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

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 01-Jul-2021 07:46:47 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/2_msa/Q8TE85_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/2_msa/Q8TE85_trimmed_msa.fasta
[00:00:00] Loaded alignment with 812 taxa and 414 sites

WARNING: Sequences tr_B4QBS0_B4QBS0_DROSI_7240 and tr_B4HN88_B4HN88_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A1D5PFL1_A0A1D5PFL1_CHICK_9031 and tr_A0A226MS04_A0A226MS04_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A1D5PFL1_A0A1D5PFL1_CHICK_9031 and tr_A0A226PLZ0_A0A226PLZ0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A7VJA9_A7VJA9_CHICK_9031 and sp_Q7T2U9_TFCP2_CHICK_9031 are exactly identical!
WARNING: Sequences tr_A7VJA9_A7VJA9_CHICK_9031 and tr_A0A226MN10_A0A226MN10_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A7VJA9_A7VJA9_CHICK_9031 and tr_A0A226NPV0_A0A226NPV0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_H2NHB0_H2NHB0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A2I3RVQ9_A0A2I3RVQ9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_H0WXF7_H0WXF7_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and sp_Q12800_TFCP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_F7H1F4_F7H1F4_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A096MPC0_A0A096MPC0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A0D9R0S6_A0A0D9R0S6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A2K5MG93_A0A2K5MG93_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A2R8ZHD7_A0A2R8ZHD7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A4FUY6_A4FUY6_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A0A2U4CBI7_A0A2U4CBI7_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A0A2Y9NF35_A0A2Y9NF35_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A0A2Y9F4B4_A0A2Y9F4B4_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_H2QIN0_H2QIN0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and sp_Q9NZI6_TF2L1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_A0A1D5R5F6_A0A1D5R5F6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_A0A0D9RVU4_A0A0D9RVU4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_A0A2K6DJU4_A0A2K6DJU4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and tr_H2QWI7_H2QWI7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and sp_Q6ISB3_GRHL2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and tr_A0A096MXW7_A0A096MXW7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and tr_A0A0D9RHT7_A0A0D9RHT7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and tr_A0A2K5XEX5_A0A2K5XEX5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and tr_A0A2R9CE02_A0A2R9CE02_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1NGZ9_G1NGZ9_MELGA_9103 and tr_U3I248_U3I248_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_F6TYZ0_F6TYZ0_HORSE_9796 are exactly identical!
WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_I3MCZ2_I3MCZ2_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_M3XA11_M3XA11_FELCA_9685 are exactly identical!
WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A091DK05_A0A091DK05_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A2U3XUS3_A0A2U3XUS3_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A2Y9KQF5_A0A2Y9KQF5_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A384D7Q7_A0A384D7Q7_URSMA_29073 are exactly identical!
WARNING: Sequences tr_F6SYN6_F6SYN6_MONDO_13616 and tr_G3WLK8_G3WLK8_SARHA_9305 are exactly identical!
WARNING: Sequences tr_A0A158Q140_A0A158Q140_BRUMA_6279 and tr_A0A158PSE0_A0A158PSE0_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_F7GLC0_F7GLC0_MACMU_9544 and tr_G7PAA7_G7PAA7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GLC0_F7GLC0_MACMU_9544 and tr_A0A2K6BBZ3_A0A2K6BBZ3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HKR5_F7HKR5_MACMU_9544 and tr_G7PCF8_G7PCF8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A015KTX4_A0A015KTX4_9GLOM_1432141 and tr_A0A2H5R4A7_A0A2H5R4A7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2I3M6I0_A0A2I3M6I0_PAPAN_9555 and tr_A0A2K5LFL3_A0A2K5LFL3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0A1P0C5_A0A0A1P0C5_9FUNG_58291 and tr_A0A367JBW1_A0A367JBW1_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0Q3MPC7_A0A0Q3MPC7_AMAAE_12930 and tr_A0A1V4K5W1_A0A1V4K5W1_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A087QTW7_A0A087QTW7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A091WHQ3_A0A091WHQ3_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A0A0AML9_A0A0A0AML9_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A093FZV6_A0A093FZV6_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A091V198_A0A091V198_NIPNI_128390 and tr_A0A087QNZ0_A0A087QNZ0_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091V198_A0A091V198_NIPNI_128390 and tr_A0A091W4H8_A0A091W4H8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A087QWA3_A0A087QWA3_APTFO_9233 and tr_A0A091VQU2_A0A091VQU2_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A087QWA3_A0A087QWA3_APTFO_9233 and tr_A0A0A0ABX4_A0A0A0ABX4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MWG8_A0A2I0MWG8_COLLI_8932 and tr_A0A1V4KH52_A0A1V4KH52_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1CLQ6_A0A0V1CLQ6_TRIBR_45882 and tr_A0A0V0UWJ2_A0A0V0UWJ2_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CLQ6_A0A0V1CLQ6_TRIBR_45882 and tr_A0A0V1P1Z5_A0A0V1P1Z5_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CLQ6_A0A0V1CLQ6_TRIBR_45882 and tr_A0A0V0U9F4_A0A0V0U9F4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0WWY0_A0A0V0WWY0_9BILA_92179 and tr_A0A0V1LN74_A0A0V1LN74_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A151IXK2_A0A151IXK2_9HYME_471704 and tr_A0A195FNV0_A0A195FNV0_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A1S3K3B4_A0A1S3K3B4_LINUN_7574 and tr_A0A1S3K3L5_A0A1S3K3L5_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3MGB0_A0A1S3MGB0_SALSA_8030 and tr_A0A060WEV4_A0A060WEV4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1D1VCR0_A0A1D1VCR0_RAMVA_947166 and tr_A0A1D1VLR9_A0A1D1VLR9_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A226MM91_A0A226MM91_CALSU_9009 and tr_A0A226PDJ0_A0A226PDJ0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0RM34_A0A2D0RM34_ICTPU_7998 and tr_A0A2D0RM37_A0A2D0RM37_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RM34_A0A2D0RM34_ICTPU_7998 and tr_A0A2D0RM42_A0A2D0RM42_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RM34_A0A2D0RM34_ICTPU_7998 and tr_A0A2D0RNP3_A0A2D0RNP3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5L7V8_A0A2K5L7V8_CERAT_9531 and tr_A0A2K5Z9W0_A0A2K5Z9W0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U4AHY5_A0A2U4AHY5_TURTR_9739 and tr_A0A2Y9PAR4_A0A2Y9PAR4_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 70

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85.raxml.reduced.phy

Alignment comprises 1 partitions and 414 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 414 / 414
Gaps: 16.28 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85.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 812 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 207 / 16560
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -507891.388608] Initial branch length optimization
[00:00:05 -408607.296932] Model parameter optimization (eps = 10.000000)
[00:01:09 -407284.636539] AUTODETECT spr round 1 (radius: 5)
[00:03:12 -246199.042849] AUTODETECT spr round 2 (radius: 10)
[00:05:19 -176847.424171] AUTODETECT spr round 3 (radius: 15)
[00:07:46 -148373.541868] AUTODETECT spr round 4 (radius: 20)
[00:10:34 -130828.636111] AUTODETECT spr round 5 (radius: 25)
[00:14:16 -120972.604363] SPR radius for FAST iterations: 25 (autodetect)
[00:14:16 -120972.604363] Model parameter optimization (eps = 3.000000)
[00:14:35 -120868.864405] FAST spr round 1 (radius: 25)
[00:16:58 -102560.403606] FAST spr round 2 (radius: 25)
[00:18:59 -101359.214363] FAST spr round 3 (radius: 25)
[00:20:36 -101262.112255] FAST spr round 4 (radius: 25)
[00:22:05 -101252.432745] FAST spr round 5 (radius: 25)
[00:23:30 -101250.652684] FAST spr round 6 (radius: 25)
[00:24:52 -101250.640972] Model parameter optimization (eps = 1.000000)
[00:25:08 -101246.485690] SLOW spr round 1 (radius: 5)
[00:27:04 -101210.697968] SLOW spr round 2 (radius: 5)
[00:28:55 -101207.539183] SLOW spr round 3 (radius: 5)
[00:30:43 -101207.299949] SLOW spr round 4 (radius: 5)
[00:32:29 -101207.299756] SLOW spr round 5 (radius: 10)
[00:34:23 -101205.433824] SLOW spr round 6 (radius: 5)
[00:36:45 -101205.066994] SLOW spr round 7 (radius: 5)
[00:38:49 -101205.066791] SLOW spr round 8 (radius: 10)
[00:40:46 -101205.066727] SLOW spr round 9 (radius: 15)
[00:43:56 -101204.132408] SLOW spr round 10 (radius: 5)
[00:46:27 -101203.384101] SLOW spr round 11 (radius: 5)
[00:48:38 -101202.824268] SLOW spr round 12 (radius: 5)
[00:50:36 -101202.824173] SLOW spr round 13 (radius: 10)
[00:51:41] [worker #1] ML tree search #2, logLikelihood: -101202.059316
[00:52:29 -101202.824143] SLOW spr round 14 (radius: 15)
[00:55:40 -101202.824114] SLOW spr round 15 (radius: 20)
[00:58:10] [worker #2] ML tree search #3, logLikelihood: -101209.359495
[01:00:24 -101200.648642] SLOW spr round 16 (radius: 5)
[01:02:59 -101200.648576] SLOW spr round 17 (radius: 10)
[01:05:24 -101200.531976] SLOW spr round 18 (radius: 5)
[01:07:41 -101200.531552] SLOW spr round 19 (radius: 10)
[01:09:45 -101200.531549] SLOW spr round 20 (radius: 15)
[01:12:49 -101198.985851] SLOW spr round 21 (radius: 5)
[01:15:19 -101198.985842] SLOW spr round 22 (radius: 10)
[01:17:38 -101198.985839] SLOW spr round 23 (radius: 15)
[01:20:31 -101198.985837] SLOW spr round 24 (radius: 20)
[01:25:21 -101198.985835] SLOW spr round 25 (radius: 25)
[01:32:12 -101198.985832] Model parameter optimization (eps = 0.100000)

[01:32:22] [worker #0] ML tree search #1, logLikelihood: -101198.704333

[01:32:22 -506999.376542] Initial branch length optimization
[01:32:27 -408614.807920] Model parameter optimization (eps = 10.000000)
[01:33:34 -407271.326478] AUTODETECT spr round 1 (radius: 5)
[01:35:42 -248173.875594] AUTODETECT spr round 2 (radius: 10)
[01:37:50 -172747.957007] AUTODETECT spr round 3 (radius: 15)
[01:40:08 -136139.134359] AUTODETECT spr round 4 (radius: 20)
[01:42:47 -119515.641686] AUTODETECT spr round 5 (radius: 25)
[01:45:46] [worker #1] ML tree search #5, logLikelihood: -101218.522226
[01:46:12 -116691.805274] SPR radius for FAST iterations: 25 (autodetect)
[01:46:12 -116691.805274] Model parameter optimization (eps = 3.000000)
[01:46:39 -116579.816433] FAST spr round 1 (radius: 25)
[01:49:00 -102221.938021] FAST spr round 2 (radius: 25)
[01:50:55 -101284.888909] FAST spr round 3 (radius: 25)
[01:52:36 -101249.851295] FAST spr round 4 (radius: 25)
[01:54:05 -101247.866182] FAST spr round 5 (radius: 25)
[01:55:30 -101247.865706] Model parameter optimization (eps = 1.000000)
[01:55:47 -101239.229237] SLOW spr round 1 (radius: 5)
[01:57:44 -101215.311464] SLOW spr round 2 (radius: 5)
[01:59:40 -101213.758228] SLOW spr round 3 (radius: 5)
[02:01:04] [worker #2] ML tree search #6, logLikelihood: -101205.147585
[02:01:32 -101212.082559] SLOW spr round 4 (radius: 5)
[02:03:27 -101211.732662] SLOW spr round 5 (radius: 5)
[02:05:16 -101211.732530] SLOW spr round 6 (radius: 10)
[02:07:09 -101211.732312] SLOW spr round 7 (radius: 15)
[02:10:28 -101211.732289] SLOW spr round 8 (radius: 20)
[02:15:20 -101211.732266] SLOW spr round 9 (radius: 25)
[02:22:14 -101211.732243] Model parameter optimization (eps = 0.100000)

[02:22:20] [worker #0] ML tree search #4, logLikelihood: -101211.699817

[02:22:20 -498794.448622] Initial branch length optimization
[02:22:24 -406523.225555] Model parameter optimization (eps = 10.000000)
[02:23:18 -405238.416972] AUTODETECT spr round 1 (radius: 5)
[02:25:21 -247677.763374] AUTODETECT spr round 2 (radius: 10)
[02:27:30 -179001.592305] AUTODETECT spr round 3 (radius: 15)
[02:29:54 -151621.655646] AUTODETECT spr round 4 (radius: 20)
[02:32:32 -134047.406855] AUTODETECT spr round 5 (radius: 25)
[02:35:30 -123976.109748] SPR radius for FAST iterations: 25 (autodetect)
[02:35:30 -123976.109748] Model parameter optimization (eps = 3.000000)
[02:35:59 -123893.883630] FAST spr round 1 (radius: 25)
[02:38:29 -102812.401059] FAST spr round 2 (radius: 25)
[02:40:32 -101334.048689] FAST spr round 3 (radius: 25)
[02:42:16 -101277.804356] FAST spr round 4 (radius: 25)
[02:43:51 -101265.331529] FAST spr round 5 (radius: 25)
[02:45:17 -101264.041566] FAST spr round 6 (radius: 25)
[02:46:42 -101264.041532] Model parameter optimization (eps = 1.000000)
[02:46:59 -101240.634081] SLOW spr round 1 (radius: 5)
[02:49:00 -101212.015306] SLOW spr round 2 (radius: 5)
[02:50:55 -101210.781218] SLOW spr round 3 (radius: 5)
[02:52:46 -101210.781065] SLOW spr round 4 (radius: 10)
[02:54:41 -101203.522717] SLOW spr round 5 (radius: 5)
[02:57:05 -101203.522601] SLOW spr round 6 (radius: 10)
[02:58:38] [worker #1] ML tree search #8, logLikelihood: -101199.864902
[02:59:17 -101203.522600] SLOW spr round 7 (radius: 15)
[03:02:18 -101203.522600] SLOW spr round 8 (radius: 20)
[03:07:21 -101203.522599] SLOW spr round 9 (radius: 25)
[03:14:28 -101203.522599] Model parameter optimization (eps = 0.100000)

[03:14:34] [worker #0] ML tree search #7, logLikelihood: -101203.443796

[03:14:34 -505671.420692] Initial branch length optimization
[03:14:39 -407861.656252] Model parameter optimization (eps = 10.000000)
[03:15:43 -406420.672862] AUTODETECT spr round 1 (radius: 5)
[03:16:45] [worker #2] ML tree search #9, logLikelihood: -101209.916267
[03:17:49 -247104.700459] AUTODETECT spr round 2 (radius: 10)
[03:19:54 -172504.253133] AUTODETECT spr round 3 (radius: 15)
[03:22:12 -140913.015494] AUTODETECT spr round 4 (radius: 20)
[03:24:57 -128974.335022] AUTODETECT spr round 5 (radius: 25)
[03:28:07 -124976.706704] SPR radius for FAST iterations: 25 (autodetect)
[03:28:07 -124976.706704] Model parameter optimization (eps = 3.000000)
[03:28:32 -124861.533532] FAST spr round 1 (radius: 25)
[03:31:02 -103543.301724] FAST spr round 2 (radius: 25)
[03:33:08 -101489.028751] FAST spr round 3 (radius: 25)
[03:34:57 -101319.258114] FAST spr round 4 (radius: 25)
[03:36:43 -101264.000570] FAST spr round 5 (radius: 25)
[03:38:12 -101248.229658] FAST spr round 6 (radius: 25)
[03:39:39 -101244.634456] FAST spr round 7 (radius: 25)
[03:41:03 -101244.634203] Model parameter optimization (eps = 1.000000)
[03:41:20 -101241.825764] SLOW spr round 1 (radius: 5)
[03:43:19 -101211.674199] SLOW spr round 2 (radius: 5)
[03:45:14 -101211.651063] SLOW spr round 3 (radius: 10)
[03:47:10 -101209.101243] SLOW spr round 4 (radius: 5)
[03:49:34 -101209.101109] SLOW spr round 5 (radius: 10)
[03:51:46 -101209.100927] SLOW spr round 6 (radius: 15)
[03:54:43 -101209.100926] SLOW spr round 7 (radius: 20)
[03:57:53] [worker #1] ML tree search #11, logLikelihood: -101215.376176
[03:59:29 -101209.100926] SLOW spr round 8 (radius: 25)
[04:06:09 -101209.100926] Model parameter optimization (eps = 0.100000)

[04:06:17] [worker #0] ML tree search #10, logLikelihood: -101208.990764

[04:06:17 -508857.816606] Initial branch length optimization
[04:06:22 -410829.707739] Model parameter optimization (eps = 10.000000)
[04:07:13 -409486.576342] AUTODETECT spr round 1 (radius: 5)
[04:09:17 -252721.881863] AUTODETECT spr round 2 (radius: 10)
[04:10:38] [worker #2] ML tree search #12, logLikelihood: -101200.066595
[04:11:19 -176086.406195] AUTODETECT spr round 3 (radius: 15)
[04:13:42 -135927.233732] AUTODETECT spr round 4 (radius: 20)
[04:16:20 -119082.506437] AUTODETECT spr round 5 (radius: 25)
[04:19:11 -115358.103241] SPR radius for FAST iterations: 25 (autodetect)
[04:19:11 -115358.103241] Model parameter optimization (eps = 3.000000)
[04:19:27 -115274.424682] FAST spr round 1 (radius: 25)
[04:21:20 -102025.919321] FAST spr round 2 (radius: 25)
[04:22:48 -101292.265996] FAST spr round 3 (radius: 25)
[04:24:11 -101250.032842] FAST spr round 4 (radius: 25)
[04:25:27 -101242.261766] FAST spr round 5 (radius: 25)
[04:26:37 -101242.261609] Model parameter optimization (eps = 1.000000)
[04:26:48 -101239.551466] SLOW spr round 1 (radius: 5)
[04:28:27 -101211.247799] SLOW spr round 2 (radius: 5)
[04:30:04 -101206.694104] SLOW spr round 3 (radius: 5)
[04:31:37 -101206.693956] SLOW spr round 4 (radius: 10)
[04:33:15 -101206.693744] SLOW spr round 5 (radius: 15)
[04:36:05 -101206.693719] SLOW spr round 6 (radius: 20)
[04:40:19 -101206.693693] SLOW spr round 7 (radius: 25)
[04:46:39 -101206.693667] Model parameter optimization (eps = 0.100000)

[04:46:44] [worker #0] ML tree search #13, logLikelihood: -101206.649876

[04:46:44 -506922.027142] Initial branch length optimization
[04:46:48 -408134.750083] Model parameter optimization (eps = 10.000000)
[04:47:33 -406796.010502] AUTODETECT spr round 1 (radius: 5)
[04:49:24 -251576.646527] AUTODETECT spr round 2 (radius: 10)
[04:51:19 -181929.544058] AUTODETECT spr round 3 (radius: 15)
[04:53:26 -148452.324974] AUTODETECT spr round 4 (radius: 20)
[04:55:42 -130229.287715] AUTODETECT spr round 5 (radius: 25)
[04:58:10 -126805.601340] SPR radius for FAST iterations: 25 (autodetect)
[04:58:10 -126805.601340] Model parameter optimization (eps = 3.000000)
[04:58:27 -126689.509768] FAST spr round 1 (radius: 25)
[05:00:23 -104045.467060] FAST spr round 2 (radius: 25)
[05:01:55 -101345.039525] FAST spr round 3 (radius: 25)
[05:03:17 -101249.385796] FAST spr round 4 (radius: 25)
[05:04:33 -101240.441019] FAST spr round 5 (radius: 25)
[05:05:47 -101238.871400] FAST spr round 6 (radius: 25)
[05:06:20] [worker #1] ML tree search #14, logLikelihood: -101208.730263
[05:06:58 -101238.871288] Model parameter optimization (eps = 1.000000)
[05:07:10 -101233.162122] SLOW spr round 1 (radius: 5)
[05:08:51 -101200.076207] SLOW spr round 2 (radius: 5)
[05:10:28 -101194.435995] SLOW spr round 3 (radius: 5)
[05:12:02 -101194.435722] SLOW spr round 4 (radius: 10)
[05:13:39 -101194.124559] SLOW spr round 5 (radius: 5)
[05:15:40 -101194.124449] SLOW spr round 6 (radius: 10)
[05:16:53] [worker #2] ML tree search #15, logLikelihood: -101216.505717
[05:17:33 -101194.124122] SLOW spr round 7 (radius: 15)
[05:20:03 -101194.123804] SLOW spr round 8 (radius: 20)
[05:24:00 -101194.123739] SLOW spr round 9 (radius: 25)
[05:29:34 -101194.123725] Model parameter optimization (eps = 0.100000)

[05:29:38] [worker #0] ML tree search #16, logLikelihood: -101194.106187

[05:29:38 -505605.957167] Initial branch length optimization
[05:29:42 -409206.201107] Model parameter optimization (eps = 10.000000)
[05:30:34 -407850.420546] AUTODETECT spr round 1 (radius: 5)
[05:32:18 -242880.851780] AUTODETECT spr round 2 (radius: 10)
[05:34:05 -171034.699035] AUTODETECT spr round 3 (radius: 15)
[05:36:05 -135777.882253] AUTODETECT spr round 4 (radius: 20)
[05:38:33 -124498.279592] AUTODETECT spr round 5 (radius: 25)
[05:41:06 -122057.894005] SPR radius for FAST iterations: 25 (autodetect)
[05:41:06 -122057.894005] Model parameter optimization (eps = 3.000000)
[05:41:27 -121941.235332] FAST spr round 1 (radius: 25)
[05:43:24 -102076.717138] FAST spr round 2 (radius: 25)
[05:44:54 -101310.762155] FAST spr round 3 (radius: 25)
[05:46:17 -101241.491936] FAST spr round 4 (radius: 25)
[05:47:34 -101237.130682] FAST spr round 5 (radius: 25)
[05:48:46 -101237.130373] Model parameter optimization (eps = 1.000000)
[05:49:00 -101228.338599] SLOW spr round 1 (radius: 5)
[05:49:39] [worker #1] ML tree search #17, logLikelihood: -101208.126141
[05:50:41 -101206.023493] SLOW spr round 2 (radius: 5)
[05:52:20 -101203.515598] SLOW spr round 3 (radius: 5)
[05:53:54 -101203.515258] SLOW spr round 4 (radius: 10)
[05:55:30 -101203.514855] SLOW spr round 5 (radius: 15)
[05:58:18 -101203.514789] SLOW spr round 6 (radius: 20)
[06:02:24 -101203.514724] SLOW spr round 7 (radius: 25)
[06:08:20 -101203.514658] Model parameter optimization (eps = 0.100000)

[06:08:29] [worker #0] ML tree search #19, logLikelihood: -101203.209376

[06:09:35] [worker #2] ML tree search #18, logLikelihood: -101221.200596
[06:32:32] [worker #1] ML tree search #20, logLikelihood: -101214.753060

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.134588,0.325141) (0.167609,0.428406) (0.361495,0.804531) (0.336307,1.765055) 
   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: -101194.106187

AIC score: 205642.212373 / AICc score: 5503154.212373 / BIC score: 212192.296313
Free parameters (model + branch lengths): 1627

WARNING: Number of free parameters (K=1627) is larger than alignment size (n=414).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85.raxml.log

Analysis started: 01-Jul-2021 07:46:47 / finished: 01-Jul-2021 14:19:20

Elapsed time: 23552.974 seconds

Consumed energy: 2128.354 Wh (= 11 km in an electric car, or 53 km with an e-scooter!)