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 03-Jul-2021 23:38:10 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/2_msa/Q8NCW0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/3_mltree/Q8NCW0 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/2_msa/Q8NCW0_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 204 sites

WARNING: Sequences tr_G1QQB8_G1QQB8_NOMLE_61853 and tr_G3QID4_G3QID4_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QQB8_G1QQB8_NOMLE_61853 and sp_Q96MU8_KREM1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QQB8_G1QQB8_NOMLE_61853 and tr_U3DHG7_U3DHG7_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1QQB8_G1QQB8_NOMLE_61853 and tr_A0A096NRI8_A0A096NRI8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QQB8_G1QQB8_NOMLE_61853 and tr_A0A0D9RBW9_A0A0D9RBW9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1QQB8_G1QQB8_NOMLE_61853 and tr_A0A2K5MRB4_A0A2K5MRB4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QQB8_G1QQB8_NOMLE_61853 and tr_A0A2K6AWS4_A0A2K6AWS4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1PKV1_G1PKV1_MYOLU_59463 and tr_F1PLW8_F1PLW8_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G3QQZ6_G3QQZ6_GORGO_9595 and sp_Q8NCW0_KREM2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QU22_G3QU22_GORGO_9595 and tr_H2QWL4_H2QWL4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QU22_G3QU22_GORGO_9595 and sp_Q7Z407_CSMD3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QU22_G3QU22_GORGO_9595 and tr_A0A2R9C8Y9_A0A2R9C8Y9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_C3YZF7_C3YZF7_BRAFL_7739 and tr_C3YZG2_C3YZG2_BRAFL_7739 are exactly identical!
WARNING: Sequences tr_C3YZF7_C3YZF7_BRAFL_7739 and tr_C3YZH4_C3YZH4_BRAFL_7739 are exactly identical!
WARNING: Sequences tr_A0A2I3RRW9_A0A2I3RRW9_PANTR_9598 and sp_Q96PZ7_CSMD1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3RRW9_A0A2I3RRW9_PANTR_9598 and tr_A0A2R9BU77_A0A2R9BU77_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q2L0_H2Q2L0_PANTR_9598 and sp_Q14520_HABP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q2L0_H2Q2L0_PANTR_9598 and tr_A0A2R9AIP9_A0A2R9AIP9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QAE7_H2QAE7_PANTR_9598 and tr_A0A2R9CBG3_A0A2R9CBG3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QS39_H2QS39_PANTR_9598 and tr_A0A2R8ZG07_A0A2R8ZG07_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QW33_H2QW33_PANTR_9598 and sp_P00750_TPA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QW33_H2QW33_PANTR_9598 and tr_A0A2R8ZEK6_A0A2R8ZEK6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FTL3_F9FTL3_FUSOF_660025 and tr_W7N216_W7N216_GIBM7_334819 are exactly identical!
WARNING: Sequences tr_F9FTL3_F9FTL3_FUSOF_660025 and tr_A0A0D2Y9X4_A0A0D2Y9X4_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FTL3_F9FTL3_FUSOF_660025 and tr_N4ULB0_N4ULB0_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FTL3_F9FTL3_FUSOF_660025 and tr_X0C6J0_X0C6J0_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FTL3_F9FTL3_FUSOF_660025 and tr_A0A2H3TRZ5_A0A2H3TRZ5_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FTL3_F9FTL3_FUSOF_660025 and tr_A0A2K0W328_A0A2K0W328_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_F9FTL3_F9FTL3_FUSOF_660025 and tr_A0A365N1D6_A0A365N1D6_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_E9EWG5_E9EWG5_METRA_655844 and tr_A0A0D9NYG3_A0A0D9NYG3_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A3B5Q161_A0A3B5Q161_XIPMA_8083 and tr_A0A087Y8V4_A0A087Y8V4_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M4AJ56_M4AJ56_XIPMA_8083 and tr_A0A087YEY6_A0A087YEY6_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A1D5Q7P1_A0A1D5Q7P1_MACMU_9544 and tr_G7PBR4_G7PBR4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5Q7P1_A0A1D5Q7P1_MACMU_9544 and tr_A0A2K5L072_A0A2K5L072_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5Q7P1_A0A1D5Q7P1_MACMU_9544 and tr_A0A2K6B1X4_A0A2K6B1X4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R240_A0A1D5R240_MACMU_9544 and tr_A0A2K5M577_A0A2K5M577_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R240_A0A1D5R240_MACMU_9544 and tr_A0A2K6CPR3_A0A2K6CPR3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R240_A0A1D5R240_MACMU_9544 and tr_A0A2K5Z8Z5_A0A2K5Z8Z5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7DAC5_F7DAC5_MACMU_9544 and tr_A0A0D9QYJ4_A0A0D9QYJ4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7DAC5_F7DAC5_MACMU_9544 and tr_A0A2K6E5N3_A0A2K6E5N3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0ZC96_H0ZC96_TAEGU_59729 and tr_U3K0U1_U3K0U1_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0ZC96_H0ZC96_TAEGU_59729 and tr_A0A093Q3X8_A0A093Q3X8_9PASS_328815 are exactly identical!
WARNING: Sequences tr_H0ZC96_H0ZC96_TAEGU_59729 and tr_A0A0A0APX8_A0A0A0APX8_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_H0ZC96_H0ZC96_TAEGU_59729 and tr_A0A093FXX7_A0A093FXX7_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A287BEL3_A0A287BEL3_PIG_9823 and tr_A0A2Y9DE63_A0A2Y9DE63_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_F2SKF2_F2SKF2_TRIRC_559305 and tr_A0A178EQN4_A0A178EQN4_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_M3WPM7_M3WPM7_FELCA_9685 and tr_A0A2U3W590_A0A2U3W590_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3WPM7_M3WPM7_FELCA_9685 and tr_A0A2Y9KU42_A0A2Y9KU42_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_U3JGU1_U3JGU1_FICAL_59894 and tr_A0A091IDP3_A0A091IDP3_CALAN_9244 are exactly identical!
WARNING: Sequences tr_U3JHY3_U3JHY3_FICAL_59894 and tr_A0A1U7RHF5_A0A1U7RHF5_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A2I3MFA6_A0A2I3MFA6_PAPAN_9555 and tr_A0A2K5KH70_A0A2K5KH70_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MFA6_A0A2I3MFA6_PAPAN_9555 and tr_A0A2K6DWW2_A0A2K6DWW2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A094EBB7_A0A094EBB7_9PEZI_1420912 and tr_A0A1B8GFZ0_A0A1B8GFZ0_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A091ETA8_A0A091ETA8_CORBR_85066 and tr_A0A091JM18_A0A091JM18_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A091ETA8_A0A091ETA8_CORBR_85066 and tr_A0A093PLA6_A0A093PLA6_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091ETA8_A0A091ETA8_CORBR_85066 and tr_A0A091VLI7_A0A091VLI7_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091ETA8_A0A091ETA8_CORBR_85066 and tr_A0A091XKM2_A0A091XKM2_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091ETA8_A0A091ETA8_CORBR_85066 and tr_A0A099ZQ31_A0A099ZQ31_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A091ETA8_A0A091ETA8_CORBR_85066 and tr_A0A0A0AUT2_A0A0A0AUT2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091ETA8_A0A091ETA8_CORBR_85066 and tr_A0A093J7W7_A0A093J7W7_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A091ULZ2_A0A091ULZ2_NIPNI_128390 and tr_A0A091FM09_A0A091FM09_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091VK56_A0A091VK56_NIPNI_128390 and tr_A0A091WEY7_A0A091WEY7_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091VWV5_A0A091VWV5_NIPNI_128390 and tr_A0A087RJX1_A0A087RJX1_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091VWV5_A0A091VWV5_NIPNI_128390 and tr_A0A0A0AJU9_A0A0A0AJU9_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A1V8UZQ1_A0A1V8UZQ1_9PEZI_1974281 and tr_A0A1V8T5Q9_A0A1V8T5Q9_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A226NG13_A0A226NG13_CALSU_9009 and tr_A0A226PCQ8_A0A226PCQ8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PNQ6_A0A2D0PNQ6_ICTPU_7998 and tr_A0A2D0PRE9_A0A2D0PRE9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QJC9_A0A2D0QJC9_ICTPU_7998 and tr_A0A2D0QJP6_A0A2D0QJP6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QYN2_A0A2D0QYN2_ICTPU_7998 and tr_A0A2D0QYP0_A0A2D0QYP0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QYN2_A0A2D0QYN2_ICTPU_7998 and tr_A0A2D0QYX3_A0A2D0QYX3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QYN2_A0A2D0QYN2_ICTPU_7998 and tr_A0A2D0R0F9_A0A2D0R0F9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QYN2_A0A2D0QYN2_ICTPU_7998 and tr_A0A2D0R0G4_A0A2D0R0G4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QYN2_A0A2D0QYN2_ICTPU_7998 and tr_A0A2D0R153_A0A2D0R153_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5MX05_A0A2K5MX05_CERAT_9531 and tr_A0A2K5YQD1_A0A2K5YQD1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U4A732_A0A2U4A732_TURTR_9739 and tr_A0A2Y9MXE6_A0A2Y9MXE6_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4A732_A0A2U4A732_TURTR_9739 and tr_A0A2Y9S6R0_A0A2Y9S6R0_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4B2S5_A0A2U4B2S5_TURTR_9739 and tr_A0A2Y9LPM1_A0A2Y9LPM1_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4B2S5_A0A2U4B2S5_TURTR_9739 and tr_A0A2Y9T6G1_A0A2Y9T6G1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4B2S5_A0A2U4B2S5_TURTR_9739 and tr_A0A384ANF6_A0A384ANF6_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2U4CJJ1_A0A2U4CJJ1_TURTR_9739 and tr_A0A383Z7V3_A0A383Z7V3_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2Y9LMD2_A0A2Y9LMD2_DELLE_9749 and tr_A0A2Y9SLW7_A0A2Y9SLW7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9SUE2_A0A2Y9SUE2_PHYCD_9755 and tr_A0A384A2W2_A0A384A2W2_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 82

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/Q8NCW0/3_mltree/Q8NCW0.raxml.reduced.phy

Alignment comprises 1 partitions and 204 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 204 / 204
Gaps: 22.40 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/3_mltree/Q8NCW0.raxml.rba

Parallelization scheme autoconfig: 4 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 / 204 / 16320
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -349300.023552] Initial branch length optimization
[00:00:05 -291350.263455] Model parameter optimization (eps = 10.000000)
[00:00:50 -290864.185411] AUTODETECT spr round 1 (radius: 5)
[00:03:23 -202906.777415] AUTODETECT spr round 2 (radius: 10)
[00:06:07 -152417.245774] AUTODETECT spr round 3 (radius: 15)
[00:09:15 -124141.905056] AUTODETECT spr round 4 (radius: 20)
[00:12:37 -115426.125928] AUTODETECT spr round 5 (radius: 25)
[00:16:21 -110077.965846] SPR radius for FAST iterations: 25 (autodetect)
[00:16:21 -110077.965846] Model parameter optimization (eps = 3.000000)
[00:16:53 -109894.576997] FAST spr round 1 (radius: 25)
[00:20:28 -94855.903105] FAST spr round 2 (radius: 25)
[00:23:18 -94128.937647] FAST spr round 3 (radius: 25)
[00:25:29 -94064.838265] FAST spr round 4 (radius: 25)
[00:27:26 -94059.860966] FAST spr round 5 (radius: 25)
[00:29:19 -94043.938792] FAST spr round 6 (radius: 25)
[00:31:06 -94043.483514] FAST spr round 7 (radius: 25)
[00:32:52 -94043.482111] Model parameter optimization (eps = 1.000000)
[00:33:19 -93997.554516] SLOW spr round 1 (radius: 5)
[00:35:41 -93957.073224] SLOW spr round 2 (radius: 5)
[00:38:00 -93955.678104] SLOW spr round 3 (radius: 5)
[00:40:17 -93954.143452] SLOW spr round 4 (radius: 5)
[00:42:33 -93952.561809] SLOW spr round 5 (radius: 5)
[00:44:48 -93951.410900] SLOW spr round 6 (radius: 5)
[00:47:05 -93951.116892] SLOW spr round 7 (radius: 5)
[00:49:18 -93951.116698] SLOW spr round 8 (radius: 10)
[00:51:38 -93949.070843] SLOW spr round 9 (radius: 5)
[00:54:30 -93944.306501] SLOW spr round 10 (radius: 5)
[00:57:00 -93943.825554] SLOW spr round 11 (radius: 5)
[00:59:19 -93943.825354] SLOW spr round 12 (radius: 10)
[01:01:41 -93943.825334] SLOW spr round 13 (radius: 15)
[01:05:56 -93941.863337] SLOW spr round 14 (radius: 5)
[01:08:48 -93941.863323] SLOW spr round 15 (radius: 10)
[01:11:36 -93941.863319] SLOW spr round 16 (radius: 15)
[01:15:30 -93941.863315] SLOW spr round 17 (radius: 20)
[01:21:23 -93938.574376] SLOW spr round 18 (radius: 5)
[01:23:18] [worker #3] ML tree search #4, logLikelihood: -93908.072440
[01:24:21 -93937.575309] SLOW spr round 19 (radius: 5)
[01:25:33] [worker #2] ML tree search #3, logLikelihood: -93903.087825
[01:26:55 -93937.575293] SLOW spr round 20 (radius: 10)
[01:29:27 -93937.575289] SLOW spr round 21 (radius: 15)
[01:33:27 -93937.575285] SLOW spr round 22 (radius: 20)
[01:35:55] [worker #1] ML tree search #2, logLikelihood: -93974.364985
[01:39:15 -93937.575281] SLOW spr round 23 (radius: 25)
[01:46:45 -93937.575277] Model parameter optimization (eps = 0.100000)

[01:46:56] [worker #0] ML tree search #1, logLikelihood: -93937.277521

[01:46:56 -352991.693659] Initial branch length optimization
[01:47:00 -290512.183735] Model parameter optimization (eps = 10.000000)
[01:47:57 -290000.427787] AUTODETECT spr round 1 (radius: 5)
[01:50:32 -205381.708134] AUTODETECT spr round 2 (radius: 10)
[01:53:23 -152802.677555] AUTODETECT spr round 3 (radius: 15)
[01:56:38 -127458.354374] AUTODETECT spr round 4 (radius: 20)
[02:00:16 -115543.626816] AUTODETECT spr round 5 (radius: 25)
[02:04:08 -109635.559132] SPR radius for FAST iterations: 25 (autodetect)
[02:04:08 -109635.559132] Model parameter optimization (eps = 3.000000)
[02:04:38 -109501.205235] FAST spr round 1 (radius: 25)
[02:08:08 -94866.124712] FAST spr round 2 (radius: 25)
[02:10:53 -94123.175147] FAST spr round 3 (radius: 25)
[02:13:11 -94052.334989] FAST spr round 4 (radius: 25)
[02:15:14 -94023.906592] FAST spr round 5 (radius: 25)
[02:17:07 -94020.711821] FAST spr round 6 (radius: 25)
[02:18:55 -94020.672991] Model parameter optimization (eps = 1.000000)
[02:19:11 -94017.110309] SLOW spr round 1 (radius: 5)
[02:21:32 -93979.155497] SLOW spr round 2 (radius: 5)
[02:23:50 -93974.312673] SLOW spr round 3 (radius: 5)
[02:26:07 -93974.304977] SLOW spr round 4 (radius: 10)
[02:28:26 -93973.738501] SLOW spr round 5 (radius: 5)
[02:31:13 -93973.737483] SLOW spr round 6 (radius: 10)
[02:33:56 -93973.737275] SLOW spr round 7 (radius: 15)
[02:37:55 -93971.294063] SLOW spr round 8 (radius: 5)
[02:40:49 -93970.652719] SLOW spr round 9 (radius: 5)
[02:43:22 -93970.651251] SLOW spr round 10 (radius: 10)
[02:45:53 -93970.651064] SLOW spr round 11 (radius: 15)
[02:49:56 -93970.651030] SLOW spr round 12 (radius: 20)
[02:51:52] [worker #1] ML tree search #6, logLikelihood: -93958.506592
[02:52:53] [worker #3] ML tree search #8, logLikelihood: -93923.747060
[02:56:03 -93970.651020] SLOW spr round 13 (radius: 25)
[03:04:08 -93970.651016] Model parameter optimization (eps = 0.100000)

[03:04:17] [worker #0] ML tree search #5, logLikelihood: -93970.564663

[03:04:17 -350901.012198] Initial branch length optimization
[03:04:21 -289071.341303] Model parameter optimization (eps = 10.000000)
[03:05:20 -288467.922572] AUTODETECT spr round 1 (radius: 5)
[03:07:53 -202124.888038] AUTODETECT spr round 2 (radius: 10)
[03:10:40 -157318.891962] AUTODETECT spr round 3 (radius: 15)
[03:14:06 -127033.090731] AUTODETECT spr round 4 (radius: 20)
[03:17:41 -114788.484253] AUTODETECT spr round 5 (radius: 25)
[03:21:28 -109783.296306] SPR radius for FAST iterations: 25 (autodetect)
[03:21:28 -109783.296306] Model parameter optimization (eps = 3.000000)
[03:22:00 -109595.089657] FAST spr round 1 (radius: 25)
[03:25:17 -94893.958377] FAST spr round 2 (radius: 25)
[03:27:50 -94075.388396] FAST spr round 3 (radius: 25)
[03:30:03 -93965.826839] FAST spr round 4 (radius: 25)
[03:32:00 -93951.715922] FAST spr round 5 (radius: 25)
[03:33:50 -93943.522547] FAST spr round 6 (radius: 25)
[03:35:36 -93942.653790] FAST spr round 7 (radius: 25)
[03:37:18 -93942.653596] Model parameter optimization (eps = 1.000000)
[03:37:48 -93923.722234] SLOW spr round 1 (radius: 5)
[03:40:03 -93901.716300] SLOW spr round 2 (radius: 5)
[03:42:20 -93898.343397] SLOW spr round 3 (radius: 5)
[03:44:34 -93898.323615] SLOW spr round 4 (radius: 10)
[03:46:54 -93897.074370] SLOW spr round 5 (radius: 5)
[03:49:41 -93897.071201] SLOW spr round 6 (radius: 10)
[03:52:25 -93897.069314] SLOW spr round 7 (radius: 15)
[03:53:49] [worker #2] ML tree search #7, logLikelihood: -93877.674533
[03:56:29 -93897.069197] SLOW spr round 8 (radius: 20)
[04:02:40 -93897.069119] SLOW spr round 9 (radius: 25)
[04:10:27 -93897.069043] Model parameter optimization (eps = 0.100000)

[04:10:53] [worker #0] ML tree search #9, logLikelihood: -93895.765803

[04:10:53 -350045.790536] Initial branch length optimization
[04:10:59 -290750.606424] Model parameter optimization (eps = 10.000000)
[04:11:55 -290207.760488] AUTODETECT spr round 1 (radius: 5)
[04:14:31 -200672.649257] AUTODETECT spr round 2 (radius: 10)
[04:17:12 -149037.874153] AUTODETECT spr round 3 (radius: 15)
[04:20:21 -122527.811973] AUTODETECT spr round 4 (radius: 20)
[04:24:12 -111340.355862] AUTODETECT spr round 5 (radius: 25)
[04:27:14] [worker #1] ML tree search #10, logLikelihood: -93898.844499
[04:28:28 -108948.024503] SPR radius for FAST iterations: 25 (autodetect)
[04:28:28 -108948.024503] Model parameter optimization (eps = 3.000000)
[04:28:56 -108809.037093] FAST spr round 1 (radius: 25)
[04:30:12] [worker #3] ML tree search #12, logLikelihood: -93913.357609
[04:32:20 -95028.697231] FAST spr round 2 (radius: 25)
[04:34:51 -94104.403694] FAST spr round 3 (radius: 25)
[04:37:03 -94018.271774] FAST spr round 4 (radius: 25)
[04:39:01 -94011.501412] FAST spr round 5 (radius: 25)
[04:40:51 -94011.497595] Model parameter optimization (eps = 1.000000)
[04:41:09 -94005.420907] SLOW spr round 1 (radius: 5)
[04:43:30 -93978.457062] SLOW spr round 2 (radius: 5)
[04:45:49 -93974.540654] SLOW spr round 3 (radius: 5)
[04:48:06 -93974.533554] SLOW spr round 4 (radius: 10)
[04:50:26 -93970.618776] SLOW spr round 5 (radius: 5)
[04:53:17 -93967.429311] SLOW spr round 6 (radius: 5)
[04:55:45 -93967.315800] SLOW spr round 7 (radius: 5)
[04:58:03 -93967.314723] SLOW spr round 8 (radius: 10)
[05:00:23 -93967.314703] SLOW spr round 9 (radius: 15)
[05:00:27] [worker #2] ML tree search #11, logLikelihood: -93958.931155
[05:04:37 -93964.906036] SLOW spr round 10 (radius: 5)
[05:07:29 -93964.905922] SLOW spr round 11 (radius: 10)
[05:10:17 -93963.447854] SLOW spr round 12 (radius: 5)
[05:12:58 -93963.447494] SLOW spr round 13 (radius: 10)
[05:15:34 -93963.447482] SLOW spr round 14 (radius: 15)
[05:19:30 -93963.447474] SLOW spr round 15 (radius: 20)
[05:25:33 -93963.447467] SLOW spr round 16 (radius: 25)
[05:33:13 -93963.447462] Model parameter optimization (eps = 0.100000)

[05:33:20] [worker #0] ML tree search #13, logLikelihood: -93963.421006

[05:33:20 -353174.591526] Initial branch length optimization
[05:33:25 -291806.568971] Model parameter optimization (eps = 10.000000)
[05:34:03 -291220.375479] AUTODETECT spr round 1 (radius: 5)
[05:36:37 -201209.905418] AUTODETECT spr round 2 (radius: 10)
[05:37:53] [worker #1] ML tree search #14, logLikelihood: -93955.494001
[05:39:23 -152776.157011] AUTODETECT spr round 3 (radius: 15)
[05:42:43 -121936.897522] AUTODETECT spr round 4 (radius: 20)
[05:46:46 -111166.176807] AUTODETECT spr round 5 (radius: 25)
[05:51:05 -108505.143757] SPR radius for FAST iterations: 25 (autodetect)
[05:51:05 -108505.143757] Model parameter optimization (eps = 3.000000)
[05:51:36 -108371.691185] FAST spr round 1 (radius: 25)
[05:54:56 -94631.163468] FAST spr round 2 (radius: 25)
[05:56:52] [worker #3] ML tree search #16, logLikelihood: -93890.261126
[05:57:26 -94060.813757] FAST spr round 3 (radius: 25)
[05:59:39 -94025.082682] FAST spr round 4 (radius: 25)
[06:01:39 -94017.530060] FAST spr round 5 (radius: 25)
[06:03:32 -94013.245142] FAST spr round 6 (radius: 25)
[06:05:19 -94007.414111] FAST spr round 7 (radius: 25)
[06:07:05 -94007.412705] Model parameter optimization (eps = 1.000000)
[06:07:21 -94000.707352] SLOW spr round 1 (radius: 5)
[06:09:41 -93971.921732] SLOW spr round 2 (radius: 5)
[06:11:58 -93968.236054] SLOW spr round 3 (radius: 5)
[06:14:14 -93967.701303] SLOW spr round 4 (radius: 5)
[06:16:27 -93967.701186] SLOW spr round 5 (radius: 10)
[06:18:43 -93966.954492] SLOW spr round 6 (radius: 5)
[06:21:28 -93966.954074] SLOW spr round 7 (radius: 10)
[06:24:07 -93966.954069] SLOW spr round 8 (radius: 15)
[06:28:03 -93964.325495] SLOW spr round 9 (radius: 5)
[06:30:55 -93964.324996] SLOW spr round 10 (radius: 10)
[06:33:46 -93961.959592] SLOW spr round 11 (radius: 5)
[06:36:25 -93961.590954] SLOW spr round 12 (radius: 5)
[06:38:49 -93961.590249] SLOW spr round 13 (radius: 10)
[06:41:14 -93959.139699] SLOW spr round 14 (radius: 5)
[06:43:57 -93959.004274] SLOW spr round 15 (radius: 5)
[06:46:22 -93959.003516] SLOW spr round 16 (radius: 10)
[06:48:46 -93959.003494] SLOW spr round 17 (radius: 15)
[06:49:53] [worker #2] ML tree search #15, logLikelihood: -93919.128740
[06:52:50 -93959.003492] SLOW spr round 18 (radius: 20)
[06:58:41 -93959.003492] SLOW spr round 19 (radius: 25)
[07:06:01 -93959.003492] Model parameter optimization (eps = 0.100000)

[07:06:14] [worker #0] ML tree search #17, logLikelihood: -93958.694569

[07:19:51] [worker #1] ML tree search #18, logLikelihood: -93914.826410
[08:01:15] [worker #3] ML tree search #20, logLikelihood: -93899.516495
[08:16:11] [worker #2] ML tree search #19, logLikelihood: -93962.861860

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.143647,0.264975) (0.071036,2.015812) (0.522237,0.882504) (0.263080,1.360292) 
   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: -93877.674533

AIC score: 191765.349065 / AICc score: 8235825.349065 / BIC score: 198418.179653
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=204).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 1 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/3_mltree/Q8NCW0.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/3_mltree/Q8NCW0.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/3_mltree/Q8NCW0.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/3_mltree/Q8NCW0.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NCW0/3_mltree/Q8NCW0.raxml.log

Analysis started: 03-Jul-2021 23:38:10 / finished: 04-Jul-2021 07:54:22

Elapsed time: 29772.082 seconds

Consumed energy: 1885.160 Wh (= 9 km in an electric car, or 47 km with an e-scooter!)