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

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 06-Jul-2021 03:15:26 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/2_msa/A0A075B6I1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/2_msa/A0A075B6I1_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 138 sites

WARNING: Sequences tr_A0A2I2YJC5_A0A2I2YJC5_GORGO_9595 and tr_A0A2I3RV96_A0A2I3RV96_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3RYP8_A0A2I3RYP8_PANTR_9598 and tr_A0A2R9AL33_A0A2R9AL33_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3S3B0_A0A2I3S3B0_PANTR_9598 and tr_A0A2R9BNT9_A0A2R9BNT9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SR69_A0A2I3SR69_PANTR_9598 and tr_A0A2R8ZB48_A0A2R8ZB48_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SXH8_A0A2I3SXH8_PANTR_9598 and tr_A0A2R9AKM0_A0A2R9AKM0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3T0N1_A0A2I3T0N1_PANTR_9598 and tr_A0A2R8ZDA9_A0A2R8ZDA9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TAX1_A0A2I3TAX1_PANTR_9598 and tr_A0A2R9AKE1_A0A2R9AKE1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TQF9_A0A2I3TQF9_PANTR_9598 and tr_A0A2R8ZQY1_A0A2R8ZQY1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TUR2_A0A2I3TUR2_PANTR_9598 and tr_A0A2R8ZX92_A0A2R8ZX92_PANPA_9597 are exactly identical!
WARNING: Sequences sp_A0A0B4J1Y8_LV949_HUMAN_9606 and tr_A0A2R9A2R6_A0A2R9A2R6_PANPA_9597 are exactly identical!
WARNING: Sequences sp_A0A0B4J2D9_KVD13_HUMAN_9606 and sp_P0DP09_KV113_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_P01593_KVD33_HUMAN_9606 and sp_P01594_KV133_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F7F215_F7F215_MACMU_9544 and tr_A0A2K6ARQ7_A0A2K6ARQ7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PHB9_G7PHB9_MACFA_9541 and tr_A0A096NSB1_A0A096NSB1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PHB9_G7PHB9_MACFA_9541 and tr_A0A2K5XPA3_A0A2K5XPA3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3LZC8_A0A2I3LZC8_PAPAN_9555 and tr_A0A2K6B468_A0A2K6B468_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3LZC8_A0A2I3LZC8_PAPAN_9555 and tr_A0A2K5XFL9_A0A2K5XFL9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3N776_A0A2I3N776_PAPAN_9555 and tr_A0A2K5NT28_A0A2K5NT28_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9RN59_A0A0D9RN59_CHLSB_60711 and tr_A0A0D9RN85_A0A0D9RN85_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2K5KMJ7_A0A2K5KMJ7_CERAT_9531 and tr_A0A2K5XYB4_A0A2K5XYB4_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 20

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.reduced.phy

Alignment comprises 1 partitions and 138 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 138 / 138
Gaps: 16.11 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 1 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 / 138 / 11040
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -189268.200094] Initial branch length optimization
[00:00:02 -166770.575282] Model parameter optimization (eps = 10.000000)
[00:00:42 -166484.192023] AUTODETECT spr round 1 (radius: 5)
[00:03:08 -119886.784772] AUTODETECT spr round 2 (radius: 10)
[00:05:46 -91709.235133] AUTODETECT spr round 3 (radius: 15)
[00:08:48 -79516.302797] AUTODETECT spr round 4 (radius: 20)
[00:12:32 -75821.114452] AUTODETECT spr round 5 (radius: 25)
[00:17:13 -73867.546221] SPR radius for FAST iterations: 25 (autodetect)
[00:17:13 -73867.546221] Model parameter optimization (eps = 3.000000)
[00:17:23 -73860.032359] FAST spr round 1 (radius: 25)
[00:20:33 -66228.849704] FAST spr round 2 (radius: 25)
[00:23:05 -65760.124339] FAST spr round 3 (radius: 25)
[00:25:19 -65716.178456] FAST spr round 4 (radius: 25)
[00:27:14 -65715.453961] FAST spr round 5 (radius: 25)
[00:29:08 -65715.453938] Model parameter optimization (eps = 1.000000)
[00:29:13 -65715.384052] SLOW spr round 1 (radius: 5)
[00:31:51 -65695.746649] SLOW spr round 2 (radius: 5)
[00:34:18 -65692.505848] SLOW spr round 3 (radius: 5)
[00:36:41 -65690.540744] SLOW spr round 4 (radius: 5)
[00:39:00 -65690.540744] SLOW spr round 5 (radius: 10)
[00:41:26 -65689.150584] SLOW spr round 6 (radius: 5)
[00:44:19 -65689.150509] SLOW spr round 7 (radius: 10)
[00:46:58 -65688.263263] SLOW spr round 8 (radius: 5)
[00:49:48 -65688.263258] SLOW spr round 9 (radius: 10)
[00:52:23 -65687.511847] SLOW spr round 10 (radius: 5)
[00:55:14 -65686.642996] SLOW spr round 11 (radius: 5)
[00:57:47 -65686.642946] SLOW spr round 12 (radius: 10)
[01:00:14 -65686.642946] SLOW spr round 13 (radius: 15)
[01:04:09 -65682.542195] SLOW spr round 14 (radius: 5)
[01:07:13 -65682.439909] SLOW spr round 15 (radius: 5)
[01:09:53 -65682.439383] SLOW spr round 16 (radius: 10)
[01:12:23 -65682.439383] SLOW spr round 17 (radius: 15)
[01:16:13 -65682.439383] SLOW spr round 18 (radius: 20)
[01:22:14 -65681.981336] SLOW spr round 19 (radius: 5)
[01:25:19 -65679.223498] SLOW spr round 20 (radius: 5)
[01:28:02 -65679.223447] SLOW spr round 21 (radius: 10)
[01:30:34 -65679.223447] SLOW spr round 22 (radius: 15)
[01:34:26 -65679.223447] SLOW spr round 23 (radius: 20)
[01:40:27 -65679.223447] SLOW spr round 24 (radius: 25)
[01:44:37] [worker #2] ML tree search #3, logLikelihood: -65431.929228
[01:48:34 -65674.151284] SLOW spr round 25 (radius: 5)
[01:51:41 -65672.079078] SLOW spr round 26 (radius: 5)
[01:54:23 -65672.079078] SLOW spr round 27 (radius: 10)
[01:56:57 -65672.079078] SLOW spr round 28 (radius: 15)
[02:00:51 -65672.079078] SLOW spr round 29 (radius: 20)
[02:06:53 -65672.079078] SLOW spr round 30 (radius: 25)
[02:10:09] [worker #1] ML tree search #2, logLikelihood: -65343.988532
[02:14:57 -65670.426556] SLOW spr round 31 (radius: 5)
[02:18:03 -65670.426550] SLOW spr round 32 (radius: 10)
[02:21:00 -65670.426550] SLOW spr round 33 (radius: 15)
[02:24:42 -65670.426550] SLOW spr round 34 (radius: 20)
[02:30:53 -65670.426550] SLOW spr round 35 (radius: 25)
[02:38:56 -65670.426550] Model parameter optimization (eps = 0.100000)

[02:39:00] [worker #0] ML tree search #1, logLikelihood: -65670.422256

[02:39:01 -190409.695561] Initial branch length optimization
[02:39:04 -167147.210171] Model parameter optimization (eps = 10.000000)
[02:39:43 -166964.654095] AUTODETECT spr round 1 (radius: 5)
[02:42:10 -120978.684618] AUTODETECT spr round 2 (radius: 10)
[02:44:50 -90984.859531] AUTODETECT spr round 3 (radius: 15)
[02:47:45 -78367.537881] AUTODETECT spr round 4 (radius: 20)
[02:51:10 -74316.883408] AUTODETECT spr round 5 (radius: 25)
[02:55:35 -73735.464432] SPR radius for FAST iterations: 25 (autodetect)
[02:55:35 -73735.464432] Model parameter optimization (eps = 3.000000)
[02:56:09 -73539.539471] FAST spr round 1 (radius: 25)
[02:59:21 -65927.082627] FAST spr round 2 (radius: 25)
[03:01:48 -65527.807732] FAST spr round 3 (radius: 25)
[03:04:02 -65493.905494] FAST spr round 4 (radius: 25)
[03:06:05 -65484.591085] FAST spr round 5 (radius: 25)
[03:08:05 -65468.108659] FAST spr round 6 (radius: 25)
[03:09:56 -65465.082186] FAST spr round 7 (radius: 25)
[03:11:45 -65465.082173] Model parameter optimization (eps = 1.000000)
[03:12:00 -65443.065101] SLOW spr round 1 (radius: 5)
[03:14:30 -65428.764355] SLOW spr round 2 (radius: 5)
[03:16:52 -65426.614786] SLOW spr round 3 (radius: 5)
[03:19:08 -65426.614657] SLOW spr round 4 (radius: 10)
[03:21:31 -65422.195272] SLOW spr round 5 (radius: 5)
[03:24:22 -65421.908107] SLOW spr round 6 (radius: 5)
[03:26:54 -65421.908107] SLOW spr round 7 (radius: 10)
[03:29:19 -65420.718725] SLOW spr round 8 (radius: 5)
[03:32:07 -65420.532134] SLOW spr round 9 (radius: 5)
[03:34:37 -65420.532077] SLOW spr round 10 (radius: 10)
[03:36:59 -65420.179274] SLOW spr round 11 (radius: 5)
[03:39:46 -65419.578395] SLOW spr round 12 (radius: 5)
[03:42:17 -65419.578365] SLOW spr round 13 (radius: 10)
[03:44:42 -65419.298383] SLOW spr round 14 (radius: 5)
[03:47:30 -65417.096367] SLOW spr round 15 (radius: 5)
[03:47:43] [worker #2] ML tree search #6, logLikelihood: -65456.857547
[03:50:02 -65417.096367] SLOW spr round 16 (radius: 10)
[03:52:26 -65417.096367] SLOW spr round 17 (radius: 15)
[03:55:53 -65412.736276] SLOW spr round 18 (radius: 5)
[03:58:51 -65408.233904] SLOW spr round 19 (radius: 5)
[04:01:25 -65408.233898] SLOW spr round 20 (radius: 10)
[04:03:49 -65408.233898] SLOW spr round 21 (radius: 15)
[04:05:48] [worker #1] ML tree search #5, logLikelihood: -65404.280658
[04:07:11 -65408.233898] SLOW spr round 22 (radius: 20)
[04:11:51 -65404.306685] SLOW spr round 23 (radius: 5)
[04:14:48 -65404.306649] SLOW spr round 24 (radius: 10)
[04:17:32 -65404.306649] SLOW spr round 25 (radius: 15)
[04:20:47 -65403.394792] SLOW spr round 26 (radius: 5)
[04:23:43 -65403.394739] SLOW spr round 27 (radius: 10)
[04:26:24 -65401.932274] SLOW spr round 28 (radius: 5)
[04:29:09 -65401.932264] SLOW spr round 29 (radius: 10)
[04:31:40 -65401.932264] SLOW spr round 30 (radius: 15)
[04:34:59 -65396.512304] SLOW spr round 31 (radius: 5)
[04:37:53 -65396.512302] SLOW spr round 32 (radius: 10)
[04:40:34 -65396.512302] SLOW spr round 33 (radius: 15)
[04:43:51 -65396.512302] SLOW spr round 34 (radius: 20)
[04:48:39 -65396.512302] SLOW spr round 35 (radius: 25)
[04:54:39 -65396.512302] Model parameter optimization (eps = 0.100000)

[04:54:45] [worker #0] ML tree search #4, logLikelihood: -65396.502495

[04:54:45 -189253.043214] Initial branch length optimization
[04:54:47 -166912.716604] Model parameter optimization (eps = 10.000000)
[04:55:22 -166641.021815] AUTODETECT spr round 1 (radius: 5)
[04:57:46 -122376.081847] AUTODETECT spr round 2 (radius: 10)
[05:00:30 -90349.332829] AUTODETECT spr round 3 (radius: 15)
[05:03:19 -76742.878150] AUTODETECT spr round 4 (radius: 20)
[05:06:33 -73578.724132] AUTODETECT spr round 5 (radius: 25)
[05:10:00 -73128.377970] SPR radius for FAST iterations: 25 (autodetect)
[05:10:00 -73128.377970] Model parameter optimization (eps = 3.000000)
[05:10:30 -72911.844414] FAST spr round 1 (radius: 25)
[05:13:40 -65972.789924] FAST spr round 2 (radius: 25)
[05:16:09 -65519.799298] FAST spr round 3 (radius: 25)
[05:18:19 -65490.629913] FAST spr round 4 (radius: 25)
[05:20:20 -65482.966576] FAST spr round 5 (radius: 25)
[05:22:13 -65479.380224] FAST spr round 6 (radius: 25)
[05:24:03 -65479.380095] Model parameter optimization (eps = 1.000000)
[05:24:20 -65462.676149] SLOW spr round 1 (radius: 5)
[05:26:51 -65442.899072] SLOW spr round 2 (radius: 5)
[05:29:20 -65434.924527] SLOW spr round 3 (radius: 5)
[05:31:40 -65434.770800] SLOW spr round 4 (radius: 5)
[05:33:59 -65434.770793] SLOW spr round 5 (radius: 10)
[05:36:20 -65433.706507] SLOW spr round 6 (radius: 5)
[05:39:15 -65425.199035] SLOW spr round 7 (radius: 5)
[05:39:52] [worker #2] ML tree search #9, logLikelihood: -65373.489484
[05:41:52 -65423.009547] SLOW spr round 8 (radius: 5)
[05:44:17 -65423.009513] SLOW spr round 9 (radius: 10)
[05:46:38 -65421.993541] SLOW spr round 10 (radius: 5)
[05:49:28 -65421.993496] SLOW spr round 11 (radius: 10)
[05:52:00 -65421.259732] SLOW spr round 12 (radius: 5)
[05:54:49 -65417.763729] SLOW spr round 13 (radius: 5)
[05:57:22 -65414.071722] SLOW spr round 14 (radius: 5)
[05:59:46 -65413.412562] SLOW spr round 15 (radius: 5)
[06:02:07 -65411.946762] SLOW spr round 16 (radius: 5)
[06:04:29 -65411.946747] SLOW spr round 17 (radius: 10)
[06:06:49 -65411.220493] SLOW spr round 18 (radius: 5)
[06:09:40 -65411.220444] SLOW spr round 19 (radius: 10)
[06:12:12 -65411.220444] SLOW spr round 20 (radius: 15)
[06:15:34 -65410.749056] SLOW spr round 21 (radius: 5)
[06:18:30 -65410.749053] SLOW spr round 22 (radius: 10)
[06:21:10 -65410.749052] SLOW spr round 23 (radius: 15)
[06:24:31 -65410.416083] SLOW spr round 24 (radius: 5)
[06:27:29 -65410.415942] SLOW spr round 25 (radius: 10)
[06:30:10 -65410.415942] SLOW spr round 26 (radius: 15)
[06:33:28 -65410.415942] SLOW spr round 27 (radius: 20)
[06:37:56 -65407.511847] SLOW spr round 28 (radius: 5)
[06:41:01 -65396.228700] SLOW spr round 29 (radius: 5)
[06:43:41 -65396.228688] SLOW spr round 30 (radius: 10)
[06:46:07 -65396.228688] SLOW spr round 31 (radius: 15)
[06:49:29 -65394.987675] SLOW spr round 32 (radius: 5)
[06:52:23 -65393.970832] SLOW spr round 33 (radius: 5)
[06:54:57 -65393.970828] SLOW spr round 34 (radius: 10)
[06:57:20 -65393.970828] SLOW spr round 35 (radius: 15)
[07:00:42 -65393.970828] SLOW spr round 36 (radius: 20)
[07:05:03 -65393.970828] SLOW spr round 37 (radius: 25)
[07:10:09 -65393.970828] Model parameter optimization (eps = 0.100000)

[07:10:15] [worker #0] ML tree search #7, logLikelihood: -65393.949601

[07:10:15 -189839.148546] Initial branch length optimization
[07:10:17 -166819.288641] Model parameter optimization (eps = 10.000000)
[07:10:55 -166623.605618] AUTODETECT spr round 1 (radius: 5)
[07:13:19 -117825.980390] AUTODETECT spr round 2 (radius: 10)
[07:16:04 -88663.627405] AUTODETECT spr round 3 (radius: 15)
[07:18:58 -78180.706896] AUTODETECT spr round 4 (radius: 20)
[07:22:15 -75370.185302] AUTODETECT spr round 5 (radius: 25)
[07:26:16 -73382.611498] SPR radius for FAST iterations: 25 (autodetect)
[07:26:16 -73382.611498] Model parameter optimization (eps = 3.000000)
[07:26:40 -73179.627123] FAST spr round 1 (radius: 25)
[07:29:42 -66048.711632] FAST spr round 2 (radius: 25)
[07:31:55] [worker #1] ML tree search #8, logLikelihood: -65421.577690
[07:32:05 -65628.256303] FAST spr round 3 (radius: 25)
[07:34:16 -65531.846745] FAST spr round 4 (radius: 25)
[07:36:17 -65510.264712] FAST spr round 5 (radius: 25)
[07:38:08 -65506.671769] FAST spr round 6 (radius: 25)
[07:40:04 -65500.087346] FAST spr round 7 (radius: 25)
[07:41:51 -65500.087335] Model parameter optimization (eps = 1.000000)
[07:42:04 -65497.057279] SLOW spr round 1 (radius: 5)
[07:44:34 -65478.493262] SLOW spr round 2 (radius: 5)
[07:46:55 -65478.294845] SLOW spr round 3 (radius: 5)
[07:49:11 -65478.294120] SLOW spr round 4 (radius: 10)
[07:51:34 -65468.637506] SLOW spr round 5 (radius: 5)
[07:54:27 -65460.811493] SLOW spr round 6 (radius: 5)
[07:56:59 -65460.811470] SLOW spr round 7 (radius: 10)
[07:59:02] [worker #2] ML tree search #12, logLikelihood: -65395.368798
[07:59:25 -65455.713118] SLOW spr round 8 (radius: 5)
[08:02:16 -65452.902443] SLOW spr round 9 (radius: 5)
[08:04:47 -65452.902436] SLOW spr round 10 (radius: 10)
[08:07:12 -65452.143128] SLOW spr round 11 (radius: 5)
[08:10:00 -65452.143080] SLOW spr round 12 (radius: 10)
[08:12:33 -65451.424343] SLOW spr round 13 (radius: 5)
[08:15:19 -65451.424308] SLOW spr round 14 (radius: 10)
[08:17:51 -65451.424308] SLOW spr round 15 (radius: 15)
[08:21:15 -65451.221006] SLOW spr round 16 (radius: 5)
[08:24:14 -65450.998180] SLOW spr round 17 (radius: 5)
[08:26:50 -65450.998124] SLOW spr round 18 (radius: 10)
[08:29:15 -65450.998123] SLOW spr round 19 (radius: 15)
[08:32:43 -65450.998123] SLOW spr round 20 (radius: 20)
[08:37:21 -65450.998123] SLOW spr round 21 (radius: 25)
[08:42:44 -65450.998123] Model parameter optimization (eps = 0.100000)

[08:42:55] [worker #0] ML tree search #10, logLikelihood: -65450.704663

[08:42:55 -189727.106390] Initial branch length optimization
[08:42:59 -166925.800528] Model parameter optimization (eps = 10.000000)
[08:43:29 -166737.065765] AUTODETECT spr round 1 (radius: 5)
[08:45:55 -121666.805441] AUTODETECT spr round 2 (radius: 10)
[08:48:33 -91503.987198] AUTODETECT spr round 3 (radius: 15)
[08:51:44 -79589.694152] AUTODETECT spr round 4 (radius: 20)
[08:55:20 -76144.283067] AUTODETECT spr round 5 (radius: 25)
[08:59:36 -75205.518145] SPR radius for FAST iterations: 25 (autodetect)
[08:59:36 -75205.518145] Model parameter optimization (eps = 3.000000)
[08:59:59 -74997.337682] FAST spr round 1 (radius: 25)
[09:03:14 -66177.544350] FAST spr round 2 (radius: 25)
[09:05:38 -65537.689574] FAST spr round 3 (radius: 25)
[09:07:46 -65493.381435] FAST spr round 4 (radius: 25)
[09:09:43 -65474.551329] FAST spr round 5 (radius: 25)
[09:11:33 -65474.551132] Model parameter optimization (eps = 1.000000)
[09:11:38 -65474.347538] SLOW spr round 1 (radius: 5)
[09:14:11 -65454.597458] SLOW spr round 2 (radius: 5)
[09:16:12] [worker #1] ML tree search #11, logLikelihood: -65401.544653
[09:16:36 -65450.010039] SLOW spr round 3 (radius: 5)
[09:18:53 -65449.800653] SLOW spr round 4 (radius: 5)
[09:21:08 -65449.800053] SLOW spr round 5 (radius: 10)
[09:23:29 -65448.734172] SLOW spr round 6 (radius: 5)
[09:26:17 -65445.979464] SLOW spr round 7 (radius: 5)
[09:28:49 -65445.979464] SLOW spr round 8 (radius: 10)
[09:31:13 -65445.082016] SLOW spr round 9 (radius: 5)
[09:34:01 -65444.641671] SLOW spr round 10 (radius: 5)
[09:36:32 -65444.641626] SLOW spr round 11 (radius: 10)
[09:38:55 -65444.039348] SLOW spr round 12 (radius: 5)
[09:41:44 -65436.367299] SLOW spr round 13 (radius: 5)
[09:44:14 -65436.367299] SLOW spr round 14 (radius: 10)
[09:46:37 -65436.107054] SLOW spr round 15 (radius: 5)
[09:47:49] [worker #2] ML tree search #15, logLikelihood: -65428.258638
[09:49:23 -65436.106994] SLOW spr round 16 (radius: 10)
[09:51:56 -65436.065758] SLOW spr round 17 (radius: 15)
[09:55:19 -65433.154015] SLOW spr round 18 (radius: 5)
[09:58:16 -65429.889589] SLOW spr round 19 (radius: 5)
[10:00:52 -65429.889587] SLOW spr round 20 (radius: 10)
[10:03:18 -65429.889587] SLOW spr round 21 (radius: 15)
[10:06:45 -65429.889587] SLOW spr round 22 (radius: 20)
[10:11:15 -65429.889587] SLOW spr round 23 (radius: 25)
[10:16:50 -65429.889587] Model parameter optimization (eps = 0.100000)

[10:17:04] [worker #0] ML tree search #13, logLikelihood: -65414.261767

[10:17:04 -189398.240036] Initial branch length optimization
[10:17:07 -166995.868819] Model parameter optimization (eps = 10.000000)
[10:17:43 -166774.319982] AUTODETECT spr round 1 (radius: 5)
[10:20:09 -121111.754481] AUTODETECT spr round 2 (radius: 10)
[10:22:47 -90471.712772] AUTODETECT spr round 3 (radius: 15)
[10:25:39 -78094.746864] AUTODETECT spr round 4 (radius: 20)
[10:29:05 -76071.066356] AUTODETECT spr round 5 (radius: 25)
[10:33:15 -74868.344737] SPR radius for FAST iterations: 25 (autodetect)
[10:33:15 -74868.344737] Model parameter optimization (eps = 3.000000)
[10:33:24 -74860.950672] FAST spr round 1 (radius: 25)
[10:36:39 -66277.192635] FAST spr round 2 (radius: 25)
[10:39:08 -65775.867556] FAST spr round 3 (radius: 25)
[10:41:23 -65692.514789] FAST spr round 4 (radius: 25)
[10:43:27 -65676.654022] FAST spr round 5 (radius: 25)
[10:45:22 -65671.607970] FAST spr round 6 (radius: 25)
[10:47:17 -65667.693091] FAST spr round 7 (radius: 25)
[10:49:06 -65667.385567] FAST spr round 8 (radius: 25)
[10:50:54 -65667.385214] Model parameter optimization (eps = 1.000000)
[10:50:59 -65666.831585] SLOW spr round 1 (radius: 5)
[10:53:33 -65631.343883] SLOW spr round 2 (radius: 5)
[10:55:59] [worker #1] ML tree search #14, logLikelihood: -65455.082910
[10:55:59 -65626.918737] SLOW spr round 3 (radius: 5)
[10:58:26 -65619.109543] SLOW spr round 4 (radius: 5)
[11:00:49 -65618.464862] SLOW spr round 5 (radius: 5)
[11:03:06 -65618.464788] SLOW spr round 6 (radius: 10)
[11:05:11] [worker #2] ML tree search #18, logLikelihood: -65377.520775
[11:05:30 -65614.372026] SLOW spr round 7 (radius: 5)
[11:08:24 -65612.526408] SLOW spr round 8 (radius: 5)
[11:10:57 -65612.526407] SLOW spr round 9 (radius: 10)
[11:13:24 -65609.881242] SLOW spr round 10 (radius: 5)
[11:16:14 -65609.881209] SLOW spr round 11 (radius: 10)
[11:18:49 -65607.621344] SLOW spr round 12 (radius: 5)
[11:21:39 -65607.085479] SLOW spr round 13 (radius: 5)
[11:24:13 -65607.085309] SLOW spr round 14 (radius: 10)
[11:26:39 -65605.505848] SLOW spr round 15 (radius: 5)
[11:29:30 -65605.505803] SLOW spr round 16 (radius: 10)
[11:32:05 -65605.028073] SLOW spr round 17 (radius: 5)
[11:34:53 -65605.026986] SLOW spr round 18 (radius: 10)
[11:37:27 -65605.026854] SLOW spr round 19 (radius: 15)
[11:40:52 -65605.026833] SLOW spr round 20 (radius: 20)
[11:45:35 -65605.026830] SLOW spr round 21 (radius: 25)
[11:51:24 -65605.026829] Model parameter optimization (eps = 0.100000)

[11:51:29] [worker #0] ML tree search #16, logLikelihood: -65604.998994

[11:51:29 -188977.186474] Initial branch length optimization
[11:51:31 -166954.497861] Model parameter optimization (eps = 10.000000)
[11:52:05 -166759.584481] AUTODETECT spr round 1 (radius: 5)
[11:54:31 -121870.101540] AUTODETECT spr round 2 (radius: 10)
[11:57:10 -92149.072916] AUTODETECT spr round 3 (radius: 15)
[12:00:11 -79897.769329] AUTODETECT spr round 4 (radius: 20)
[12:03:40 -75609.372662] AUTODETECT spr round 5 (radius: 25)
[12:08:01 -74419.824747] SPR radius for FAST iterations: 25 (autodetect)
[12:08:01 -74419.824747] Model parameter optimization (eps = 3.000000)
[12:08:37 -74182.936732] FAST spr round 1 (radius: 25)
[12:11:53 -66027.512597] FAST spr round 2 (radius: 25)
[12:14:19 -65519.459400] FAST spr round 3 (radius: 25)
[12:16:31 -65447.179557] FAST spr round 4 (radius: 25)
[12:17:17] [worker #1] ML tree search #17, logLikelihood: -65445.525996
[12:18:36 -65424.501879] FAST spr round 5 (radius: 25)
[12:20:28 -65423.456354] FAST spr round 6 (radius: 25)
[12:22:18 -65423.456351] Model parameter optimization (eps = 1.000000)
[12:22:30 -65415.520796] SLOW spr round 1 (radius: 5)
[12:25:03 -65403.914924] SLOW spr round 2 (radius: 5)
[12:27:26 -65403.913811] SLOW spr round 3 (radius: 10)
[12:29:46 -65403.340847] SLOW spr round 4 (radius: 5)
[12:32:34 -65403.340696] SLOW spr round 5 (radius: 10)
[12:35:07 -65403.013002] SLOW spr round 6 (radius: 5)
[12:37:52 -65403.012974] SLOW spr round 7 (radius: 10)
[12:40:24 -65402.040478] SLOW spr round 8 (radius: 5)
[12:43:11 -65397.288052] SLOW spr round 9 (radius: 5)
[12:45:42 -65396.957606] SLOW spr round 10 (radius: 5)
[12:48:04 -65396.957603] SLOW spr round 11 (radius: 10)
[12:50:24 -65396.868048] SLOW spr round 12 (radius: 15)
[12:53:48 -65396.236266] SLOW spr round 13 (radius: 5)
[12:56:42 -65396.235635] SLOW spr round 14 (radius: 10)
[12:59:22 -65396.235628] SLOW spr round 15 (radius: 15)
[13:02:34 -65396.235628] SLOW spr round 16 (radius: 20)
[13:07:08 -65396.235628] SLOW spr round 17 (radius: 25)
[13:12:29 -65395.877440] SLOW spr round 18 (radius: 5)
[13:15:27 -65395.061901] SLOW spr round 19 (radius: 5)
[13:18:04 -65395.061881] SLOW spr round 20 (radius: 10)
[13:20:30 -65395.061881] SLOW spr round 21 (radius: 15)
[13:23:47 -65395.061881] SLOW spr round 22 (radius: 20)
[13:28:19 -65395.061881] SLOW spr round 23 (radius: 25)
[13:33:42 -65395.061881] Model parameter optimization (eps = 0.100000)

[13:33:46] [worker #0] ML tree search #19, logLikelihood: -65395.053068

[14:14:02] [worker #1] ML tree search #20, logLikelihood: -65420.316273

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.217460,0.434856) (0.113194,0.480450) (0.487856,0.856489) (0.181489,2.386961) 
   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: -65343.988532

AIC score: 134697.977065 / AICc score: 8178757.977065 / BIC score: 140567.120704
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=138).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 71 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A0A075B6I1/3_mltree/A0A075B6I1.raxml.log

Analysis started: 06-Jul-2021 03:15:26 / finished: 06-Jul-2021 17:29:28

Elapsed time: 51242.562 seconds