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 09-Jul-2021 01:46:05 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/2_msa/Q9BYZ2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/3_mltree/Q9BYZ2 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/2_msa/Q9BYZ2_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 325 sites

WARNING: Sequences tr_E1BTT8_E1BTT8_CHICK_9031 and sp_P00340_LDHA_CHICK_9031 are exactly identical!
WARNING: Sequences tr_A0A2I3HFC4_A0A2I3HFC4_NOMLE_61853 and tr_G3RGX1_G3RGX1_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3HFC4_A0A2I3HFC4_NOMLE_61853 and tr_H2NDY3_H2NDY3_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3HFC4_A0A2I3HFC4_NOMLE_61853 and sp_Q5R1W9_LDHA_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3HFC4_A0A2I3HFC4_NOMLE_61853 and tr_A0A2R9CIM6_A0A2R9CIM6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_A0A2J8XXL0_A0A2J8XXL0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and sp_A5A6N7_LDHB_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_H2Q5L1_H2Q5L1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and sp_P07195_LDHB_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_F7HQ10_F7HQ10_MACMU_9544 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_G7PCH4_G7PCH4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_J9QRH6_J9QRH6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_A0A0D9R6G5_A0A0D9R6G5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_A0A2K5NSL6_A0A2K5NSL6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_A0A2K6C201_A0A2K6C201_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_A0A2R9AUG7_A0A2R9AUG7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3ZCH6_M3ZCH6_NOMLE_61853 and tr_A0A2U3WAZ0_A0A2U3WAZ0_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A2I2Z7D8_A0A2I2Z7D8_GORGO_9595 and tr_A0A2J8P4T2_A0A2J8P4T2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Z7D8_A0A2I2Z7D8_GORGO_9595 and sp_Q6ZMR3_LDH6A_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z7D8_A0A2I2Z7D8_GORGO_9595 and tr_A0A2R8ZQY6_A0A2R8ZQY6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q9I9_H2Q9I9_PANTR_9598 and tr_A0A2R8ZGL5_A0A2R8ZGL5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A088A9S2_A0A088A9S2_APIME_7460 and tr_A0A2A3EN13_A0A2A3EN13_APICC_94128 are exactly identical!
WARNING: Sequences sp_P07864_LDHC_HUMAN_9606 and tr_A0A2R9BUA1_A0A2R9BUA1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0FZW4_A0A0E0FZW4_ORYNI_4536 and tr_A2WZU6_A2WZU6_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0FZW4_A0A0E0FZW4_ORYNI_4536 and tr_I1NWD6_I1NWD6_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0FZW4_A0A0E0FZW4_ORYNI_4536 and tr_A0A0E0N8K9_A0A0E0N8K9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0FZW4_A0A0E0FZW4_ORYNI_4536 and tr_A0A0D3EZK0_A0A0D3EZK0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0FZW4_A0A0E0FZW4_ORYNI_4536 and tr_A0A0D9YL33_A0A0D9YL33_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0FZW4_A0A0E0FZW4_ORYNI_4536 and tr_Q0E4Q5_Q0E4Q5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0HJN2_A0A0E0HJN2_ORYNI_4536 and tr_A2Y8B2_A2Y8B2_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HJN2_A0A0E0HJN2_ORYNI_4536 and tr_I1PYR5_I1PYR5_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HJN2_A0A0E0HJN2_ORYNI_4536 and tr_A0A0E0E2E6_A0A0E0E2E6_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0HJN2_A0A0E0HJN2_ORYNI_4536 and tr_A0A0E0PSE6_A0A0E0PSE6_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HJN2_A0A0E0HJN2_ORYNI_4536 and tr_A0A0D3GBU0_A0A0D3GBU0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0HJN2_A0A0E0HJN2_ORYNI_4536 and tr_A0A0E0A3W6_A0A0E0A3W6_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0HJN2_A0A0E0HJN2_ORYNI_4536 and tr_Q9LWZ6_Q9LWZ6_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A1D5QFP8_A0A1D5QFP8_MACMU_9544 and tr_G7PQL2_G7PQL2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QFP8_A0A1D5QFP8_MACMU_9544 and tr_A0A2I3LUW8_A0A2I3LUW8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QFP8_A0A1D5QFP8_MACMU_9544 and tr_A0A2K6CCL6_A0A2K6CCL6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6QUY2_F6QUY2_MACMU_9544 and tr_Q4R6K1_Q4R6K1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GNJ6_F7GNJ6_MACMU_9544 and tr_A0A096N1N0_A0A096N1N0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7GNJ6_F7GNJ6_MACMU_9544 and tr_A0A2K6DJA5_A0A2K6DJA5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1B8XY05_A0A1B8XY05_XENTR_8364 and sp_Q66KB7_UEVLD_XENTR_8364 are exactly identical!
WARNING: Sequences tr_J9QRH9_J9QRH9_CALJA_9483 and tr_A0A384C8X4_A0A384C8X4_URSMA_29073 are exactly identical!
WARNING: Sequences tr_F1SR05_F1SR05_PIG_9823 and sp_P00336_LDHB_PIG_9823 are exactly identical!
WARNING: Sequences tr_M4EBT1_M4EBT1_BRARP_51351 and tr_A0A078I074_A0A078I074_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A067F5R0_A0A067F5R0_CITSI_2711 and tr_V4T0C0_V4T0C0_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A096N757_A0A096N757_PAPAN_9555 and tr_A0A2K5XY12_A0A2K5XY12_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A078HD00_A0A078HD00_BRANA_3708 and tr_A0A0D3A7D3_A0A0D3A7D3_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0A1MUL3_A0A0A1MUL3_9FUNG_58291 and tr_A0A367J3I5_A0A367J3I5_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V0SBV7_A0A0V0SBV7_9BILA_6336 and tr_A0A0V1D991_A0A0V1D991_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0SBV7_A0A0V0SBV7_9BILA_6336 and tr_A0A0V0WDL7_A0A0V0WDL7_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0SBV7_A0A0V0SBV7_9BILA_6336 and tr_A0A0V0V2U1_A0A0V0V2U1_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0SBV7_A0A0V0SBV7_9BILA_6336 and tr_A0A0V1LRJ7_A0A0V1LRJ7_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0SBV7_A0A0V0SBV7_9BILA_6336 and tr_A0A0V0ZL22_A0A0V0ZL22_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0SBV7_A0A0V0SBV7_9BILA_6336 and tr_A0A0V1MBQ0_A0A0V1MBQ0_9BILA_268474 are exactly identical!
WARNING: Sequences tr_A0A0V0SBV7_A0A0V0SBV7_9BILA_6336 and tr_A0A0V0TU43_A0A0V0TU43_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1Y1Y7K2_A0A1Y1Y7K2_9FUNG_1314790 and tr_A0A1Y1Y7Y8_A0A1Y1Y7Y8_9FUNG_1314790 are exactly identical!
WARNING: Sequences tr_A0A226MSL3_A0A226MSL3_CALSU_9009 and tr_A0A226P544_A0A226P544_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226MU85_A0A226MU85_CALSU_9009 and tr_A0A226P273_A0A226P273_COLVI_9014 are exactly identical!
WARNING: Duplicate sequences found: 60

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/Q9BYZ2/3_mltree/Q9BYZ2.raxml.reduced.phy

Alignment comprises 1 partitions and 325 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 325 / 325
Gaps: 4.85 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/3_mltree/Q9BYZ2.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 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 / 325 / 26000
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -470788.282165] Initial branch length optimization
[00:00:08 -388983.613718] Model parameter optimization (eps = 10.000000)
[00:01:19 -385645.630850] AUTODETECT spr round 1 (radius: 5)
[00:05:51 -287597.084538] AUTODETECT spr round 2 (radius: 10)
[00:10:57 -218309.726391] AUTODETECT spr round 3 (radius: 15)
[00:16:26 -179399.088842] AUTODETECT spr round 4 (radius: 20)
[00:22:23 -159569.488021] AUTODETECT spr round 5 (radius: 25)
[00:29:34 -152099.433390] SPR radius for FAST iterations: 25 (autodetect)
[00:29:34 -152099.433390] Model parameter optimization (eps = 3.000000)
[00:30:11 -151774.774099] FAST spr round 1 (radius: 25)
[00:35:49 -130886.658937] FAST spr round 2 (radius: 25)
[00:39:55 -129877.357972] FAST spr round 3 (radius: 25)
[00:43:27 -129766.396439] FAST spr round 4 (radius: 25)
[00:46:55 -129536.591322] FAST spr round 5 (radius: 25)
[00:50:05 -129377.705277] FAST spr round 6 (radius: 25)
[00:53:07 -129321.933351] FAST spr round 7 (radius: 25)
[00:56:00 -129321.933236] Model parameter optimization (eps = 1.000000)
[00:56:23 -129317.716694] SLOW spr round 1 (radius: 5)
[01:00:16 -129292.263478] SLOW spr round 2 (radius: 5)
[01:04:09 -129279.932381] SLOW spr round 3 (radius: 5)
[01:08:01 -129279.277081] SLOW spr round 4 (radius: 5)
[01:11:49 -129278.855899] SLOW spr round 5 (radius: 5)
[01:15:34 -129278.855814] SLOW spr round 6 (radius: 10)
[01:19:28 -129278.806969] SLOW spr round 7 (radius: 15)
[01:25:58 -129274.187364] SLOW spr round 8 (radius: 5)
[01:31:00 -129270.132949] SLOW spr round 9 (radius: 5)
[01:35:17 -129270.132833] SLOW spr round 10 (radius: 10)
[01:39:27 -129270.132761] SLOW spr round 11 (radius: 15)
[01:45:42 -129270.132690] SLOW spr round 12 (radius: 20)
[01:54:50 -129270.132678] SLOW spr round 13 (radius: 25)
[02:08:14 -129270.132676] Model parameter optimization (eps = 0.100000)

[02:08:24] [worker #0] ML tree search #1, logLikelihood: -129270.039182

[02:08:24 -468955.935919] Initial branch length optimization
[02:08:31 -386979.013651] Model parameter optimization (eps = 10.000000)
[02:10:08 -383567.680748] AUTODETECT spr round 1 (radius: 5)
[02:14:39 -289414.913463] AUTODETECT spr round 2 (radius: 10)
[02:19:43 -220779.582997] AUTODETECT spr round 3 (radius: 15)
[02:25:07 -187801.050471] AUTODETECT spr round 4 (radius: 20)
[02:31:42 -167735.252151] AUTODETECT spr round 5 (radius: 25)
[02:38:22 -156430.882562] SPR radius for FAST iterations: 25 (autodetect)
[02:38:22 -156430.882562] Model parameter optimization (eps = 3.000000)
[02:38:41 -156414.712303] FAST spr round 1 (radius: 25)
[02:44:36 -130993.244892] FAST spr round 2 (radius: 25)
[02:48:51 -129672.860761] FAST spr round 3 (radius: 25)
[02:52:30 -129566.786900] FAST spr round 4 (radius: 25)
[02:55:48 -129542.286142] FAST spr round 5 (radius: 25)
[02:58:47 -129541.537717] FAST spr round 6 (radius: 25)
[03:01:41 -129541.537533] Model parameter optimization (eps = 1.000000)
[03:02:11 -129316.729270] SLOW spr round 1 (radius: 5)
[03:06:16 -129273.883428] SLOW spr round 2 (radius: 5)
[03:10:07 -129269.791971] SLOW spr round 3 (radius: 5)
[03:12:13] [worker #4] ML tree search #5, logLikelihood: -129263.855291
[03:13:52 -129269.790841] SLOW spr round 4 (radius: 10)
[03:17:50 -129269.200460] SLOW spr round 5 (radius: 5)
[03:22:30 -129269.200373] SLOW spr round 6 (radius: 10)
[03:24:48] [worker #1] ML tree search #2, logLikelihood: -129289.218099
[03:27:00 -129269.200358] SLOW spr round 7 (radius: 15)
[03:30:25] [worker #3] ML tree search #4, logLikelihood: -129270.014617
[03:33:16 -129269.200352] SLOW spr round 8 (radius: 20)
[03:42:43 -129269.200349] SLOW spr round 9 (radius: 25)
[03:56:43 -129268.583257] SLOW spr round 10 (radius: 5)
[04:01:54 -129268.195243] SLOW spr round 11 (radius: 5)
[04:06:20 -129268.195021] SLOW spr round 12 (radius: 10)
[04:10:41 -129268.195019] SLOW spr round 13 (radius: 15)
[04:10:50] [worker #2] ML tree search #3, logLikelihood: -129275.913267
[04:17:02 -129268.195012] SLOW spr round 14 (radius: 20)
[04:26:24 -129268.195011] SLOW spr round 15 (radius: 25)
[04:40:28 -129267.943248] SLOW spr round 16 (radius: 5)
[04:45:37 -129267.764422] SLOW spr round 17 (radius: 5)
[04:50:03 -129267.764360] SLOW spr round 18 (radius: 10)
[04:54:25 -129267.764358] SLOW spr round 19 (radius: 15)
[05:00:46 -129267.764357] SLOW spr round 20 (radius: 20)
[05:10:09 -129267.044893] SLOW spr round 21 (radius: 5)
[05:15:15 -129267.044874] SLOW spr round 22 (radius: 10)
[05:20:17 -129267.044873] SLOW spr round 23 (radius: 15)
[05:26:31 -129267.044871] SLOW spr round 24 (radius: 20)
[05:35:55 -129267.044870] SLOW spr round 25 (radius: 25)
[05:49:52 -129267.044868] Model parameter optimization (eps = 0.100000)

[05:50:01] [worker #0] ML tree search #6, logLikelihood: -129267.033659

[05:50:01 -472828.006817] Initial branch length optimization
[05:50:09 -390075.426727] Model parameter optimization (eps = 10.000000)
[05:51:19 -386597.699810] AUTODETECT spr round 1 (radius: 5)
[05:55:48 -289313.493074] AUTODETECT spr round 2 (radius: 10)
[06:00:56 -222769.466115] AUTODETECT spr round 3 (radius: 15)
[06:01:25] [worker #1] ML tree search #7, logLikelihood: -129297.185547
[06:06:12 -184670.063390] AUTODETECT spr round 4 (radius: 20)
[06:12:21 -161360.028868] AUTODETECT spr round 5 (radius: 25)
[06:12:43] [worker #4] ML tree search #10, logLikelihood: -129269.171232
[06:19:23 -154880.249591] SPR radius for FAST iterations: 25 (autodetect)
[06:19:23 -154880.249591] Model parameter optimization (eps = 3.000000)
[06:20:05 -154602.663086] FAST spr round 1 (radius: 25)
[06:25:34 -130549.011649] FAST spr round 2 (radius: 25)
[06:29:51 -129622.284589] FAST spr round 3 (radius: 25)
[06:33:27 -129538.246695] FAST spr round 4 (radius: 25)
[06:36:41 -129531.071594] FAST spr round 5 (radius: 25)
[06:39:43 -129531.071171] Model parameter optimization (eps = 1.000000)
[06:40:08 -129520.345625] SLOW spr round 1 (radius: 5)
[06:41:49] [worker #2] ML tree search #8, logLikelihood: -131112.998903
[06:44:10 -129490.192968] SLOW spr round 2 (radius: 5)
[06:48:09 -129484.888954] SLOW spr round 3 (radius: 5)
[06:51:58 -129484.888500] SLOW spr round 4 (radius: 10)
[06:56:00 -129480.324617] SLOW spr round 5 (radius: 5)
[07:00:41 -129480.324326] SLOW spr round 6 (radius: 10)
[07:05:12 -129477.713854] SLOW spr round 7 (radius: 5)
[07:09:56 -129474.865825] SLOW spr round 8 (radius: 5)
[07:12:28] [worker #3] ML tree search #9, logLikelihood: -129274.935799
[07:14:12 -129473.342300] SLOW spr round 9 (radius: 5)
[07:18:05 -129473.342125] SLOW spr round 10 (radius: 10)
[07:22:03 -129473.342064] SLOW spr round 11 (radius: 15)
[07:28:21 -129473.342004] SLOW spr round 12 (radius: 20)
[07:37:29 -129473.341944] SLOW spr round 13 (radius: 25)
[07:50:44 -129468.391949] SLOW spr round 14 (radius: 5)
[07:55:52 -129468.044815] SLOW spr round 15 (radius: 5)
[08:00:19 -129468.044745] SLOW spr round 16 (radius: 10)
[08:04:36 -129468.044684] SLOW spr round 17 (radius: 15)
[08:10:43 -129468.044624] SLOW spr round 18 (radius: 20)
[08:19:54 -129468.044563] SLOW spr round 19 (radius: 25)
[08:33:05 -129468.044502] Model parameter optimization (eps = 0.100000)

[08:33:21] [worker #0] ML tree search #11, logLikelihood: -129467.901602

[08:33:21 -471305.867250] Initial branch length optimization
[08:33:28 -390141.072873] Model parameter optimization (eps = 10.000000)
[08:34:39 -386603.366999] AUTODETECT spr round 1 (radius: 5)
[08:37:37] [worker #4] ML tree search #15, logLikelihood: -129271.557512
[08:39:08 -285376.732198] AUTODETECT spr round 2 (radius: 10)
[08:40:51] [worker #1] ML tree search #12, logLikelihood: -129280.617508
[08:44:13 -221552.121045] AUTODETECT spr round 3 (radius: 15)
[08:49:43 -184252.232121] AUTODETECT spr round 4 (radius: 20)
[08:55:58 -164978.106180] AUTODETECT spr round 5 (radius: 25)
[09:03:23 -156828.347647] SPR radius for FAST iterations: 25 (autodetect)
[09:03:23 -156828.347647] Model parameter optimization (eps = 3.000000)
[09:04:01 -156505.772631] FAST spr round 1 (radius: 25)
[09:09:51 -130728.342074] FAST spr round 2 (radius: 25)
[09:14:10 -129416.524097] FAST spr round 3 (radius: 25)
[09:17:39 -129365.789420] FAST spr round 4 (radius: 25)
[09:20:51 -129354.213137] FAST spr round 5 (radius: 25)
[09:23:51 -129347.464178] FAST spr round 6 (radius: 25)
[09:26:47 -129345.605998] FAST spr round 7 (radius: 25)
[09:29:43 -129345.292377] FAST spr round 8 (radius: 25)
[09:32:49 -129345.292278] Model parameter optimization (eps = 1.000000)
[09:33:16 -129339.245337] SLOW spr round 1 (radius: 5)
[09:37:32 -129301.493428] SLOW spr round 2 (radius: 5)
[09:41:32 -129298.924219] SLOW spr round 3 (radius: 5)
[09:45:22 -129298.923821] SLOW spr round 4 (radius: 10)
[09:49:17 -129298.871570] SLOW spr round 5 (radius: 15)
[09:55:43 -129296.872582] SLOW spr round 6 (radius: 5)
[10:00:40 -129293.999177] SLOW spr round 7 (radius: 5)
[10:05:00 -129293.999047] SLOW spr round 8 (radius: 10)
[10:07:44] [worker #3] ML tree search #14, logLikelihood: -129267.052055
[10:09:10 -129293.999016] SLOW spr round 9 (radius: 15)
[10:10:27] [worker #2] ML tree search #13, logLikelihood: -129276.027031
[10:15:26 -129293.999016] SLOW spr round 10 (radius: 20)
[10:24:49 -129293.999015] SLOW spr round 11 (radius: 25)
[10:38:33 -129289.050986] SLOW spr round 12 (radius: 5)
[10:43:43 -129288.703380] SLOW spr round 13 (radius: 5)
[10:48:10 -129288.703350] SLOW spr round 14 (radius: 10)
[10:52:28 -129288.703350] SLOW spr round 15 (radius: 15)
[10:58:40 -129288.703349] SLOW spr round 16 (radius: 20)
[11:08:04 -129288.703349] SLOW spr round 17 (radius: 25)
[11:16:31] [worker #1] ML tree search #17, logLikelihood: -129281.744724
[11:21:46 -129288.703348] Model parameter optimization (eps = 0.100000)

[11:21:58] [worker #0] ML tree search #16, logLikelihood: -129288.549372

[12:30:25] [worker #4] ML tree search #20, logLikelihood: -129263.612052
[13:33:50] [worker #3] ML tree search #19, logLikelihood: -129295.326675
[14:04:32] [worker #2] ML tree search #18, logLikelihood: -129268.584037

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.188864,0.622144) (0.231377,0.513119) (0.354686,0.854429) (0.225072,2.046992) 
   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: -129263.612052

AIC score: 262537.224105 / AICc score: 8306597.224105 / BIC score: 270123.793596
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=325).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 147 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/3_mltree/Q9BYZ2.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/3_mltree/Q9BYZ2.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/3_mltree/Q9BYZ2.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/3_mltree/Q9BYZ2.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9BYZ2/3_mltree/Q9BYZ2.raxml.log

Analysis started: 09-Jul-2021 01:46:05 / finished: 09-Jul-2021 15:50:38

Elapsed time: 50672.586 seconds