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 16-Jul-2021 07:43:47 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/2_msa/Q6NT32_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/3_mltree/Q6NT32 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/2_msa/Q6NT32_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 520 sites

WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_M3Y017_M3Y017_MUSPF_9669 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2I3H6M2_A0A2I3H6M2_NOMLE_61853 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_G1P8A4_G1P8A4_MYOLU_59463 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_G3RBW3_G3RBW3_GORGO_9595 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_H2PVY8_H2PVY8_PONAB_9601 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_G1TYL9_G1TYL9_RABIT_9986 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_F1Q3I9_F1Q3I9_CANLF_9615 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2I3RYY1_A0A2I3RYY1_PANTR_9598 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_F6UIF6_F6UIF6_HORSE_9796 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_I3MQG8_I3MQG8_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_H0Y111_H0Y111_OTOGA_30611 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A286XBR3_A0A286XBR3_CAVPO_10141 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_G7NRV3_G7NRV3_MACMU_9544 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_G1MC29_G1MC29_AILME_9646 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_L5KW21_L5KW21_PTEAL_9402 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2I2UDX2_A0A2I2UDX2_FELCA_9685 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A091CW20_A0A091CW20_FUKDA_885580 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A0D9RG79_A0A0D9RG79_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A3Q0DMF7_A0A3Q0DMF7_TARSY_1868482 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2K5MHG7_A0A2K5MHG7_CERAT_9531 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2K6DL61_A0A2K6DL61_MACNE_9545 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2K5YQ23_A0A2K5YQ23_MANLE_9568 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2R9A7T8_A0A2R9A7T8_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2U3VNI4_A0A2U3VNI4_ODORO_9708 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2Y9DSC6_A0A2Y9DSC6_TRIMA_127582 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2Y9LF14_A0A2Y9LF14_ENHLU_391180 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2Y9M4T8_A0A2Y9M4T8_DELLE_9749 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A2Y9F3J5_A0A2Y9F3J5_PHYCD_9755 are exactly identical!
WARNING: Sequences sp_Q8BYM5_NLGN3_MOUSE_10090 and tr_A0A384A8J7_A0A384A8J7_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G3I7K0_G3I7K0_CRIGR_10029 and tr_A0A1U8CN00_A0A1U8CN00_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3I7K0_G3I7K0_CRIGR_10029 and tr_A0A2U3Y1E8_A0A2U3Y1E8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_G3QGN3_G3QGN3_GORGO_9595 and tr_A0A2J8Q8V8_A0A2J8Q8V8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QGN3_G3QGN3_GORGO_9595 and tr_A0A2R9B1H5_A0A2R9B1H5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_A0A2J8L771_A0A2J8L771_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_F6RUI6_F6RUI6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_U3FSR0_U3FSR0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_G7NZE2_G7NZE2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_A0A096N102_A0A096N102_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_A0A2K5L7H3_A0A2K5L7H3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_A0A2K6CTK8_A0A2K6CTK8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_A0A2K5XCK1_A0A2K5XCK1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3QNJ3_G3QNJ3_GORGO_9595 and tr_A0A2R9A9V3_A0A2R9A9V3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5Q544_W5Q544_SHEEP_9940 and tr_G3MXP5_G3MXP5_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_Q62888_NLGN2_RAT_10116 and tr_A0A1U8BV67_A0A1U8BV67_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M4AAM2_M4AAM2_XIPMA_8083 and tr_A0A096MAY8_A0A096MAY8_POEFO_48698 are exactly identical!
WARNING: Sequences sp_Q8NFZ4_NLGN2_HUMAN_9606 and tr_F6WCL3_F6WCL3_CALJA_9483 are exactly identical!
WARNING: Sequences sp_Q8NFZ4_NLGN2_HUMAN_9606 and tr_A0A096P2P8_A0A096P2P8_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_Q8NFZ4_NLGN2_HUMAN_9606 and tr_A0A0D9RH57_A0A0D9RH57_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q8NFZ4_NLGN2_HUMAN_9606 and tr_A0A1S2ZNE7_A0A1S2ZNE7_ERIEU_9365 are exactly identical!
WARNING: Sequences sp_Q8NFZ4_NLGN2_HUMAN_9606 and tr_A0A2K6B7J7_A0A2K6B7J7_MACNE_9545 are exactly identical!
WARNING: Sequences sp_Q8NFZ4_NLGN2_HUMAN_9606 and tr_A0A2U3VTB8_A0A2U3VTB8_ODORO_9708 are exactly identical!
WARNING: Sequences sp_Q8NFZ4_NLGN2_HUMAN_9606 and tr_A0A2Y9T4P8_A0A2Y9T4P8_PHYCD_9755 are exactly identical!
WARNING: Sequences sp_Q9NZ94_NLGN3_HUMAN_9606 and tr_A0A1S3AJB4_A0A1S3AJB4_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_F6UGL5_F6UGL5_MACMU_9544 and tr_G7Q259_G7Q259_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6UGL5_F6UGL5_MACMU_9544 and tr_A0A2K5P6E8_A0A2K5P6E8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6UGL5_F6UGL5_MACMU_9544 and tr_A0A2K6CZZ8_A0A2K6CZZ8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6UGL5_F6UGL5_MACMU_9544 and tr_A0A2K5Z653_A0A2K5Z653_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7HPD8_F7HPD8_MACMU_9544 and tr_A0A2K6DEC1_A0A2K6DEC1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A091FHC2_A0A091FHC2_CORBR_85066 and tr_A0A093PKH9_A0A093PKH9_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091V4Q2_A0A091V4Q2_NIPNI_128390 and tr_A0A087QSP2_A0A087QSP2_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091V4Q2_A0A091V4Q2_NIPNI_128390 and tr_A0A093I3P5_A0A093I3P5_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091V4Q2_A0A091V4Q2_NIPNI_128390 and tr_A0A091GC26_A0A091GC26_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091V4Q2_A0A091V4Q2_NIPNI_128390 and tr_A0A0A0ASH1_A0A0A0ASH1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091FSI0_A0A091FSI0_9AVES_55661 and tr_A0A091IHX0_A0A091IHX0_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A2I0MKY4_A0A2I0MKY4_COLLI_8932 and tr_A0A1V4JCQ3_A0A1V4JCQ3_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1MQ84_A0A0V1MQ84_9BILA_268474 and tr_A0A0V1HH09_A0A0V1HH09_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A2R2MTQ6_A0A2R2MTQ6_LINUN_7574 and tr_A0A2R2MTU1_A0A2R2MTU1_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A226N871_A0A226N871_CALSU_9009 and tr_A0A226PJX6_A0A226PJX6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2U4C4F2_A0A2U4C4F2_TURTR_9739 and tr_A0A2Y9M7D8_A0A2Y9M7D8_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 69

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/Q6NT32/3_mltree/Q6NT32.raxml.reduced.phy

Alignment comprises 1 partitions and 520 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 520 / 520
Gaps: 6.09 %
Invariant sites: 0.19 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/3_mltree/Q6NT32.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 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 / 260 / 20800
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -919662.553527] Initial branch length optimization
[00:00:09 -762592.750850] Model parameter optimization (eps = 10.000000)
[00:01:07 -761505.726810] AUTODETECT spr round 1 (radius: 5)
[00:05:14 -527344.517257] AUTODETECT spr round 2 (radius: 10)
[00:09:46 -416100.324898] AUTODETECT spr round 3 (radius: 15)
[00:15:15 -313135.226290] AUTODETECT spr round 4 (radius: 20)
[00:21:13 -300970.410055] AUTODETECT spr round 5 (radius: 25)
[00:28:17 -299944.727454] SPR radius for FAST iterations: 25 (autodetect)
[00:28:17 -299944.727454] Model parameter optimization (eps = 3.000000)
[00:28:49 -299761.561588] FAST spr round 1 (radius: 25)
[00:33:38 -265832.380116] FAST spr round 2 (radius: 25)
[00:37:01 -265045.594142] FAST spr round 3 (radius: 25)
[00:40:02 -264959.135300] FAST spr round 4 (radius: 25)
[00:42:55 -264929.346558] FAST spr round 5 (radius: 25)
[00:45:34 -264920.436148] FAST spr round 6 (radius: 25)
[00:48:10 -264918.024491] FAST spr round 7 (radius: 25)
[00:50:44 -264918.024453] Model parameter optimization (eps = 1.000000)
[00:51:00 -264912.763057] SLOW spr round 1 (radius: 5)
[00:54:23 -264845.430268] SLOW spr round 2 (radius: 5)
[00:57:48 -264834.179816] SLOW spr round 3 (radius: 5)
[01:01:13 -264827.566964] SLOW spr round 4 (radius: 5)
[01:04:36 -264825.743620] SLOW spr round 5 (radius: 5)
[01:07:53 -264825.743577] SLOW spr round 6 (radius: 10)
[01:11:22 -264825.743517] SLOW spr round 7 (radius: 15)
[01:17:07 -264825.743491] SLOW spr round 8 (radius: 20)
[01:25:45 -264825.743491] SLOW spr round 9 (radius: 25)
[01:27:56] [worker #1] ML tree search #2, logLikelihood: -264817.418739
[01:36:58 -264825.743491] Model parameter optimization (eps = 0.100000)

[01:37:09] [worker #0] ML tree search #1, logLikelihood: -264825.472343

[01:37:09 -918059.728824] Initial branch length optimization
[01:37:20 -772467.161297] Model parameter optimization (eps = 10.000000)
[01:38:30 -771472.442322] AUTODETECT spr round 1 (radius: 5)
[01:38:38] [worker #2] ML tree search #3, logLikelihood: -264827.012096
[01:42:42 -524794.168853] AUTODETECT spr round 2 (radius: 10)
[01:47:14 -389005.565299] AUTODETECT spr round 3 (radius: 15)
[01:52:04 -314090.938393] AUTODETECT spr round 4 (radius: 20)
[01:57:32 -297529.527644] AUTODETECT spr round 5 (radius: 25)
[02:04:18 -296869.278425] SPR radius for FAST iterations: 25 (autodetect)
[02:04:18 -296869.278425] Model parameter optimization (eps = 3.000000)
[02:04:51 -296631.917978] FAST spr round 1 (radius: 25)
[02:10:07 -266306.459824] FAST spr round 2 (radius: 25)
[02:14:01 -265062.017286] FAST spr round 3 (radius: 25)
[02:17:11 -264969.291775] FAST spr round 4 (radius: 25)
[02:19:59 -264959.141738] FAST spr round 5 (radius: 25)
[02:22:36 -264959.141719] Model parameter optimization (eps = 1.000000)
[02:22:57 -264946.701055] SLOW spr round 1 (radius: 5)
[02:26:38 -264875.792673] SLOW spr round 2 (radius: 5)
[02:30:17 -264864.992270] SLOW spr round 3 (radius: 5)
[02:33:52 -264860.325815] SLOW spr round 4 (radius: 5)
[02:37:14 -264857.868414] SLOW spr round 5 (radius: 5)
[02:40:33 -264857.868277] SLOW spr round 6 (radius: 10)
[02:44:06 -264854.644274] SLOW spr round 7 (radius: 5)
[02:48:24 -264853.667233] SLOW spr round 8 (radius: 5)
[02:52:08 -264853.667225] SLOW spr round 9 (radius: 10)
[02:55:38 -264853.667225] SLOW spr round 10 (radius: 15)
[03:01:14 -264853.667223] SLOW spr round 11 (radius: 20)
[03:09:41 -264853.667223] SLOW spr round 12 (radius: 25)
[03:14:57] [worker #1] ML tree search #5, logLikelihood: -264847.228056
[03:19:00] [worker #2] ML tree search #6, logLikelihood: -264807.210273
[03:20:21 -264853.667223] Model parameter optimization (eps = 0.100000)

[03:20:34] [worker #0] ML tree search #4, logLikelihood: -264852.967283

[03:20:35 -918358.137908] Initial branch length optimization
[03:20:44 -765943.814560] Model parameter optimization (eps = 10.000000)
[03:22:01 -764915.359746] AUTODETECT spr round 1 (radius: 5)
[03:26:11 -514678.143481] AUTODETECT spr round 2 (radius: 10)
[03:30:44 -392735.766507] AUTODETECT spr round 3 (radius: 15)
[03:35:07 -326775.868903] AUTODETECT spr round 4 (radius: 20)
[03:40:25 -308875.899845] AUTODETECT spr round 5 (radius: 25)
[03:48:16 -299677.421354] SPR radius for FAST iterations: 25 (autodetect)
[03:48:16 -299677.421354] Model parameter optimization (eps = 3.000000)
[03:48:49 -299561.557844] FAST spr round 1 (radius: 25)
[03:54:07 -265950.241224] FAST spr round 2 (radius: 25)
[03:57:52 -265045.963790] FAST spr round 3 (radius: 25)
[04:01:10 -264906.419877] FAST spr round 4 (radius: 25)
[04:04:03 -264897.464327] FAST spr round 5 (radius: 25)
[04:06:43 -264894.783964] FAST spr round 6 (radius: 25)
[04:09:17 -264894.783906] Model parameter optimization (eps = 1.000000)
[04:09:38 -264884.895375] SLOW spr round 1 (radius: 5)
[04:13:20 -264817.948453] SLOW spr round 2 (radius: 5)
[04:16:54 -264810.682240] SLOW spr round 3 (radius: 5)
[04:20:15 -264805.611045] SLOW spr round 4 (radius: 5)
[04:23:30 -264805.610983] SLOW spr round 5 (radius: 10)
[04:26:56 -264805.610967] SLOW spr round 6 (radius: 15)
[04:32:42 -264805.610956] SLOW spr round 7 (radius: 20)
[04:41:09 -264805.610945] SLOW spr round 8 (radius: 25)
[04:42:07] [worker #2] ML tree search #9, logLikelihood: -264800.011073
[04:45:21] [worker #1] ML tree search #8, logLikelihood: -264828.011700
[04:52:00 -264805.610935] Model parameter optimization (eps = 0.100000)

[04:52:18] [worker #0] ML tree search #7, logLikelihood: -264805.504904

[04:52:18 -915962.874739] Initial branch length optimization
[04:52:26 -768498.818711] Model parameter optimization (eps = 10.000000)
[04:53:25 -767263.736162] AUTODETECT spr round 1 (radius: 5)
[04:57:32 -516059.184013] AUTODETECT spr round 2 (radius: 10)
[05:02:01 -400390.751760] AUTODETECT spr round 3 (radius: 15)
[05:06:43 -354796.430246] AUTODETECT spr round 4 (radius: 20)
[05:12:00 -338839.325439] AUTODETECT spr round 5 (radius: 25)
[05:18:16 -314371.788596] SPR radius for FAST iterations: 25 (autodetect)
[05:18:16 -314371.788596] Model parameter optimization (eps = 3.000000)
[05:18:51 -314271.830954] FAST spr round 1 (radius: 25)
[05:24:08 -266985.133631] FAST spr round 2 (radius: 25)
[05:27:49 -265286.210273] FAST spr round 3 (radius: 25)
[05:31:02 -265133.826199] FAST spr round 4 (radius: 25)
[05:33:54 -265101.799022] FAST spr round 5 (radius: 25)
[05:36:39 -265081.740051] FAST spr round 6 (radius: 25)
[05:39:15 -265077.032288] FAST spr round 7 (radius: 25)
[05:41:48 -265077.032196] Model parameter optimization (eps = 1.000000)
[05:42:04 -265073.295502] SLOW spr round 1 (radius: 5)
[05:45:40 -265025.209081] SLOW spr round 2 (radius: 5)
[05:49:04 -265017.109126] SLOW spr round 3 (radius: 5)
[05:52:24 -265017.107149] SLOW spr round 4 (radius: 10)
[05:55:50 -265017.106951] SLOW spr round 5 (radius: 15)
[06:01:36 -265015.717527] SLOW spr round 6 (radius: 5)
[06:06:06 -265015.717512] SLOW spr round 7 (radius: 10)
[06:10:03 -265015.717512] SLOW spr round 8 (radius: 15)
[06:11:04] [worker #2] ML tree search #12, logLikelihood: -264826.162230
[06:14:00] [worker #1] ML tree search #11, logLikelihood: -264967.506735
[06:15:31 -265015.717511] SLOW spr round 9 (radius: 20)
[06:24:20 -265015.717511] SLOW spr round 10 (radius: 25)
[06:35:08 -265015.717504] Model parameter optimization (eps = 0.100000)

[06:35:32] [worker #0] ML tree search #10, logLikelihood: -265015.403078

[06:35:32 -922674.665534] Initial branch length optimization
[06:35:41 -768196.376391] Model parameter optimization (eps = 10.000000)
[06:37:06 -766984.835901] AUTODETECT spr round 1 (radius: 5)
[06:41:17 -511141.950518] AUTODETECT spr round 2 (radius: 10)
[06:45:50 -391148.541524] AUTODETECT spr round 3 (radius: 15)
[06:50:24 -348836.546432] AUTODETECT spr round 4 (radius: 20)
[06:56:00 -308750.391644] AUTODETECT spr round 5 (radius: 25)
[07:02:07 -302013.550905] SPR radius for FAST iterations: 25 (autodetect)
[07:02:07 -302013.550905] Model parameter optimization (eps = 3.000000)
[07:02:38 -301895.157744] FAST spr round 1 (radius: 25)
[07:07:53 -265716.381134] FAST spr round 2 (radius: 25)
[07:11:34 -264922.636638] FAST spr round 3 (radius: 25)
[07:14:34 -264894.976907] FAST spr round 4 (radius: 25)
[07:17:17 -264888.279863] FAST spr round 5 (radius: 25)
[07:19:51 -264888.279710] Model parameter optimization (eps = 1.000000)
[07:20:18 -264882.761369] SLOW spr round 1 (radius: 5)
[07:23:53 -264829.368257] SLOW spr round 2 (radius: 5)
[07:27:19 -264827.255566] SLOW spr round 3 (radius: 5)
[07:30:37 -264827.255491] SLOW spr round 4 (radius: 10)
[07:34:04 -264827.255490] SLOW spr round 5 (radius: 15)
[07:38:21] [worker #1] ML tree search #14, logLikelihood: -264819.625474
[07:39:36 -264827.255490] SLOW spr round 6 (radius: 20)
[07:47:42 -264827.255490] SLOW spr round 7 (radius: 25)
[07:51:23] [worker #2] ML tree search #15, logLikelihood: -264817.606464
[07:58:14 -264827.255490] Model parameter optimization (eps = 0.100000)

[07:58:21] [worker #0] ML tree search #13, logLikelihood: -264827.216526

[07:58:21 -919290.215891] Initial branch length optimization
[07:58:29 -766818.096776] Model parameter optimization (eps = 10.000000)
[07:59:39 -765633.323349] AUTODETECT spr round 1 (radius: 5)
[08:03:48 -525128.506974] AUTODETECT spr round 2 (radius: 10)
[08:08:23 -395344.867786] AUTODETECT spr round 3 (radius: 15)
[08:13:02 -338214.868374] AUTODETECT spr round 4 (radius: 20)
[08:18:38 -307942.834072] AUTODETECT spr round 5 (radius: 25)
[08:25:01 -303434.024507] SPR radius for FAST iterations: 25 (autodetect)
[08:25:01 -303434.024507] Model parameter optimization (eps = 3.000000)
[08:25:33 -303190.446156] FAST spr round 1 (radius: 25)
[08:30:39 -267175.617211] FAST spr round 2 (radius: 25)
[08:34:17 -265104.800109] FAST spr round 3 (radius: 25)
[08:37:34 -264944.364173] FAST spr round 4 (radius: 25)
[08:40:31 -264926.197973] FAST spr round 5 (radius: 25)
[08:43:17 -264911.982464] FAST spr round 6 (radius: 25)
[08:45:52 -264911.361791] FAST spr round 7 (radius: 25)
[08:48:27 -264909.317554] FAST spr round 8 (radius: 25)
[08:51:01 -264909.317554] Model parameter optimization (eps = 1.000000)
[08:51:26 -264905.909520] SLOW spr round 1 (radius: 5)
[08:54:52 -264846.438004] SLOW spr round 2 (radius: 5)
[08:58:18 -264840.019105] SLOW spr round 3 (radius: 5)
[09:01:40 -264840.017903] SLOW spr round 4 (radius: 10)
[09:05:15 -264838.032507] SLOW spr round 5 (radius: 5)
[09:09:39 -264834.368988] SLOW spr round 6 (radius: 5)
[09:13:29 -264831.255414] SLOW spr round 7 (radius: 5)
[09:17:01 -264831.255318] SLOW spr round 8 (radius: 10)
[09:20:01] [worker #1] ML tree search #17, logLikelihood: -264806.623975
[09:20:35 -264831.255285] SLOW spr round 9 (radius: 15)
[09:26:10 -264831.255281] SLOW spr round 10 (radius: 20)
[09:29:04] [worker #2] ML tree search #18, logLikelihood: -264825.350030
[09:34:39 -264831.255281] SLOW spr round 11 (radius: 25)
[09:44:33 -264831.255281] Model parameter optimization (eps = 0.100000)

[09:44:59] [worker #0] ML tree search #16, logLikelihood: -264828.335240

[09:44:59 -924554.349371] Initial branch length optimization
[09:45:11 -773422.609155] Model parameter optimization (eps = 10.000000)
[09:46:15 -772351.883738] AUTODETECT spr round 1 (radius: 5)
[09:50:26 -526264.036227] AUTODETECT spr round 2 (radius: 10)
[09:54:58 -398511.047029] AUTODETECT spr round 3 (radius: 15)
[09:59:41 -326160.691658] AUTODETECT spr round 4 (radius: 20)
[10:04:59 -317195.618398] AUTODETECT spr round 5 (radius: 25)
[10:10:53 -302682.185695] SPR radius for FAST iterations: 25 (autodetect)
[10:10:53 -302682.185695] Model parameter optimization (eps = 3.000000)
[10:11:22 -302524.064125] FAST spr round 1 (radius: 25)
[10:16:30 -266770.138672] FAST spr round 2 (radius: 25)
[10:20:19 -265159.509138] FAST spr round 3 (radius: 25)
[10:23:43 -264930.753270] FAST spr round 4 (radius: 25)
[10:26:38 -264907.149772] FAST spr round 5 (radius: 25)
[10:29:13 -264904.977313] FAST spr round 6 (radius: 25)
[10:31:44 -264904.977280] Model parameter optimization (eps = 1.000000)
[10:32:07 -264894.557074] SLOW spr round 1 (radius: 5)
[10:35:44 -264825.821759] SLOW spr round 2 (radius: 5)
[10:39:05 -264820.876827] SLOW spr round 3 (radius: 5)
[10:42:27 -264817.609846] SLOW spr round 4 (radius: 5)
[10:45:42 -264817.609687] SLOW spr round 5 (radius: 10)
[10:49:03] [worker #1] ML tree search #20, logLikelihood: -264845.266244
[10:49:11 -264813.801474] SLOW spr round 6 (radius: 5)
[10:53:27 -264812.939760] SLOW spr round 7 (radius: 5)
[10:57:11 -264812.939729] SLOW spr round 8 (radius: 10)
[11:00:42 -264812.939729] SLOW spr round 9 (radius: 15)
[11:06:11 -264812.939722] SLOW spr round 10 (radius: 20)
[11:14:50 -264812.939722] SLOW spr round 11 (radius: 25)
[11:25:25 -264812.939722] Model parameter optimization (eps = 0.100000)

[11:25:32] [worker #0] ML tree search #19, logLikelihood: -264812.902050


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.133396,0.261309) (0.185271,0.395256) (0.349731,0.955194) (0.331603,1.682293) 
   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: -264800.011073

AIC score: 533610.022145 / AICc score: 8577670.022145 / BIC score: 542138.948913
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=520).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/3_mltree/Q6NT32.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/3_mltree/Q6NT32.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/3_mltree/Q6NT32.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6NT32/3_mltree/Q6NT32.raxml.log

Analysis started: 16-Jul-2021 07:43:47 / finished: 16-Jul-2021 19:09:19

Elapsed time: 41132.470 seconds