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 03:29:23 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12791/2_msa/Q12791_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12791/3_mltree/Q12791 --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/Q12791/2_msa/Q12791_trimmed_msa.fasta
[00:00:00] Loaded alignment with 465 taxa and 981 sites

WARNING: Sequences sp_Q08460_KCMA1_MOUSE_10090 and tr_A0A1U8CS04_A0A1U8CS04_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A2I3GF78_A0A2I3GF78_NOMLE_61853 and tr_A0A2I3R9W8_A0A2I3R9W8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GF78_A0A2I3GF78_NOMLE_61853 and tr_F7EYH8_F7EYH8_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3GF78_A0A2I3GF78_NOMLE_61853 and tr_A0A2I3M8Q1_A0A2I3M8Q1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3GF78_A0A2I3GF78_NOMLE_61853 and tr_A0A2K6DQP1_A0A2K6DQP1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3GF78_A0A2I3GF78_NOMLE_61853 and tr_A0A2K5ZF12_A0A2K5ZF12_MANLE_9568 are exactly identical!
WARNING: Sequences sp_Q9BG98_KCMA1_RABIT_9986 and sp_O18867_KCMA1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G0N0Z1_G0N0Z1_CAEBE_135651 and tr_A0A2G5TTG7_A0A2G5TTG7_9PELO_1611254 are exactly identical!
WARNING: Sequences sp_O18866_KCMA1_PIG_9823 and sp_Q28204_KCMA1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A0N4TSU4_A0A0N4TSU4_BRUPA_6280 and tr_A0A0R3RMY6_A0A0R3RMY6_9BILA_1147741 are exactly identical!
WARNING: Sequences tr_A0A0N0U5N4_A0A0N0U5N4_9HYME_166423 and tr_A0A154PC45_A0A154PC45_9HYME_178035 are exactly identical!
WARNING: Sequences tr_A0A091JD96_A0A091JD96_EGRGA_188379 and tr_A0A091UM38_A0A091UM38_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JD96_A0A091JD96_EGRGA_188379 and tr_A0A093HLR7_A0A093HLR7_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091JD96_A0A091JD96_EGRGA_188379 and tr_A0A091WGX6_A0A091WGX6_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091JD96_A0A091JD96_EGRGA_188379 and tr_A0A093GE02_A0A093GE02_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A091JD96_A0A091JD96_EGRGA_188379 and tr_A0A091JA57_A0A091JA57_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A0V1CPP8_A0A0V1CPP8_TRIBR_45882 and tr_A0A0V0UX49_A0A0V0UX49_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CPP8_A0A0V1CPP8_TRIBR_45882 and tr_A0A0V1A3F4_A0A0V1A3F4_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1CPP8_A0A0V1CPP8_TRIBR_45882 and tr_A0A0V0U529_A0A0V0U529_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0X0E2_A0A0V0X0E2_9BILA_92179 and tr_A0A0V1L4R9_A0A0V1L4R9_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1MU74_A0A0V1MU74_9BILA_268474 and tr_A0A0V1HX77_A0A0V1HX77_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A0V1P5N5_A0A0V1P5N5_9BILA_92180 and tr_A0A0V0U4V5_A0A0V0U4V5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1I7U4G8_A0A1I7U4G8_9PELO_1561998 and tr_A0A1I7U4G9_A0A1I7U4G9_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1D1UFK0_A0A1D1UFK0_RAMVA_947166 and tr_A0A1D1UJ56_A0A1D1UJ56_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1D1VF74_A0A1D1VF74_RAMVA_947166 and tr_A0A1D1VP35_A0A1D1VP35_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A1D1VH94_A0A1D1VH94_RAMVA_947166 and tr_A0A1D1VKM6_A0A1D1VKM6_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A2U3W5J4_A0A2U3W5J4_ODORO_9708 and tr_A0A2Y9J537_A0A2Y9J537_ENHLU_391180 are exactly identical!
WARNING: Duplicate sequences found: 27

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/Q12791/3_mltree/Q12791.raxml.reduced.phy

Alignment comprises 1 partitions and 981 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 981 / 981
Gaps: 33.02 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12791/3_mltree/Q12791.raxml.rba

Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 465 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 246 / 19680
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -402820.540205] Initial branch length optimization
[00:00:04 -308310.429962] Model parameter optimization (eps = 10.000000)
[00:01:14 -306582.062425] AUTODETECT spr round 1 (radius: 5)
[00:02:07 -214408.757728] AUTODETECT spr round 2 (radius: 10)
[00:03:08 -163271.633111] AUTODETECT spr round 3 (radius: 15)
[00:04:18 -152920.809055] AUTODETECT spr round 4 (radius: 20)
[00:05:54 -136954.641472] AUTODETECT spr round 5 (radius: 25)
[00:07:42 -136571.834803] SPR radius for FAST iterations: 25 (autodetect)
[00:07:42 -136571.834803] Model parameter optimization (eps = 3.000000)
[00:08:15 -135472.383959] FAST spr round 1 (radius: 25)
[00:09:45 -120443.494432] FAST spr round 2 (radius: 25)
[00:10:49 -120020.769884] FAST spr round 3 (radius: 25)
[00:11:44 -119978.219215] FAST spr round 4 (radius: 25)
[00:12:34 -119961.056491] FAST spr round 5 (radius: 25)
[00:13:21 -119961.030383] Model parameter optimization (eps = 1.000000)
[00:13:34 -119955.533634] SLOW spr round 1 (radius: 5)
[00:14:41 -119932.496089] SLOW spr round 2 (radius: 5)
[00:15:50 -119930.502831] SLOW spr round 3 (radius: 5)
[00:16:53 -119930.501454] SLOW spr round 4 (radius: 10)
[00:18:10 -119930.153688] SLOW spr round 5 (radius: 5)
[00:19:35 -119930.152574] SLOW spr round 6 (radius: 10)
[00:20:59 -119930.152528] SLOW spr round 7 (radius: 15)
[00:23:10 -119930.152522] SLOW spr round 8 (radius: 20)
[00:26:36 -119923.842684] SLOW spr round 9 (radius: 5)
[00:28:11 -119923.841969] SLOW spr round 10 (radius: 10)
[00:29:44 -119923.841946] SLOW spr round 11 (radius: 15)
[00:31:52 -119923.841944] SLOW spr round 12 (radius: 20)
[00:35:17 -119923.841944] SLOW spr round 13 (radius: 25)
[00:39:02 -119923.230555] SLOW spr round 14 (radius: 5)
[00:40:24] [worker #1] ML tree search #2, logLikelihood: -119955.108789
[00:40:36 -119923.229411] SLOW spr round 15 (radius: 10)
[00:42:15 -119923.229344] SLOW spr round 16 (radius: 15)
[00:44:25 -119923.229322] SLOW spr round 17 (radius: 20)
[00:47:52 -119923.229314] SLOW spr round 18 (radius: 25)
[00:51:40 -119922.217536] SLOW spr round 19 (radius: 5)
[00:53:16 -119922.216847] SLOW spr round 20 (radius: 10)
[00:54:55 -119922.216839] SLOW spr round 21 (radius: 15)
[00:57:05 -119922.216839] SLOW spr round 22 (radius: 20)
[01:00:35 -119922.216838] SLOW spr round 23 (radius: 25)
[01:04:26 -119922.216838] Model parameter optimization (eps = 0.100000)

[01:04:34] [worker #0] ML tree search #1, logLikelihood: -119922.100486

[01:04:34 -405789.203187] Initial branch length optimization
[01:04:36 -312903.817377] Model parameter optimization (eps = 10.000000)
[01:05:18 -311308.351530] AUTODETECT spr round 1 (radius: 5)
[01:06:09 -214295.713828] AUTODETECT spr round 2 (radius: 10)
[01:07:08 -165497.039742] AUTODETECT spr round 3 (radius: 15)
[01:08:32 -138090.451997] AUTODETECT spr round 4 (radius: 20)
[01:10:16 -130371.912467] AUTODETECT spr round 5 (radius: 25)
[01:12:02 -129417.225534] SPR radius for FAST iterations: 25 (autodetect)
[01:12:02 -129417.225534] Model parameter optimization (eps = 3.000000)
[01:12:34 -128518.608539] FAST spr round 1 (radius: 25)
[01:14:03 -120406.823263] FAST spr round 2 (radius: 25)
[01:15:07 -120043.582756] FAST spr round 3 (radius: 25)
[01:16:02 -120021.442496] FAST spr round 4 (radius: 25)
[01:16:50 -120011.408433] FAST spr round 5 (radius: 25)
[01:17:35 -120011.396705] Model parameter optimization (eps = 1.000000)
[01:17:47 -120005.151576] SLOW spr round 1 (radius: 5)
[01:18:52 -119979.560956] SLOW spr round 2 (radius: 5)
[01:19:58 -119978.556424] SLOW spr round 3 (radius: 5)
[01:21:01 -119978.555318] SLOW spr round 4 (radius: 10)
[01:22:14 -119969.175023] SLOW spr round 5 (radius: 5)
[01:23:41 -119966.267755] SLOW spr round 6 (radius: 5)
[01:24:55 -119966.267378] SLOW spr round 7 (radius: 10)
[01:26:12 -119966.267349] SLOW spr round 8 (radius: 15)
[01:27:44] [worker #1] ML tree search #4, logLikelihood: -119899.183731
[01:28:30 -119965.971536] SLOW spr round 9 (radius: 5)
[01:30:03 -119965.971372] SLOW spr round 10 (radius: 10)
[01:31:32 -119965.971286] SLOW spr round 11 (radius: 15)
[01:33:42 -119965.971281] SLOW spr round 12 (radius: 20)
[01:37:02 -119965.971278] SLOW spr round 13 (radius: 25)
[01:40:50 -119965.971275] Model parameter optimization (eps = 0.100000)

[01:40:57] [worker #0] ML tree search #3, logLikelihood: -119965.681773

[01:40:58 -406909.978404] Initial branch length optimization
[01:41:00 -310302.585258] Model parameter optimization (eps = 10.000000)
[01:41:39 -308754.707380] AUTODETECT spr round 1 (radius: 5)
[01:42:30 -219966.785060] AUTODETECT spr round 2 (radius: 10)
[01:43:29 -181622.523335] AUTODETECT spr round 3 (radius: 15)
[01:44:40 -156732.275267] AUTODETECT spr round 4 (radius: 20)
[01:46:09 -148568.488959] AUTODETECT spr round 5 (radius: 25)
[01:47:52 -142343.480656] SPR radius for FAST iterations: 25 (autodetect)
[01:47:52 -142343.480656] Model parameter optimization (eps = 3.000000)
[01:48:28 -141324.104683] FAST spr round 1 (radius: 25)
[01:50:03 -121304.008497] FAST spr round 2 (radius: 25)
[01:51:17 -120130.084625] FAST spr round 3 (radius: 25)
[01:52:18 -120043.475300] FAST spr round 4 (radius: 25)
[01:53:09 -120016.375426] FAST spr round 5 (radius: 25)
[01:53:56 -120014.455393] FAST spr round 6 (radius: 25)
[01:54:40 -120014.454573] Model parameter optimization (eps = 1.000000)
[01:54:54 -120000.815192] SLOW spr round 1 (radius: 5)
[01:56:06 -119967.453910] SLOW spr round 2 (radius: 5)
[01:57:18 -119964.055639] SLOW spr round 3 (radius: 5)
[01:58:26 -119961.129325] SLOW spr round 4 (radius: 5)
[01:59:33 -119961.103214] SLOW spr round 5 (radius: 10)
[02:00:50 -119956.134204] SLOW spr round 6 (radius: 5)
[02:02:17 -119956.085762] SLOW spr round 7 (radius: 10)
[02:03:39 -119956.061568] SLOW spr round 8 (radius: 15)
[02:05:48 -119949.743272] SLOW spr round 9 (radius: 5)
[02:07:19 -119949.741488] SLOW spr round 10 (radius: 10)
[02:08:46 -119949.741403] SLOW spr round 11 (radius: 15)
[02:10:51 -119949.741368] SLOW spr round 12 (radius: 20)
[02:14:25 -119949.741349] SLOW spr round 13 (radius: 25)
[02:14:51] [worker #1] ML tree search #6, logLikelihood: -119919.795141
[02:18:24 -119949.741337] Model parameter optimization (eps = 0.100000)

[02:18:35] [worker #0] ML tree search #5, logLikelihood: -119949.252092

[02:18:35 -408023.324998] Initial branch length optimization
[02:18:37 -312941.108961] Model parameter optimization (eps = 10.000000)
[02:19:11 -311219.000390] AUTODETECT spr round 1 (radius: 5)
[02:20:02 -216932.136369] AUTODETECT spr round 2 (radius: 10)
[02:21:04 -175168.268150] AUTODETECT spr round 3 (radius: 15)
[02:22:26 -147610.858494] AUTODETECT spr round 4 (radius: 20)
[02:24:13 -135041.835472] AUTODETECT spr round 5 (radius: 25)
[02:26:09 -133529.309696] SPR radius for FAST iterations: 25 (autodetect)
[02:26:09 -133529.309696] Model parameter optimization (eps = 3.000000)
[02:26:43 -132449.818747] FAST spr round 1 (radius: 25)
[02:28:04 -120367.815028] FAST spr round 2 (radius: 25)
[02:29:04 -120031.136379] FAST spr round 3 (radius: 25)
[02:29:59 -119975.072520] FAST spr round 4 (radius: 25)
[02:30:49 -119968.455538] FAST spr round 5 (radius: 25)
[02:31:35 -119968.443188] Model parameter optimization (eps = 1.000000)
[02:31:48 -119962.169224] SLOW spr round 1 (radius: 5)
[02:32:55 -119946.590149] SLOW spr round 2 (radius: 5)
[02:34:01 -119945.854893] SLOW spr round 3 (radius: 5)
[02:35:06 -119945.854529] SLOW spr round 4 (radius: 10)
[02:36:21 -119944.539008] SLOW spr round 5 (radius: 5)
[02:37:47 -119944.213611] SLOW spr round 6 (radius: 5)
[02:39:01 -119944.213373] SLOW spr round 7 (radius: 10)
[02:40:19 -119944.213353] SLOW spr round 8 (radius: 15)
[02:42:34 -119944.213349] SLOW spr round 9 (radius: 20)
[02:46:05 -119944.213348] SLOW spr round 10 (radius: 25)
[02:49:55 -119944.213347] Model parameter optimization (eps = 0.100000)

[02:49:59] [worker #0] ML tree search #7, logLikelihood: -119944.184940

[02:49:59 -403561.329280] Initial branch length optimization
[02:50:01 -309866.429321] Model parameter optimization (eps = 10.000000)
[02:50:37 -308286.206718] AUTODETECT spr round 1 (radius: 5)
[02:51:27 -219995.658997] AUTODETECT spr round 2 (radius: 10)
[02:52:28 -172700.196456] AUTODETECT spr round 3 (radius: 15)
[02:53:42 -144227.455783] AUTODETECT spr round 4 (radius: 20)
[02:54:43] [worker #1] ML tree search #8, logLikelihood: -119957.869889
[02:55:25 -136457.438657] AUTODETECT spr round 5 (radius: 25)
[02:57:28 -134651.313330] SPR radius for FAST iterations: 25 (autodetect)
[02:57:28 -134651.313330] Model parameter optimization (eps = 3.000000)
[02:58:01 -133676.558452] FAST spr round 1 (radius: 25)
[02:59:33 -121018.406694] FAST spr round 2 (radius: 25)
[03:00:38 -120060.028032] FAST spr round 3 (radius: 25)
[03:01:33 -120001.436204] FAST spr round 4 (radius: 25)
[03:02:21 -119999.647780] FAST spr round 5 (radius: 25)
[03:03:07 -119999.646822] Model parameter optimization (eps = 1.000000)
[03:03:21 -119994.221445] SLOW spr round 1 (radius: 5)
[03:04:29 -119976.940716] SLOW spr round 2 (radius: 5)
[03:05:37 -119976.733861] SLOW spr round 3 (radius: 5)
[03:06:43 -119976.722458] SLOW spr round 4 (radius: 10)
[03:08:01 -119953.359644] SLOW spr round 5 (radius: 5)
[03:09:30 -119949.586738] SLOW spr round 6 (radius: 5)
[03:10:44 -119949.586041] SLOW spr round 7 (radius: 10)
[03:12:02 -119948.306409] SLOW spr round 8 (radius: 5)
[03:13:27 -119948.305682] SLOW spr round 9 (radius: 10)
[03:14:50 -119948.305663] SLOW spr round 10 (radius: 15)
[03:17:00 -119948.305653] SLOW spr round 11 (radius: 20)
[03:20:35 -119948.305648] SLOW spr round 12 (radius: 25)
[03:24:32 -119948.305645] Model parameter optimization (eps = 0.100000)

[03:24:40] [worker #0] ML tree search #9, logLikelihood: -119948.048013

[03:24:40 -398882.169657] Initial branch length optimization
[03:24:43 -306787.142416] Model parameter optimization (eps = 10.000000)
[03:25:18 -305093.763687] AUTODETECT spr round 1 (radius: 5)
[03:26:10 -224774.901555] AUTODETECT spr round 2 (radius: 10)
[03:27:10 -181761.559850] AUTODETECT spr round 3 (radius: 15)
[03:28:28 -158083.735330] AUTODETECT spr round 4 (radius: 20)
[03:28:55] [worker #1] ML tree search #10, logLikelihood: -119969.205060
[03:29:52 -142705.490149] AUTODETECT spr round 5 (radius: 25)
[03:31:24 -139209.696728] SPR radius for FAST iterations: 25 (autodetect)
[03:31:24 -139209.696728] Model parameter optimization (eps = 3.000000)
[03:31:56 -138184.895448] FAST spr round 1 (radius: 25)
[03:33:29 -120852.044903] FAST spr round 2 (radius: 25)
[03:34:38 -120117.807487] FAST spr round 3 (radius: 25)
[03:35:35 -120041.044424] FAST spr round 4 (radius: 25)
[03:36:26 -120034.771543] FAST spr round 5 (radius: 25)
[03:37:12 -120034.466546] FAST spr round 6 (radius: 25)
[03:37:57 -120034.454614] Model parameter optimization (eps = 1.000000)
[03:38:12 -120015.856708] SLOW spr round 1 (radius: 5)
[03:39:21 -119981.987097] SLOW spr round 2 (radius: 5)
[03:40:29 -119978.664584] SLOW spr round 3 (radius: 5)
[03:41:33 -119978.642467] SLOW spr round 4 (radius: 10)
[03:42:52 -119978.392118] SLOW spr round 5 (radius: 5)
[03:44:16 -119978.391867] SLOW spr round 6 (radius: 10)
[03:45:43 -119978.391855] SLOW spr round 7 (radius: 15)
[03:48:01 -119977.374617] SLOW spr round 8 (radius: 5)
[03:49:35 -119976.993100] SLOW spr round 9 (radius: 5)
[03:50:54 -119976.992910] SLOW spr round 10 (radius: 10)
[03:52:18 -119976.992906] SLOW spr round 11 (radius: 15)
[03:54:37 -119976.992902] SLOW spr round 12 (radius: 20)
[03:58:19 -119975.937420] SLOW spr round 13 (radius: 5)
[03:59:54 -119975.932209] SLOW spr round 14 (radius: 10)
[04:01:31 -119975.932205] SLOW spr round 15 (radius: 15)
[04:03:44 -119975.932201] SLOW spr round 16 (radius: 20)
[04:07:09] [worker #1] ML tree search #12, logLikelihood: -119936.947946
[04:07:25 -119975.932195] SLOW spr round 17 (radius: 25)
[04:11:21 -119975.932191] Model parameter optimization (eps = 0.100000)

[04:11:29] [worker #0] ML tree search #11, logLikelihood: -119975.728146

[04:11:29 -404525.967366] Initial branch length optimization
[04:11:32 -312793.336126] Model parameter optimization (eps = 10.000000)
[04:11:59 -311345.507246] AUTODETECT spr round 1 (radius: 5)
[04:12:49 -212127.066724] AUTODETECT spr round 2 (radius: 10)
[04:13:50 -169059.835523] AUTODETECT spr round 3 (radius: 15)
[04:15:06 -151710.556565] AUTODETECT spr round 4 (radius: 20)
[04:16:34 -137152.557880] AUTODETECT spr round 5 (radius: 25)
[04:18:15 -132365.562513] SPR radius for FAST iterations: 25 (autodetect)
[04:18:15 -132365.562513] Model parameter optimization (eps = 3.000000)
[04:18:50 -131483.600705] FAST spr round 1 (radius: 25)
[04:20:11 -120527.024693] FAST spr round 2 (radius: 25)
[04:21:11 -120068.128151] FAST spr round 3 (radius: 25)
[04:22:06 -120003.137152] FAST spr round 4 (radius: 25)
[04:22:59 -120002.762813] FAST spr round 5 (radius: 25)
[04:23:45 -120002.760398] Model parameter optimization (eps = 1.000000)
[04:23:57 -119999.264640] SLOW spr round 1 (radius: 5)
[04:25:04 -119966.878528] SLOW spr round 2 (radius: 5)
[04:26:12 -119966.875648] SLOW spr round 3 (radius: 10)
[04:27:29 -119964.989853] SLOW spr round 4 (radius: 5)
[04:28:55 -119964.988154] SLOW spr round 5 (radius: 10)
[04:30:18 -119964.988100] SLOW spr round 6 (radius: 15)
[04:32:29 -119958.768358] SLOW spr round 7 (radius: 5)
[04:34:03 -119945.176085] SLOW spr round 8 (radius: 5)
[04:35:22 -119945.173029] SLOW spr round 9 (radius: 10)
[04:36:41 -119945.172908] SLOW spr round 10 (radius: 15)
[04:38:55 -119942.981847] SLOW spr round 11 (radius: 5)
[04:40:28 -119942.980430] SLOW spr round 12 (radius: 10)
[04:41:58 -119942.980004] SLOW spr round 13 (radius: 15)
[04:44:05 -119942.979823] SLOW spr round 14 (radius: 20)
[04:47:25 -119942.979731] SLOW spr round 15 (radius: 25)
[04:51:18 -119940.783187] SLOW spr round 16 (radius: 5)
[04:51:32] [worker #1] ML tree search #14, logLikelihood: -119969.954211
[04:52:55 -119939.740556] SLOW spr round 17 (radius: 5)
[04:54:18 -119939.652254] SLOW spr round 18 (radius: 10)
[04:55:39 -119939.649333] SLOW spr round 19 (radius: 15)
[04:57:51 -119939.215540] SLOW spr round 20 (radius: 5)
[04:59:22 -119939.212918] SLOW spr round 21 (radius: 10)
[05:00:53 -119939.211439] SLOW spr round 22 (radius: 15)
[05:03:02 -119939.210629] SLOW spr round 23 (radius: 20)
[05:06:25 -119939.210161] SLOW spr round 24 (radius: 25)
[05:10:17 -119939.209885] Model parameter optimization (eps = 0.100000)

[05:10:24] [worker #0] ML tree search #13, logLikelihood: -119939.106778

[05:10:25 -408000.156677] Initial branch length optimization
[05:10:27 -312095.592513] Model parameter optimization (eps = 10.000000)
[05:11:03 -310269.207524] AUTODETECT spr round 1 (radius: 5)
[05:11:56 -215225.736485] AUTODETECT spr round 2 (radius: 10)
[05:12:59 -166378.962396] AUTODETECT spr round 3 (radius: 15)
[05:14:17 -143556.212271] AUTODETECT spr round 4 (radius: 20)
[05:15:50 -134309.675513] AUTODETECT spr round 5 (radius: 25)
[05:17:38 -133607.493599] SPR radius for FAST iterations: 25 (autodetect)
[05:17:38 -133607.493599] Model parameter optimization (eps = 3.000000)
[05:18:11 -132483.683323] FAST spr round 1 (radius: 25)
[05:19:33 -120647.674356] FAST spr round 2 (radius: 25)
[05:20:33 -120062.256764] FAST spr round 3 (radius: 25)
[05:21:30 -120002.264241] FAST spr round 4 (radius: 25)
[05:22:20 -119996.628562] FAST spr round 5 (radius: 25)
[05:23:06 -119995.377752] FAST spr round 6 (radius: 25)
[05:23:51 -119995.376756] Model parameter optimization (eps = 1.000000)
[05:24:05 -119987.166764] SLOW spr round 1 (radius: 5)
[05:25:13 -119969.754150] SLOW spr round 2 (radius: 5)
[05:26:18 -119969.752111] SLOW spr round 3 (radius: 10)
[05:27:36 -119948.582201] SLOW spr round 4 (radius: 5)
[05:29:01 -119948.328750] SLOW spr round 5 (radius: 5)
[05:30:14 -119948.328378] SLOW spr round 6 (radius: 10)
[05:31:33 -119948.328264] SLOW spr round 7 (radius: 15)
[05:31:43] [worker #1] ML tree search #16, logLikelihood: -119892.288535
[05:33:46 -119946.945402] SLOW spr round 8 (radius: 5)
[05:35:19 -119946.899575] SLOW spr round 9 (radius: 10)
[05:36:51 -119946.702925] SLOW spr round 10 (radius: 5)
[05:38:17 -119946.674030] SLOW spr round 11 (radius: 10)
[05:39:39 -119946.674020] SLOW spr round 12 (radius: 15)
[05:41:51 -119946.674017] SLOW spr round 13 (radius: 20)
[05:45:30 -119946.674015] SLOW spr round 14 (radius: 25)
[05:49:27 -119944.429658] SLOW spr round 15 (radius: 5)
[05:51:03 -119943.263642] SLOW spr round 16 (radius: 5)
[05:52:24 -119943.260653] SLOW spr round 17 (radius: 10)
[05:53:42 -119943.260471] SLOW spr round 18 (radius: 15)
[05:55:50 -119943.260432] SLOW spr round 19 (radius: 20)
[05:59:24 -119943.260422] SLOW spr round 20 (radius: 25)
[06:03:22 -119943.260417] Model parameter optimization (eps = 0.100000)

[06:03:31] [worker #0] ML tree search #15, logLikelihood: -119942.778586

[06:03:31 -404716.449621] Initial branch length optimization
[06:03:33 -312213.393624] Model parameter optimization (eps = 10.000000)
[06:04:04 -310522.839527] AUTODETECT spr round 1 (radius: 5)
[06:04:54 -222868.515659] AUTODETECT spr round 2 (radius: 10)
[06:05:57 -166254.972692] AUTODETECT spr round 3 (radius: 15)
[06:07:13 -146438.576413] AUTODETECT spr round 4 (radius: 20)
[06:08:33 -137293.792165] AUTODETECT spr round 5 (radius: 25)
[06:09:15] [worker #1] ML tree search #18, logLikelihood: -119974.585154
[06:10:00 -133772.975338] SPR radius for FAST iterations: 25 (autodetect)
[06:10:00 -133772.975338] Model parameter optimization (eps = 3.000000)
[06:10:31 -132805.424786] FAST spr round 1 (radius: 25)
[06:12:00 -120854.164678] FAST spr round 2 (radius: 25)
[06:13:08 -120272.333971] FAST spr round 3 (radius: 25)
[06:13:59 -120016.123083] FAST spr round 4 (radius: 25)
[06:14:47 -120013.476138] FAST spr round 5 (radius: 25)
[06:15:33 -120013.450183] Model parameter optimization (eps = 1.000000)
[06:15:48 -120000.715601] SLOW spr round 1 (radius: 5)
[06:16:56 -119974.227604] SLOW spr round 2 (radius: 5)
[06:18:03 -119973.888231] SLOW spr round 3 (radius: 5)
[06:19:10 -119973.876443] SLOW spr round 4 (radius: 10)
[06:20:31 -119954.885698] SLOW spr round 5 (radius: 5)
[06:21:57 -119954.882468] SLOW spr round 6 (radius: 10)
[06:23:21 -119954.287151] SLOW spr round 7 (radius: 5)
[06:24:45 -119954.287050] SLOW spr round 8 (radius: 10)
[06:26:08 -119954.287024] SLOW spr round 9 (radius: 15)
[06:28:19 -119946.345691] SLOW spr round 10 (radius: 5)
[06:29:51 -119946.316953] SLOW spr round 11 (radius: 10)
[06:31:21 -119946.214043] SLOW spr round 12 (radius: 5)
[06:32:45 -119946.183448] SLOW spr round 13 (radius: 10)
[06:34:07 -119946.183430] SLOW spr round 14 (radius: 15)
[06:36:15 -119946.183422] SLOW spr round 15 (radius: 20)
[06:39:43 -119946.183416] SLOW spr round 16 (radius: 25)
[06:43:35 -119946.183410] Model parameter optimization (eps = 0.100000)

[06:43:42] [worker #0] ML tree search #17, logLikelihood: -119946.112854

[06:43:42 -408024.297891] Initial branch length optimization
[06:43:45 -311997.283784] Model parameter optimization (eps = 10.000000)
[06:44:25 -310281.111010] AUTODETECT spr round 1 (radius: 5)
[06:45:18 -223840.044743] AUTODETECT spr round 2 (radius: 10)
[06:46:21 -165155.451368] AUTODETECT spr round 3 (radius: 15)
[06:47:35 -146089.944049] AUTODETECT spr round 4 (radius: 20)
[06:48:57 -141338.582507] AUTODETECT spr round 5 (radius: 25)
[06:50:47 -135517.829734] SPR radius for FAST iterations: 25 (autodetect)
[06:50:47 -135517.829734] Model parameter optimization (eps = 3.000000)
[06:51:18 -134375.814697] FAST spr round 1 (radius: 25)
[06:52:48 -120523.624638] FAST spr round 2 (radius: 25)
[06:53:59 -120041.168322] FAST spr round 3 (radius: 25)
[06:54:51 -120023.734552] FAST spr round 4 (radius: 25)
[06:55:41 -120017.620661] FAST spr round 5 (radius: 25)
[06:56:27 -120017.607959] Model parameter optimization (eps = 1.000000)
[06:56:41 -120008.003570] SLOW spr round 1 (radius: 5)
[06:57:48 -119989.405677] SLOW spr round 2 (radius: 5)
[06:58:54 -119988.091652] SLOW spr round 3 (radius: 5)
[07:00:02 -119983.077720] SLOW spr round 4 (radius: 5)
[07:01:07 -119982.272876] SLOW spr round 5 (radius: 5)
[07:02:11 -119982.272670] SLOW spr round 6 (radius: 10)
[07:03:31 -119966.192329] SLOW spr round 7 (radius: 5)
[07:03:41] [worker #1] ML tree search #20, logLikelihood: -119903.129098
[07:04:56 -119963.748540] SLOW spr round 8 (radius: 5)
[07:06:08 -119963.736585] SLOW spr round 9 (radius: 10)
[07:07:29 -119959.278267] SLOW spr round 10 (radius: 5)
[07:08:52 -119959.277551] SLOW spr round 11 (radius: 10)
[07:10:13 -119959.277436] SLOW spr round 12 (radius: 15)
[07:12:23 -119956.724545] SLOW spr round 13 (radius: 5)
[07:13:51 -119956.720889] SLOW spr round 14 (radius: 10)
[07:15:19 -119956.719800] SLOW spr round 15 (radius: 15)
[07:17:26 -119956.719431] SLOW spr round 16 (radius: 20)
[07:21:03 -119956.719274] SLOW spr round 17 (radius: 25)
[07:24:54 -119954.604079] SLOW spr round 18 (radius: 5)
[07:26:27 -119954.503920] SLOW spr round 19 (radius: 5)
[07:27:44 -119954.502650] SLOW spr round 20 (radius: 10)
[07:29:03 -119953.756532] SLOW spr round 21 (radius: 5)
[07:30:25 -119952.894663] SLOW spr round 22 (radius: 5)
[07:31:35 -119952.564400] SLOW spr round 23 (radius: 5)
[07:32:40 -119952.561527] SLOW spr round 24 (radius: 10)
[07:33:55 -119952.561049] SLOW spr round 25 (radius: 15)
[07:36:11 -119952.560906] SLOW spr round 26 (radius: 20)
[07:39:48 -119952.560815] SLOW spr round 27 (radius: 25)
[07:43:41 -119952.560731] Model parameter optimization (eps = 0.100000)

[07:43:45] [worker #0] ML tree search #19, logLikelihood: -119952.526999


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.265854,0.611042) (0.168751,0.669206) (0.365175,0.805620) (0.200219,2.149793) 
   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: -119892.288535

AIC score: 241650.577069 / AICc score: 278732.364303 / BIC score: 246211.615174
Free parameters (model + branch lengths): 933

Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12791/3_mltree/Q12791.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12791/3_mltree/Q12791.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12791/3_mltree/Q12791.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q12791/3_mltree/Q12791.raxml.log

Analysis started: 03-Jul-2021 03:29:23 / finished: 03-Jul-2021 11:13:08

Elapsed time: 27825.208 seconds

Consumed energy: 2322.465 Wh (= 12 km in an electric car, or 58 km with an e-scooter!)