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 01-Jul-2021 02:50:32 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/2_msa/A6NKB5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/3_mltree/A6NKB5 --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/A6NKB5/2_msa/A6NKB5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 575 taxa and 753 sites

WARNING: Sequences tr_M3YJQ5_M3YJQ5_MUSPF_9669 and tr_A0A2Y9JRJ8_A0A2Y9JRJ8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3IDN1_G3IDN1_CRIGR_10029 and tr_A0A3Q0CGJ3_A0A3Q0CGJ3_MESAU_10036 are exactly identical!
WARNING: Sequences tr_H2NLP3_H2NLP3_PONAB_9601 and tr_A0A0D9RKI0_A0A0D9RKI0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2NLP3_H2NLP3_PONAB_9601 and tr_A0A2K6AXL3_A0A2K6AXL3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2Q440_H2Q440_PANTR_9598 and sp_Q9H6A9_PCX3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_K7D0I2_K7D0I2_PANTR_9598 and tr_A0A2R9BP55_A0A2R9BP55_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A3B5QZG5_A0A3B5QZG5_XIPMA_8083 and tr_A0A3B5JYT3_A0A3B5JYT3_TAKRU_31033 are exactly identical!
WARNING: Sequences tr_A0A1D5RCI2_A0A1D5RCI2_MACMU_9544 and tr_A0A2K6A543_A0A2K6A543_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6SXG8_F6SXG8_MACMU_9544 and tr_A0A2K5KWN4_A0A2K5KWN4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6SXG8_F6SXG8_MACMU_9544 and tr_A0A2K5Y438_A0A2K5Y438_MANLE_9568 are exactly identical!
WARNING: Sequences tr_U3JQQ3_U3JQQ3_FICAL_59894 and tr_A0A091FQU7_A0A091FQU7_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3JQQ3_U3JQQ3_FICAL_59894 and tr_A0A093PSB3_A0A093PSB3_9PASS_328815 are exactly identical!
WARNING: Sequences tr_U3J9R6_U3J9R6_ANAPL_8839 and tr_A0A091JEZ9_A0A091JEZ9_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_U3J9R6_U3J9R6_ANAPL_8839 and tr_A0A091VXD4_A0A091VXD4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_U3J9R6_U3J9R6_ANAPL_8839 and tr_A0A087R229_A0A087R229_APTFO_9233 are exactly identical!
WARNING: Sequences tr_U3J9R6_U3J9R6_ANAPL_8839 and tr_A0A091WJ66_A0A091WJ66_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_U3J9R6_U3J9R6_ANAPL_8839 and tr_A0A091FMF2_A0A091FMF2_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A096MWG6_A0A096MWG6_PAPAN_9555 and tr_A0A2K6AMF1_A0A2K6AMF1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MSU9_A0A2I3MSU9_PAPAN_9555 and tr_A0A2K5L3D2_A0A2K5L3D2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A151MAW8_A0A151MAW8_ALLMI_8496 and tr_A0A3Q0FVZ4_A0A3Q0FVZ4_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A2I0MQ05_A0A2I0MQ05_COLLI_8932 and tr_A0A1V4KF75_A0A1V4KF75_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V0WQ93_A0A0V0WQ93_9BILA_92179 and tr_A0A0V1LQW7_A0A0V1LQW7_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0WQ93_A0A0V0WQ93_9BILA_92179 and tr_A0A0V1A6L6_A0A0V1A6L6_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0WQ93_A0A0V0WQ93_9BILA_92179 and tr_A0A0V1NYY5_A0A0V1NYY5_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A1S3R6Q9_A0A1S3R6Q9_SALSA_8030 and tr_A0A060Y9I1_A0A060Y9I1_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2D0QKL7_A0A2D0QKL7_ICTPU_7998 and tr_A0A2D0QL58_A0A2D0QL58_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T1B1_A0A2D0T1B1_ICTPU_7998 and tr_A0A2D0T1W0_A0A2D0T1W0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2A3ED84_A0A2A3ED84_APICC_94128 and tr_A0A2A3EEN7_A0A2A3EEN7_APICC_94128 are exactly identical!
WARNING: Duplicate sequences found: 28

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/A6NKB5/3_mltree/A6NKB5.raxml.reduced.phy

Alignment comprises 1 partitions and 753 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 753 / 753
Gaps: 18.52 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/3_mltree/A6NKB5.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 575 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 189 / 15120
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -549795.801535] Initial branch length optimization
[00:00:03 -422882.181999] Model parameter optimization (eps = 10.000000)
[00:00:28 -420515.252581] AUTODETECT spr round 1 (radius: 5)
[00:01:23 -266732.701826] AUTODETECT spr round 2 (radius: 10)
[00:02:26 -198673.830159] AUTODETECT spr round 3 (radius: 15)
[00:03:47 -164528.513500] AUTODETECT spr round 4 (radius: 20)
[00:05:14 -149561.043940] AUTODETECT spr round 5 (radius: 25)
[00:07:15 -144771.752340] SPR radius for FAST iterations: 25 (autodetect)
[00:07:15 -144771.752340] Model parameter optimization (eps = 3.000000)
[00:07:38 -144468.457778] FAST spr round 1 (radius: 25)
[00:09:06 -128540.225614] FAST spr round 2 (radius: 25)
[00:10:18 -127809.598130] FAST spr round 3 (radius: 25)
[00:11:20 -127742.676515] FAST spr round 4 (radius: 25)
[00:12:07 -127741.729282] FAST spr round 5 (radius: 25)
[00:12:53 -127741.729028] Model parameter optimization (eps = 1.000000)
[00:13:04 -127736.641158] SLOW spr round 1 (radius: 5)
[00:14:09 -127717.228705] SLOW spr round 2 (radius: 5)
[00:15:12 -127714.298055] SLOW spr round 3 (radius: 5)
[00:16:14 -127713.338472] SLOW spr round 4 (radius: 5)
[00:17:15 -127713.337099] SLOW spr round 5 (radius: 10)
[00:18:27 -127707.683324] SLOW spr round 6 (radius: 5)
[00:19:46 -127707.683254] SLOW spr round 7 (radius: 10)
[00:21:07 -127707.683185] SLOW spr round 8 (radius: 15)
[00:23:05 -127701.548588] SLOW spr round 9 (radius: 5)
[00:24:33 -127700.566739] SLOW spr round 10 (radius: 5)
[00:25:48 -127700.074217] SLOW spr round 11 (radius: 5)
[00:26:54 -127700.070203] SLOW spr round 12 (radius: 10)
[00:28:08 -127698.255215] SLOW spr round 13 (radius: 5)
[00:29:26 -127698.229215] SLOW spr round 14 (radius: 10)
[00:30:44 -127697.864389] SLOW spr round 15 (radius: 5)
[00:31:41] [worker #1] ML tree search #2, logLikelihood: -127696.752694
[00:32:01 -127697.864167] SLOW spr round 16 (radius: 10)
[00:33:20 -127697.864094] SLOW spr round 17 (radius: 15)
[00:35:15 -127697.864025] SLOW spr round 18 (radius: 20)
[00:38:09 -127697.863956] SLOW spr round 19 (radius: 25)
[00:41:21 -127697.863888] Model parameter optimization (eps = 0.100000)

[00:41:25] [worker #0] ML tree search #1, logLikelihood: -127697.777809

[00:41:25 -565589.973052] Initial branch length optimization
[00:41:29 -431482.306597] Model parameter optimization (eps = 10.000000)
[00:42:01 -429105.521579] AUTODETECT spr round 1 (radius: 5)
[00:42:59 -265963.099281] AUTODETECT spr round 2 (radius: 10)
[00:44:04 -185196.138051] AUTODETECT spr round 3 (radius: 15)
[00:45:18 -162933.660469] AUTODETECT spr round 4 (radius: 20)
[00:46:49 -147016.152594] AUTODETECT spr round 5 (radius: 25)
[00:48:42 -144808.783329] SPR radius for FAST iterations: 25 (autodetect)
[00:48:42 -144808.783329] Model parameter optimization (eps = 3.000000)
[00:49:08 -144445.854219] FAST spr round 1 (radius: 25)
[00:50:35 -128481.443062] FAST spr round 2 (radius: 25)
[00:51:46 -127884.629462] FAST spr round 3 (radius: 25)
[00:52:46 -127733.153550] FAST spr round 4 (radius: 25)
[00:53:35 -127729.152042] FAST spr round 5 (radius: 25)
[00:54:21 -127729.151717] Model parameter optimization (eps = 1.000000)
[00:54:32 -127723.750301] SLOW spr round 1 (radius: 5)
[00:55:36 -127704.759225] SLOW spr round 2 (radius: 5)
[00:56:40 -127703.611325] SLOW spr round 3 (radius: 5)
[00:57:41 -127703.608314] SLOW spr round 4 (radius: 10)
[00:58:51 -127701.738740] SLOW spr round 5 (radius: 5)
[01:00:11 -127701.735597] SLOW spr round 6 (radius: 10)
[01:01:29 -127701.735179] SLOW spr round 7 (radius: 15)
[01:03:19 -127701.182513] SLOW spr round 8 (radius: 5)
[01:04:45 -127701.127717] SLOW spr round 9 (radius: 10)
[01:06:07 -127701.127327] SLOW spr round 10 (radius: 15)
[01:07:57 -127701.126968] SLOW spr round 11 (radius: 20)
[01:10:36 -127701.126610] SLOW spr round 12 (radius: 25)
[01:13:39 -127700.867414] SLOW spr round 13 (radius: 5)
[01:15:08 -127700.866549] SLOW spr round 14 (radius: 10)
[01:16:35] [worker #1] ML tree search #4, logLikelihood: -127694.530198
[01:16:35 -127700.866052] SLOW spr round 15 (radius: 15)
[01:18:24 -127700.865623] SLOW spr round 16 (radius: 20)
[01:21:01 -127700.865225] SLOW spr round 17 (radius: 25)
[01:24:03 -127700.864845] Model parameter optimization (eps = 0.100000)

[01:24:08] [worker #0] ML tree search #3, logLikelihood: -127700.848488

[01:24:08 -547999.829247] Initial branch length optimization
[01:24:11 -421888.826469] Model parameter optimization (eps = 10.000000)
[01:24:49 -419564.820269] AUTODETECT spr round 1 (radius: 5)
[01:25:45 -271389.887216] AUTODETECT spr round 2 (radius: 10)
[01:26:48 -192905.926961] AUTODETECT spr round 3 (radius: 15)
[01:28:06 -165196.673307] AUTODETECT spr round 4 (radius: 20)
[01:29:34 -153584.513173] AUTODETECT spr round 5 (radius: 25)
[01:31:37 -147453.271222] SPR radius for FAST iterations: 25 (autodetect)
[01:31:37 -147453.271222] Model parameter optimization (eps = 3.000000)
[01:31:58 -147193.951520] FAST spr round 1 (radius: 25)
[01:33:28 -129772.277307] FAST spr round 2 (radius: 25)
[01:34:37 -127812.975802] FAST spr round 3 (radius: 25)
[01:35:36 -127740.300168] FAST spr round 4 (radius: 25)
[01:36:26 -127730.323962] FAST spr round 5 (radius: 25)
[01:37:12 -127730.320679] Model parameter optimization (eps = 1.000000)
[01:37:23 -127723.856959] SLOW spr round 1 (radius: 5)
[01:38:28 -127699.169262] SLOW spr round 2 (radius: 5)
[01:39:30 -127699.167357] SLOW spr round 3 (radius: 10)
[01:40:39 -127699.166813] SLOW spr round 4 (radius: 15)
[01:42:34 -127698.445928] SLOW spr round 5 (radius: 5)
[01:44:00 -127698.445758] SLOW spr round 6 (radius: 10)
[01:45:24 -127698.445645] SLOW spr round 7 (radius: 15)
[01:47:15 -127698.247312] SLOW spr round 8 (radius: 5)
[01:48:43 -127697.119938] SLOW spr round 9 (radius: 5)
[01:49:58 -127696.311039] SLOW spr round 10 (radius: 5)
[01:51:03 -127696.309923] SLOW spr round 11 (radius: 10)
[01:52:17 -127694.938009] SLOW spr round 12 (radius: 5)
[01:53:36 -127694.832707] SLOW spr round 13 (radius: 5)
[01:54:45 -127694.795185] SLOW spr round 14 (radius: 10)
[01:56:00 -127694.788541] SLOW spr round 15 (radius: 15)
[01:57:56 -127694.205290] SLOW spr round 16 (radius: 5)
[01:59:22 -127694.205016] SLOW spr round 17 (radius: 10)
[02:00:46 -127694.204958] SLOW spr round 18 (radius: 15)
[02:02:39 -127694.204904] SLOW spr round 19 (radius: 20)
[02:03:09] [worker #1] ML tree search #6, logLikelihood: -127691.475797
[02:05:23 -127693.815477] SLOW spr round 20 (radius: 5)
[02:06:52 -127692.042815] SLOW spr round 21 (radius: 5)
[02:08:07 -127692.042643] SLOW spr round 22 (radius: 10)
[02:09:23 -127692.042541] SLOW spr round 23 (radius: 15)
[02:11:15 -127692.042459] SLOW spr round 24 (radius: 20)
[02:13:56 -127692.042387] SLOW spr round 25 (radius: 25)
[02:16:58 -127692.042315] Model parameter optimization (eps = 0.100000)

[02:17:06] [worker #0] ML tree search #5, logLikelihood: -127691.650785

[02:17:06 -557005.850637] Initial branch length optimization
[02:17:08 -430556.776728] Model parameter optimization (eps = 10.000000)
[02:17:38 -427998.597565] AUTODETECT spr round 1 (radius: 5)
[02:18:34 -275660.702417] AUTODETECT spr round 2 (radius: 10)
[02:19:36 -191600.493546] AUTODETECT spr round 3 (radius: 15)
[02:20:48 -162072.627295] AUTODETECT spr round 4 (radius: 20)
[02:22:17 -148924.213179] AUTODETECT spr round 5 (radius: 25)
[02:23:58 -145868.492014] SPR radius for FAST iterations: 25 (autodetect)
[02:23:58 -145868.492014] Model parameter optimization (eps = 3.000000)
[02:24:17 -145579.139479] FAST spr round 1 (radius: 25)
[02:25:47 -129346.839390] FAST spr round 2 (radius: 25)
[02:27:01 -127790.444368] FAST spr round 3 (radius: 25)
[02:28:00 -127738.781308] FAST spr round 4 (radius: 25)
[02:28:49 -127735.799997] FAST spr round 5 (radius: 25)
[02:29:35 -127735.785956] Model parameter optimization (eps = 1.000000)
[02:29:46 -127726.291574] SLOW spr round 1 (radius: 5)
[02:30:48 -127703.220901] SLOW spr round 2 (radius: 5)
[02:31:47 -127702.497794] SLOW spr round 3 (radius: 5)
[02:32:44 -127702.497425] SLOW spr round 4 (radius: 10)
[02:33:49 -127702.497394] SLOW spr round 5 (radius: 15)
[02:35:23] [worker #1] ML tree search #8, logLikelihood: -127693.359927
[02:35:45 -127702.367730] SLOW spr round 6 (radius: 5)
[02:37:10 -127702.231837] SLOW spr round 7 (radius: 5)
[02:38:23 -127702.230124] SLOW spr round 8 (radius: 10)
[02:39:38 -127702.229349] SLOW spr round 9 (radius: 15)
[02:41:32 -127702.228995] SLOW spr round 10 (radius: 20)
[02:44:11 -127700.304148] SLOW spr round 11 (radius: 5)
[02:45:35 -127700.293251] SLOW spr round 12 (radius: 10)
[02:47:01 -127700.289433] SLOW spr round 13 (radius: 15)
[02:48:55 -127700.289217] SLOW spr round 14 (radius: 20)
[02:51:42 -127700.289212] SLOW spr round 15 (radius: 25)
[02:54:53 -127700.289210] Model parameter optimization (eps = 0.100000)

[02:54:56] [worker #0] ML tree search #7, logLikelihood: -127700.258014

[02:54:56 -556073.054760] Initial branch length optimization
[02:54:59 -424058.924272] Model parameter optimization (eps = 10.000000)
[02:55:28 -421688.213332] AUTODETECT spr round 1 (radius: 5)
[02:56:24 -273435.029054] AUTODETECT spr round 2 (radius: 10)
[02:57:27 -198850.170402] AUTODETECT spr round 3 (radius: 15)
[02:58:37 -169025.406418] AUTODETECT spr round 4 (radius: 20)
[03:00:02 -156359.117999] AUTODETECT spr round 5 (radius: 25)
[03:02:08 -148554.080348] SPR radius for FAST iterations: 25 (autodetect)
[03:02:08 -148554.080348] Model parameter optimization (eps = 3.000000)
[03:02:28 -148129.727064] FAST spr round 1 (radius: 25)
[03:03:57 -129972.007844] FAST spr round 2 (radius: 25)
[03:05:00 -127825.219743] FAST spr round 3 (radius: 25)
[03:05:57 -127750.534085] FAST spr round 4 (radius: 25)
[03:06:45 -127749.545850] FAST spr round 5 (radius: 25)
[03:07:31 -127748.664927] FAST spr round 6 (radius: 25)
[03:08:17 -127746.959274] FAST spr round 7 (radius: 25)
[03:09:01 -127746.957972] Model parameter optimization (eps = 1.000000)
[03:09:13 -127738.604684] SLOW spr round 1 (radius: 5)
[03:10:14 -127718.956181] SLOW spr round 2 (radius: 5)
[03:10:31] [worker #1] ML tree search #10, logLikelihood: -127695.490872
[03:11:18 -127712.399047] SLOW spr round 3 (radius: 5)
[03:12:19 -127712.398057] SLOW spr round 4 (radius: 10)
[03:13:27 -127712.234937] SLOW spr round 5 (radius: 5)
[03:14:46 -127712.195867] SLOW spr round 6 (radius: 10)
[03:16:04 -127712.195341] SLOW spr round 7 (radius: 15)
[03:17:55 -127708.236841] SLOW spr round 8 (radius: 5)
[03:19:23 -127705.882709] SLOW spr round 9 (radius: 5)
[03:20:36 -127705.876310] SLOW spr round 10 (radius: 10)
[03:21:52 -127705.757834] SLOW spr round 11 (radius: 5)
[03:23:10 -127705.718936] SLOW spr round 12 (radius: 10)
[03:24:28 -127705.718417] SLOW spr round 13 (radius: 15)
[03:26:15 -127705.718086] SLOW spr round 14 (radius: 20)
[03:28:58 -127702.149603] SLOW spr round 15 (radius: 5)
[03:30:27 -127701.650258] SLOW spr round 16 (radius: 5)
[03:31:41 -127701.626852] SLOW spr round 17 (radius: 10)
[03:32:58 -127701.625271] SLOW spr round 18 (radius: 15)
[03:34:47 -127699.616967] SLOW spr round 19 (radius: 5)
[03:36:13 -127699.615869] SLOW spr round 20 (radius: 10)
[03:37:36 -127699.615561] SLOW spr round 21 (radius: 15)
[03:39:24 -127699.615376] SLOW spr round 22 (radius: 20)
[03:42:06 -127699.615257] SLOW spr round 23 (radius: 25)
[03:45:10 -127699.615172] Model parameter optimization (eps = 0.100000)

[03:45:16] [worker #0] ML tree search #9, logLikelihood: -127699.474522

[03:45:16 -545779.522189] Initial branch length optimization
[03:45:20 -422569.251676] Model parameter optimization (eps = 10.000000)
[03:45:42 -420145.524208] AUTODETECT spr round 1 (radius: 5)
[03:46:36 -263404.799325] AUTODETECT spr round 2 (radius: 10)
[03:47:38 -195507.187995] AUTODETECT spr round 3 (radius: 15)
[03:48:52 -161568.190452] AUTODETECT spr round 4 (radius: 20)
[03:50:23 -147008.395373] AUTODETECT spr round 5 (radius: 25)
[03:52:06 -145716.092796] SPR radius for FAST iterations: 25 (autodetect)
[03:52:06 -145716.092796] Model parameter optimization (eps = 3.000000)
[03:52:27 -145383.449796] FAST spr round 1 (radius: 25)
[03:53:49 -128737.773047] FAST spr round 2 (radius: 25)
[03:54:50 -127798.548895] FAST spr round 3 (radius: 25)
[03:55:46 -127751.183211] FAST spr round 4 (radius: 25)
[03:56:33 -127742.690641] FAST spr round 5 (radius: 25)
[03:57:19 -127734.157355] FAST spr round 6 (radius: 25)
[03:58:06 -127724.981759] FAST spr round 7 (radius: 25)
[03:58:49 -127724.980188] Model parameter optimization (eps = 1.000000)
[03:59:04 -127712.173925] SLOW spr round 1 (radius: 5)
[04:00:05 -127692.743626] SLOW spr round 2 (radius: 5)
[04:01:07 -127692.424941] SLOW spr round 3 (radius: 5)
[04:02:09 -127692.424456] SLOW spr round 4 (radius: 10)
[04:03:19 -127692.424169] SLOW spr round 5 (radius: 15)
[04:05:17 -127691.575777] SLOW spr round 6 (radius: 5)
[04:05:41] [worker #1] ML tree search #12, logLikelihood: -127702.212555
[04:06:43 -127691.574690] SLOW spr round 7 (radius: 10)
[04:08:10 -127691.574521] SLOW spr round 8 (radius: 15)
[04:10:07 -127691.574422] SLOW spr round 9 (radius: 20)
[04:13:00 -127691.574343] SLOW spr round 10 (radius: 25)
[04:16:16 -127691.574275] Model parameter optimization (eps = 0.100000)

[04:16:20] [worker #0] ML tree search #11, logLikelihood: -127691.502646

[04:16:20 -553705.325862] Initial branch length optimization
[04:16:23 -424422.369252] Model parameter optimization (eps = 10.000000)
[04:17:02 -422170.001378] AUTODETECT spr round 1 (radius: 5)
[04:17:57 -261235.037883] AUTODETECT spr round 2 (radius: 10)
[04:19:00 -187612.097608] AUTODETECT spr round 3 (radius: 15)
[04:20:19 -163182.534624] AUTODETECT spr round 4 (radius: 20)
[04:22:01 -143711.777288] AUTODETECT spr round 5 (radius: 25)
[04:23:45 -142023.504706] SPR radius for FAST iterations: 25 (autodetect)
[04:23:45 -142023.504706] Model parameter optimization (eps = 3.000000)
[04:24:06 -141702.430922] FAST spr round 1 (radius: 25)
[04:25:32 -128522.246236] FAST spr round 2 (radius: 25)
[04:26:35 -127762.031823] FAST spr round 3 (radius: 25)
[04:27:27 -127750.076929] FAST spr round 4 (radius: 25)
[04:28:15 -127743.218012] FAST spr round 5 (radius: 25)
[04:29:01 -127736.884502] FAST spr round 6 (radius: 25)
[04:29:45 -127736.510061] FAST spr round 7 (radius: 25)
[04:30:29 -127736.506903] Model parameter optimization (eps = 1.000000)
[04:30:40 -127732.023031] SLOW spr round 1 (radius: 5)
[04:31:41 -127696.599284] SLOW spr round 2 (radius: 5)
[04:32:43 -127693.972197] SLOW spr round 3 (radius: 5)
[04:33:44 -127693.972089] SLOW spr round 4 (radius: 10)
[04:34:52 -127693.972021] SLOW spr round 5 (radius: 15)
[04:36:49 -127693.190189] SLOW spr round 6 (radius: 5)
[04:38:14 -127693.047536] SLOW spr round 7 (radius: 5)
[04:39:25 -127693.047367] SLOW spr round 8 (radius: 10)
[04:40:40 -127693.047258] SLOW spr round 9 (radius: 15)
[04:42:36 -127693.047176] SLOW spr round 10 (radius: 20)
[04:43:43] [worker #1] ML tree search #14, logLikelihood: -127694.104918
[04:45:26 -127693.047107] SLOW spr round 11 (radius: 25)
[04:48:44 -127693.047042] Model parameter optimization (eps = 0.100000)

[04:48:51] [worker #0] ML tree search #13, logLikelihood: -127692.897594

[04:48:51 -544960.374961] Initial branch length optimization
[04:48:53 -419861.711566] Model parameter optimization (eps = 10.000000)
[04:49:17 -417352.264680] AUTODETECT spr round 1 (radius: 5)
[04:50:12 -276734.650097] AUTODETECT spr round 2 (radius: 10)
[04:51:16 -204231.425691] AUTODETECT spr round 3 (radius: 15)
[04:52:27 -168193.562558] AUTODETECT spr round 4 (radius: 20)
[04:53:51 -149720.471512] AUTODETECT spr round 5 (radius: 25)
[04:55:41 -143513.284586] SPR radius for FAST iterations: 25 (autodetect)
[04:55:41 -143513.284586] Model parameter optimization (eps = 3.000000)
[04:56:03 -143204.187602] FAST spr round 1 (radius: 25)
[04:57:31 -128512.363124] FAST spr round 2 (radius: 25)
[04:58:38 -127858.758316] FAST spr round 3 (radius: 25)
[04:59:33 -127785.626520] FAST spr round 4 (radius: 25)
[05:00:22 -127777.773123] FAST spr round 5 (radius: 25)
[05:01:09 -127760.059537] FAST spr round 6 (radius: 25)
[05:01:54 -127760.058108] Model parameter optimization (eps = 1.000000)
[05:02:05 -127755.533245] SLOW spr round 1 (radius: 5)
[05:03:06 -127710.800908] SLOW spr round 2 (radius: 5)
[05:04:10 -127704.483293] SLOW spr round 3 (radius: 5)
[05:05:12 -127704.468599] SLOW spr round 4 (radius: 10)
[05:06:21 -127702.267184] SLOW spr round 5 (radius: 5)
[05:07:42 -127699.430949] SLOW spr round 6 (radius: 5)
[05:08:50 -127699.428264] SLOW spr round 7 (radius: 10)
[05:10:03 -127699.427373] SLOW spr round 8 (radius: 15)
[05:11:56 -127698.285282] SLOW spr round 9 (radius: 5)
[05:13:21 -127698.270494] SLOW spr round 10 (radius: 10)
[05:14:44 -127698.270397] SLOW spr round 11 (radius: 15)
[05:14:59] [worker #1] ML tree search #16, logLikelihood: -127690.972045
[05:16:33 -127698.270327] SLOW spr round 12 (radius: 20)
[05:19:20 -127698.270268] SLOW spr round 13 (radius: 25)
[05:22:27 -127698.270216] Model parameter optimization (eps = 0.100000)

[05:22:31] [worker #0] ML tree search #15, logLikelihood: -127698.263545

[05:22:31 -551582.522308] Initial branch length optimization
[05:22:34 -421605.336351] Model parameter optimization (eps = 10.000000)
[05:23:01 -419093.814270] AUTODETECT spr round 1 (radius: 5)
[05:23:57 -271319.235349] AUTODETECT spr round 2 (radius: 10)
[05:25:01 -184825.997797] AUTODETECT spr round 3 (radius: 15)
[05:26:15 -161799.413553] AUTODETECT spr round 4 (radius: 20)
[05:27:44 -145831.396661] AUTODETECT spr round 5 (radius: 25)
[05:29:26 -143154.063100] SPR radius for FAST iterations: 25 (autodetect)
[05:29:26 -143154.063100] Model parameter optimization (eps = 3.000000)
[05:29:49 -142812.718566] FAST spr round 1 (radius: 25)
[05:31:13 -128642.806941] FAST spr round 2 (radius: 25)
[05:32:14 -127807.920394] FAST spr round 3 (radius: 25)
[05:33:09 -127752.081789] FAST spr round 4 (radius: 25)
[05:33:58 -127748.522317] FAST spr round 5 (radius: 25)
[05:34:46 -127748.519645] Model parameter optimization (eps = 1.000000)
[05:34:59 -127744.731192] SLOW spr round 1 (radius: 5)
[05:36:06 -127712.652489] SLOW spr round 2 (radius: 5)
[05:37:12 -127710.790320] SLOW spr round 3 (radius: 5)
[05:38:13 -127710.789201] SLOW spr round 4 (radius: 10)
[05:39:24 -127705.513078] SLOW spr round 5 (radius: 5)
[05:40:47 -127697.096559] SLOW spr round 6 (radius: 5)
[05:41:59 -127694.762482] SLOW spr round 7 (radius: 5)
[05:43:05 -127693.124235] SLOW spr round 8 (radius: 5)
[05:44:07 -127693.123033] SLOW spr round 9 (radius: 10)
[05:45:18 -127690.867644] SLOW spr round 10 (radius: 5)
[05:46:37 -127690.865695] SLOW spr round 11 (radius: 10)
[05:47:41] [worker #1] ML tree search #18, logLikelihood: -127689.842950
[05:47:55 -127690.865191] SLOW spr round 12 (radius: 15)
[05:49:49 -127689.732582] SLOW spr round 13 (radius: 5)
[05:51:17 -127689.231831] SLOW spr round 14 (radius: 5)
[05:52:30 -127689.230078] SLOW spr round 15 (radius: 10)
[05:53:46 -127689.229404] SLOW spr round 16 (radius: 15)
[05:55:41 -127689.228998] SLOW spr round 17 (radius: 20)
[05:58:28 -127689.228665] SLOW spr round 18 (radius: 25)
[06:01:27 -127689.228351] Model parameter optimization (eps = 0.100000)

[06:01:32] [worker #0] ML tree search #17, logLikelihood: -127689.204136

[06:01:32 -552880.383583] Initial branch length optimization
[06:01:35 -425752.780170] Model parameter optimization (eps = 10.000000)
[06:01:59 -423551.456068] AUTODETECT spr round 1 (radius: 5)
[06:02:52 -272439.337783] AUTODETECT spr round 2 (radius: 10)
[06:03:55 -192961.633403] AUTODETECT spr round 3 (radius: 15)
[06:05:10 -161079.333254] AUTODETECT spr round 4 (radius: 20)
[06:06:34 -142675.533815] AUTODETECT spr round 5 (radius: 25)
[06:08:06 -141374.534165] SPR radius for FAST iterations: 25 (autodetect)
[06:08:06 -141374.534165] Model parameter optimization (eps = 3.000000)
[06:08:31 -141084.778587] FAST spr round 1 (radius: 25)
[06:09:51 -128748.239933] FAST spr round 2 (radius: 25)
[06:10:57 -128173.467788] FAST spr round 3 (radius: 25)
[06:11:50 -128031.607340] FAST spr round 4 (radius: 25)
[06:12:42 -127773.593733] FAST spr round 5 (radius: 25)
[06:13:28 -127773.277257] FAST spr round 6 (radius: 25)
[06:14:12 -127772.961337] FAST spr round 7 (radius: 25)
[06:14:56 -127772.959616] Model parameter optimization (eps = 1.000000)
[06:15:06 -127766.334405] SLOW spr round 1 (radius: 5)
[06:16:08 -127716.565283] SLOW spr round 2 (radius: 5)
[06:17:11 -127713.529994] SLOW spr round 3 (radius: 5)
[06:18:14 -127713.502832] SLOW spr round 4 (radius: 10)
[06:19:28 -127713.501356] SLOW spr round 5 (radius: 15)
[06:21:33 -127712.459167] SLOW spr round 6 (radius: 5)
[06:23:06 -127712.432709] SLOW spr round 7 (radius: 10)
[06:24:35 -127712.429069] SLOW spr round 8 (radius: 15)
[06:25:43] [worker #1] ML tree search #20, logLikelihood: -127691.769487
[06:26:34 -127712.427398] SLOW spr round 9 (radius: 20)
[06:29:31 -127712.426632] SLOW spr round 10 (radius: 25)
[06:32:55 -127708.703088] SLOW spr round 11 (radius: 5)
[06:34:32 -127708.701022] SLOW spr round 12 (radius: 10)
[06:36:07 -127708.700266] SLOW spr round 13 (radius: 15)
[06:38:08 -127708.699905] SLOW spr round 14 (radius: 20)
[06:41:06 -127701.003427] SLOW spr round 15 (radius: 5)
[06:42:41 -127700.867792] SLOW spr round 16 (radius: 5)
[06:44:00 -127700.867711] SLOW spr round 17 (radius: 10)
[06:45:23 -127700.867598] SLOW spr round 18 (radius: 15)
[06:47:22 -127700.867544] SLOW spr round 19 (radius: 20)
[06:50:19 -127700.867491] SLOW spr round 20 (radius: 25)
[06:53:43 -127700.867439] Model parameter optimization (eps = 0.100000)

[06:53:46] [worker #0] ML tree search #19, logLikelihood: -127700.815847


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.228078,0.549459) (0.259488,1.310068) (0.411610,0.752936) (0.100824,2.229807) 
   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: -127689.204136

AIC score: 257684.408272 / AICc score: 2918808.408272 / BIC score: 263015.955480
Free parameters (model + branch lengths): 1153

WARNING: Number of free parameters (K=1153) is larger than alignment size (n=753).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 92 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/3_mltree/A6NKB5.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/3_mltree/A6NKB5.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/3_mltree/A6NKB5.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/3_mltree/A6NKB5.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKB5/3_mltree/A6NKB5.raxml.log

Analysis started: 01-Jul-2021 02:50:32 / finished: 01-Jul-2021 09:44:19

Elapsed time: 24827.056 seconds

Consumed energy: 2153.507 Wh (= 11 km in an electric car, or 54 km with an e-scooter!)