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 03-Jul-2021 20:31:55 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/2_msa/Q9UQE7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/3_mltree/Q9UQE7 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/2_msa/Q9UQE7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1168 sites

WARNING: Sequences tr_Q8AWB8_Q8AWB8_CHICK_9031 and tr_A0A218UUD8_A0A218UUD8_9PASE_299123 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and sp_Q5R4K5_SMC3_PONAB_9601 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_G1T0Q6_G1T0Q6_RABIT_9986 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_E2R7T4_E2R7T4_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_H2R1R2_H2R1R2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_W5PJ45_W5PJ45_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_H0WM80_H0WM80_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and sp_Q9UQE7_SMC3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_F2Z5G2_F2Z5G2_PIG_9823 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A7Z065_A7Z065_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_M3WDH5_M3WDH5_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A1U7SZ70_A0A1U7SZ70_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A1U7QCR4_A0A1U7QCR4_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2R9AH80_A0A2R9AH80_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2U3V0N4_A0A2U3V0N4_TURTR_9739 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2U3WQY7_A0A2U3WQY7_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2U3XWK0_A0A2U3XWK0_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2Y9DHS0_A0A2Y9DHS0_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2Y9J3U7_A0A2Y9J3U7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2Y9MU97_A0A2Y9MU97_DELLE_9749 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A2Y9F527_A0A2Y9F527_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A384BKK3_A0A384BKK3_URSMA_29073 are exactly identical!
WARNING: Sequences tr_M3XSK3_M3XSK3_MUSPF_9669 and tr_A0A383ZD68_A0A383ZD68_BALAS_310752 are exactly identical!
WARNING: Sequences tr_J3KF79_J3KF79_COCIM_246410 and tr_E9D886_E9D886_COCPS_443226 are exactly identical!
WARNING: Sequences tr_E9F0V1_E9F0V1_METRA_655844 and tr_A0A0D9NUV0_A0A0D9NUV0_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A1P6BLU6_A0A1P6BLU6_BRUMA_6279 and tr_A0A0R3QQ37_A0A0R3QQ37_9BILA_42155 are exactly identical!
WARNING: Sequences tr_G7X564_G7X564_ASPKW_1033177 and tr_A0A146FLY8_A0A146FLY8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_H0ZK70_H0ZK70_TAEGU_59729 and tr_U3JHY8_U3JHY8_FICAL_59894 are exactly identical!
WARNING: Sequences tr_G2YMY6_G2YMY6_BOTF4_999810 and tr_M7TQE3_M7TQE3_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_G3Y311_G3Y311_ASPNA_380704 and tr_A0A319AUB0_A0A319AUB0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7PDY3_G7PDY3_MACFA_9541 and tr_A0A096P0C9_A0A096P0C9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PDY3_G7PDY3_MACFA_9541 and tr_A0A0D9QYP0_A0A0D9QYP0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7PDY3_G7PDY3_MACFA_9541 and tr_A0A2K6AI75_A0A2K6AI75_MANLE_9568 are exactly identical!
WARNING: Sequences tr_W2Q3V9_W2Q3V9_PHYPN_761204 and tr_W2KZA9_W2KZA9_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015IBU8_A0A015IBU8_9GLOM_1432141 and tr_A0A2H5U1P0_A0A2H5U1P0_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0F8WMM7_A0A0F8WMM7_9EURO_308745 and tr_A0A2T5LTR2_A0A2T5LTR2_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A151NVY3_A0A151NVY3_ALLMI_8496 and tr_A0A226MX32_A0A226MX32_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A091JFH1_A0A091JFH1_EGRGA_188379 and tr_A0A091VRG0_A0A091VRG0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JFH1_A0A091JFH1_EGRGA_188379 and tr_A0A087QZF8_A0A087QZF8_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JFH1_A0A091JFH1_EGRGA_188379 and tr_A0A0A0A9A2_A0A0A0A9A2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091JFH1_A0A091JFH1_EGRGA_188379 and tr_A0A091HSD2_A0A091HSD2_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A093HKG6_A0A093HKG6_STRCA_441894 and tr_A0A091VDU4_A0A091VDU4_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A0V0UIX4_A0A0V0UIX4_9BILA_181606 and tr_A0A0V0UJD9_A0A0V0UJD9_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0Z461_A0A0V0Z461_9BILA_990121 and tr_A0A0V0T3J0_A0A0V0T3J0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A124BV09_A0A124BV09_ASPNG_5061 and tr_A0A1L9NAP3_A0A1L9NAP3_ASPTU_767770 are exactly identical!
WARNING: Duplicate sequences found: 45

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/Q9UQE7/3_mltree/Q9UQE7.raxml.reduced.phy

Alignment comprises 1 partitions and 1168 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1168 / 1168
Gaps: 12.74 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/3_mltree/Q9UQE7.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 / 146 / 11680
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1822785.788595] Initial branch length optimization
[00:00:06 -1557581.869922] Model parameter optimization (eps = 10.000000)
[00:00:41 -1554848.643543] AUTODETECT spr round 1 (radius: 5)
[00:03:26 -1147068.714112] AUTODETECT spr round 2 (radius: 10)
[00:06:31 -840071.407782] AUTODETECT spr round 3 (radius: 15)
[00:09:39 -718533.470113] AUTODETECT spr round 4 (radius: 20)
[00:13:07 -668149.635283] AUTODETECT spr round 5 (radius: 25)
[00:17:13 -663359.352036] SPR radius for FAST iterations: 25 (autodetect)
[00:17:13 -663359.352036] Model parameter optimization (eps = 3.000000)
[00:17:36 -663234.094507] FAST spr round 1 (radius: 25)
[00:21:44 -592353.277440] FAST spr round 2 (radius: 25)
[00:24:47 -588956.499990] FAST spr round 3 (radius: 25)
[00:27:18 -588523.579494] FAST spr round 4 (radius: 25)
[00:29:40 -588447.791765] FAST spr round 5 (radius: 25)
[00:31:53 -588446.523803] FAST spr round 6 (radius: 25)
[00:33:55 -588446.522988] Model parameter optimization (eps = 1.000000)
[00:34:12 -588442.326834] SLOW spr round 1 (radius: 5)
[00:36:59 -588304.471271] SLOW spr round 2 (radius: 5)
[00:39:47 -588289.863543] SLOW spr round 3 (radius: 5)
[00:42:28 -588289.860958] SLOW spr round 4 (radius: 10)
[00:45:28 -588289.860334] SLOW spr round 5 (radius: 15)
[00:51:09 -588288.605364] SLOW spr round 6 (radius: 5)
[00:54:50 -588288.604880] SLOW spr round 7 (radius: 10)
[00:58:20 -588288.604415] SLOW spr round 8 (radius: 15)
[01:03:35 -588288.603959] SLOW spr round 9 (radius: 20)
[01:11:57 -588288.603507] SLOW spr round 10 (radius: 25)
[01:22:33 -588288.603058] Model parameter optimization (eps = 0.100000)

[01:22:40] ML tree search #1, logLikelihood: -588288.584126

[01:22:40 -1821804.180023] Initial branch length optimization
[01:22:47 -1553742.324584] Model parameter optimization (eps = 10.000000)
[01:23:19 -1551186.731020] AUTODETECT spr round 1 (radius: 5)
[01:25:59 -1160976.112540] AUTODETECT spr round 2 (radius: 10)
[01:29:07 -833716.626204] AUTODETECT spr round 3 (radius: 15)
[01:32:20 -735076.222019] AUTODETECT spr round 4 (radius: 20)
[01:36:09 -671950.833610] AUTODETECT spr round 5 (radius: 25)
[01:39:55 -663021.387817] SPR radius for FAST iterations: 25 (autodetect)
[01:39:55 -663021.387817] Model parameter optimization (eps = 3.000000)
[01:40:15 -662913.249034] FAST spr round 1 (radius: 25)
[01:44:40 -591349.655035] FAST spr round 2 (radius: 25)
[01:47:52 -588700.602203] FAST spr round 3 (radius: 25)
[01:50:38 -588450.934272] FAST spr round 4 (radius: 25)
[01:52:55 -588425.519256] FAST spr round 5 (radius: 25)
[01:55:04 -588422.314741] FAST spr round 6 (radius: 25)
[01:57:05 -588422.314348] Model parameter optimization (eps = 1.000000)
[01:57:20 -588416.680131] SLOW spr round 1 (radius: 5)
[02:00:15 -588295.881995] SLOW spr round 2 (radius: 5)
[02:02:52 -588287.462078] SLOW spr round 3 (radius: 5)
[02:05:05 -588287.457750] SLOW spr round 4 (radius: 10)
[02:07:35 -588287.457364] SLOW spr round 5 (radius: 15)
[02:12:19 -588285.913095] SLOW spr round 6 (radius: 5)
[02:15:22 -588285.911795] SLOW spr round 7 (radius: 10)
[02:18:20 -588285.911408] SLOW spr round 8 (radius: 15)
[02:22:48 -588285.911175] SLOW spr round 9 (radius: 20)
[02:31:09 -588285.910989] SLOW spr round 10 (radius: 25)
[02:42:35 -588285.910818] Model parameter optimization (eps = 0.100000)

[02:42:45] ML tree search #2, logLikelihood: -588285.228106

[02:42:45 -1819941.084047] Initial branch length optimization
[02:42:51 -1556258.137161] Model parameter optimization (eps = 10.000000)
[02:43:26 -1553668.576936] AUTODETECT spr round 1 (radius: 5)
[02:46:15 -1150109.421215] AUTODETECT spr round 2 (radius: 10)
[02:49:27 -870991.980936] AUTODETECT spr round 3 (radius: 15)
[02:52:56 -727543.415744] AUTODETECT spr round 4 (radius: 20)
[02:56:34 -669288.837601] AUTODETECT spr round 5 (radius: 25)
[03:01:00 -658222.623643] SPR radius for FAST iterations: 25 (autodetect)
[03:01:00 -658222.623643] Model parameter optimization (eps = 3.000000)
[03:01:22 -658098.960157] FAST spr round 1 (radius: 25)
[03:05:31 -590507.792812] FAST spr round 2 (radius: 25)
[03:08:51 -588574.780876] FAST spr round 3 (radius: 25)
[03:11:39 -588428.418368] FAST spr round 4 (radius: 25)
[03:13:57 -588427.397561] FAST spr round 5 (radius: 25)
[03:16:56 -588426.301992] FAST spr round 6 (radius: 25)
[03:20:41 -588426.301486] Model parameter optimization (eps = 1.000000)
[03:20:59 -588425.161473] SLOW spr round 1 (radius: 5)
[03:23:59 -588300.348201] SLOW spr round 2 (radius: 5)
[03:26:53 -588297.260929] SLOW spr round 3 (radius: 5)
[03:29:44 -588297.260483] SLOW spr round 4 (radius: 10)
[03:32:56 -588296.001053] SLOW spr round 5 (radius: 5)
[03:36:36 -588296.000725] SLOW spr round 6 (radius: 10)
[03:40:08 -588296.000397] SLOW spr round 7 (radius: 15)
[03:45:46 -588295.750693] SLOW spr round 8 (radius: 5)
[03:49:40 -588295.749403] SLOW spr round 9 (radius: 10)
[03:53:26 -588295.748888] SLOW spr round 10 (radius: 15)
[03:59:00 -588295.748502] SLOW spr round 11 (radius: 20)
[04:07:35 -588295.748156] SLOW spr round 12 (radius: 25)
[04:18:21 -588295.747820] Model parameter optimization (eps = 0.100000)

[04:18:27] ML tree search #3, logLikelihood: -588295.729267

[04:18:27 -1827290.388368] Initial branch length optimization
[04:18:33 -1546067.843749] Model parameter optimization (eps = 10.000000)
[04:19:06 -1543651.366081] AUTODETECT spr round 1 (radius: 5)
[04:21:56 -1151279.713967] AUTODETECT spr round 2 (radius: 10)
[04:25:09 -884677.277389] AUTODETECT spr round 3 (radius: 15)
[04:28:41 -724699.593890] AUTODETECT spr round 4 (radius: 20)
[04:32:17 -679859.215780] AUTODETECT spr round 5 (radius: 25)
[04:36:06 -677565.025897] SPR radius for FAST iterations: 25 (autodetect)
[04:36:06 -677565.025897] Model parameter optimization (eps = 3.000000)
[04:36:26 -677475.790070] FAST spr round 1 (radius: 25)
[04:40:20 -590803.002996] FAST spr round 2 (radius: 25)
[04:43:14 -588652.252998] FAST spr round 3 (radius: 25)
[04:45:34 -588528.150784] FAST spr round 4 (radius: 25)
[04:47:33 -588524.549813] FAST spr round 5 (radius: 25)
[04:49:23 -588524.549488] Model parameter optimization (eps = 1.000000)
[04:49:37 -588517.748555] SLOW spr round 1 (radius: 5)
[04:52:14 -588342.608080] SLOW spr round 2 (radius: 5)
[04:54:45 -588336.203352] SLOW spr round 3 (radius: 5)
[04:57:10 -588334.468061] SLOW spr round 4 (radius: 5)
[04:59:33 -588334.467884] SLOW spr round 5 (radius: 10)
[05:02:15 -588316.739921] SLOW spr round 6 (radius: 5)
[05:05:22 -588316.242150] SLOW spr round 7 (radius: 5)
[05:08:07 -588309.458083] SLOW spr round 8 (radius: 5)
[05:10:40 -588309.454017] SLOW spr round 9 (radius: 10)
[05:13:21 -588309.453865] SLOW spr round 10 (radius: 15)
[05:18:10 -588309.453713] SLOW spr round 11 (radius: 20)
[05:25:25 -588302.976976] SLOW spr round 12 (radius: 5)
[05:28:46 -588302.976789] SLOW spr round 13 (radius: 10)
[05:31:59 -588302.976637] SLOW spr round 14 (radius: 15)
[05:36:36 -588302.976486] SLOW spr round 15 (radius: 20)
[05:43:54 -588302.976334] SLOW spr round 16 (radius: 25)
[05:53:12 -588302.976183] Model parameter optimization (eps = 0.100000)

[05:53:22] ML tree search #4, logLikelihood: -588302.826654

[05:53:22 -1828462.710101] Initial branch length optimization
[05:53:27 -1558666.839542] Model parameter optimization (eps = 10.000000)
[05:53:59 -1556192.280539] AUTODETECT spr round 1 (radius: 5)
[05:56:19 -1137748.821151] AUTODETECT spr round 2 (radius: 10)
[05:58:59 -860464.957717] AUTODETECT spr round 3 (radius: 15)
[06:02:03 -720975.478747] AUTODETECT spr round 4 (radius: 20)
[06:05:23 -665577.600207] AUTODETECT spr round 5 (radius: 25)
[06:09:00 -662529.844767] SPR radius for FAST iterations: 25 (autodetect)
[06:09:00 -662529.844767] Model parameter optimization (eps = 3.000000)
[06:09:18 -662454.563949] FAST spr round 1 (radius: 25)
[06:12:56 -590672.753734] FAST spr round 2 (radius: 25)
[06:15:39 -588527.554286] FAST spr round 3 (radius: 25)
[06:17:56 -588433.104774] FAST spr round 4 (radius: 25)
[06:19:55 -588419.658188] FAST spr round 5 (radius: 25)
[06:21:47 -588419.250019] FAST spr round 6 (radius: 25)
[06:23:33 -588419.248096] Model parameter optimization (eps = 1.000000)
[06:23:54 -588410.424753] SLOW spr round 1 (radius: 5)
[06:26:31 -588298.591506] SLOW spr round 2 (radius: 5)
[06:29:08 -588296.311925] SLOW spr round 3 (radius: 5)
[06:31:47 -588296.309376] SLOW spr round 4 (radius: 10)
[06:34:43 -588295.170060] SLOW spr round 5 (radius: 5)
[06:38:04 -588295.167913] SLOW spr round 6 (radius: 10)
[06:41:19 -588292.967642] SLOW spr round 7 (radius: 5)
[06:44:36 -588292.877333] SLOW spr round 8 (radius: 10)
[06:47:48 -588292.877175] SLOW spr round 9 (radius: 15)
[06:53:00 -588291.626691] SLOW spr round 10 (radius: 5)
[06:56:35 -588291.626536] SLOW spr round 11 (radius: 10)
[07:00:02 -588291.626381] SLOW spr round 12 (radius: 15)
[07:04:43 -588291.626226] SLOW spr round 13 (radius: 20)
[07:11:57 -588291.626071] SLOW spr round 14 (radius: 25)
[07:21:10 -588291.626004] Model parameter optimization (eps = 0.100000)

[07:21:24] ML tree search #5, logLikelihood: -588291.497180

[07:21:24 -1810398.577529] Initial branch length optimization
[07:21:31 -1544895.873455] Model parameter optimization (eps = 10.000000)
[07:22:05 -1542195.222741] AUTODETECT spr round 1 (radius: 5)
[07:24:21 -1163852.877835] AUTODETECT spr round 2 (radius: 10)
[07:27:00 -928808.965592] AUTODETECT spr round 3 (radius: 15)
[07:30:05 -721670.480961] AUTODETECT spr round 4 (radius: 20)
[07:33:11 -675743.820555] AUTODETECT spr round 5 (radius: 25)
[07:36:35 -668719.668706] SPR radius for FAST iterations: 25 (autodetect)
[07:36:35 -668719.668706] Model parameter optimization (eps = 3.000000)
[07:36:53 -668599.263652] FAST spr round 1 (radius: 25)
[07:40:02 -592136.473606] FAST spr round 2 (radius: 25)
[07:42:26 -588590.966654] FAST spr round 3 (radius: 25)
[07:44:34 -588456.116546] FAST spr round 4 (radius: 25)
[07:46:24 -588441.157094] FAST spr round 5 (radius: 25)
[07:48:06 -588441.156361] Model parameter optimization (eps = 1.000000)
[07:48:16 -588438.078684] SLOW spr round 1 (radius: 5)
[07:50:35 -588309.408232] SLOW spr round 2 (radius: 5)
[07:52:50 -588306.736523] SLOW spr round 3 (radius: 5)
[07:55:04 -588306.735674] SLOW spr round 4 (radius: 10)
[07:57:34 -588306.735217] SLOW spr round 5 (radius: 15)
[08:02:08 -588306.483784] SLOW spr round 6 (radius: 5)
[08:05:12 -588306.482577] SLOW spr round 7 (radius: 10)
[08:08:09 -588306.482215] SLOW spr round 8 (radius: 15)
[08:12:31 -588306.481999] SLOW spr round 9 (radius: 20)
[08:19:20 -588306.385787] SLOW spr round 10 (radius: 25)
[08:28:04 -588300.036558] SLOW spr round 11 (radius: 5)
[08:31:16 -588298.939424] SLOW spr round 12 (radius: 5)
[08:33:59 -588296.577844] SLOW spr round 13 (radius: 5)
[08:36:26 -588296.577154] SLOW spr round 14 (radius: 10)
[08:39:01 -588296.576386] SLOW spr round 15 (radius: 15)
[08:43:33 -588296.576233] SLOW spr round 16 (radius: 20)
[08:50:23 -588289.492353] SLOW spr round 17 (radius: 5)
[08:53:32 -588289.492200] SLOW spr round 18 (radius: 10)
[08:56:34 -588289.492047] SLOW spr round 19 (radius: 15)
[09:01:00 -588289.491894] SLOW spr round 20 (radius: 20)
[09:07:58 -588289.491741] SLOW spr round 21 (radius: 25)
[09:17:22 -588289.491588] Model parameter optimization (eps = 0.100000)

[09:17:31] ML tree search #6, logLikelihood: -588289.445997

[09:17:31 -1817970.509281] Initial branch length optimization
[09:17:36 -1540206.236557] Model parameter optimization (eps = 10.000000)
[09:18:04 -1537649.275642] AUTODETECT spr round 1 (radius: 5)
[09:20:26 -1160750.608047] AUTODETECT spr round 2 (radius: 10)
[09:23:13 -881923.250127] AUTODETECT spr round 3 (radius: 15)
[09:26:18 -728194.695236] AUTODETECT spr round 4 (radius: 20)
[09:29:45 -684367.252964] AUTODETECT spr round 5 (radius: 25)
[09:33:33 -674729.202019] SPR radius for FAST iterations: 25 (autodetect)
[09:33:33 -674729.202019] Model parameter optimization (eps = 3.000000)
[09:34:00 -674463.060882] FAST spr round 1 (radius: 25)
[09:37:39 -591061.118459] FAST spr round 2 (radius: 25)
[09:40:17 -588518.534870] FAST spr round 3 (radius: 25)
[09:42:26 -588481.198378] FAST spr round 4 (radius: 25)
[09:44:19 -588440.453655] FAST spr round 5 (radius: 25)
[09:46:02 -588440.451866] Model parameter optimization (eps = 1.000000)
[09:46:13 -588438.542923] SLOW spr round 1 (radius: 5)
[09:48:39 -588315.962652] SLOW spr round 2 (radius: 5)
[09:51:05 -588298.003387] SLOW spr round 3 (radius: 5)
[09:53:22 -588297.988813] SLOW spr round 4 (radius: 10)
[09:55:54 -588296.734756] SLOW spr round 5 (radius: 5)
[09:58:48 -588296.734414] SLOW spr round 6 (radius: 10)
[10:01:36 -588296.734208] SLOW spr round 7 (radius: 15)
[10:06:03 -588296.176273] SLOW spr round 8 (radius: 5)
[10:09:08 -588296.175616] SLOW spr round 9 (radius: 10)
[10:12:05 -588296.175328] SLOW spr round 10 (radius: 15)
[10:16:30 -588296.175130] SLOW spr round 11 (radius: 20)
[10:23:17 -588296.174958] SLOW spr round 12 (radius: 25)
[10:32:02 -588296.174795] Model parameter optimization (eps = 0.100000)

[10:32:09] ML tree search #7, logLikelihood: -588296.024715

[10:32:09 -1813953.700487] Initial branch length optimization
[10:32:13 -1547027.277658] Model parameter optimization (eps = 10.000000)
[10:32:44 -1544569.697843] AUTODETECT spr round 1 (radius: 5)
[10:34:54 -1152233.701296] AUTODETECT spr round 2 (radius: 10)
[10:37:26 -895104.050980] AUTODETECT spr round 3 (radius: 15)
[10:40:29 -713332.536076] AUTODETECT spr round 4 (radius: 20)
[10:43:35 -669547.543906] AUTODETECT spr round 5 (radius: 25)
[10:47:10 -666674.515857] SPR radius for FAST iterations: 25 (autodetect)
[10:47:10 -666674.515857] Model parameter optimization (eps = 3.000000)
[10:47:27 -666569.585958] FAST spr round 1 (radius: 25)
[10:50:59 -591674.045161] FAST spr round 2 (radius: 25)
[10:53:41 -588624.617658] FAST spr round 3 (radius: 25)
[10:55:51 -588433.943522] FAST spr round 4 (radius: 25)
[10:57:42 -588420.927082] FAST spr round 5 (radius: 25)
[10:59:26 -588420.925465] Model parameter optimization (eps = 1.000000)
[10:59:38 -588417.839174] SLOW spr round 1 (radius: 5)
[11:02:02 -588304.848702] SLOW spr round 2 (radius: 5)
[11:04:19 -588300.552432] SLOW spr round 3 (radius: 5)
[11:06:33 -588300.549083] SLOW spr round 4 (radius: 10)
[11:09:05 -588294.533547] SLOW spr round 5 (radius: 5)
[11:11:57 -588293.786682] SLOW spr round 6 (radius: 5)
[11:14:29 -588293.786256] SLOW spr round 7 (radius: 10)
[11:17:04 -588293.785981] SLOW spr round 8 (radius: 15)
[11:21:34 -588293.655914] SLOW spr round 9 (radius: 5)
[11:24:37 -588293.655712] SLOW spr round 10 (radius: 10)
[11:27:33 -588293.655528] SLOW spr round 11 (radius: 15)
[11:31:55 -588293.655358] SLOW spr round 12 (radius: 20)
[11:38:49 -588293.655198] SLOW spr round 13 (radius: 25)
[11:47:35 -588293.655047] Model parameter optimization (eps = 0.100000)

[11:47:45] ML tree search #8, logLikelihood: -588293.009520

[11:47:45 -1813581.214156] Initial branch length optimization
[11:47:50 -1544815.873004] Model parameter optimization (eps = 10.000000)
[11:48:17 -1542408.824456] AUTODETECT spr round 1 (radius: 5)
[11:50:24 -1162807.114494] AUTODETECT spr round 2 (radius: 10)
[11:52:57 -891668.414455] AUTODETECT spr round 3 (radius: 15)
[11:55:55 -765689.706168] AUTODETECT spr round 4 (radius: 20)
[11:59:11 -682316.725318] AUTODETECT spr round 5 (radius: 25)
[12:02:27 -673475.728988] SPR radius for FAST iterations: 25 (autodetect)
[12:02:27 -673475.728988] Model parameter optimization (eps = 3.000000)
[12:02:44 -673370.782991] FAST spr round 1 (radius: 25)
[12:06:22 -590730.080129] FAST spr round 2 (radius: 25)
[12:08:51 -588647.854042] FAST spr round 3 (radius: 25)
[12:10:58 -588498.645541] FAST spr round 4 (radius: 25)
[12:12:48 -588482.279393] FAST spr round 5 (radius: 25)
[12:14:30 -588482.278174] Model parameter optimization (eps = 1.000000)
[12:14:40 -588478.716669] SLOW spr round 1 (radius: 5)
[12:16:56 -588320.903090] SLOW spr round 2 (radius: 5)
[12:19:17 -588299.774144] SLOW spr round 3 (radius: 5)
[12:21:35 -588298.273928] SLOW spr round 4 (radius: 5)
[12:23:49 -588298.272664] SLOW spr round 5 (radius: 10)
[12:26:19 -588285.957417] SLOW spr round 6 (radius: 5)
[12:29:13 -588282.031578] SLOW spr round 7 (radius: 5)
[12:31:44 -588282.029598] SLOW spr round 8 (radius: 10)
[12:34:21 -588282.029372] SLOW spr round 9 (radius: 15)
[12:38:58 -588281.635727] SLOW spr round 10 (radius: 5)
[12:42:01 -588281.634590] SLOW spr round 11 (radius: 10)
[12:44:59 -588281.634377] SLOW spr round 12 (radius: 15)
[12:49:29 -588281.634315] SLOW spr round 13 (radius: 20)
[12:56:36 -588281.634295] SLOW spr round 14 (radius: 25)
[13:05:32 -588281.634287] Model parameter optimization (eps = 0.100000)

[13:05:40] ML tree search #9, logLikelihood: -588281.387100

[13:05:40 -1828370.938888] Initial branch length optimization
[13:05:46 -1557261.569432] Model parameter optimization (eps = 10.000000)
[13:06:13 -1554818.632666] AUTODETECT spr round 1 (radius: 5)
[13:08:23 -1160948.195555] AUTODETECT spr round 2 (radius: 10)
[13:10:58 -886948.957947] AUTODETECT spr round 3 (radius: 15)
[13:13:55 -715766.935636] AUTODETECT spr round 4 (radius: 20)
[13:16:56 -671315.692048] AUTODETECT spr round 5 (radius: 25)
[13:20:13 -661618.654524] SPR radius for FAST iterations: 25 (autodetect)
[13:20:13 -661618.654524] Model parameter optimization (eps = 3.000000)
[13:20:33 -661500.686725] FAST spr round 1 (radius: 25)
[13:24:02 -590510.878678] FAST spr round 2 (radius: 25)
[13:26:34 -588589.836236] FAST spr round 3 (radius: 25)
[13:28:39 -588455.185653] FAST spr round 4 (radius: 25)
[13:30:30 -588450.960427] FAST spr round 5 (radius: 25)
[13:32:13 -588450.934504] Model parameter optimization (eps = 1.000000)
[13:32:22 -588443.597211] SLOW spr round 1 (radius: 5)
[13:34:38 -588293.175579] SLOW spr round 2 (radius: 5)
[13:36:54 -588292.679627] SLOW spr round 3 (radius: 5)
[13:39:07 -588292.679199] SLOW spr round 4 (radius: 10)
[13:41:35 -588292.678748] SLOW spr round 5 (radius: 15)
[13:46:10 -588291.014146] SLOW spr round 6 (radius: 5)
[13:49:12 -588291.012852] SLOW spr round 7 (radius: 10)
[13:52:07 -588291.012455] SLOW spr round 8 (radius: 15)
[13:56:28 -588291.012210] SLOW spr round 9 (radius: 20)
[14:03:19 -588291.012012] SLOW spr round 10 (radius: 25)
[14:12:02 -588291.011835] Model parameter optimization (eps = 0.100000)

[14:12:09] ML tree search #10, logLikelihood: -588290.694805

[14:12:09 -1820448.173998] Initial branch length optimization
[14:12:14 -1542290.014263] Model parameter optimization (eps = 10.000000)
[14:12:46 -1539666.505167] AUTODETECT spr round 1 (radius: 5)
[14:14:56 -1147261.401039] AUTODETECT spr round 2 (radius: 10)
[14:17:25 -852629.339869] AUTODETECT spr round 3 (radius: 15)
[14:20:04 -702243.375707] AUTODETECT spr round 4 (radius: 20)
[14:22:58 -674481.288200] AUTODETECT spr round 5 (radius: 25)
[14:26:38 -670458.303255] SPR radius for FAST iterations: 25 (autodetect)
[14:26:38 -670458.303255] Model parameter optimization (eps = 3.000000)
[14:26:58 -670375.075538] FAST spr round 1 (radius: 25)
[14:30:38 -591188.765325] FAST spr round 2 (radius: 25)
[14:33:19 -588574.808333] FAST spr round 3 (radius: 25)
[14:35:32 -588476.052935] FAST spr round 4 (radius: 25)
[14:37:28 -588461.507800] FAST spr round 5 (radius: 25)
[14:39:13 -588457.847972] FAST spr round 6 (radius: 25)
[14:40:54 -588457.847092] Model parameter optimization (eps = 1.000000)
[14:41:05 -588451.824586] SLOW spr round 1 (radius: 5)
[14:43:25 -588322.512113] SLOW spr round 2 (radius: 5)
[14:45:45 -588308.609182] SLOW spr round 3 (radius: 5)
[14:47:59 -588307.673132] SLOW spr round 4 (radius: 5)
[14:50:13 -588307.672695] SLOW spr round 5 (radius: 10)
[14:52:47 -588300.049301] SLOW spr round 6 (radius: 5)
[14:55:40 -588294.872918] SLOW spr round 7 (radius: 5)
[14:58:11 -588294.872205] SLOW spr round 8 (radius: 10)
[15:00:48 -588294.871841] SLOW spr round 9 (radius: 15)
[15:05:17 -588294.642617] SLOW spr round 10 (radius: 5)
[15:08:21 -588294.641428] SLOW spr round 11 (radius: 10)
[15:11:18 -588294.641067] SLOW spr round 12 (radius: 15)
[15:15:41 -588294.640853] SLOW spr round 13 (radius: 20)
[15:22:29 -588294.640682] SLOW spr round 14 (radius: 25)
[15:31:11 -588294.640524] Model parameter optimization (eps = 0.100000)

[15:31:15] ML tree search #11, logLikelihood: -588294.583870

[15:31:16 -1826717.241753] Initial branch length optimization
[15:31:22 -1559783.413205] Model parameter optimization (eps = 10.000000)
[15:31:50 -1557268.852314] AUTODETECT spr round 1 (radius: 5)
[15:33:58 -1164167.837801] AUTODETECT spr round 2 (radius: 10)
[15:36:35 -874460.609308] AUTODETECT spr round 3 (radius: 15)
[15:39:20 -721235.890116] AUTODETECT spr round 4 (radius: 20)
[15:42:21 -676591.497988] AUTODETECT spr round 5 (radius: 25)
[15:45:48 -667265.537884] SPR radius for FAST iterations: 25 (autodetect)
[15:45:48 -667265.537884] Model parameter optimization (eps = 3.000000)
[15:46:14 -667147.165821] FAST spr round 1 (radius: 25)
[15:49:30 -590709.675171] FAST spr round 2 (radius: 25)
[15:51:56 -588579.998891] FAST spr round 3 (radius: 25)
[15:54:01 -588488.604639] FAST spr round 4 (radius: 25)
[15:55:52 -588470.791132] FAST spr round 5 (radius: 25)
[15:57:34 -588470.790225] Model parameter optimization (eps = 1.000000)
[15:57:49 -588458.463773] SLOW spr round 1 (radius: 5)
[16:00:07 -588324.827626] SLOW spr round 2 (radius: 5)
[16:02:24 -588317.424223] SLOW spr round 3 (radius: 5)
[16:04:39 -588317.423687] SLOW spr round 4 (radius: 10)
[16:07:08 -588316.167520] SLOW spr round 5 (radius: 5)
[16:10:02 -588316.167193] SLOW spr round 6 (radius: 10)
[16:12:48 -588316.166874] SLOW spr round 7 (radius: 15)
[16:17:11 -588316.166558] SLOW spr round 8 (radius: 20)
[16:23:51 -588316.165638] SLOW spr round 9 (radius: 25)
[16:32:32 -588316.165328] Model parameter optimization (eps = 0.100000)

[16:32:37] ML tree search #12, logLikelihood: -588316.112203

[16:32:37 -1822985.638795] Initial branch length optimization
[16:32:42 -1563640.787579] Model parameter optimization (eps = 10.000000)
[16:33:08 -1561093.938207] AUTODETECT spr round 1 (radius: 5)
[16:35:17 -1147429.929522] AUTODETECT spr round 2 (radius: 10)
[16:37:50 -870693.329071] AUTODETECT spr round 3 (radius: 15)
[16:40:49 -722517.213105] AUTODETECT spr round 4 (radius: 20)
[16:43:37 -671383.896325] AUTODETECT spr round 5 (radius: 25)
[16:46:49 -668575.438673] SPR radius for FAST iterations: 25 (autodetect)
[16:46:49 -668575.438673] Model parameter optimization (eps = 3.000000)
[16:47:08 -668464.952366] FAST spr round 1 (radius: 25)
[16:50:53 -592792.207878] FAST spr round 2 (radius: 25)
[16:53:23 -588523.352992] FAST spr round 3 (radius: 25)
[16:55:30 -588442.012425] FAST spr round 4 (radius: 25)
[16:57:20 -588437.178417] FAST spr round 5 (radius: 25)
[16:59:03 -588432.779323] FAST spr round 6 (radius: 25)
[17:00:42 -588432.778806] Model parameter optimization (eps = 1.000000)
[17:00:54 -588431.618051] SLOW spr round 1 (radius: 5)
[17:03:10 -588294.042473] SLOW spr round 2 (radius: 5)
[17:05:27 -588292.355944] SLOW spr round 3 (radius: 5)
[17:07:40 -588292.355296] SLOW spr round 4 (radius: 10)
[17:10:11 -588292.354047] SLOW spr round 5 (radius: 15)
[17:14:49 -588290.747406] SLOW spr round 6 (radius: 5)
[17:17:52 -588290.745642] SLOW spr round 7 (radius: 10)
[17:20:52 -588290.745243] SLOW spr round 8 (radius: 15)
[17:25:18 -588290.745027] SLOW spr round 9 (radius: 20)
[17:32:12 -588290.744851] SLOW spr round 10 (radius: 25)
[17:41:02 -588290.744687] Model parameter optimization (eps = 0.100000)

[17:41:06] ML tree search #13, logLikelihood: -588290.692793

[17:41:06 -1811573.686600] Initial branch length optimization
[17:41:12 -1541196.599398] Model parameter optimization (eps = 10.000000)
[17:41:40 -1538525.515696] AUTODETECT spr round 1 (radius: 5)
[17:43:50 -1151151.992470] AUTODETECT spr round 2 (radius: 10)
[17:46:23 -838985.625124] AUTODETECT spr round 3 (radius: 15)
[17:49:06 -711670.329259] AUTODETECT spr round 4 (radius: 20)
[17:52:06 -650709.562702] AUTODETECT spr round 5 (radius: 25)
[17:55:37 -646403.862668] SPR radius for FAST iterations: 25 (autodetect)
[17:55:37 -646403.862668] Model parameter optimization (eps = 3.000000)
[17:55:53 -646259.435886] FAST spr round 1 (radius: 25)
[17:59:18 -590521.998034] FAST spr round 2 (radius: 25)
[18:01:52 -588482.040748] FAST spr round 3 (radius: 25)
[18:04:00 -588408.657991] FAST spr round 4 (radius: 25)
[18:05:51 -588392.644863] FAST spr round 5 (radius: 25)
[18:07:34 -588392.627725] Model parameter optimization (eps = 1.000000)
[18:07:44 -588387.982409] SLOW spr round 1 (radius: 5)
[18:10:10 -588292.796715] SLOW spr round 2 (radius: 5)
[18:12:25 -588292.733457] SLOW spr round 3 (radius: 10)
[18:15:00 -588290.567056] SLOW spr round 4 (radius: 5)
[18:17:53 -588290.566837] SLOW spr round 5 (radius: 10)
[18:20:41 -588290.566646] SLOW spr round 6 (radius: 15)
[18:25:08 -588290.241970] SLOW spr round 7 (radius: 5)
[18:28:12 -588290.240741] SLOW spr round 8 (radius: 10)
[18:31:11 -588290.240374] SLOW spr round 9 (radius: 15)
[18:35:35 -588290.240155] SLOW spr round 10 (radius: 20)
[18:43:23 -588290.239980] SLOW spr round 11 (radius: 25)
[18:54:22 -588290.239819] Model parameter optimization (eps = 0.100000)

[18:54:28] ML tree search #14, logLikelihood: -588290.140045

[18:54:29 -1819941.825114] Initial branch length optimization
[18:54:35 -1549640.640587] Model parameter optimization (eps = 10.000000)
[18:55:08 -1547140.022531] AUTODETECT spr round 1 (radius: 5)
[18:57:51 -1147927.823000] AUTODETECT spr round 2 (radius: 10)
[19:01:05 -846844.832234] AUTODETECT spr round 3 (radius: 15)
[19:04:26 -739788.310638] AUTODETECT spr round 4 (radius: 20)
[19:08:05 -671501.268927] AUTODETECT spr round 5 (radius: 25)
[19:12:33 -664607.894189] SPR radius for FAST iterations: 25 (autodetect)
[19:12:33 -664607.894189] Model parameter optimization (eps = 3.000000)
[19:12:53 -664518.204025] FAST spr round 1 (radius: 25)
[19:17:25 -593175.862011] FAST spr round 2 (radius: 25)
[19:20:52 -588721.208124] FAST spr round 3 (radius: 25)
[19:23:45 -588459.645066] FAST spr round 4 (radius: 25)
[19:26:07 -588446.096661] FAST spr round 5 (radius: 25)
[19:28:16 -588440.485684] FAST spr round 6 (radius: 25)
[19:30:19 -588440.484451] Model parameter optimization (eps = 1.000000)
[19:30:36 -588433.947330] SLOW spr round 1 (radius: 5)
[19:33:34 -588321.803529] SLOW spr round 2 (radius: 5)
[19:36:25 -588315.053302] SLOW spr round 3 (radius: 5)
[19:38:54 -588315.024812] SLOW spr round 4 (radius: 10)
[19:41:32 -588306.069845] SLOW spr round 5 (radius: 5)
[19:45:08 -588305.274750] SLOW spr round 6 (radius: 5)
[19:48:17 -588305.272831] SLOW spr round 7 (radius: 10)
[19:51:32 -588305.272252] SLOW spr round 8 (radius: 15)
[19:57:04 -588305.128904] SLOW spr round 9 (radius: 5)
[20:00:55 -588305.127854] SLOW spr round 10 (radius: 10)
[20:04:33 -588305.127643] SLOW spr round 11 (radius: 15)
[20:09:57 -588305.127580] SLOW spr round 12 (radius: 20)
[20:18:33 -588303.014176] SLOW spr round 13 (radius: 5)
[20:22:29 -588303.014171] SLOW spr round 14 (radius: 10)
[20:26:14 -588303.014169] SLOW spr round 15 (radius: 15)
[20:31:39 -588298.666997] SLOW spr round 16 (radius: 5)
[20:35:30 -588298.666997] SLOW spr round 17 (radius: 10)
[20:39:10 -588298.666961] SLOW spr round 18 (radius: 15)
[20:44:36 -588298.666961] SLOW spr round 19 (radius: 20)
[20:53:11 -588298.666960] SLOW spr round 20 (radius: 25)
[21:04:09 -588298.666960] Model parameter optimization (eps = 0.100000)

[21:04:24] ML tree search #15, logLikelihood: -588297.224312

[21:04:24 -1833876.979919] Initial branch length optimization
[21:04:36 -1564542.771154] Model parameter optimization (eps = 10.000000)
[21:05:07 -1561953.883846] AUTODETECT spr round 1 (radius: 5)
[21:07:47 -1148939.029345] AUTODETECT spr round 2 (radius: 10)
[21:10:55 -875049.609837] AUTODETECT spr round 3 (radius: 15)
[21:14:17 -723926.608227] AUTODETECT spr round 4 (radius: 20)
[21:17:53 -663103.453215] AUTODETECT spr round 5 (radius: 25)
[21:22:04 -650295.016832] SPR radius for FAST iterations: 25 (autodetect)
[21:22:04 -650295.016832] Model parameter optimization (eps = 3.000000)
[21:22:27 -650156.369566] FAST spr round 1 (radius: 25)
[21:26:40 -590156.942690] FAST spr round 2 (radius: 25)
[21:29:49 -588587.303045] FAST spr round 3 (radius: 25)
[21:32:25 -588458.598898] FAST spr round 4 (radius: 25)
[21:34:38 -588458.511979] Model parameter optimization (eps = 1.000000)
[21:34:52 -588456.349656] SLOW spr round 1 (radius: 5)
[21:37:51 -588323.883319] SLOW spr round 2 (radius: 5)
[21:40:45 -588316.754643] SLOW spr round 3 (radius: 5)
[21:43:34 -588316.754091] SLOW spr round 4 (radius: 10)
[21:46:42 -588316.753426] SLOW spr round 5 (radius: 15)
[21:52:26 -588316.209411] SLOW spr round 6 (radius: 5)
[21:56:13 -588316.208430] SLOW spr round 7 (radius: 10)
[21:59:57 -588316.207802] SLOW spr round 8 (radius: 15)
[22:05:24 -588316.207265] SLOW spr round 9 (radius: 20)
[22:13:54 -588316.206756] SLOW spr round 10 (radius: 25)
[22:24:52 -588316.206255] Model parameter optimization (eps = 0.100000)

[22:25:01] ML tree search #16, logLikelihood: -588316.055313

[22:25:01 -1819558.321149] Initial branch length optimization
[22:25:07 -1554138.458291] Model parameter optimization (eps = 10.000000)
[22:25:43 -1551643.681596] AUTODETECT spr round 1 (radius: 5)
[22:28:23 -1147171.621043] AUTODETECT spr round 2 (radius: 10)
[22:31:31 -859078.981738] AUTODETECT spr round 3 (radius: 15)
[22:35:00 -722490.686606] AUTODETECT spr round 4 (radius: 20)
[22:38:37 -675715.216293] AUTODETECT spr round 5 (radius: 25)
[22:42:28 -666004.298956] SPR radius for FAST iterations: 25 (autodetect)
[22:42:28 -666004.298956] Model parameter optimization (eps = 3.000000)
[22:42:47 -665942.291763] FAST spr round 1 (radius: 25)
[22:47:04 -591145.818616] FAST spr round 2 (radius: 25)
[22:50:18 -588557.809956] FAST spr round 3 (radius: 25)
[22:53:09 -588452.905841] FAST spr round 4 (radius: 25)
[22:55:27 -588442.591155] FAST spr round 5 (radius: 25)
[22:57:37 -588441.151632] FAST spr round 6 (radius: 25)
[22:59:42 -588441.139691] Model parameter optimization (eps = 1.000000)
[22:59:54 -588436.357263] SLOW spr round 1 (radius: 5)
[23:02:46 -588312.055278] SLOW spr round 2 (radius: 5)
[23:05:39 -588301.437703] SLOW spr round 3 (radius: 5)
[23:08:28 -588300.168091] SLOW spr round 4 (radius: 5)
[23:11:15 -588300.167039] SLOW spr round 5 (radius: 10)
[23:14:23 -588289.284452] SLOW spr round 6 (radius: 5)
[23:18:00 -588289.283778] SLOW spr round 7 (radius: 10)
[23:21:27 -588289.283254] SLOW spr round 8 (radius: 15)
[23:27:04 -588288.031652] SLOW spr round 9 (radius: 5)
[23:30:53 -588288.031207] SLOW spr round 10 (radius: 10)
[23:34:34 -588288.030770] SLOW spr round 11 (radius: 15)
[23:40:06 -588288.030336] SLOW spr round 12 (radius: 20)
[23:48:46 -588288.029904] SLOW spr round 13 (radius: 25)
[23:59:56 -588288.029471] Model parameter optimization (eps = 0.100000)

[24:00:04] ML tree search #17, logLikelihood: -588287.847799

[24:00:04 -1821081.678127] Initial branch length optimization
[24:00:10 -1553824.526386] Model parameter optimization (eps = 10.000000)
[24:00:57 -1551407.165698] AUTODETECT spr round 1 (radius: 5)
[24:03:38 -1145516.695223] AUTODETECT spr round 2 (radius: 10)
[24:06:44 -882810.726480] AUTODETECT spr round 3 (radius: 15)
[24:10:22 -751582.791824] AUTODETECT spr round 4 (radius: 20)
[24:14:25 -681076.619851] AUTODETECT spr round 5 (radius: 25)
[24:18:43 -678101.750949] SPR radius for FAST iterations: 25 (autodetect)
[24:18:43 -678101.750949] Model parameter optimization (eps = 3.000000)
[24:19:02 -677981.625513] FAST spr round 1 (radius: 25)
[24:23:20 -591594.777746] FAST spr round 2 (radius: 25)
[24:26:18 -588655.412309] FAST spr round 3 (radius: 25)
[24:28:44 -588409.611822] FAST spr round 4 (radius: 25)
[24:31:03 -588403.209790] FAST spr round 5 (radius: 25)
[24:33:11 -588397.991215] FAST spr round 6 (radius: 25)
[24:35:17 -588397.990313] Model parameter optimization (eps = 1.000000)
[24:35:39 -588394.688279] SLOW spr round 1 (radius: 5)
[24:38:38 -588297.534132] SLOW spr round 2 (radius: 5)
[24:41:30 -588293.845036] SLOW spr round 3 (radius: 5)
[24:44:16 -588293.839146] SLOW spr round 4 (radius: 10)
[24:47:31 -588291.677527] SLOW spr round 5 (radius: 5)
[24:51:10 -588291.676701] SLOW spr round 6 (radius: 10)
[24:54:44 -588291.676103] SLOW spr round 7 (radius: 15)
[25:00:18 -588291.375135] SLOW spr round 8 (radius: 5)
[25:04:11 -588291.373661] SLOW spr round 9 (radius: 10)
[25:07:58 -588291.372971] SLOW spr round 10 (radius: 15)
[25:13:27 -588291.372427] SLOW spr round 11 (radius: 20)
[25:21:59 -588291.371924] SLOW spr round 12 (radius: 25)
[25:32:49 -588291.371434] Model parameter optimization (eps = 0.100000)

[25:32:55] ML tree search #18, logLikelihood: -588291.317934

[25:32:55 -1830557.804431] Initial branch length optimization
[25:33:06 -1563562.587717] Model parameter optimization (eps = 10.000000)
[25:33:54 -1561018.676944] AUTODETECT spr round 1 (radius: 5)
[25:36:38 -1151171.251283] AUTODETECT spr round 2 (radius: 10)
[25:39:52 -897551.051152] AUTODETECT spr round 3 (radius: 15)
[25:43:35 -749442.843498] AUTODETECT spr round 4 (radius: 20)
[25:47:26 -678152.303084] AUTODETECT spr round 5 (radius: 25)
[25:51:37 -668970.253013] SPR radius for FAST iterations: 25 (autodetect)
[25:51:38 -668970.253013] Model parameter optimization (eps = 3.000000)
[25:52:00 -668841.084562] FAST spr round 1 (radius: 25)
[25:56:37 -591049.522771] FAST spr round 2 (radius: 25)
[25:59:57 -588657.872101] FAST spr round 3 (radius: 25)
[26:02:40 -588448.131028] FAST spr round 4 (radius: 25)
[26:04:57 -588418.184282] FAST spr round 5 (radius: 25)
[26:07:06 -588417.754457] FAST spr round 6 (radius: 25)
[26:09:12 -588417.731087] Model parameter optimization (eps = 1.000000)
[26:09:26 -588414.368284] SLOW spr round 1 (radius: 5)
[26:12:19 -588299.434581] SLOW spr round 2 (radius: 5)
[26:15:09 -588297.423723] SLOW spr round 3 (radius: 5)
[26:17:57 -588297.421272] SLOW spr round 4 (radius: 10)
[26:21:09 -588297.420598] SLOW spr round 5 (radius: 15)
[26:26:51 -588295.539054] SLOW spr round 6 (radius: 5)
[26:30:44 -588295.538108] SLOW spr round 7 (radius: 10)
[26:34:30 -588295.537458] SLOW spr round 8 (radius: 15)
[26:39:58 -588295.536958] SLOW spr round 9 (radius: 20)
[26:48:24 -588295.536482] SLOW spr round 10 (radius: 25)
[26:59:00 -588295.536013] Model parameter optimization (eps = 0.100000)

[26:59:06] ML tree search #19, logLikelihood: -588295.503479

[26:59:06 -1819963.485710] Initial branch length optimization
[26:59:12 -1549364.363727] Model parameter optimization (eps = 10.000000)
[26:59:48 -1546793.162918] AUTODETECT spr round 1 (radius: 5)
[27:02:36 -1117822.348009] AUTODETECT spr round 2 (radius: 10)
[27:05:48 -810547.265017] AUTODETECT spr round 3 (radius: 15)
[27:09:00 -710862.034493] AUTODETECT spr round 4 (radius: 20)
[27:12:57 -667055.873975] AUTODETECT spr round 5 (radius: 25)
[27:18:21 -658980.101988] SPR radius for FAST iterations: 25 (autodetect)
[27:18:21 -658980.101988] Model parameter optimization (eps = 3.000000)
[27:18:29 -658967.428574] FAST spr round 1 (radius: 25)
[27:22:37 -590266.395944] FAST spr round 2 (radius: 25)
[27:25:40 -588571.759376] FAST spr round 3 (radius: 25)
[27:28:15 -588507.471569] FAST spr round 4 (radius: 25)
[27:30:27 -588507.471027] Model parameter optimization (eps = 1.000000)
[27:30:46 -588422.770965] SLOW spr round 1 (radius: 5)
[27:33:47 -588323.317109] SLOW spr round 2 (radius: 5)
[27:36:42 -588314.467883] SLOW spr round 3 (radius: 5)
[27:39:30 -588314.467241] SLOW spr round 4 (radius: 10)
[27:42:40 -588314.466702] SLOW spr round 5 (radius: 15)
[27:48:20 -588314.083177] SLOW spr round 6 (radius: 5)
[27:52:14 -588314.081414] SLOW spr round 7 (radius: 10)
[27:55:54 -588314.080711] SLOW spr round 8 (radius: 15)
[28:01:19 -588314.080161] SLOW spr round 9 (radius: 20)
[28:09:57 -588314.079654] SLOW spr round 10 (radius: 25)
[28:20:55 -588314.079158] Model parameter optimization (eps = 0.100000)

[28:21:03] ML tree search #20, logLikelihood: -588314.041992


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.188877,0.213425) (0.184500,0.306303) (0.351952,0.920650) (0.274671,2.108527) 
   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: -588281.387100

AIC score: 1180572.774199 / AICc score: 9224632.774199 / BIC score: 1190724.185767
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1168).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/3_mltree/Q9UQE7.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/3_mltree/Q9UQE7.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/3_mltree/Q9UQE7.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQE7/3_mltree/Q9UQE7.raxml.log

Analysis started: 03-Jul-2021 20:31:55 / finished: 05-Jul-2021 00:52:59

Elapsed time: 102063.919 seconds

Consumed energy: 6896.539 Wh (= 34 km in an electric car, or 172 km with an e-scooter!)