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

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

RAxML-NG was called at 06-Jul-2021 21:52:46 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/2_msa/A6NLU0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/3_mltree/A6NLU0 --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/A6NLU0/2_msa/A6NLU0_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 397 sites

WARNING: Sequences sp_Q62158_TRI27_MOUSE_10090 and tr_A0A1U7R5Y1_A0A1U7R5Y1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_F1P646_F1P646_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_G1M498_G1M498_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A2U3ZPJ8_A0A2U3ZPJ8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A2U3XSM4_A0A2U3XSM4_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A2Y9JZW9_A0A2Y9JZW9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A384C9P1_A0A384C9P1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I3HMI9_A0A2I3HMI9_NOMLE_61853 and tr_G3R4G7_G3R4G7_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_G3RIJ4_G3RIJ4_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_K7EUW2_K7EUW2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_H2QSK5_H2QSK5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and sp_P14373_TRI27_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_F7DCK3_F7DCK3_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A096NLL9_A0A096NLL9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A0D9R6T3_A0A0D9R6T3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2K5N1H5_A0A2K5N1H5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2K6B8E9_A0A2K6B8E9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2K5YG76_A0A2K5YG76_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2R9BGL3_A0A2R9BGL3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_G3RJV6_G3RJV6_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and sp_Q1XHU0_TRI39_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and sp_Q9HCM9_TRI39_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_F7BHH4_F7BHH4_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2I3NHT9_A0A2I3NHT9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2K5P029_A0A2K5P029_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2K6CGL3_A0A2K6CGL3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2K5YXE4_A0A2K5YXE4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RI87_G1RI87_NOMLE_61853 and tr_M3ZBJ4_M3ZBJ4_NOMLE_61853 are exactly identical!
WARNING: Sequences tr_H2PIE3_H2PIE3_PONAB_9601 and tr_A0A2R8MSH2_A0A2R8MSH2_CALJA_9483 are exactly identical!
WARNING: Sequences tr_H2PIE3_H2PIE3_PONAB_9601 and tr_A0A0D9R725_A0A0D9R725_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2PIE3_H2PIE3_PONAB_9601 and tr_A0A1U7V4Q4_A0A1U7V4Q4_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_H2Q2Y1_H2Q2Y1_PANTR_9598 and sp_P19474_RO52_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q2Y1_H2Q2Y1_PANTR_9598 and tr_A0A2R9CHV1_A0A2R9CHV1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q2Y4_H2Q2Y4_PANTR_9598 and tr_A0A2R9BG02_A0A2R9BG02_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QSH7_H2QSH7_PANTR_9598 and tr_A0A2R9BIQ5_A0A2R9BIQ5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7BVH2_K7BVH2_PANTR_9598 and sp_Q96F44_TRI11_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_K7BVH2_K7BVH2_PANTR_9598 and tr_A0A2R8ZKT7_A0A2R8ZKT7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_K7GND2_K7GND2_PIG_9823 are exactly identical!
WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_Q1LZA9_Q1LZA9_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_A0A2U3VAG6_A0A2U3VAG6_TURTR_9739 are exactly identical!
WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_A0A2Y9M7Y8_A0A2Y9M7Y8_DELLE_9749 are exactly identical!
WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_A0A383ZVH3_A0A383ZVH3_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A1D5QTX6_A0A1D5QTX6_MACMU_9544 and tr_A0A2K5M5M7_A0A2K5M5M7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6U9E0_F6U9E0_MACMU_9544 and tr_G7P3M3_G7P3M3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6W0V1_F6W0V1_MACMU_9544 and tr_G7P6Q0_G7P6Q0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6W0V1_F6W0V1_MACMU_9544 and tr_A0A2K5YPH2_A0A2K5YPH2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7C1A0_F7C1A0_MACMU_9544 and tr_A0A2K6B3T4_A0A2K6B3T4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GJW9_F7GJW9_MACMU_9544 and tr_A0A096N7V8_A0A096N7V8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7GJW9_F7GJW9_MACMU_9544 and tr_A0A2K5MWE8_A0A2K5MWE8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GJW9_F7GJW9_MACMU_9544 and tr_A0A2K6BDB8_A0A2K6BDB8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GSV0_F7GSV0_MACMU_9544 and tr_A0A0D9QW75_A0A0D9QW75_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7GSV0_F7GSV0_MACMU_9544 and tr_A0A2K6D5I5_A0A2K6D5I5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3T9K8_G3T9K8_LOXAF_9785 and tr_A0A2Y9E543_A0A2Y9E543_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_G7P2K9_G7P2K9_MACFA_9541 and tr_A0A2K5L9F1_A0A2K5L9F1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7P2K9_G7P2K9_MACFA_9541 and tr_A0A2K6E3W7_A0A2K6E3W7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7P2K9_G7P2K9_MACFA_9541 and tr_A0A2K6A532_A0A2K6A532_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7P2P4_G7P2P4_MACFA_9541 and tr_A0A2K6EB40_A0A2K6EB40_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NAM1_A0A096NAM1_PAPAN_9555 and tr_A0A2K5LKX8_A0A2K5LKX8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NAM1_A0A096NAM1_PAPAN_9555 and tr_A0A2K5YAG4_A0A2K5YAG4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NLH8_A0A096NLH8_PAPAN_9555 and tr_A0A2K5YWX2_A0A2K5YWX2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151M5R0_A0A151M5R0_ALLMI_8496 and tr_A0A1U8DHU9_A0A1U8DHU9_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091JG56_A0A091JG56_EGRGA_188379 and tr_A0A091UZ29_A0A091UZ29_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A2D0QFK5_A0A2D0QFK5_ICTPU_7998 and tr_W5U984_W5U984_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3V9R2_A0A2U3V9R2_TURTR_9739 and tr_A0A2Y9MAZ9_A0A2Y9MAZ9_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3WQ74_A0A2U3WQ74_ODORO_9708 and tr_A0A2U3Y010_A0A2U3Y010_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9MXG3_A0A2Y9MXG3_DELLE_9749 and tr_A0A2Y9EPM4_A0A2Y9EPM4_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9MXG3_A0A2Y9MXG3_DELLE_9749 and tr_A0A384B2Y7_A0A384B2Y7_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 67

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/A6NLU0/3_mltree/A6NLU0.raxml.reduced.phy

Alignment comprises 1 partitions and 397 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 397 / 397
Gaps: 18.01 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/3_mltree/A6NLU0.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 / 199 / 15920
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -654480.633019] Initial branch length optimization
[00:00:09 -569067.610367] Model parameter optimization (eps = 10.000000)
[00:01:01 -567554.204443] AUTODETECT spr round 1 (radius: 5)
[00:04:11 -385805.407260] AUTODETECT spr round 2 (radius: 10)
[00:07:40 -268022.262443] AUTODETECT spr round 3 (radius: 15)
[00:11:16 -213937.271630] AUTODETECT spr round 4 (radius: 20)
[00:15:53 -201185.151165] AUTODETECT spr round 5 (radius: 25)
[00:22:18 -200011.819189] SPR radius for FAST iterations: 25 (autodetect)
[00:22:18 -200011.819189] Model parameter optimization (eps = 3.000000)
[00:22:48 -199820.905881] FAST spr round 1 (radius: 25)
[00:26:29 -178433.810706] FAST spr round 2 (radius: 25)
[00:29:16 -177818.365207] FAST spr round 3 (radius: 25)
[00:31:43 -177793.036991] FAST spr round 4 (radius: 25)
[00:33:57 -177791.358879] FAST spr round 5 (radius: 25)
[00:36:06 -177791.358841] Model parameter optimization (eps = 1.000000)
[00:36:24 -177785.121872] SLOW spr round 1 (radius: 5)
[00:39:24 -177725.455644] SLOW spr round 2 (radius: 5)
[00:42:19 -177693.842572] SLOW spr round 3 (radius: 5)
[00:45:13 -177689.596887] SLOW spr round 4 (radius: 5)
[00:48:06 -177687.642224] SLOW spr round 5 (radius: 5)
[00:50:51 -177687.641306] SLOW spr round 6 (radius: 10)
[00:53:38 -177686.622609] SLOW spr round 7 (radius: 5)
[00:57:06 -177686.622594] SLOW spr round 8 (radius: 10)
[01:00:09 -177686.622591] SLOW spr round 9 (radius: 15)
[01:04:34 -177686.441898] SLOW spr round 10 (radius: 5)
[01:08:12 -177686.441895] SLOW spr round 11 (radius: 10)
[01:11:23 -177686.441895] SLOW spr round 12 (radius: 15)
[01:15:44 -177686.441895] SLOW spr round 13 (radius: 20)
[01:23:57 -177686.441895] SLOW spr round 14 (radius: 25)
[01:27:41] [worker #2] ML tree search #3, logLikelihood: -177668.512158
[01:30:59] [worker #1] ML tree search #2, logLikelihood: -177669.995930
[01:35:10 -177686.441895] Model parameter optimization (eps = 0.100000)

[01:35:27] [worker #0] ML tree search #1, logLikelihood: -177686.271098

[01:35:28 -651754.234331] Initial branch length optimization
[01:35:33 -571052.056938] Model parameter optimization (eps = 10.000000)
[01:36:23 -569549.025890] AUTODETECT spr round 1 (radius: 5)
[01:39:36 -394292.164517] AUTODETECT spr round 2 (radius: 10)
[01:43:08 -267661.769423] AUTODETECT spr round 3 (radius: 15)
[01:46:57 -219478.077901] AUTODETECT spr round 4 (radius: 20)
[01:51:20 -204783.050554] AUTODETECT spr round 5 (radius: 25)
[01:56:50 -203052.491857] SPR radius for FAST iterations: 25 (autodetect)
[01:56:50 -203052.491857] Model parameter optimization (eps = 3.000000)
[01:57:19 -202916.839049] FAST spr round 1 (radius: 25)
[02:01:18 -178714.056287] FAST spr round 2 (radius: 25)
[02:04:15 -177853.999085] FAST spr round 3 (radius: 25)
[02:06:55 -177756.126632] FAST spr round 4 (radius: 25)
[02:09:19 -177730.129707] FAST spr round 5 (radius: 25)
[02:11:29 -177727.943347] FAST spr round 6 (radius: 25)
[02:13:36 -177726.867688] FAST spr round 7 (radius: 25)
[02:15:42 -177726.867273] Model parameter optimization (eps = 1.000000)
[02:16:02 -177720.851219] SLOW spr round 1 (radius: 5)
[02:19:06 -177696.926166] SLOW spr round 2 (radius: 5)
[02:22:06 -177688.411247] SLOW spr round 3 (radius: 5)
[02:25:00 -177683.251048] SLOW spr round 4 (radius: 5)
[02:27:45 -177683.250969] SLOW spr round 5 (radius: 10)
[02:30:31 -177682.339891] SLOW spr round 6 (radius: 5)
[02:34:00 -177682.339516] SLOW spr round 7 (radius: 10)
[02:37:00 -177682.339516] SLOW spr round 8 (radius: 15)
[02:41:16 -177682.339516] SLOW spr round 9 (radius: 20)
[02:49:06 -177682.339516] SLOW spr round 10 (radius: 25)
[02:58:31] [worker #1] ML tree search #5, logLikelihood: -177725.892528
[02:59:47 -177682.339516] Model parameter optimization (eps = 0.100000)

[02:59:54] [worker #0] ML tree search #4, logLikelihood: -177682.276139

[02:59:54 -652462.924715] Initial branch length optimization
[03:00:02 -568729.455225] Model parameter optimization (eps = 10.000000)
[03:01:03 -567228.767817] AUTODETECT spr round 1 (radius: 5)
[03:04:24 -377662.000731] AUTODETECT spr round 2 (radius: 10)
[03:08:02 -267846.280479] AUTODETECT spr round 3 (radius: 15)
[03:10:27] [worker #2] ML tree search #6, logLikelihood: -177679.689596
[03:11:51 -217588.227810] AUTODETECT spr round 4 (radius: 20)
[03:16:42 -202609.816331] AUTODETECT spr round 5 (radius: 25)
[03:23:17 -201110.162007] SPR radius for FAST iterations: 25 (autodetect)
[03:23:17 -201110.162007] Model parameter optimization (eps = 3.000000)
[03:23:44 -200963.985738] FAST spr round 1 (radius: 25)
[03:27:37 -179293.308786] FAST spr round 2 (radius: 25)
[03:30:35 -177871.395986] FAST spr round 3 (radius: 25)
[03:33:11 -177806.176978] FAST spr round 4 (radius: 25)
[03:35:30 -177802.168176] FAST spr round 5 (radius: 25)
[03:37:43 -177800.997839] FAST spr round 6 (radius: 25)
[03:39:56 -177798.290816] FAST spr round 7 (radius: 25)
[03:42:07 -177797.290560] FAST spr round 8 (radius: 25)
[03:44:16 -177797.288866] Model parameter optimization (eps = 1.000000)
[03:44:35 -177789.638256] SLOW spr round 1 (radius: 5)
[03:47:45 -177704.258841] SLOW spr round 2 (radius: 5)
[03:50:48 -177680.537750] SLOW spr round 3 (radius: 5)
[03:53:44 -177678.663661] SLOW spr round 4 (radius: 5)
[03:56:41 -177677.853373] SLOW spr round 5 (radius: 5)
[03:59:34 -177677.853348] SLOW spr round 6 (radius: 10)
[04:02:26 -177677.118659] SLOW spr round 7 (radius: 5)
[04:06:05 -177671.438735] SLOW spr round 8 (radius: 5)
[04:09:19 -177671.438251] SLOW spr round 9 (radius: 10)
[04:12:15 -177671.438201] SLOW spr round 10 (radius: 15)
[04:16:47 -177671.249577] SLOW spr round 11 (radius: 5)
[04:20:28 -177671.249574] SLOW spr round 12 (radius: 10)
[04:23:42 -177671.249574] SLOW spr round 13 (radius: 15)
[04:28:03 -177671.249574] SLOW spr round 14 (radius: 20)
[04:30:01] [worker #1] ML tree search #8, logLikelihood: -177678.792549
[04:36:01 -177671.249574] SLOW spr round 15 (radius: 25)
[04:46:48 -177671.249574] Model parameter optimization (eps = 0.100000)

[04:46:58] [worker #0] ML tree search #7, logLikelihood: -177671.085305

[04:46:58 -653155.339131] Initial branch length optimization
[04:47:07 -569680.907313] Model parameter optimization (eps = 10.000000)
[04:48:10 -568208.358158] AUTODETECT spr round 1 (radius: 5)
[04:48:16] [worker #2] ML tree search #9, logLikelihood: -177698.095349
[04:51:30 -390231.788381] AUTODETECT spr round 2 (radius: 10)
[04:55:03 -269480.975916] AUTODETECT spr round 3 (radius: 15)
[04:58:49 -216928.621480] AUTODETECT spr round 4 (radius: 20)
[05:03:26 -203616.109801] AUTODETECT spr round 5 (radius: 25)
[05:09:35 -201086.569853] SPR radius for FAST iterations: 25 (autodetect)
[05:09:35 -201086.569853] Model parameter optimization (eps = 3.000000)
[05:10:02 -200902.329408] FAST spr round 1 (radius: 25)
[05:13:53 -179624.849531] FAST spr round 2 (radius: 25)
[05:16:58 -177894.337075] FAST spr round 3 (radius: 25)
[05:19:42 -177796.748610] FAST spr round 4 (radius: 25)
[05:22:16 -177774.458003] FAST spr round 5 (radius: 25)
[05:24:43 -177771.738003] FAST spr round 6 (radius: 25)
[05:26:59 -177771.737489] Model parameter optimization (eps = 1.000000)
[05:27:18 -177764.329033] SLOW spr round 1 (radius: 5)
[05:30:32 -177703.751543] SLOW spr round 2 (radius: 5)
[05:33:34 -177699.500160] SLOW spr round 3 (radius: 5)
[05:36:32 -177696.259643] SLOW spr round 4 (radius: 5)
[05:39:29 -177696.259406] SLOW spr round 5 (radius: 10)
[05:42:31 -177689.857325] SLOW spr round 6 (radius: 5)
[05:46:20 -177683.254440] SLOW spr round 7 (radius: 5)
[05:48:57] [worker #1] ML tree search #11, logLikelihood: -177666.070634
[05:49:40 -177676.652391] SLOW spr round 8 (radius: 5)
[05:52:51 -177676.651474] SLOW spr round 9 (radius: 10)
[05:55:57 -177676.651244] SLOW spr round 10 (radius: 15)
[06:00:52 -177676.651072] SLOW spr round 11 (radius: 20)
[06:09:11 -177676.451611] SLOW spr round 12 (radius: 5)
[06:13:05 -177676.451446] SLOW spr round 13 (radius: 10)
[06:16:31 -177676.451282] SLOW spr round 14 (radius: 15)
[06:21:05 -177676.451118] SLOW spr round 15 (radius: 20)
[06:22:35] [worker #2] ML tree search #12, logLikelihood: -177665.917973
[06:29:38 -177676.450953] SLOW spr round 16 (radius: 25)
[06:41:22 -177676.450788] Model parameter optimization (eps = 0.100000)

[06:41:35] [worker #0] ML tree search #10, logLikelihood: -177676.032624

[06:41:35 -654197.566282] Initial branch length optimization
[06:41:43 -570552.866409] Model parameter optimization (eps = 10.000000)
[06:42:31 -569178.838569] AUTODETECT spr round 1 (radius: 5)
[06:45:57 -391129.845342] AUTODETECT spr round 2 (radius: 10)
[06:49:43 -260971.254459] AUTODETECT spr round 3 (radius: 15)
[06:53:23 -221878.879459] AUTODETECT spr round 4 (radius: 20)
[06:58:18 -202405.486291] AUTODETECT spr round 5 (radius: 25)
[07:04:48 -199962.485823] SPR radius for FAST iterations: 25 (autodetect)
[07:04:48 -199962.485823] Model parameter optimization (eps = 3.000000)
[07:05:16 -199705.412197] FAST spr round 1 (radius: 25)
[07:09:06 -178666.990183] FAST spr round 2 (radius: 25)
[07:12:05 -177837.167205] FAST spr round 3 (radius: 25)
[07:14:47 -177771.358535] FAST spr round 4 (radius: 25)
[07:17:13 -177755.226891] FAST spr round 5 (radius: 25)
[07:19:02] [worker #1] ML tree search #14, logLikelihood: -177664.200431
[07:19:32 -177748.615546] FAST spr round 6 (radius: 25)
[07:21:45 -177748.615404] Model parameter optimization (eps = 1.000000)
[07:22:04 -177745.680154] SLOW spr round 1 (radius: 5)
[07:25:15 -177688.307587] SLOW spr round 2 (radius: 5)
[07:28:20 -177677.646936] SLOW spr round 3 (radius: 5)
[07:31:11 -177677.646701] SLOW spr round 4 (radius: 10)
[07:34:05 -177671.112241] SLOW spr round 5 (radius: 5)
[07:37:41 -177670.359667] SLOW spr round 6 (radius: 5)
[07:40:52 -177670.359641] SLOW spr round 7 (radius: 10)
[07:43:50 -177670.359640] SLOW spr round 8 (radius: 15)
[07:46:04] [worker #2] ML tree search #15, logLikelihood: -177675.470709
[07:48:20 -177670.359639] SLOW spr round 9 (radius: 20)
[07:56:06 -177670.162751] SLOW spr round 10 (radius: 5)
[07:59:56 -177670.162751] SLOW spr round 11 (radius: 10)
[08:03:19 -177670.162751] SLOW spr round 12 (radius: 15)
[08:07:37 -177670.162751] SLOW spr round 13 (radius: 20)
[08:15:22 -177670.162751] SLOW spr round 14 (radius: 25)
[08:26:13 -177670.162751] Model parameter optimization (eps = 0.100000)

[08:26:26] [worker #0] ML tree search #13, logLikelihood: -177669.513327

[08:26:26 -652615.953181] Initial branch length optimization
[08:26:33 -568278.305880] Model parameter optimization (eps = 10.000000)
[08:27:24 -566762.350752] AUTODETECT spr round 1 (radius: 5)
[08:30:42 -384356.608832] AUTODETECT spr round 2 (radius: 10)
[08:34:15 -267274.838296] AUTODETECT spr round 3 (radius: 15)
[08:38:01 -220452.852442] AUTODETECT spr round 4 (radius: 20)
[08:42:37 -202051.130843] AUTODETECT spr round 5 (radius: 25)
[08:49:22 -199939.686518] SPR radius for FAST iterations: 25 (autodetect)
[08:49:22 -199939.686518] Model parameter optimization (eps = 3.000000)
[08:49:49 -199746.391999] FAST spr round 1 (radius: 25)
[08:53:46 -178524.851739] FAST spr round 2 (radius: 25)
[08:54:51] [worker #1] ML tree search #17, logLikelihood: -177716.292125
[08:56:44 -177833.063122] FAST spr round 3 (radius: 25)
[08:59:21 -177763.817167] FAST spr round 4 (radius: 25)
[09:01:43 -177760.430386] FAST spr round 5 (radius: 25)
[09:03:57 -177760.232462] FAST spr round 6 (radius: 25)
[09:06:07 -177760.232274] Model parameter optimization (eps = 1.000000)
[09:06:25 -177758.111840] SLOW spr round 1 (radius: 5)
[09:09:26 -177694.153203] SLOW spr round 2 (radius: 5)
[09:12:20 -177690.672036] SLOW spr round 3 (radius: 5)
[09:15:08 -177690.671913] SLOW spr round 4 (radius: 10)
[09:18:00 -177688.895691] SLOW spr round 5 (radius: 5)
[09:21:20] [worker #2] ML tree search #18, logLikelihood: -177676.073060
[09:21:37 -177687.486727] SLOW spr round 6 (radius: 5)
[09:24:45 -177687.486532] SLOW spr round 7 (radius: 10)
[09:27:40 -177687.486510] SLOW spr round 8 (radius: 15)
[09:32:12 -177687.486507] SLOW spr round 9 (radius: 20)
[09:40:11 -177687.486506] SLOW spr round 10 (radius: 25)
[09:51:16 -177687.486506] Model parameter optimization (eps = 0.100000)

[09:51:22] [worker #0] ML tree search #16, logLikelihood: -177687.443403

[09:51:23 -650008.804056] Initial branch length optimization
[09:51:32 -568474.239625] Model parameter optimization (eps = 10.000000)
[09:52:27 -566815.067647] AUTODETECT spr round 1 (radius: 5)
[09:55:44 -374385.284687] AUTODETECT spr round 2 (radius: 10)
[09:59:11 -263106.217319] AUTODETECT spr round 3 (radius: 15)
[10:02:54 -217033.796458] AUTODETECT spr round 4 (radius: 20)
[10:07:04 -205027.864269] AUTODETECT spr round 5 (radius: 25)
[10:12:48 -201889.163636] SPR radius for FAST iterations: 25 (autodetect)
[10:12:48 -201889.163636] Model parameter optimization (eps = 3.000000)
[10:13:18 -201767.148257] FAST spr round 1 (radius: 25)
[10:17:22 -178752.433169] FAST spr round 2 (radius: 25)
[10:20:21 -177789.907293] FAST spr round 3 (radius: 25)
[10:22:58 -177739.743806] FAST spr round 4 (radius: 25)
[10:25:16 -177733.899966] FAST spr round 5 (radius: 25)
[10:27:30 -177728.751471] FAST spr round 6 (radius: 25)
[10:27:38] [worker #1] ML tree search #20, logLikelihood: -177667.156912
[10:29:39 -177728.751471] Model parameter optimization (eps = 1.000000)
[10:30:02 -177725.232677] SLOW spr round 1 (radius: 5)
[10:33:08 -177688.683279] SLOW spr round 2 (radius: 5)
[10:36:01 -177686.381665] SLOW spr round 3 (radius: 5)
[10:38:49 -177686.227611] SLOW spr round 4 (radius: 5)
[10:41:35 -177686.227594] SLOW spr round 5 (radius: 10)
[10:44:23 -177685.320905] SLOW spr round 6 (radius: 5)
[10:47:53 -177685.320532] SLOW spr round 7 (radius: 10)
[10:50:57 -177685.320532] SLOW spr round 8 (radius: 15)
[10:55:23 -177685.320532] SLOW spr round 9 (radius: 20)
[11:03:34 -177685.320532] SLOW spr round 10 (radius: 25)
[11:14:33 -177685.131101] SLOW spr round 11 (radius: 5)
[11:18:18 -177685.131101] SLOW spr round 12 (radius: 10)
[11:21:38 -177685.131098] SLOW spr round 13 (radius: 15)
[11:26:00 -177685.131098] SLOW spr round 14 (radius: 20)
[11:34:14 -177685.131098] SLOW spr round 15 (radius: 25)
[11:45:04 -177685.131098] Model parameter optimization (eps = 0.100000)

[11:45:11] [worker #0] ML tree search #19, logLikelihood: -177685.110382


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.097493,0.275798) (0.102053,0.394962) (0.429539,0.849953) (0.370914,1.530586) 
   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: -177664.200431

AIC score: 359338.400862 / AICc score: 8403398.400862 / BIC score: 367326.193105
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=397).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 130 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/3_mltree/A6NLU0.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/3_mltree/A6NLU0.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/3_mltree/A6NLU0.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/3_mltree/A6NLU0.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NLU0/3_mltree/A6NLU0.raxml.log

Analysis started: 06-Jul-2021 21:52:46 / finished: 07-Jul-2021 09:37:58

Elapsed time: 42311.718 seconds