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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 07-Jul-2021 19:08:28 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P1Y6/2_msa/Q9P1Y6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P1Y6/3_mltree/Q9P1Y6 --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/Q9P1Y6/2_msa/Q9P1Y6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 836 sites

WARNING: Sequences tr_H2NG23_H2NG23_PONAB_9601 and tr_F7FU78_F7FU78_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NG23_H2NG23_PONAB_9601 and tr_A0A2K6AYQ9_A0A2K6AYQ9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A179UA60_A0A179UA60_BLAGS_559298 and tr_C5GI05_C5GI05_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A179UFL7_A0A179UFL7_BLAGS_559298 and tr_C5GAB4_C5GAB4_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_C6HC01_C6HC01_AJECH_544712 and tr_F0UB51_F0UB51_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J4KR17_J4KR17_BEAB2_655819 and tr_A0A2N6NPU4_A0A2N6NPU4_BEABA_176275 are exactly identical!
WARNING: Sequences tr_Q2UB30_Q2UB30_ASPOR_510516 and tr_A0A1S9DSQ9_A0A1S9DSQ9_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0E0I601_A0A0E0I601_ORYNI_4536 and tr_I1QDF9_I1QDF9_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0I601_A0A0E0I601_ORYNI_4536 and tr_A0A0E0QD19_A0A0E0QD19_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0K0JSR2_A0A0K0JSR2_BRUMA_6279 and tr_A0A158PXD4_A0A158PXD4_BRUMA_6279 are exactly identical!
WARNING: Sequences tr_F6RK87_F6RK87_MACMU_9544 and tr_A0A0A0MUI3_A0A0A0MUI3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6RK87_F6RK87_MACMU_9544 and tr_A0A2K5M301_A0A2K5M301_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7XVN5_G7XVN5_ASPKW_1033177 and tr_A0A146FKG7_A0A146FKG7_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A0E0PWF3_A0A0E0PWF3_ORYRU_4529 and tr_A0A0E0A864_A0A0E0A864_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0PWF3_A0A0E0PWF3_ORYRU_4529 and tr_Q5VMR7_Q5VMR7_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_U5H310_U5H310_USTV1_683840 and tr_A0A2X0PCB3_A0A2X0PCB3_9BASI_796604 are exactly identical!
WARNING: Sequences tr_V2Y576_V2Y576_MONRO_1381753 and tr_A0A0W0FC55_A0A0W0FC55_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A044SVA6_A0A044SVA6_ONCVO_6282 and tr_A0A182EFB3_A0A182EFB3_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A1S3XUV3_A0A1S3XUV3_TOBAC_4097 and tr_A0A1U7VBV9_A0A1U7VBV9_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2D0SEW4_A0A2D0SEW4_ICTPU_7998 and tr_A0A2D0SEX6_A0A2D0SEX6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T467_A0A2D0T467_ICTPU_7998 and tr_A0A2D0T4F9_A0A2D0T4F9_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 21

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/Q9P1Y6/3_mltree/Q9P1Y6.raxml.reduced.phy

Alignment comprises 1 partitions and 836 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 836 / 836
Gaps: 38.70 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P1Y6/3_mltree/Q9P1Y6.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 209 / 16720
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1252149.116326] Initial branch length optimization
[00:00:12 -1070988.974395] Model parameter optimization (eps = 10.000000)
[00:01:40 -1066960.319777] AUTODETECT spr round 1 (radius: 5)
[00:05:49 -790156.773449] AUTODETECT spr round 2 (radius: 10)
[00:10:12 -597369.081557] AUTODETECT spr round 3 (radius: 15)
[00:14:45 -504659.553151] AUTODETECT spr round 4 (radius: 20)
[00:19:58 -474420.641231] AUTODETECT spr round 5 (radius: 25)
[00:25:16 -470175.446166] SPR radius for FAST iterations: 25 (autodetect)
[00:25:16 -470175.446166] Model parameter optimization (eps = 3.000000)
[00:26:17 -469856.586840] FAST spr round 1 (radius: 25)
[00:32:09 -424422.319855] FAST spr round 2 (radius: 25)
[00:36:49 -422737.528501] FAST spr round 3 (radius: 25)
[00:40:36 -422623.274070] FAST spr round 4 (radius: 25)
[00:43:46 -422606.558624] FAST spr round 5 (radius: 25)
[00:46:34 -422606.558191] Model parameter optimization (eps = 1.000000)
[00:46:58 -422605.012210] SLOW spr round 1 (radius: 5)
[00:50:42 -422541.054804] SLOW spr round 2 (radius: 5)
[00:55:20 -422539.202043] SLOW spr round 3 (radius: 5)
[01:01:03 -422539.201586] SLOW spr round 4 (radius: 10)
[01:05:17 -422537.547040] SLOW spr round 5 (radius: 5)
[01:09:37 -422537.546727] SLOW spr round 6 (radius: 10)
[01:14:12 -422537.281818] SLOW spr round 7 (radius: 5)
[01:18:21 -422537.281707] SLOW spr round 8 (radius: 10)
[01:22:50 -422537.281624] SLOW spr round 9 (radius: 15)
[01:30:11 -422536.491759] SLOW spr round 10 (radius: 5)
[01:34:43 -422535.246590] SLOW spr round 11 (radius: 5)
[01:38:37 -422535.246040] SLOW spr round 12 (radius: 10)
[01:42:51 -422535.246000] SLOW spr round 13 (radius: 15)
[01:50:17 -422535.245989] SLOW spr round 14 (radius: 20)
[02:01:31 -422535.245979] SLOW spr round 15 (radius: 25)
[02:14:24 -422535.245970] Model parameter optimization (eps = 0.100000)

[02:14:45] [worker #0] ML tree search #1, logLikelihood: -422535.002387

[02:14:45 -1247949.023761] Initial branch length optimization
[02:14:53 -1064499.453569] Model parameter optimization (eps = 10.000000)
[02:16:03 -1060372.595827] AUTODETECT spr round 1 (radius: 5)
[02:19:36 -778898.566649] AUTODETECT spr round 2 (radius: 10)
[02:23:24 -614038.280873] AUTODETECT spr round 3 (radius: 15)
[02:27:44 -514268.565540] AUTODETECT spr round 4 (radius: 20)
[02:28:53] [worker #1] ML tree search #2, logLikelihood: -422522.395054
[02:32:49 -474685.591046] AUTODETECT spr round 5 (radius: 25)
[02:38:01 -468427.490246] SPR radius for FAST iterations: 25 (autodetect)
[02:38:01 -468427.490246] Model parameter optimization (eps = 3.000000)
[02:38:43 -467966.367799] FAST spr round 1 (radius: 25)
[02:45:02 -424080.987677] FAST spr round 2 (radius: 25)
[02:49:39 -422721.729907] FAST spr round 3 (radius: 25)
[02:53:16 -422615.059699] FAST spr round 4 (radius: 25)
[02:56:16 -422599.239042] FAST spr round 5 (radius: 25)
[02:59:01 -422597.810861] FAST spr round 6 (radius: 25)
[03:01:40 -422596.531616] FAST spr round 7 (radius: 25)
[03:04:17 -422596.529566] Model parameter optimization (eps = 1.000000)
[03:04:46 -422584.835952] SLOW spr round 1 (radius: 5)
[03:08:30 -422541.534719] SLOW spr round 2 (radius: 5)
[03:12:02 -422538.298873] SLOW spr round 3 (radius: 5)
[03:15:33 -422534.585329] SLOW spr round 4 (radius: 5)
[03:18:55 -422534.585176] SLOW spr round 5 (radius: 10)
[03:22:57 -422532.914006] SLOW spr round 6 (radius: 5)
[03:27:14 -422532.123816] SLOW spr round 7 (radius: 5)
[03:31:01 -422532.123483] SLOW spr round 8 (radius: 10)
[03:35:15 -422532.123482] SLOW spr round 9 (radius: 15)
[03:43:04 -422530.907765] SLOW spr round 10 (radius: 5)
[03:47:33 -422530.856942] SLOW spr round 11 (radius: 10)
[03:52:34 -422530.854158] SLOW spr round 12 (radius: 15)
[04:00:01 -422530.853155] SLOW spr round 13 (radius: 20)
[04:11:49 -422530.852793] SLOW spr round 14 (radius: 25)
[04:25:36 -422530.852661] Model parameter optimization (eps = 0.100000)

[04:25:59] [worker #0] ML tree search #3, logLikelihood: -422530.783860

[04:25:59 -1249212.086656] Initial branch length optimization
[04:26:14 -1064659.671198] Model parameter optimization (eps = 10.000000)
[04:28:59 -1060543.367579] AUTODETECT spr round 1 (radius: 5)
[04:32:33 -796200.145197] AUTODETECT spr round 2 (radius: 10)
[04:34:07] [worker #1] ML tree search #4, logLikelihood: -422512.126535
[04:36:26 -601702.637125] AUTODETECT spr round 3 (radius: 15)
[04:40:47 -521651.463032] AUTODETECT spr round 4 (radius: 20)
[04:45:42 -477556.017026] AUTODETECT spr round 5 (radius: 25)
[04:51:36 -466377.879691] SPR radius for FAST iterations: 25 (autodetect)
[04:51:36 -466377.879691] Model parameter optimization (eps = 3.000000)
[04:52:15 -465906.411689] FAST spr round 1 (radius: 25)
[04:58:33 -424328.872439] FAST spr round 2 (radius: 25)
[05:03:18 -422720.051656] FAST spr round 3 (radius: 25)
[05:07:09 -422621.573782] FAST spr round 4 (radius: 25)
[05:10:15 -422603.828738] FAST spr round 5 (radius: 25)
[05:13:05 -422597.471478] FAST spr round 6 (radius: 25)
[05:15:49 -422591.132246] FAST spr round 7 (radius: 25)
[05:18:28 -422591.131123] Model parameter optimization (eps = 1.000000)
[05:18:53 -422583.246279] SLOW spr round 1 (radius: 5)
[05:22:40 -422521.519381] SLOW spr round 2 (radius: 5)
[05:26:17 -422517.968196] SLOW spr round 3 (radius: 5)
[05:29:45 -422516.053138] SLOW spr round 4 (radius: 5)
[05:33:14 -422514.628365] SLOW spr round 5 (radius: 5)
[05:36:43 -422512.818698] SLOW spr round 6 (radius: 5)
[05:40:05 -422512.817232] SLOW spr round 7 (radius: 10)
[05:43:58 -422511.930656] SLOW spr round 8 (radius: 5)
[05:48:16 -422511.930635] SLOW spr round 9 (radius: 10)
[05:52:51 -422511.672597] SLOW spr round 10 (radius: 5)
[05:57:09 -422508.398007] SLOW spr round 11 (radius: 5)
[06:00:53 -422508.390380] SLOW spr round 12 (radius: 10)
[06:05:00 -422508.050840] SLOW spr round 13 (radius: 5)
[06:09:14 -422508.016040] SLOW spr round 14 (radius: 10)
[06:13:45 -422508.013971] SLOW spr round 15 (radius: 15)
[06:20:50 -422506.568795] SLOW spr round 16 (radius: 5)
[06:25:17 -422506.568672] SLOW spr round 17 (radius: 10)
[06:30:06 -422506.568646] SLOW spr round 18 (radius: 15)
[06:37:02 -422506.568638] SLOW spr round 19 (radius: 20)
[06:47:51 -422506.568634] SLOW spr round 20 (radius: 25)
[07:00:37 -422506.568631] Model parameter optimization (eps = 0.100000)

[07:01:03] [worker #0] ML tree search #5, logLikelihood: -422506.421071

[07:01:03 -1250983.872433] Initial branch length optimization
[07:01:21 -1067297.787218] Model parameter optimization (eps = 10.000000)
[07:03:26 -1063317.052628] AUTODETECT spr round 1 (radius: 5)
[07:07:39 -793599.113081] AUTODETECT spr round 2 (radius: 10)
[07:11:28 -614007.039734] AUTODETECT spr round 3 (radius: 15)
[07:16:13 -521459.995147] AUTODETECT spr round 4 (radius: 20)
[07:16:50] [worker #1] ML tree search #6, logLikelihood: -422505.306991
[07:21:29 -487766.262337] AUTODETECT spr round 5 (radius: 25)
[07:26:44 -470777.875758] SPR radius for FAST iterations: 25 (autodetect)
[07:26:44 -470777.875758] Model parameter optimization (eps = 3.000000)
[07:27:22 -470166.106066] FAST spr round 1 (radius: 25)
[07:33:38 -424130.570886] FAST spr round 2 (radius: 25)
[07:38:16 -422722.860708] FAST spr round 3 (radius: 25)
[07:41:56 -422616.285408] FAST spr round 4 (radius: 25)
[07:44:59 -422613.624840] FAST spr round 5 (radius: 25)
[07:47:52 -422603.071332] FAST spr round 6 (radius: 25)
[07:50:35 -422600.661647] FAST spr round 7 (radius: 25)
[07:53:11 -422600.657069] Model parameter optimization (eps = 1.000000)
[07:53:35 -422597.809387] SLOW spr round 1 (radius: 5)
[07:57:23 -422526.637522] SLOW spr round 2 (radius: 5)
[08:01:00 -422515.068266] SLOW spr round 3 (radius: 5)
[08:06:18 -422515.067374] SLOW spr round 4 (radius: 10)
[08:10:54 -422511.502149] SLOW spr round 5 (radius: 5)
[08:15:11 -422510.727087] SLOW spr round 6 (radius: 5)
[08:18:56 -422510.726281] SLOW spr round 7 (radius: 10)
[08:23:06 -422510.726239] SLOW spr round 8 (radius: 15)
[08:30:43 -422510.726230] SLOW spr round 9 (radius: 20)
[08:42:20 -422510.726224] SLOW spr round 10 (radius: 25)
[08:55:58 -422510.726219] Model parameter optimization (eps = 0.100000)

[08:56:21] [worker #0] ML tree search #7, logLikelihood: -422510.353657

[08:56:21 -1251050.610459] Initial branch length optimization
[08:56:34 -1069860.285951] Model parameter optimization (eps = 10.000000)
[08:58:39 -1065640.095925] AUTODETECT spr round 1 (radius: 5)
[09:03:40 -782377.953465] AUTODETECT spr round 2 (radius: 10)
[09:07:26 -597537.030108] AUTODETECT spr round 3 (radius: 15)
[09:11:41 -513168.318606] AUTODETECT spr round 4 (radius: 20)
[09:16:19 -483306.979093] AUTODETECT spr round 5 (radius: 25)
[09:20:37] [worker #1] ML tree search #8, logLikelihood: -422512.937754
[09:21:35 -476157.446669] SPR radius for FAST iterations: 25 (autodetect)
[09:21:35 -476157.446669] Model parameter optimization (eps = 3.000000)
[09:22:17 -475654.675773] FAST spr round 1 (radius: 25)
[09:28:38 -424395.237435] FAST spr round 2 (radius: 25)
[09:33:16 -422722.954341] FAST spr round 3 (radius: 25)
[09:36:55 -422660.645908] FAST spr round 4 (radius: 25)
[09:40:01 -422628.791391] FAST spr round 5 (radius: 25)
[09:42:53 -422612.843851] FAST spr round 6 (radius: 25)
[09:45:35 -422610.371774] FAST spr round 7 (radius: 25)
[09:48:11 -422610.371549] Model parameter optimization (eps = 1.000000)
[09:48:34 -422606.264572] SLOW spr round 1 (radius: 5)
[09:52:11 -422527.237786] SLOW spr round 2 (radius: 5)
[09:55:40 -422515.689757] SLOW spr round 3 (radius: 5)
[09:59:02 -422515.688869] SLOW spr round 4 (radius: 10)
[10:03:00 -422513.401187] SLOW spr round 5 (radius: 5)
[10:07:18 -422513.400613] SLOW spr round 6 (radius: 10)
[10:12:01 -422513.172932] SLOW spr round 7 (radius: 5)
[10:16:11 -422513.172810] SLOW spr round 8 (radius: 10)
[10:20:45 -422513.172799] SLOW spr round 9 (radius: 15)
[10:28:22 -422513.172792] SLOW spr round 10 (radius: 20)
[10:40:12 -422512.082954] SLOW spr round 11 (radius: 5)
[10:44:49 -422508.136421] SLOW spr round 12 (radius: 5)
[10:48:44 -422508.136117] SLOW spr round 13 (radius: 10)
[10:53:03 -422508.135968] SLOW spr round 14 (radius: 15)
[11:00:43 -422508.135893] SLOW spr round 15 (radius: 20)
[11:12:26 -422508.135854] SLOW spr round 16 (radius: 25)
[11:21:12] [worker #1] ML tree search #10, logLikelihood: -422501.948128
[11:26:02 -422507.794244] SLOW spr round 17 (radius: 5)
[11:30:43 -422507.586119] SLOW spr round 18 (radius: 5)
[11:34:42 -422507.582956] SLOW spr round 19 (radius: 10)
[11:39:08 -422507.582454] SLOW spr round 20 (radius: 15)
[11:46:52 -422507.582373] SLOW spr round 21 (radius: 20)
[11:58:41 -422507.582356] SLOW spr round 22 (radius: 25)
[12:12:18 -422507.582349] Model parameter optimization (eps = 0.100000)

[12:12:37] [worker #0] ML tree search #9, logLikelihood: -422507.381186

[12:12:38 -1257900.046041] Initial branch length optimization
[12:12:51 -1076312.248734] Model parameter optimization (eps = 10.000000)
[12:13:59 -1072321.086621] AUTODETECT spr round 1 (radius: 5)
[12:17:40 -779838.877371] AUTODETECT spr round 2 (radius: 10)
[12:21:34 -598776.073764] AUTODETECT spr round 3 (radius: 15)
[12:26:02 -493092.210042] AUTODETECT spr round 4 (radius: 20)
[12:30:52 -470233.587917] AUTODETECT spr round 5 (radius: 25)
[12:36:24 -463673.925178] SPR radius for FAST iterations: 25 (autodetect)
[12:36:24 -463673.925178] Model parameter optimization (eps = 3.000000)
[12:37:06 -463323.814951] FAST spr round 1 (radius: 25)
[12:43:06 -424175.908953] FAST spr round 2 (radius: 25)
[12:47:51 -422816.677603] FAST spr round 3 (radius: 25)
[12:51:27 -422616.691360] FAST spr round 4 (radius: 25)
[12:54:28 -422612.973299] FAST spr round 5 (radius: 25)
[12:57:10 -422612.966213] Model parameter optimization (eps = 1.000000)
[12:57:41 -422569.537669] SLOW spr round 1 (radius: 5)
[13:01:25 -422518.084635] SLOW spr round 2 (radius: 5)
[13:04:58 -422510.886041] SLOW spr round 3 (radius: 5)
[13:08:19 -422510.883024] SLOW spr round 4 (radius: 10)
[13:12:15 -422510.352326] SLOW spr round 5 (radius: 5)
[13:16:29 -422509.722817] SLOW spr round 6 (radius: 5)
[13:20:15 -422509.505733] SLOW spr round 7 (radius: 5)
[13:23:45 -422509.502272] SLOW spr round 8 (radius: 10)
[13:27:45 -422509.501314] SLOW spr round 9 (radius: 15)
[13:28:26] [worker #1] ML tree search #12, logLikelihood: -422518.952230
[13:35:42 -422509.500979] SLOW spr round 10 (radius: 20)
[13:47:35 -422509.500860] SLOW spr round 11 (radius: 25)
[14:04:11 -422509.500817] Model parameter optimization (eps = 0.100000)

[14:04:22] [worker #0] ML tree search #11, logLikelihood: -422509.274226

[14:04:23 -1257553.455828] Initial branch length optimization
[14:04:33 -1077955.709668] Model parameter optimization (eps = 10.000000)
[14:06:21 -1073820.087206] AUTODETECT spr round 1 (radius: 5)
[14:10:01 -796822.930565] AUTODETECT spr round 2 (radius: 10)
[14:13:59 -598012.229715] AUTODETECT spr round 3 (radius: 15)
[14:18:21 -506596.963339] AUTODETECT spr round 4 (radius: 20)
[14:23:08 -474024.760542] AUTODETECT spr round 5 (radius: 25)
[14:32:03 -470281.259956] SPR radius for FAST iterations: 25 (autodetect)
[14:32:03 -470281.259956] Model parameter optimization (eps = 3.000000)
[14:32:50 -469863.759585] FAST spr round 1 (radius: 25)
[14:39:43 -423998.862897] FAST spr round 2 (radius: 25)
[14:44:25 -422666.388041] FAST spr round 3 (radius: 25)
[14:47:59 -422582.927032] FAST spr round 4 (radius: 25)
[14:50:58 -422579.284787] FAST spr round 5 (radius: 25)
[14:53:44 -422579.243505] Model parameter optimization (eps = 1.000000)
[14:53:58 -422578.750075] SLOW spr round 1 (radius: 5)
[14:57:38 -422529.262337] SLOW spr round 2 (radius: 5)
[15:01:13 -422513.941133] SLOW spr round 3 (radius: 5)
[15:04:38 -422505.094192] SLOW spr round 4 (radius: 5)
[15:08:00 -422503.827341] SLOW spr round 5 (radius: 5)
[15:11:19 -422503.826590] SLOW spr round 6 (radius: 10)
[15:15:19 -422501.227271] SLOW spr round 7 (radius: 5)
[15:19:34 -422496.610978] SLOW spr round 8 (radius: 5)
[15:23:18 -422496.610023] SLOW spr round 9 (radius: 10)
[15:27:34 -422495.557239] SLOW spr round 10 (radius: 5)
[15:31:42 -422495.557164] SLOW spr round 11 (radius: 10)
[15:32:03] [worker #1] ML tree search #14, logLikelihood: -422509.389761
[15:36:28 -422495.557132] SLOW spr round 12 (radius: 15)
[15:44:11 -422495.557114] SLOW spr round 13 (radius: 20)
[15:56:53 -422495.224295] SLOW spr round 14 (radius: 5)
[16:01:28 -422495.221970] SLOW spr round 15 (radius: 10)
[16:06:45 -422495.221402] SLOW spr round 16 (radius: 15)
[16:14:22 -422495.221233] SLOW spr round 17 (radius: 20)
[16:27:04 -422495.221177] SLOW spr round 18 (radius: 25)
[16:44:49 -422495.221157] Model parameter optimization (eps = 0.100000)

[16:45:10] [worker #0] ML tree search #13, logLikelihood: -422494.884048

[16:45:10 -1260674.391188] Initial branch length optimization
[16:45:20 -1073238.861059] Model parameter optimization (eps = 10.000000)
[16:47:10 -1069643.305697] AUTODETECT spr round 1 (radius: 5)
[16:50:51 -786528.666354] AUTODETECT spr round 2 (radius: 10)
[16:54:46 -608918.081503] AUTODETECT spr round 3 (radius: 15)
[16:59:15 -525550.812364] AUTODETECT spr round 4 (radius: 20)
[17:03:56 -485717.555457] AUTODETECT spr round 5 (radius: 25)
[17:08:47 -477708.219909] SPR radius for FAST iterations: 25 (autodetect)
[17:08:47 -477708.219909] Model parameter optimization (eps = 3.000000)
[17:09:32 -477320.507148] FAST spr round 1 (radius: 25)
[17:15:16 -425540.863150] FAST spr round 2 (radius: 25)
[17:19:30 -422728.862239] FAST spr round 3 (radius: 25)
[17:23:02 -422658.027185] FAST spr round 4 (radius: 25)
[17:26:05 -422645.223959] FAST spr round 5 (radius: 25)
[17:26:38] [worker #1] ML tree search #16, logLikelihood: -422518.424366
[17:28:55 -422632.129066] FAST spr round 6 (radius: 25)
[17:31:38 -422632.129010] Model parameter optimization (eps = 1.000000)
[17:32:11 -422613.638927] SLOW spr round 1 (radius: 5)
[17:35:49 -422544.662316] SLOW spr round 2 (radius: 5)
[17:39:20 -422543.702465] SLOW spr round 3 (radius: 5)
[17:42:45 -422543.701660] SLOW spr round 4 (radius: 10)
[17:46:41 -422543.701539] SLOW spr round 5 (radius: 15)
[17:54:26 -422542.274150] SLOW spr round 6 (radius: 5)
[17:58:59 -422542.274113] SLOW spr round 7 (radius: 10)
[18:03:55 -422542.274106] SLOW spr round 8 (radius: 15)
[18:11:12 -422542.274103] SLOW spr round 9 (radius: 20)
[18:23:16 -422542.274100] SLOW spr round 10 (radius: 25)
[18:36:42 -422542.274099] Model parameter optimization (eps = 0.100000)

[18:37:06] [worker #0] ML tree search #15, logLikelihood: -422541.756541

[18:37:06 -1253799.636050] Initial branch length optimization
[18:37:15 -1069554.626817] Model parameter optimization (eps = 10.000000)
[18:38:59 -1064692.567220] AUTODETECT spr round 1 (radius: 5)
[18:42:38 -794486.989800] AUTODETECT spr round 2 (radius: 10)
[18:46:31 -597432.725637] AUTODETECT spr round 3 (radius: 15)
[18:50:52 -522302.861477] AUTODETECT spr round 4 (radius: 20)
[18:55:34 -477919.517787] AUTODETECT spr round 5 (radius: 25)
[19:00:40 -470990.299950] SPR radius for FAST iterations: 25 (autodetect)
[19:00:40 -470990.299950] Model parameter optimization (eps = 3.000000)
[19:01:30 -470450.044888] FAST spr round 1 (radius: 25)
[19:07:43 -424207.695735] FAST spr round 2 (radius: 25)
[19:13:34 -422763.247916] FAST spr round 3 (radius: 25)
[19:17:18 -422654.156096] FAST spr round 4 (radius: 25)
[19:20:22 -422641.206040] FAST spr round 5 (radius: 25)
[19:25:22 -422640.646097] FAST spr round 6 (radius: 25)
[19:27:59 -422640.641994] Model parameter optimization (eps = 1.000000)
[19:28:22 -422637.316690] SLOW spr round 1 (radius: 5)
[19:29:52] [worker #1] ML tree search #18, logLikelihood: -422506.660565
[19:32:13 -422544.555055] SLOW spr round 2 (radius: 5)
[19:35:53 -422521.486323] SLOW spr round 3 (radius: 5)
[19:39:19 -422520.354153] SLOW spr round 4 (radius: 5)
[19:42:44 -422519.516163] SLOW spr round 5 (radius: 5)
[19:46:08 -422519.029125] SLOW spr round 6 (radius: 5)
[19:49:32 -422519.027130] SLOW spr round 7 (radius: 10)
[19:53:30 -422518.722894] SLOW spr round 8 (radius: 5)
[19:57:45 -422518.718127] SLOW spr round 9 (radius: 10)
[20:02:30 -422518.717719] SLOW spr round 10 (radius: 15)
[20:10:04 -422513.160063] SLOW spr round 11 (radius: 5)
[20:14:42 -422511.194377] SLOW spr round 12 (radius: 5)
[20:18:38 -422511.190455] SLOW spr round 13 (radius: 10)
[20:23:00 -422511.189845] SLOW spr round 14 (radius: 15)
[20:30:37 -422511.189725] SLOW spr round 15 (radius: 20)
[20:42:27 -422511.189689] SLOW spr round 16 (radius: 25)
[20:55:52 -422511.087663] SLOW spr round 17 (radius: 5)
[21:00:31 -422510.981107] SLOW spr round 18 (radius: 5)
[21:04:29 -422510.980036] SLOW spr round 19 (radius: 10)
[21:08:50 -422510.979747] SLOW spr round 20 (radius: 15)
[21:10:29] [worker #1] ML tree search #20, logLikelihood: -422516.705717
[21:16:13 -422510.979658] SLOW spr round 21 (radius: 20)
[21:27:49 -422510.979626] SLOW spr round 22 (radius: 25)
[21:41:06 -422510.979613] Model parameter optimization (eps = 0.100000)

[21:41:30] [worker #0] ML tree search #17, logLikelihood: -422510.055739

[21:41:30 -1258210.105248] Initial branch length optimization
[21:41:40 -1071049.140305] Model parameter optimization (eps = 10.000000)
[21:43:15 -1066629.706258] AUTODETECT spr round 1 (radius: 5)
[21:46:47 -792406.869561] AUTODETECT spr round 2 (radius: 10)
[21:50:34 -615328.891590] AUTODETECT spr round 3 (radius: 15)
[21:54:48 -510599.962832] AUTODETECT spr round 4 (radius: 20)
[21:59:31 -472159.215318] AUTODETECT spr round 5 (radius: 25)
[22:04:33 -469588.375685] SPR radius for FAST iterations: 25 (autodetect)
[22:04:33 -469588.375685] Model parameter optimization (eps = 3.000000)
[22:05:29 -469196.820542] FAST spr round 1 (radius: 25)
[22:11:23 -423894.266453] FAST spr round 2 (radius: 25)
[22:15:50 -422720.753438] FAST spr round 3 (radius: 25)
[22:19:28 -422628.926089] FAST spr round 4 (radius: 25)
[22:22:22 -422618.371094] FAST spr round 5 (radius: 25)
[22:25:01 -422618.330514] Model parameter optimization (eps = 1.000000)
[22:25:32 -422608.835565] SLOW spr round 1 (radius: 5)
[22:29:23 -422505.766263] SLOW spr round 2 (radius: 5)
[22:32:54 -422496.654502] SLOW spr round 3 (radius: 5)
[22:36:15 -422495.767671] SLOW spr round 4 (radius: 5)
[22:39:31 -422495.766552] SLOW spr round 5 (radius: 10)
[22:43:23 -422494.070884] SLOW spr round 6 (radius: 5)
[22:47:36 -422492.140483] SLOW spr round 7 (radius: 5)
[22:51:17 -422492.135683] SLOW spr round 8 (radius: 10)
[22:55:24 -422492.135667] SLOW spr round 9 (radius: 15)
[23:03:03 -422492.135659] SLOW spr round 10 (radius: 20)
[23:14:58 -422492.135655] SLOW spr round 11 (radius: 25)
[23:28:33 -422492.135652] Model parameter optimization (eps = 0.100000)

[23:28:49] [worker #0] ML tree search #19, logLikelihood: -422491.594767


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.087219,0.634276) (0.016275,0.565331) (0.255126,0.716561) (0.641380,1.173508) 
   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: -422491.594767

AIC score: 848993.189534 / AICc score: 8893053.189534 / BIC score: 858474.089903
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=836).
         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/Q9P1Y6/3_mltree/Q9P1Y6.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P1Y6/3_mltree/Q9P1Y6.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P1Y6/3_mltree/Q9P1Y6.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P1Y6/3_mltree/Q9P1Y6.raxml.log

Analysis started: 07-Jul-2021 19:08:28 / finished: 08-Jul-2021 18:37:18

Elapsed time: 84529.806 seconds

Consumed energy: 5999.216 Wh (= 30 km in an electric car, or 150 km with an e-scooter!)