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 06-Jul-2021 14:18:31 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95996/2_msa/O95996_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95996/3_mltree/O95996 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95996/2_msa/O95996_trimmed_msa.fasta
[00:00:00] Loaded alignment with 350 taxa and 390 sites

WARNING: Sequences tr_B4QSH8_B4QSH8_DROSI_7240 and tr_Q9Y1T2_Q9Y1T2_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QSH8_B4QSH8_DROSI_7240 and tr_B4HGJ4_B4HGJ4_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_K7G530_K7G530_PELSI_13735 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A151PIC9_A0A151PIC9_ALLMI_8496 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A091IQM6_A0A091IQM6_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A087RBK3_A0A087RBK3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A093I673_A0A093I673_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A091G6L1_A0A091G6L1_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A2I0M8T0_A0A2I0M8T0_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A091J9Y2_A0A091J9Y2_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A1D5PC88_A0A1D5PC88_CHICK_9031 and tr_A0A3Q0GXG2_A0A3Q0GXG2_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A1D5PQ21_A0A1D5PQ21_CHICK_9031 and tr_A0A226MHF4_A0A226MHF4_CALSU_9009 are exactly identical!
WARNING: Sequences tr_M3YMP0_M3YMP0_MUSPF_9669 and tr_A0A2Y9JRK4_A0A2Y9JRK4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_Q9VAS9_Q9VAS9_DROME_7227 and tr_B4HZ21_B4HZ21_DROSE_7238 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_G1PQS9_G1PQS9_MYOLU_59463 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_G3RRG6_G3RRG6_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_K7EU19_K7EU19_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_G1T9V0_G1T9V0_RABIT_9986 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_H2QRB5_H2QRB5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_F6Y0R6_F6Y0R6_HORSE_9796 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A287CRY0_A0A287CRY0_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_H0UWJ7_H0UWJ7_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A1D5Q593_A0A1D5Q593_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_F7IA27_F7IA27_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_G1M1X1_G1M1X1_AILME_9646 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_G8F2K9_G8F2K9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_L5KLB3_L5KLB3_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2I2V347_A0A2I2V347_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2I3MTS7_A0A2I3MTS7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A0D9RR03_A0A0D9RR03_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A1S3WST2_A0A1S3WST2_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2K5LKU8_A0A2K5LKU8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2K6E1Z5_A0A2K6E1Z5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2K6A0C3_A0A2K6A0C3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2R9AUR0_A0A2R9AUR0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2U4BTA8_A0A2U4BTA8_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2U3W0P1_A0A2U3W0P1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2U3YVT6_A0A2U3YVT6_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2Y9PNP0_A0A2Y9PNP0_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A2Y9SMQ3_A0A2Y9SMQ3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A384D7V3_A0A384D7V3_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G1RLE9_G1RLE9_NOMLE_61853 and tr_A0A384AXK8_A0A384AXK8_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A1D5R589_A0A1D5R589_MACMU_9544 and tr_A0A2K5NTS0_A0A2K5NTS0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R589_A0A1D5R589_MACMU_9544 and tr_A0A2K6C325_A0A2K6C325_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G5BA32_G5BA32_HETGA_10181 and tr_A0A2Y9QWJ4_A0A2Y9QWJ4_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_H0YRX9_H0YRX9_TAEGU_59729 and tr_U3JB97_U3JB97_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0YRX9_H0YRX9_TAEGU_59729 and tr_A0A218UVN0_A0A218UVN0_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A044V9H8_A0A044V9H8_ONCVO_6282 and tr_A0A182DZA1_A0A182DZA1_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0Q3PSV0_A0A0Q3PSV0_AMAAE_12930 and tr_A0A093PPX0_A0A093PPX0_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A0N1PJB9_A0A0N1PJB9_PAPMA_76193 and tr_A0A194Q2E2_A0A194Q2E2_PAPXU_66420 are exactly identical!
WARNING: Sequences tr_A0A0V1D7N4_A0A0V1D7N4_TRIBR_45882 and tr_A0A0V0VDF6_A0A0V0VDF6_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1LE15_A0A0V1LE15_9BILA_6335 and tr_A0A0V1P553_A0A0V1P553_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A1I7UBZ9_A0A1I7UBZ9_9PELO_1561998 and tr_A0A1I7UC00_A0A1I7UC00_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1I7UBZ9_A0A1I7UBZ9_9PELO_1561998 and tr_A0A1I7UC01_A0A1I7UC01_9PELO_1561998 are exactly identical!
WARNING: Duplicate sequences found: 54

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/O95996/3_mltree/O95996.raxml.reduced.phy

Alignment comprises 1 partitions and 390 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 390 / 390
Gaps: 12.43 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95996/3_mltree/O95996.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 350 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 195 / 15600
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -157862.461428] Initial branch length optimization
[00:00:01 -118417.545025] Model parameter optimization (eps = 10.000000)
[00:00:29 -117826.365574] AUTODETECT spr round 1 (radius: 5)
[00:00:51 -88211.403272] AUTODETECT spr round 2 (radius: 10)
[00:01:19 -62662.423791] AUTODETECT spr round 3 (radius: 15)
[00:01:53 -51420.118556] AUTODETECT spr round 4 (radius: 20)
[00:02:32 -47927.893745] AUTODETECT spr round 5 (radius: 25)
[00:03:21 -46693.914422] SPR radius for FAST iterations: 25 (autodetect)
[00:03:21 -46693.914422] Model parameter optimization (eps = 3.000000)
[00:03:32 -46474.802077] FAST spr round 1 (radius: 25)
[00:04:09 -40955.524898] FAST spr round 2 (radius: 25)
[00:04:34 -40631.659456] FAST spr round 3 (radius: 25)
[00:04:57 -40619.048893] FAST spr round 4 (radius: 25)
[00:05:19 -40616.472345] FAST spr round 5 (radius: 25)
[00:05:37 -40616.469866] Model parameter optimization (eps = 1.000000)
[00:05:50 -40612.122138] SLOW spr round 1 (radius: 5)
[00:06:17 -40596.916453] SLOW spr round 2 (radius: 5)
[00:06:46 -40596.562098] SLOW spr round 3 (radius: 5)
[00:07:14 -40596.390075] SLOW spr round 4 (radius: 5)
[00:07:40 -40596.388194] SLOW spr round 5 (radius: 10)
[00:08:10 -40596.301837] SLOW spr round 6 (radius: 15)
[00:08:56 -40595.885681] SLOW spr round 7 (radius: 5)
[00:09:33 -40595.885457] SLOW spr round 8 (radius: 10)
[00:10:05] [worker #1] ML tree search #2, logLikelihood: -40606.481468
[00:10:10 -40595.885356] SLOW spr round 9 (radius: 15)
[00:10:55 -40595.885268] SLOW spr round 10 (radius: 20)
[00:11:47 -40595.044537] SLOW spr round 11 (radius: 5)
[00:12:27 -40594.276541] SLOW spr round 12 (radius: 5)
[00:13:00 -40594.224434] SLOW spr round 13 (radius: 10)
[00:13:33 -40594.224314] SLOW spr round 14 (radius: 15)
[00:14:16 -40594.224273] SLOW spr round 15 (radius: 20)
[00:15:07 -40594.224246] SLOW spr round 16 (radius: 25)
[00:16:02 -40594.224220] Model parameter optimization (eps = 0.100000)

[00:16:11] [worker #0] ML tree search #1, logLikelihood: -40593.430380

[00:16:11 -160614.824935] Initial branch length optimization
[00:16:12 -120333.464598] Model parameter optimization (eps = 10.000000)
[00:16:38 -119653.597256] AUTODETECT spr round 1 (radius: 5)
[00:16:43] [worker #2] ML tree search #3, logLikelihood: -40590.175664
[00:16:59 -82949.239365] AUTODETECT spr round 2 (radius: 10)
[00:17:27 -62061.977679] AUTODETECT spr round 3 (radius: 15)
[00:18:02 -47664.882802] AUTODETECT spr round 4 (radius: 20)
[00:18:42 -46679.107033] AUTODETECT spr round 5 (radius: 25)
[00:19:19 -46417.307483] SPR radius for FAST iterations: 25 (autodetect)
[00:19:19 -46417.307483] Model parameter optimization (eps = 3.000000)
[00:19:37 -46146.390505] FAST spr round 1 (radius: 25)
[00:20:11 -40847.386839] FAST spr round 2 (radius: 25)
[00:20:38 -40638.220293] FAST spr round 3 (radius: 25)
[00:21:00 -40613.083981] FAST spr round 4 (radius: 25)
[00:21:19 -40613.083713] Model parameter optimization (eps = 1.000000)
[00:21:27 -40607.802392] SLOW spr round 1 (radius: 5)
[00:21:54 -40597.949533] SLOW spr round 2 (radius: 5)
[00:22:23 -40597.844226] SLOW spr round 3 (radius: 5)
[00:22:49 -40597.842178] SLOW spr round 4 (radius: 10)
[00:23:19 -40597.841515] SLOW spr round 5 (radius: 15)
[00:24:07 -40594.643794] SLOW spr round 6 (radius: 5)
[00:24:47 -40593.148721] SLOW spr round 7 (radius: 5)
[00:25:20 -40593.137638] SLOW spr round 8 (radius: 10)
[00:25:53 -40593.136271] SLOW spr round 9 (radius: 15)
[00:26:38] [worker #1] ML tree search #5, logLikelihood: -40589.946901
[00:26:40 -40593.135761] SLOW spr round 10 (radius: 20)
[00:27:35 -40593.135546] SLOW spr round 11 (radius: 25)
[00:28:29 -40591.543847] SLOW spr round 12 (radius: 5)
[00:29:08 -40591.543748] SLOW spr round 13 (radius: 10)
[00:29:48 -40591.543708] SLOW spr round 14 (radius: 15)
[00:30:35 -40591.543670] SLOW spr round 15 (radius: 20)
[00:31:30 -40591.543633] SLOW spr round 16 (radius: 25)
[00:32:24 -40591.543596] Model parameter optimization (eps = 0.100000)

[00:32:29] [worker #0] ML tree search #4, logLikelihood: -40590.996037

[00:32:29 -159515.126763] Initial branch length optimization
[00:32:30 -119300.141388] Model parameter optimization (eps = 10.000000)
[00:33:04 -118547.510352] AUTODETECT spr round 1 (radius: 5)
[00:33:26 -85964.676603] AUTODETECT spr round 2 (radius: 10)
[00:33:53 -64251.345103] AUTODETECT spr round 3 (radius: 15)
[00:34:27 -51482.191325] AUTODETECT spr round 4 (radius: 20)
[00:35:02 -47316.502782] AUTODETECT spr round 5 (radius: 25)
[00:35:37 -44869.297622] SPR radius for FAST iterations: 25 (autodetect)
[00:35:37 -44869.297622] Model parameter optimization (eps = 3.000000)
[00:35:52 -44611.883595] FAST spr round 1 (radius: 25)
[00:36:12] [worker #2] ML tree search #6, logLikelihood: -40589.585010
[00:36:27 -40881.031511] FAST spr round 2 (radius: 25)
[00:36:52 -40654.723498] FAST spr round 3 (radius: 25)
[00:37:15 -40624.167058] FAST spr round 4 (radius: 25)
[00:37:35 -40619.329987] FAST spr round 5 (radius: 25)
[00:37:54 -40617.486928] FAST spr round 6 (radius: 25)
[00:38:12 -40617.486876] Model parameter optimization (eps = 1.000000)
[00:38:20 -40608.903601] SLOW spr round 1 (radius: 5)
[00:38:47 -40595.199868] SLOW spr round 2 (radius: 5)
[00:39:16 -40595.019161] SLOW spr round 3 (radius: 5)
[00:39:44 -40595.016621] SLOW spr round 4 (radius: 10)
[00:40:15 -40595.015781] SLOW spr round 5 (radius: 15)
[00:41:00 -40592.900807] SLOW spr round 6 (radius: 5)
[00:41:39 -40592.873972] SLOW spr round 7 (radius: 10)
[00:42:15 -40592.873474] SLOW spr round 8 (radius: 15)
[00:42:59 -40592.873325] SLOW spr round 9 (radius: 20)
[00:43:54 -40592.873253] SLOW spr round 10 (radius: 25)
[00:43:56] [worker #1] ML tree search #8, logLikelihood: -40584.929586
[00:44:55 -40592.400672] SLOW spr round 11 (radius: 5)
[00:45:35 -40592.400614] SLOW spr round 12 (radius: 10)
[00:46:12 -40592.400597] SLOW spr round 13 (radius: 15)
[00:46:56 -40592.400584] SLOW spr round 14 (radius: 20)
[00:47:51 -40592.400573] SLOW spr round 15 (radius: 25)
[00:48:50 -40592.400563] Model parameter optimization (eps = 0.100000)

[00:48:56] [worker #0] ML tree search #7, logLikelihood: -40592.078051

[00:48:56 -160986.584672] Initial branch length optimization
[00:48:57 -119506.832710] Model parameter optimization (eps = 10.000000)
[00:49:24 -118817.025385] AUTODETECT spr round 1 (radius: 5)
[00:49:46 -89435.243497] AUTODETECT spr round 2 (radius: 10)
[00:50:13 -65601.944391] AUTODETECT spr round 3 (radius: 15)
[00:50:43 -55393.280928] AUTODETECT spr round 4 (radius: 20)
[00:50:56] [worker #2] ML tree search #9, logLikelihood: -40584.652063
[00:51:16 -51660.857429] AUTODETECT spr round 5 (radius: 25)
[00:51:48 -45256.872210] SPR radius for FAST iterations: 25 (autodetect)
[00:51:48 -45256.872210] Model parameter optimization (eps = 3.000000)
[00:52:01 -44994.523897] FAST spr round 1 (radius: 25)
[00:52:35 -40882.695151] FAST spr round 2 (radius: 25)
[00:53:04 -40644.326193] FAST spr round 3 (radius: 25)
[00:53:26 -40620.137131] FAST spr round 4 (radius: 25)
[00:53:44 -40619.593419] FAST spr round 5 (radius: 25)
[00:54:02 -40619.592984] Model parameter optimization (eps = 1.000000)
[00:54:10 -40609.263220] SLOW spr round 1 (radius: 5)
[00:54:36 -40600.568581] SLOW spr round 2 (radius: 5)
[00:55:04 -40600.467090] SLOW spr round 3 (radius: 5)
[00:55:31 -40600.466291] SLOW spr round 4 (radius: 10)
[00:56:01 -40600.407410] SLOW spr round 5 (radius: 15)
[00:56:40] [worker #1] ML tree search #11, logLikelihood: -40602.418275
[00:56:46 -40600.002426] SLOW spr round 6 (radius: 5)
[00:57:24 -40599.646828] SLOW spr round 7 (radius: 5)
[00:57:56 -40599.635219] SLOW spr round 8 (radius: 10)
[00:58:28 -40599.634032] SLOW spr round 9 (radius: 15)
[00:59:11 -40599.633233] SLOW spr round 10 (radius: 20)
[01:00:04 -40599.342894] SLOW spr round 11 (radius: 5)
[01:00:43 -40599.297846] SLOW spr round 12 (radius: 10)
[01:01:21 -40598.549432] SLOW spr round 13 (radius: 5)
[01:01:54 -40598.548004] SLOW spr round 14 (radius: 10)
[01:02:27 -40598.547819] SLOW spr round 15 (radius: 15)
[01:03:09 -40598.140013] SLOW spr round 16 (radius: 5)
[01:03:47 -40598.139619] SLOW spr round 17 (radius: 10)
[01:04:23 -40598.139582] SLOW spr round 18 (radius: 15)
[01:05:06 -40598.139554] SLOW spr round 19 (radius: 20)
[01:05:59 -40598.139540] SLOW spr round 20 (radius: 25)
[01:06:57 -40598.139540] Model parameter optimization (eps = 0.100000)

[01:07:05] [worker #0] ML tree search #10, logLikelihood: -40597.943195

[01:07:05 -160422.825062] Initial branch length optimization
[01:07:06 -120481.705077] Model parameter optimization (eps = 10.000000)
[01:07:35 -119769.067710] AUTODETECT spr round 1 (radius: 5)
[01:07:57 -89717.730069] AUTODETECT spr round 2 (radius: 10)
[01:08:24 -67347.036754] AUTODETECT spr round 3 (radius: 15)
[01:08:56 -51833.530413] AUTODETECT spr round 4 (radius: 20)
[01:09:38 -47678.133806] AUTODETECT spr round 5 (radius: 25)
[01:10:19 -47630.647077] SPR radius for FAST iterations: 25 (autodetect)
[01:10:19 -47630.647077] Model parameter optimization (eps = 3.000000)
[01:10:34 -47328.933691] FAST spr round 1 (radius: 25)
[01:11:10 -41704.686666] FAST spr round 2 (radius: 25)
[01:11:35 -40746.679688] FAST spr round 3 (radius: 25)
[01:11:57 -40629.589490] FAST spr round 4 (radius: 25)
[01:12:16 -40628.457837] FAST spr round 5 (radius: 25)
[01:12:32 -40628.457354] Model parameter optimization (eps = 1.000000)
[01:12:41 -40621.699277] SLOW spr round 1 (radius: 5)
[01:13:08 -40606.981698] SLOW spr round 2 (radius: 5)
[01:13:34 -40606.169046] SLOW spr round 3 (radius: 5)
[01:14:02 -40604.720649] SLOW spr round 4 (radius: 5)
[01:14:28 -40604.720208] SLOW spr round 5 (radius: 10)
[01:14:59 -40598.224060] SLOW spr round 6 (radius: 5)
[01:15:35 -40594.600362] SLOW spr round 7 (radius: 5)
[01:15:48] [worker #1] ML tree search #14, logLikelihood: -40594.831686
[01:16:05 -40594.598390] SLOW spr round 8 (radius: 10)
[01:16:36 -40594.597853] SLOW spr round 9 (radius: 15)
[01:17:23 -40588.488912] SLOW spr round 10 (radius: 5)
[01:18:00 -40588.312600] SLOW spr round 11 (radius: 5)
[01:18:31 -40588.312540] SLOW spr round 12 (radius: 10)
[01:19:03 -40588.312494] SLOW spr round 13 (radius: 15)
[01:19:47 -40588.312455] SLOW spr round 14 (radius: 20)
[01:20:42 -40588.312415] SLOW spr round 15 (radius: 25)
[01:21:47 -40587.682423] SLOW spr round 16 (radius: 5)
[01:22:27 -40587.655765] SLOW spr round 17 (radius: 10)
[01:23:04] [worker #2] ML tree search #12, logLikelihood: -40583.497538
[01:23:05 -40587.654270] SLOW spr round 18 (radius: 15)
[01:23:50 -40587.653857] SLOW spr round 19 (radius: 20)
[01:24:47 -40587.653742] SLOW spr round 20 (radius: 25)
[01:25:50 -40587.653692] Model parameter optimization (eps = 0.100000)

[01:25:56] [worker #0] ML tree search #13, logLikelihood: -40587.168432

[01:25:56 -160646.752789] Initial branch length optimization
[01:25:57 -120220.504407] Model parameter optimization (eps = 10.000000)
[01:26:25 -119509.510044] AUTODETECT spr round 1 (radius: 5)
[01:26:46 -89393.241510] AUTODETECT spr round 2 (radius: 10)
[01:27:12 -67580.859040] AUTODETECT spr round 3 (radius: 15)
[01:27:46 -54824.802235] AUTODETECT spr round 4 (radius: 20)
[01:28:22 -54097.623566] AUTODETECT spr round 5 (radius: 25)
[01:29:04 -51524.130417] SPR radius for FAST iterations: 25 (autodetect)
[01:29:04 -51524.130417] Model parameter optimization (eps = 3.000000)
[01:29:17 -51197.957400] FAST spr round 1 (radius: 25)
[01:29:53 -42128.154569] FAST spr round 2 (radius: 25)
[01:30:21 -40730.845049] FAST spr round 3 (radius: 25)
[01:30:45 -40666.488463] FAST spr round 4 (radius: 25)
[01:31:04 -40652.428875] FAST spr round 5 (radius: 25)
[01:31:21 -40649.632641] FAST spr round 6 (radius: 25)
[01:31:38 -40644.719247] FAST spr round 7 (radius: 25)
[01:31:54 -40644.717221] Model parameter optimization (eps = 1.000000)
[01:32:04 -40625.335552] SLOW spr round 1 (radius: 5)
[01:32:31 -40610.665585] SLOW spr round 2 (radius: 5)
[01:32:57 -40609.318880] SLOW spr round 3 (radius: 5)
[01:33:24 -40609.318541] SLOW spr round 4 (radius: 10)
[01:33:54 -40609.318439] SLOW spr round 5 (radius: 15)
[01:34:39 -40609.088646] SLOW spr round 6 (radius: 5)
[01:35:17 -40609.088569] SLOW spr round 7 (radius: 10)
[01:35:34] [worker #1] ML tree search #17, logLikelihood: -40590.961505
[01:35:54 -40609.088530] SLOW spr round 8 (radius: 15)
[01:36:32] [worker #2] ML tree search #15, logLikelihood: -40618.808983
[01:36:36 -40609.088494] SLOW spr round 9 (radius: 20)
[01:37:33 -40609.088458] SLOW spr round 10 (radius: 25)
[01:38:36 -40605.591247] SLOW spr round 11 (radius: 5)
[01:39:17 -40604.877991] SLOW spr round 12 (radius: 5)
[01:39:51 -40604.877571] SLOW spr round 13 (radius: 10)
[01:40:25 -40603.489397] SLOW spr round 14 (radius: 5)
[01:40:59 -40603.489337] SLOW spr round 15 (radius: 10)
[01:41:34 -40603.489297] SLOW spr round 16 (radius: 15)
[01:42:17 -40603.426453] SLOW spr round 17 (radius: 20)
[01:43:13 -40603.426382] SLOW spr round 18 (radius: 25)
[01:44:15 -40603.426336] Model parameter optimization (eps = 0.100000)

[01:44:18] [worker #0] ML tree search #16, logLikelihood: -40603.378643

[01:44:18 -161221.468858] Initial branch length optimization
[01:44:19 -119482.670096] Model parameter optimization (eps = 10.000000)
[01:44:44 -118826.419259] AUTODETECT spr round 1 (radius: 5)
[01:45:05 -89581.886983] AUTODETECT spr round 2 (radius: 10)
[01:45:31 -69015.000744] AUTODETECT spr round 3 (radius: 15)
[01:46:01] [worker #1] ML tree search #20, logLikelihood: -40597.732101
[01:46:07 -54241.239650] AUTODETECT spr round 4 (radius: 20)
[01:46:47 -51107.778880] AUTODETECT spr round 5 (radius: 25)
[01:47:31 -48370.041509] SPR radius for FAST iterations: 25 (autodetect)
[01:47:31 -48370.041509] Model parameter optimization (eps = 3.000000)
[01:47:47 -48085.794609] FAST spr round 1 (radius: 25)
[01:48:22 -40827.448507] FAST spr round 2 (radius: 25)
[01:48:49 -40621.269806] FAST spr round 3 (radius: 25)
[01:49:09] [worker #2] ML tree search #18, logLikelihood: -40604.107695
[01:49:11 -40606.631528] FAST spr round 4 (radius: 25)
[01:49:30 -40606.584115] Model parameter optimization (eps = 1.000000)
[01:49:36 -40601.636460] SLOW spr round 1 (radius: 5)
[01:50:03 -40599.129202] SLOW spr round 2 (radius: 5)
[01:50:29 -40599.127062] SLOW spr round 3 (radius: 10)
[01:50:58 -40598.682686] SLOW spr round 4 (radius: 5)
[01:51:34 -40598.679911] SLOW spr round 5 (radius: 10)
[01:52:08 -40598.679369] SLOW spr round 6 (radius: 15)
[01:52:49 -40597.013259] SLOW spr round 7 (radius: 5)
[01:53:27 -40597.011825] SLOW spr round 8 (radius: 10)
[01:54:04 -40597.011481] SLOW spr round 9 (radius: 15)
[01:54:48 -40597.011391] SLOW spr round 10 (radius: 20)
[01:55:40 -40597.011361] SLOW spr round 11 (radius: 25)
[01:56:36 -40597.011347] Model parameter optimization (eps = 0.100000)

[01:56:39] [worker #0] ML tree search #19, logLikelihood: -40596.988538


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.343053,0.592193) (0.096307,0.782179) (0.372583,0.844060) (0.188057,2.164422) 
   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: -40583.497538

AIC score: 82572.995075 / AICc score: 1072396.995075 / BIC score: 85361.196233
Free parameters (model + branch lengths): 703

WARNING: Number of free parameters (K=703) is larger than alignment size (n=390).
         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/O95996/3_mltree/O95996.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95996/3_mltree/O95996.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95996/3_mltree/O95996.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95996/3_mltree/O95996.raxml.log

Analysis started: 06-Jul-2021 14:18:31 / finished: 06-Jul-2021 16:15:11

Elapsed time: 6999.348 seconds

Consumed energy: 629.795 Wh (= 3 km in an electric car, or 16 km with an e-scooter!)