738] Model parameter optimization (eps = 0.100000)

[11:48:15] ML tree search #18, logLikelihood: -203516.775034

[11:48:15 -923629.486294] Initial branch length optimization
[11:48:18 -764609.475762] Model parameter optimization (eps = 10.000000)
[11:48:47 -761283.908017] AUTODETECT spr round 1 (radius: 5)
[11:50:32 -478824.786047] AUTODETECT spr round 2 (radius: 10)
[11:52:43 -357734.832610] AUTODETECT spr round 3 (radius: 15)
[11:54:47 -283063.797221] AUTODETECT spr round 4 (radius: 20)
[11:57:08 -251809.593343] AUTODETECT spr round 5 (radius: 25)
[11:59:45 -239293.852259] SPR radius for FAST iterations: 25 (autodetect)
[11:59:45 -239293.852259] Model parameter optimization (eps = 3.000000)
[12:00:08 -239052.885258] FAST spr round 1 (radius: 25)
[12:02:09 -204724.373345] FAST spr round 2 (radius: 25)
[12:03:45 -203723.082933] FAST spr round 3 (radius: 25)
[12:05:13 -203621.139521] FAST spr round 4 (radius: 25)
[12:06:36 -203607.324828] FAST spr round 5 (radius: 25)
[12:07:55 -203605.958830] FAST spr round 6 (radius: 25)
[12:09:13 -203605.958828] Model parameter optimization (eps = 1.000000)
[12:09:26 -203594.243880] SLOW spr round 1 (radius: 5)
[12:11:09 -203540.005927] SLOW spr round 2 (radius: 5)
[12:12:48 -203538.843976] SLOW spr round 3 (radius: 5)
[12:14:25 -203538.843972] SLOW spr round 4 (radius: 10)
[12:16:03 -203538.843972] SLOW spr round 5 (radius: 15)
[12:18:27 -203538.843971] SLOW spr round 6 (radius: 20)
[12:21:54 -203538.843971] SLOW spr round 7 (radius: 25)
[12:26:14 -203538.843971] Model parameter optimization (eps = 0.100000)

[12:26:25] ML tree search #19, logLikelihood: -203538.541844

[12:26:25 -924508.803171] Initial branch length optimization
[12:26:28 -764659.590490] Model parameter optimization (eps = 10.000000)
[12:26:55 -761291.017623] AUTODETECT spr round 1 (radius: 5)
[12:28:38 -481247.513537] AUTODETECT spr round 2 (radius: 10)
[12:30:38 -338041.869963] AUTODETECT spr round 3 (radius: 15)
[12:32:34 -277573.246613] AUTODETECT spr round 4 (radius: 20)
[12:35:15 -237331.910355] AUTODETECT spr round 5 (radius: 25)
[12:38:00 -235480.267057] SPR radius for FAST iterations: 25 (autodetect)
[12:38:00 -235480.267057] Model parameter optimization (eps = 3.000000)
[12:38:18 -235234.533706] FAST spr round 1 (radius: 25)
[12:40:22 -204528.315910] FAST spr round 2 (radius: 25)
[12:41:58 -203663.792711] FAST spr round 3 (radius: 25)
[12:43:25 -203601.214493] FAST spr round 4 (radius: 25)
[12:44:47 -203587.789244] FAST spr round 5 (radius: 25)
[12:46:06 -203585.050974] FAST spr round 6 (radius: 25)
[12:47:26 -203585.050971] Model parameter optimization (eps = 1.000000)
[12:47:39 -203564.339851] SLOW spr round 1 (radius: 5)
[12:49:23 -203524.352202] SLOW spr round 2 (radius: 5)
[12:51:04 -203524.021290] SLOW spr round 3 (radius: 5)
[12:52:44 -203524.021288] SLOW spr round 4 (radius: 10)
[12:54:23 -203524.021288] SLOW spr round 5 (radius: 15)
[12:56:52 -203524.021287] SLOW spr round 6 (radius: 20)
[13:00:19 -203524.021287] SLOW spr round 7 (radius: 25)
[13:04:36 -203524.021287] Model parameter optimization (eps = 0.100000)

[13:04:45] ML tree search #20, logLikelihood: -203523.896012


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.314317,0.586182) (0.349464,0.671048) (0.281836,1.545449) (0.054383,2.678839) 
   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: -203514.733542

AIC score: 411039.467083 / AICc score: 8455099.467083 / BIC score: 419680.853231
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=550).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 129 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/3_mltree/P51798.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/3_mltree/P51798.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/3_mltree/P51798.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/3_mltree/P51798.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51798/3_mltree/P51798.raxml.log

Analysis started: 02-Jul-2021 09:23:08 / finished: 02-Jul-2021 22:27:54

Elapsed time: 47085.348 seconds

Consumed energy: 4026.068 Wh (= 20 km in an electric car, or 101 km with an e-scooter!)