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 03-Jul-2021 06:51:09 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/2_msa/Q8IX07_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07 --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/Q8IX07/2_msa/Q8IX07_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 302 sites

WARNING: Sequences tr_A0A1D5PTA6_A0A1D5PTA6_CHICK_9031 and tr_A0A0Q3UQM2_A0A0Q3UQM2_AMAAE_12930 are exactly identical!
WARNING: Sequences sp_Q9JHX2_SP5_MOUSE_10090 and tr_A0A0G2JUC1_A0A0G2JUC1_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3Y3N3_M3Y3N3_MUSPF_9669 and tr_A0A2Y9JA88_A0A2Y9JA88_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Y5J1_M3Y5J1_MUSPF_9669 and tr_A0A2Y9IJV5_A0A2Y9IJV5_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I3H1U9_A0A2I3H1U9_NOMLE_61853 and tr_H2PHU9_H2PHU9_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2X7_A0A2I2Z2X7_GORGO_9595 and tr_A0A2R9B8D5_A0A2R9B8D5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R6U6_G3R6U6_GORGO_9595 and tr_A0A2J8JLM8_A0A2J8JLM8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R6U6_G3R6U6_GORGO_9595 and sp_Q8NHY6_ZFP28_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R6U6_G3R6U6_GORGO_9595 and tr_A0A2R9BYG1_A0A2R9BYG1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2J8U2Q0_A0A2J8U2Q0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_H2QUK7_H2QUK7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and sp_Q13422_IKZF1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_F6YC72_F6YC72_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2R8MF47_A0A2R8MF47_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_G7P1S2_G7P1S2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A096NWV9_A0A096NWV9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A0D9RTY8_A0A0D9RTY8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K5NH61_A0A2K5NH61_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K6C676_A0A2K6C676_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K5ZPN0_A0A2K5ZPN0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2R9B7I4_A0A2R9B7I4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2NU92_H2NU92_PONAB_9601 and sp_Q9UKT9_IKZF3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NU92_H2NU92_PONAB_9601 and tr_A0A2R8ZNQ3_A0A2R8ZNQ3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2PR04_H2PR04_PONAB_9601 and tr_K7D552_K7D552_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2PR04_H2PR04_PONAB_9601 and sp_Q8WW38_FOG2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PR04_H2PR04_PONAB_9601 and tr_F7D828_F7D828_CALJA_9483 are exactly identical!
WARNING: Sequences tr_H2PR04_H2PR04_PONAB_9601 and tr_A0A2R8ZET5_A0A2R8ZET5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q28Z81_Q28Z81_DROPS_46245 and tr_B4GI51_B4GI51_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B3FXQ6_B3FXQ6_CANLF_9615 and tr_M3WAS0_M3WAS0_FELCA_9685 are exactly identical!
WARNING: Sequences tr_H2R6E5_H2R6E5_PANTR_9598 and sp_Q6BEB4_SP5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R6E5_H2R6E5_PANTR_9598 and tr_F6SBI0_F6SBI0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_F6VNV7_F6VNV7_MACMU_9544 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_D2H553_D2H553_AILME_9646 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_A0A096N980_A0A096N980_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_A0A0D9SCG4_A0A0D9SCG4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_A0A1S3A6E3_A0A1S3A6E3_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_A0A2K5L0G8_A0A2K5L0G8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_A0A2K6B1E0_A0A2K6B1E0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_A0A2K5XTR3_A0A2K5XTR3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_W5Q1N1_W5Q1N1_SHEEP_9940 and tr_D3K5N4_D3K5N4_PIG_9823 are exactly identical!
WARNING: Sequences tr_W5Q1N1_W5Q1N1_SHEEP_9940 and tr_A0A384ANP9_A0A384ANP9_BALAS_310752 are exactly identical!
WARNING: Sequences tr_M4ATS7_M4ATS7_XIPMA_8083 and tr_A0A087XNQ0_A0A087XNQ0_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A088A8X5_A0A088A8X5_APIME_7460 and tr_A0A2A3E4C8_A0A2A3E4C8_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NQJ2_A0A158NQJ2_ATTCE_12957 and tr_A0A195BSR0_A0A195BSR0_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NQJ2_A0A158NQJ2_ATTCE_12957 and tr_A0A195EQI1_A0A195EQI1_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A158NXH8_A0A158NXH8_ATTCE_12957 and tr_A0A195B6W8_A0A195B6W8_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_G7PUM7_G7PUM7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A096P5D4_A0A096P5D4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A0D9S376_A0A0D9S376_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A2K5LW35_A0A2K5LW35_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A2K6CKM4_A0A2K6CKM4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A2K5YZH0_A0A2K5YZH0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7HPZ3_F7HPZ3_MACMU_9544 and tr_A0A2K6D4H8_A0A2K6D4H8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PCH3_G7PCH3_MACFA_9541 and tr_A0A2K6CDW7_A0A2K6CDW7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A087XB33_A0A087XB33_POEFO_48698 and tr_A0A087YDR4_A0A087YDR4_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 and tr_A0A2K5NZC2_A0A2K5NZC2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 and tr_A0A2K6E8I7_A0A2K6E8I7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 and tr_A0A2K6A449_A0A2K6A449_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3N9S4_A0A2I3N9S4_PAPAN_9555 and tr_A0A2K5ZJV2_A0A2K5ZJV2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D9RR78_A0A0D9RR78_CHLSB_60711 and tr_A0A2K5NKQ4_A0A2K5NKQ4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A151P596_A0A151P596_ALLMI_8496 and tr_A0A1U7RMB5_A0A1U7RMB5_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091JVH6_A0A091JVH6_EGRGA_188379 and tr_A0A093PXA5_A0A093PXA5_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091JVH6_A0A091JVH6_EGRGA_188379 and tr_A0A091WJL8_A0A091WJL8_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JVH6_A0A091JVH6_EGRGA_188379 and tr_A0A087QWC4_A0A087QWC4_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JVH6_A0A091JVH6_EGRGA_188379 and tr_A0A093HZL6_A0A093HZL6_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091JVH6_A0A091JVH6_EGRGA_188379 and tr_A0A0A0AYS7_A0A0A0AYS7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091JVH6_A0A091JVH6_EGRGA_188379 and tr_A0A091J7G4_A0A091J7G4_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A091V0K6_A0A091V0K6_NIPNI_128390 and tr_A0A099ZVT7_A0A099ZVT7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091VQM4_A0A091VQM4_NIPNI_128390 and tr_A0A091WL71_A0A091WL71_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091VQM4_A0A091VQM4_NIPNI_128390 and tr_A0A0A0ACN0_A0A0A0ACN0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091VQM4_A0A091VQM4_NIPNI_128390 and tr_A0A2I0MWG0_A0A2I0MWG0_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A1S3PWM5_A0A1S3PWM5_SALSA_8030 and tr_A0A060WWC2_A0A060WWC2_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226MZ88_A0A226MZ88_CALSU_9009 and tr_A0A226P0A3_A0A226P0A3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NGA3_A0A226NGA3_CALSU_9009 and tr_A0A226PKU0_A0A226PKU0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2U4ATQ9_A0A2U4ATQ9_TURTR_9739 and tr_A0A2Y9S2H1_A0A2Y9S2H1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9F1H3_A0A2Y9F1H3_PHYCD_9755 and tr_A0A383ZRT4_A0A383ZRT4_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 76

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/Q8IX07/3_mltree/Q8IX07.raxml.reduced.phy

Alignment comprises 1 partitions and 302 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 302 / 302
Gaps: 24.60 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07.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 / 302 / 24160
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -495376.319145] Initial branch length optimization
[00:00:12 -423600.313915] Model parameter optimization (eps = 10.000000)
[00:01:32 -422296.629000] AUTODETECT spr round 1 (radius: 5)
[00:05:52 -294377.905449] AUTODETECT spr round 2 (radius: 10)
[00:10:20 -227461.144771] AUTODETECT spr round 3 (radius: 15)
[00:15:48 -189167.412610] AUTODETECT spr round 4 (radius: 20)
[00:21:53 -176316.366860] AUTODETECT spr round 5 (radius: 25)
[00:28:46 -174190.904666] SPR radius for FAST iterations: 25 (autodetect)
[00:28:46 -174190.904666] Model parameter optimization (eps = 3.000000)
[00:29:26 -174068.025852] FAST spr round 1 (radius: 25)
[00:36:48 -161558.507403] FAST spr round 2 (radius: 25)
[00:42:21 -160330.149655] FAST spr round 3 (radius: 25)
[00:46:53 -160236.784304] FAST spr round 4 (radius: 25)
[00:50:57 -160210.468974] FAST spr round 5 (radius: 25)
[00:54:34 -160198.475921] FAST spr round 6 (radius: 25)
[00:57:50 -160193.753885] FAST spr round 7 (radius: 25)
[01:00:58 -160193.752048] Model parameter optimization (eps = 1.000000)
[01:01:16 -160192.307594] SLOW spr round 1 (radius: 5)
[01:05:32 -160153.766567] SLOW spr round 2 (radius: 5)
[01:09:39 -160146.184823] SLOW spr round 3 (radius: 5)
[01:13:42 -160145.659288] SLOW spr round 4 (radius: 5)
[01:17:38 -160144.602562] SLOW spr round 5 (radius: 5)
[01:21:31 -160144.602272] SLOW spr round 6 (radius: 10)
[01:25:43 -160142.566488] SLOW spr round 7 (radius: 5)
[01:30:20 -160142.561331] SLOW spr round 8 (radius: 10)
[01:35:11 -160142.560415] SLOW spr round 9 (radius: 15)
[01:42:51 -160135.270131] SLOW spr round 10 (radius: 5)
[01:47:39 -160135.256778] SLOW spr round 11 (radius: 10)
[01:52:46 -160135.256416] SLOW spr round 12 (radius: 15)
[02:00:18 -160135.256292] SLOW spr round 13 (radius: 20)
[02:11:34 -160134.411108] SLOW spr round 14 (radius: 5)
[02:16:30 -160134.223507] SLOW spr round 15 (radius: 5)
[02:20:56 -160134.175418] SLOW spr round 16 (radius: 10)
[02:25:36 -160131.335823] SLOW spr round 17 (radius: 5)
[02:30:18 -160130.514538] SLOW spr round 18 (radius: 5)
[02:34:29 -160130.513224] SLOW spr round 19 (radius: 10)
[02:38:53 -160130.513074] SLOW spr round 20 (radius: 15)
[02:46:44 -160130.513021] SLOW spr round 21 (radius: 20)
[02:57:58 -160130.512988] SLOW spr round 22 (radius: 25)
[03:11:20 -160117.599713] SLOW spr round 23 (radius: 5)
[03:16:32 -160111.811190] SLOW spr round 24 (radius: 5)
[03:21:05 -160110.064652] SLOW spr round 25 (radius: 5)
[03:25:25 -160108.685771] SLOW spr round 26 (radius: 5)
[03:26:22] [worker #4] ML tree search #5, logLikelihood: -160058.996190
[03:29:32 -160108.632835] SLOW spr round 27 (radius: 10)
[03:33:49 -160107.779511] SLOW spr round 28 (radius: 5)
[03:38:27 -160107.641934] SLOW spr round 29 (radius: 5)
[03:42:40 -160107.641866] SLOW spr round 30 (radius: 10)
[03:47:05 -160107.641856] SLOW spr round 31 (radius: 15)
[03:49:44] [worker #1] ML tree search #2, logLikelihood: -160096.531201
[03:54:59 -160106.961383] SLOW spr round 32 (radius: 5)
[03:59:52 -160106.460546] SLOW spr round 33 (radius: 5)
[04:04:10 -160106.459319] SLOW spr round 34 (radius: 10)
[04:08:42 -160106.459275] SLOW spr round 35 (radius: 15)
[04:16:45 -160106.459270] SLOW spr round 36 (radius: 20)
[04:20:55] [worker #3] ML tree search #4, logLikelihood: -160078.308041
[04:28:12 -160106.459269] SLOW spr round 37 (radius: 25)
[04:41:31 -160106.459269] Model parameter optimization (eps = 0.100000)

[04:41:41] [worker #0] ML tree search #1, logLikelihood: -160106.383503

[04:41:42 -493030.817194] Initial branch length optimization
[04:41:53 -420206.328967] Model parameter optimization (eps = 10.000000)
[04:43:21 -418891.865721] AUTODETECT spr round 1 (radius: 5)
[04:47:43 -294542.722432] AUTODETECT spr round 2 (radius: 10)
[04:52:16 -233883.263598] AUTODETECT spr round 3 (radius: 15)
[04:53:54] [worker #2] ML tree search #3, logLikelihood: -160101.479788
[04:57:18 -204376.027966] AUTODETECT spr round 4 (radius: 20)
[05:03:15 -182678.004760] AUTODETECT spr round 5 (radius: 25)
[05:10:00 -176722.163747] SPR radius for FAST iterations: 25 (autodetect)
[05:10:00 -176722.163747] Model parameter optimization (eps = 3.000000)
[05:10:35 -176578.397431] FAST spr round 1 (radius: 25)
[05:17:16 -161697.704794] FAST spr round 2 (radius: 25)
[05:22:35 -160440.686437] FAST spr round 3 (radius: 25)
[05:27:05 -160238.009951] FAST spr round 4 (radius: 25)
[05:31:01 -160219.898592] FAST spr round 5 (radius: 25)
[05:34:40 -160189.856426] FAST spr round 6 (radius: 25)
[05:38:04 -160177.492354] FAST spr round 7 (radius: 25)
[05:41:16 -160173.451528] FAST spr round 8 (radius: 25)
[05:44:20 -160173.450656] Model parameter optimization (eps = 1.000000)
[05:44:45 -160168.616501] SLOW spr round 1 (radius: 5)
[05:48:59 -160142.274853] SLOW spr round 2 (radius: 5)
[05:53:11 -160137.227631] SLOW spr round 3 (radius: 5)
[05:57:14 -160137.226612] SLOW spr round 4 (radius: 10)
[06:01:29 -160136.058033] SLOW spr round 5 (radius: 5)
[06:06:16 -160135.465809] SLOW spr round 6 (radius: 5)
[06:10:34 -160135.463660] SLOW spr round 7 (radius: 10)
[06:15:04 -160135.463421] SLOW spr round 8 (radius: 15)
[06:23:13 -160129.701227] SLOW spr round 9 (radius: 5)
[06:28:16 -160125.391120] SLOW spr round 10 (radius: 5)
[06:32:42 -160125.369130] SLOW spr round 11 (radius: 10)
[06:37:18 -160125.369029] SLOW spr round 12 (radius: 15)
[06:45:13 -160124.634429] SLOW spr round 13 (radius: 5)
[06:50:08 -160124.064897] SLOW spr round 14 (radius: 5)
[06:54:32 -160124.063339] SLOW spr round 15 (radius: 10)
[06:59:09 -160124.063195] SLOW spr round 16 (radius: 15)
[07:07:05 -160124.063162] SLOW spr round 17 (radius: 20)
[07:18:30 -160120.005234] SLOW spr round 18 (radius: 5)
[07:23:37 -160115.785533] SLOW spr round 19 (radius: 5)
[07:28:06 -160114.138141] SLOW spr round 20 (radius: 5)
[07:32:17 -160112.177802] SLOW spr round 21 (radius: 5)
[07:36:18 -160112.177166] SLOW spr round 22 (radius: 10)
[07:40:36 -160112.177147] SLOW spr round 23 (radius: 15)
[07:48:57 -160112.177146] SLOW spr round 24 (radius: 20)
[08:00:21 -160112.002124] SLOW spr round 25 (radius: 5)
[08:05:21 -160112.001641] SLOW spr round 26 (radius: 10)
[08:09:53] [worker #1] ML tree search #7, logLikelihood: -160057.599442
[08:10:56 -160112.001621] SLOW spr round 27 (radius: 15)
[08:18:45 -160112.001620] SLOW spr round 28 (radius: 20)
[08:30:13 -160111.950024] SLOW spr round 29 (radius: 25)
[08:42:35 -160111.949750] Model parameter optimization (eps = 0.100000)

[08:42:43] [worker #0] ML tree search #6, logLikelihood: -160111.905994

[08:42:43 -495322.679068] Initial branch length optimization
[08:42:55 -424437.680285] Model parameter optimization (eps = 10.000000)
[08:44:20 -423242.881426] AUTODETECT spr round 1 (radius: 5)
[08:48:38 -293606.530768] AUTODETECT spr round 2 (radius: 10)
[08:53:12 -222946.294308] AUTODETECT spr round 3 (radius: 15)
[08:58:13 -193119.769191] AUTODETECT spr round 4 (radius: 20)
[09:04:10 -180505.902441] AUTODETECT spr round 5 (radius: 25)
[09:11:01 -176031.792189] SPR radius for FAST iterations: 25 (autodetect)
[09:11:01 -176031.792189] Model parameter optimization (eps = 3.000000)
[09:11:50 -175857.914156] FAST spr round 1 (radius: 25)
[09:17:02] [worker #4] ML tree search #10, logLikelihood: -160086.253748
[09:19:24 -161425.962895] FAST spr round 2 (radius: 25)
[09:25:04 -160422.038712] FAST spr round 3 (radius: 25)
[09:29:32 -160278.289965] FAST spr round 4 (radius: 25)
[09:31:30] [worker #2] ML tree search #8, logLikelihood: -160074.724979
[09:33:34 -160242.378911] FAST spr round 5 (radius: 25)
[09:37:12 -160231.746454] FAST spr round 6 (radius: 25)
[09:40:31 -160231.743449] Model parameter optimization (eps = 1.000000)
[09:40:55 -160229.944241] SLOW spr round 1 (radius: 5)
[09:45:13 -160176.822079] SLOW spr round 2 (radius: 5)
[09:49:25 -160166.058301] SLOW spr round 3 (radius: 5)
[09:53:32 -160163.642626] SLOW spr round 4 (radius: 5)
[09:57:30 -160163.641472] SLOW spr round 5 (radius: 10)
[10:01:45 -160159.248258] SLOW spr round 6 (radius: 5)
[10:06:32 -160156.556436] SLOW spr round 7 (radius: 5)
[10:10:52 -160155.701321] SLOW spr round 8 (radius: 5)
[10:15:01 -160153.880525] SLOW spr round 9 (radius: 5)
[10:19:07 -160150.527951] SLOW spr round 10 (radius: 5)
[10:23:08 -160150.372233] SLOW spr round 11 (radius: 5)
[10:27:06 -160150.371829] SLOW spr round 12 (radius: 10)
[10:31:17 -160150.371735] SLOW spr round 13 (radius: 15)
[10:38:53 -160149.452563] SLOW spr round 14 (radius: 5)
[10:43:53 -160148.538789] SLOW spr round 15 (radius: 5)
[10:48:18 -160147.772615] SLOW spr round 16 (radius: 5)
[10:52:26 -160147.772252] SLOW spr round 17 (radius: 10)
[10:56:43 -160147.772161] SLOW spr round 18 (radius: 15)
[11:04:07 -160147.772121] SLOW spr round 19 (radius: 20)
[11:14:31 -160140.225666] SLOW spr round 20 (radius: 5)
[11:19:35 -160137.083567] SLOW spr round 21 (radius: 5)
[11:24:04 -160136.602701] SLOW spr round 22 (radius: 5)
[11:28:13 -160136.602669] SLOW spr round 23 (radius: 10)
[11:28:54] [worker #1] ML tree search #12, logLikelihood: -160063.045087
[11:32:32 -160136.602662] SLOW spr round 24 (radius: 15)
[11:39:52 -160136.602657] SLOW spr round 25 (radius: 20)
[11:50:19 -160136.602653] SLOW spr round 26 (radius: 25)
[12:02:30 -160135.771196] SLOW spr round 27 (radius: 5)
[12:07:31] [worker #3] ML tree search #9, logLikelihood: -160070.379950
[12:07:35 -160135.371736] SLOW spr round 28 (radius: 5)
[12:12:05 -160135.369845] SLOW spr round 29 (radius: 10)
[12:16:43 -160135.369749] SLOW spr round 30 (radius: 15)
[12:23:58 -160135.369733] SLOW spr round 31 (radius: 20)
[12:31:50] [worker #4] ML tree search #15, logLikelihood: -160036.239994
[12:34:27 -160135.369728] SLOW spr round 32 (radius: 25)
[12:46:34 -160135.369724] Model parameter optimization (eps = 0.100000)

[12:46:48] [worker #0] ML tree search #11, logLikelihood: -160135.146009

[12:46:48 -493716.914348] Initial branch length optimization
[12:46:58 -421314.901818] Model parameter optimization (eps = 10.000000)
[12:48:02 -419966.205177] AUTODETECT spr round 1 (radius: 5)
[12:52:23 -296378.082849] AUTODETECT spr round 2 (radius: 10)
[12:56:57 -239073.051150] AUTODETECT spr round 3 (radius: 15)
[13:02:13 -202006.746406] AUTODETECT spr round 4 (radius: 20)
[13:08:22 -186794.255202] AUTODETECT spr round 5 (radius: 25)
[13:15:50 -178931.114643] SPR radius for FAST iterations: 25 (autodetect)
[13:15:50 -178931.114643] Model parameter optimization (eps = 3.000000)
[13:16:29 -178801.755175] FAST spr round 1 (radius: 25)
[13:24:12 -162565.059174] FAST spr round 2 (radius: 25)
[13:29:54 -161134.623798] FAST spr round 3 (radius: 25)
[13:34:26 -160425.951500] FAST spr round 4 (radius: 25)
[13:38:25 -160218.030183] FAST spr round 5 (radius: 25)
[13:41:56 -160208.310992] FAST spr round 6 (radius: 25)
[13:45:18 -160184.220496] FAST spr round 7 (radius: 25)
[13:48:25 -160182.096704] FAST spr round 8 (radius: 25)
[13:51:29 -160182.081443] Model parameter optimization (eps = 1.000000)
[13:51:45 -160175.306883] SLOW spr round 1 (radius: 5)
[13:55:57 -160119.913899] SLOW spr round 2 (radius: 5)
[14:00:06 -160109.212778] SLOW spr round 3 (radius: 5)
[14:04:09 -160109.212285] SLOW spr round 4 (radius: 10)
[14:08:30 -160103.561727] SLOW spr round 5 (radius: 5)
[14:13:18 -160103.400374] SLOW spr round 6 (radius: 5)
[14:17:37 -160103.400234] SLOW spr round 7 (radius: 10)
[14:22:11 -160102.436370] SLOW spr round 8 (radius: 5)
[14:26:54 -160102.435977] SLOW spr round 9 (radius: 10)
[14:30:21] [worker #1] ML tree search #17, logLikelihood: -160065.941686
[14:31:51 -160101.143727] SLOW spr round 10 (radius: 5)
[14:36:35 -160099.533205] SLOW spr round 11 (radius: 5)
[14:40:59 -160097.998909] SLOW spr round 12 (radius: 5)
[14:45:07 -160097.998001] SLOW spr round 13 (radius: 10)
[14:49:26 -160097.997903] SLOW spr round 14 (radius: 15)
[14:57:25 -160087.769846] SLOW spr round 15 (radius: 5)
[15:02:27 -160084.329667] SLOW spr round 16 (radius: 5)
[15:06:55 -160083.963604] SLOW spr round 17 (radius: 5)
[15:11:04 -160083.962897] SLOW spr round 18 (radius: 10)
[15:15:26 -160083.382449] SLOW spr round 19 (radius: 5)
[15:20:08 -160083.382109] SLOW spr round 20 (radius: 10)
[15:25:00 -160083.382067] SLOW spr round 21 (radius: 15)
[15:32:01] [worker #2] ML tree search #13, logLikelihood: -160065.562193
[15:32:52 -160083.382040] SLOW spr round 22 (radius: 20)
[15:44:18 -160080.932403] SLOW spr round 23 (radius: 5)
[15:49:19 -160080.931079] SLOW spr round 24 (radius: 10)
[15:54:43 -160080.930979] SLOW spr round 25 (radius: 15)
[16:02:20 -160080.930932] SLOW spr round 26 (radius: 20)
[16:13:11 -160079.160365] SLOW spr round 27 (radius: 5)
[16:18:15 -160076.524463] SLOW spr round 28 (radius: 5)
[16:22:22] [worker #4] ML tree search #20, logLikelihood: -160071.132085
[16:22:43 -160076.523420] SLOW spr round 29 (radius: 10)
[16:27:18 -160076.523347] SLOW spr round 30 (radius: 15)
[16:35:02 -160075.621282] SLOW spr round 31 (radius: 5)
[16:40:01 -160072.426591] SLOW spr round 32 (radius: 5)
[16:44:26 -160072.237716] SLOW spr round 33 (radius: 5)
[16:48:32 -160072.237313] SLOW spr round 34 (radius: 10)
[16:52:51 -160072.237296] SLOW spr round 35 (radius: 15)
[16:58:18] [worker #3] ML tree search #14, logLikelihood: -160115.529205
[17:00:57 -160072.237291] SLOW spr round 36 (radius: 20)
[17:11:52 -160072.237289] SLOW spr round 37 (radius: 25)
[17:24:44 -160071.704028] SLOW spr round 38 (radius: 5)
[17:29:44 -160071.703894] SLOW spr round 39 (radius: 10)
[17:35:16 -160071.703892] SLOW spr round 40 (radius: 15)
[17:42:56 -160071.703891] SLOW spr round 41 (radius: 20)
[17:53:57 -160071.703890] SLOW spr round 42 (radius: 25)
[18:06:48 -160071.703890] Model parameter optimization (eps = 0.100000)

[18:06:58] [worker #0] ML tree search #16, logLikelihood: -160071.624230

[18:28:51] [worker #2] ML tree search #18, logLikelihood: -160085.436353
[20:55:00] [worker #3] ML tree search #19, logLikelihood: -160036.550406

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.127931,0.274276) (0.088546,0.719984) (0.447190,0.904032) (0.336333,1.477362) 
   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: -160036.239994

AIC score: 324082.479988 / AICc score: 8368142.479988 / BIC score: 331521.886157
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=302).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 47 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07.raxml.log

Analysis started: 03-Jul-2021 06:51:09 / finished: 04-Jul-2021 03:46:10

Elapsed time: 75301.078 seconds