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 06-Jul-2021 17:09:52 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86SU0/2_msa/Q86SU0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86SU0/3_mltree/Q86SU0 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86SU0/2_msa/Q86SU0_trimmed_msa.fasta
[00:00:00] Loaded alignment with 247 taxa and 124 sites

WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2I3HDE8_A0A2I3HDE8_NOMLE_61853 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_G3QYQ4_G3QYQ4_GORGO_9595 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_H2N4W1_H2N4W1_PONAB_9601 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2J8LM05_A0A2J8LM05_PANTR_9598 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and sp_Q71H61_ILDR2_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A1D5QTG4_A0A1D5QTG4_MACMU_9544 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_G7NU38_G7NU38_MACFA_9541 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A096NPM9_A0A096NPM9_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A0D9REH8_A0A0D9REH8_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2K5LPY7_A0A2K5LPY7_CERAT_9531 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2K6DRE5_A0A2K6DRE5_MACNE_9545 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2K6A5N9_A0A2K6A5N9_MANLE_9568 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2R9BEQ8_A0A2R9BEQ8_PANPA_9597 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2Y9M240_A0A2Y9M240_DELLE_9749 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A2Y9S1F5_A0A2Y9S1F5_PHYCD_9755 are exactly identical!
WARNING: Sequences sp_B5TVM2_ILDR2_MOUSE_10090 and tr_A0A383ZC15_A0A383ZC15_BALAS_310752 are exactly identical!
WARNING: Sequences sp_Q8CBR1_ILDR1_MOUSE_10090 and tr_E9PSR6_E9PSR6_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3YW67_M3YW67_MUSPF_9669 and tr_A0A2Y9JTQ2_A0A2Y9JTQ2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1QHD1_G1QHD1_NOMLE_61853 and tr_G3QKD5_G3QKD5_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QHD1_G1QHD1_NOMLE_61853 and tr_A0A2J8W1Y7_A0A2J8W1Y7_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1QHD1_G1QHD1_NOMLE_61853 and sp_Q5R8C7_ILDR1_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1QHD1_G1QHD1_NOMLE_61853 and tr_A0A2J8M3R5_A0A2J8M3R5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QHD1_G1QHD1_NOMLE_61853 and sp_Q86SU0_ILDR1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QHD1_G1QHD1_NOMLE_61853 and tr_A0A2R9CLH7_A0A2R9CLH7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RQZ9_G3RQZ9_GORGO_9595 and tr_H2NYF1_H2NYF1_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RQZ9_G3RQZ9_GORGO_9595 and tr_A0A2J8QH70_A0A2J8QH70_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RQZ9_G3RQZ9_GORGO_9595 and sp_Q86X29_LSR_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RQZ9_G3RQZ9_GORGO_9595 and tr_A0A0A0MWW0_A0A0A0MWW0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3RQZ9_G3RQZ9_GORGO_9595 and tr_A0A2R8ZUV9_A0A2R8ZUV9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1NNP5_G1NNP5_MELGA_9103 and tr_A0A226MX04_A0A226MX04_CALSU_9009 are exactly identical!
WARNING: Sequences tr_G1NNP5_G1NNP5_MELGA_9103 and tr_A0A226P970_A0A226P970_COLVI_9014 are exactly identical!
WARNING: Sequences tr_G1T1H5_G1T1H5_RABIT_9986 and tr_M3WA36_M3WA36_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1T1H5_G1T1H5_RABIT_9986 and tr_A0A2U4AB10_A0A2U4AB10_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G1T1H5_G1T1H5_RABIT_9986 and tr_A0A2Y9F032_A0A2Y9F032_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G1T1H5_G1T1H5_RABIT_9986 and tr_A0A383ZKQ2_A0A383ZKQ2_BALAS_310752 are exactly identical!
WARNING: Sequences tr_U3KM95_U3KM95_RABIT_9986 and tr_G3SWV4_G3SWV4_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_U3KM95_U3KM95_RABIT_9986 and tr_A0A2Y9E453_A0A2Y9E453_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_F1PBS5_F1PBS5_CANLF_9615 and tr_G1M6Q3_G1M6Q3_AILME_9646 are exactly identical!
WARNING: Sequences tr_F1PBS5_F1PBS5_CANLF_9615 and tr_A0A2U3VBV5_A0A2U3VBV5_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F1PBS5_F1PBS5_CANLF_9615 and tr_A0A2U3XL00_A0A2U3XL00_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_W5QFT9_W5QFT9_SHEEP_9940 and tr_I3LBB5_I3LBB5_PIG_9823 are exactly identical!
WARNING: Sequences tr_W5QFT9_W5QFT9_SHEEP_9940 and tr_A0A1S3WT44_A0A1S3WT44_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_H0WH79_H0WH79_OTOGA_30611 and tr_A0A096N9E2_A0A096N9E2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H0WH79_H0WH79_OTOGA_30611 and tr_A0A0D9R4R1_A0A0D9R4R1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A286XX14_A0A286XX14_CAVPO_10141 and tr_A0A1S3FE44_A0A1S3FE44_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_F6RE05_F6RE05_MACMU_9544 and tr_F7GPP4_F7GPP4_CALJA_9483 are exactly identical!
WARNING: Sequences tr_F6RE05_F6RE05_MACMU_9544 and tr_G7NXR3_G7NXR3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6RE05_F6RE05_MACMU_9544 and tr_A0A2K6BVV9_A0A2K6BVV9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6RE05_F6RE05_MACMU_9544 and tr_A0A2K5ZPZ8_A0A2K5ZPZ8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0ZTG6_H0ZTG6_TAEGU_59729 and tr_U3JFQ0_U3JFQ0_FICAL_59894 are exactly identical!
WARNING: Sequences tr_G1KZG9_G1KZG9_AILME_9646 and tr_A0A384CMK4_A0A384CMK4_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A151M7B0_A0A151M7B0_ALLMI_8496 and tr_A0A1U7STR6_A0A1U7STR6_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A1S3MUR5_A0A1S3MUR5_SALSA_8030 and tr_A0A1S3QFC9_A0A1S3QFC9_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3MUR5_A0A1S3MUR5_SALSA_8030 and tr_A0A1S3QPP1_A0A1S3QPP1_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3PQA4_A0A1S3PQA4_SALSA_8030 and tr_A0A1S3QP97_A0A1S3QP97_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3RW92_A0A1S3RW92_SALSA_8030 and tr_B5X416_B5X416_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A226N4N0_A0A226N4N0_CALSU_9009 and tr_A0A226PVB6_A0A226PVB6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0Q5S4_A0A2D0Q5S4_ICTPU_7998 and tr_A0A2D0Q8H0_A0A2D0Q8H0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5LUE8_A0A2K5LUE8_CERAT_9531 and tr_A0A2K6CTH0_A0A2K6CTH0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5LUE8_A0A2K5LUE8_CERAT_9531 and tr_A0A2K5YPI9_A0A2K5YPI9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U3WHY9_A0A2U3WHY9_ODORO_9708 and tr_A0A2U3Z9D7_A0A2U3Z9D7_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 61

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/Q86SU0/3_mltree/Q86SU0.raxml.reduced.phy

Alignment comprises 1 partitions and 124 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 124 / 124
Gaps: 1.48 %
Invariant sites: 6.45 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86SU0/3_mltree/Q86SU0.raxml.rba

Parallelization scheme autoconfig: 2 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 247 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 124 / 9920
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -44490.765115] Initial branch length optimization
[00:00:00 -35484.334930] Model parameter optimization (eps = 10.000000)
[00:00:07 -35448.233005] AUTODETECT spr round 1 (radius: 5)
[00:00:14 -16619.499151] AUTODETECT spr round 2 (radius: 10)
[00:00:24 -12523.728330] AUTODETECT spr round 3 (radius: 15)
[00:00:35 -11494.361748] AUTODETECT spr round 4 (radius: 20)
[00:00:46 -10163.272315] AUTODETECT spr round 5 (radius: 25)
[00:00:59 -10157.370474] SPR radius for FAST iterations: 25 (autodetect)
[00:00:59 -10157.370474] Model parameter optimization (eps = 3.000000)
[00:01:04 -10142.840484] FAST spr round 1 (radius: 25)
[00:01:13 -9162.881520] FAST spr round 2 (radius: 25)
[00:01:21 -8951.271156] FAST spr round 3 (radius: 25)
[00:01:28 -8926.529088] FAST spr round 4 (radius: 25)
[00:01:34 -8924.796781] FAST spr round 5 (radius: 25)
[00:01:39 -8924.796536] Model parameter optimization (eps = 1.000000)
[00:01:46 -8922.484464] SLOW spr round 1 (radius: 5)
[00:01:56 -8920.921293] SLOW spr round 2 (radius: 5)
[00:02:06 -8920.419922] SLOW spr round 3 (radius: 5)
[00:02:15 -8920.418358] SLOW spr round 4 (radius: 10)
[00:02:26 -8918.818133] SLOW spr round 5 (radius: 5)
[00:02:40 -8917.853152] SLOW spr round 6 (radius: 5)
[00:02:52 -8917.853115] SLOW spr round 7 (radius: 10)
[00:03:02 -8917.853113] SLOW spr round 8 (radius: 15)
[00:03:16 -8917.853113] SLOW spr round 9 (radius: 20)
[00:03:29] [worker #1] ML tree search #2, logLikelihood: -8920.713561
[00:03:30 -8917.853113] SLOW spr round 10 (radius: 25)
[00:03:43 -8917.853113] Model parameter optimization (eps = 0.100000)

[00:03:53] [worker #0] ML tree search #1, logLikelihood: -8917.325284

[00:03:53 -43260.404024] Initial branch length optimization
[00:03:53 -34285.491315] Model parameter optimization (eps = 10.000000)
[00:03:59 -34251.466629] AUTODETECT spr round 1 (radius: 5)
[00:04:07 -17095.545457] AUTODETECT spr round 2 (radius: 10)
[00:04:17 -12180.135772] AUTODETECT spr round 3 (radius: 15)
[00:04:27 -10424.058552] AUTODETECT spr round 4 (radius: 20)
[00:04:40 -10222.689248] AUTODETECT spr round 5 (radius: 25)
[00:04:52 -10066.895294] SPR radius for FAST iterations: 25 (autodetect)
[00:04:52 -10066.895294] Model parameter optimization (eps = 3.000000)
[00:04:56 -10046.861944] FAST spr round 1 (radius: 25)
[00:05:04 -9051.034105] FAST spr round 2 (radius: 25)
[00:05:11 -8928.511578] FAST spr round 3 (radius: 25)
[00:05:18 -8925.988032] FAST spr round 4 (radius: 25)
[00:05:23 -8925.987965] Model parameter optimization (eps = 1.000000)
[00:05:29 -8923.548759] SLOW spr round 1 (radius: 5)
[00:05:39 -8917.409186] SLOW spr round 2 (radius: 5)
[00:05:49 -8917.408825] SLOW spr round 3 (radius: 10)
[00:06:00 -8917.408814] SLOW spr round 4 (radius: 15)
[00:06:15 -8917.408814] SLOW spr round 5 (radius: 20)
[00:06:30 -8917.050152] SLOW spr round 6 (radius: 5)
[00:06:47 -8917.050125] SLOW spr round 7 (radius: 10)
[00:07:02 -8917.050121] SLOW spr round 8 (radius: 15)
[00:07:15 -8917.050121] SLOW spr round 9 (radius: 20)
[00:07:18] [worker #1] ML tree search #4, logLikelihood: -8911.021394
[00:07:31 -8917.050121] SLOW spr round 10 (radius: 25)
[00:07:47 -8917.050121] Model parameter optimization (eps = 0.100000)

[00:07:50] [worker #0] ML tree search #3, logLikelihood: -8916.874284

[00:07:50 -43243.993602] Initial branch length optimization
[00:07:50 -34662.891533] Model parameter optimization (eps = 10.000000)
[00:07:56 -34623.265221] AUTODETECT spr round 1 (radius: 5)
[00:08:04 -14837.021110] AUTODETECT spr round 2 (radius: 10)
[00:08:14 -11492.604080] AUTODETECT spr round 3 (radius: 15)
[00:08:26 -9869.315780] AUTODETECT spr round 4 (radius: 20)
[00:08:39 -9708.924423] AUTODETECT spr round 5 (radius: 25)
[00:08:53 -9708.923116] SPR radius for FAST iterations: 20 (autodetect)
[00:08:53 -9708.923116] Model parameter optimization (eps = 3.000000)
[00:09:00 -9691.483872] FAST spr round 1 (radius: 20)
[00:09:10 -8967.030682] FAST spr round 2 (radius: 20)
[00:09:18 -8926.195780] FAST spr round 3 (radius: 20)
[00:09:25 -8920.615031] FAST spr round 4 (radius: 20)
[00:09:32 -8920.614575] Model parameter optimization (eps = 1.000000)
[00:09:35 -8918.444052] SLOW spr round 1 (radius: 5)
[00:09:46 -8914.629657] SLOW spr round 2 (radius: 5)
[00:09:57 -8914.629203] SLOW spr round 3 (radius: 10)
[00:10:08 -8914.629199] SLOW spr round 4 (radius: 15)
[00:10:23 -8914.629197] SLOW spr round 5 (radius: 20)
[00:10:39 -8914.629197] SLOW spr round 6 (radius: 25)
[00:10:53 -8914.629197] Model parameter optimization (eps = 0.100000)

[00:10:54] [worker #0] ML tree search #5, logLikelihood: -8914.583152

[00:10:54 -42449.923299] Initial branch length optimization
[00:10:54 -33224.064571] Model parameter optimization (eps = 10.000000)
[00:11:00 -33197.121121] AUTODETECT spr round 1 (radius: 5)
[00:11:08 -17809.683840] AUTODETECT spr round 2 (radius: 10)
[00:11:18 -12080.325932] AUTODETECT spr round 3 (radius: 15)
[00:11:31 -10060.116764] AUTODETECT spr round 4 (radius: 20)
[00:11:45 -9997.411828] AUTODETECT spr round 5 (radius: 25)
[00:12:00 -9997.407602] SPR radius for FAST iterations: 20 (autodetect)
[00:12:00 -9997.407602] Model parameter optimization (eps = 3.000000)
[00:12:10 -9977.838380] FAST spr round 1 (radius: 20)
[00:12:19 -9098.952522] FAST spr round 2 (radius: 20)
[00:12:28 -8981.396492] FAST spr round 3 (radius: 20)
[00:12:34] [worker #1] ML tree search #6, logLikelihood: -8917.569658
[00:12:36 -8952.881434] FAST spr round 4 (radius: 20)
[00:12:43 -8949.742452] FAST spr round 5 (radius: 20)
[00:12:50 -8949.742338] Model parameter optimization (eps = 1.000000)
[00:12:54 -8948.955294] SLOW spr round 1 (radius: 5)
[00:13:06 -8942.591928] SLOW spr round 2 (radius: 5)
[00:13:18 -8942.459743] SLOW spr round 3 (radius: 5)
[00:13:29 -8942.459648] SLOW spr round 4 (radius: 10)
[00:13:40 -8942.459645] SLOW spr round 5 (radius: 15)
[00:13:54 -8941.589750] SLOW spr round 6 (radius: 5)
[00:14:10 -8936.385257] SLOW spr round 7 (radius: 5)
[00:14:25 -8936.272082] SLOW spr round 8 (radius: 5)
[00:14:37 -8936.271877] SLOW spr round 9 (radius: 10)
[00:14:48 -8936.271874] SLOW spr round 10 (radius: 15)
[00:15:03 -8928.374373] SLOW spr round 11 (radius: 5)
[00:15:20 -8927.915962] SLOW spr round 12 (radius: 5)
[00:15:33 -8927.915886] SLOW spr round 13 (radius: 10)
[00:15:39] [worker #1] ML tree search #8, logLikelihood: -8923.735800
[00:15:45 -8926.637212] SLOW spr round 14 (radius: 5)
[00:16:00 -8925.717942] SLOW spr round 15 (radius: 5)
[00:16:13 -8925.546514] SLOW spr round 16 (radius: 5)
[00:16:24 -8925.546356] SLOW spr round 17 (radius: 10)
[00:16:35 -8925.546356] SLOW spr round 18 (radius: 15)
[00:16:50 -8925.546356] SLOW spr round 19 (radius: 20)
[00:17:04 -8925.546356] SLOW spr round 20 (radius: 25)
[00:17:18 -8925.546356] Model parameter optimization (eps = 0.100000)

[00:17:20] [worker #0] ML tree search #7, logLikelihood: -8925.497455

[00:17:20 -44320.363518] Initial branch length optimization
[00:17:20 -35858.125853] Model parameter optimization (eps = 10.000000)
[00:17:27 -35801.971548] AUTODETECT spr round 1 (radius: 5)
[00:17:35 -16774.957036] AUTODETECT spr round 2 (radius: 10)
[00:17:45 -12149.252531] AUTODETECT spr round 3 (radius: 15)
[00:17:57 -10447.335025] AUTODETECT spr round 4 (radius: 20)
[00:18:09 -10040.956416] AUTODETECT spr round 5 (radius: 25)
[00:18:22 -9899.677150] SPR radius for FAST iterations: 25 (autodetect)
[00:18:22 -9899.677150] Model parameter optimization (eps = 3.000000)
[00:18:26 -9879.437134] FAST spr round 1 (radius: 25)
[00:18:35 -8969.455001] FAST spr round 2 (radius: 25)
[00:18:43 -8933.787667] FAST spr round 3 (radius: 25)
[00:18:50 -8929.785013] FAST spr round 4 (radius: 25)
[00:18:56 -8929.784818] Model parameter optimization (eps = 1.000000)
[00:19:02 -8926.267885] SLOW spr round 1 (radius: 5)
[00:19:13 -8925.681414] SLOW spr round 2 (radius: 5)
[00:19:23 -8925.681390] SLOW spr round 3 (radius: 10)
[00:19:33 -8925.681389] SLOW spr round 4 (radius: 15)
[00:19:38] [worker #1] ML tree search #10, logLikelihood: -8915.304968
[00:19:48 -8925.681389] SLOW spr round 5 (radius: 20)
[00:20:03 -8925.681389] SLOW spr round 6 (radius: 25)
[00:20:17 -8925.681389] Model parameter optimization (eps = 0.100000)

[00:20:18] [worker #0] ML tree search #9, logLikelihood: -8925.678392

[00:20:18 -44251.361607] Initial branch length optimization
[00:20:18 -34767.864438] Model parameter optimization (eps = 10.000000)
[00:20:24 -34693.342051] AUTODETECT spr round 1 (radius: 5)
[00:20:32 -17328.950378] AUTODETECT spr round 2 (radius: 10)
[00:20:43 -12342.380010] AUTODETECT spr round 3 (radius: 15)
[00:20:55 -11064.313747] AUTODETECT spr round 4 (radius: 20)
[00:21:09 -10103.988110] AUTODETECT spr round 5 (radius: 25)
[00:21:23 -9932.093754] SPR radius for FAST iterations: 25 (autodetect)
[00:21:23 -9932.093754] Model parameter optimization (eps = 3.000000)
[00:21:28 -9906.245636] FAST spr round 1 (radius: 25)
[00:21:39 -8973.739348] FAST spr round 2 (radius: 25)
[00:21:47 -8939.411247] FAST spr round 3 (radius: 25)
[00:21:54 -8939.400229] Model parameter optimization (eps = 1.000000)
[00:21:56 -8938.486637] SLOW spr round 1 (radius: 5)
[00:22:07 -8932.642803] SLOW spr round 2 (radius: 5)
[00:22:18 -8931.315067] SLOW spr round 3 (radius: 5)
[00:22:28 -8931.314274] SLOW spr round 4 (radius: 10)
[00:22:40 -8919.450905] SLOW spr round 5 (radius: 5)
[00:22:55 -8919.450324] SLOW spr round 6 (radius: 10)
[00:23:00] [worker #1] ML tree search #12, logLikelihood: -8920.036227
[00:23:08 -8917.999473] SLOW spr round 7 (radius: 5)
[00:23:23 -8917.965366] SLOW spr round 8 (radius: 10)
[00:23:36 -8917.963589] SLOW spr round 9 (radius: 15)
[00:23:50 -8917.963583] SLOW spr round 10 (radius: 20)
[00:24:05 -8917.963583] SLOW spr round 11 (radius: 25)
[00:24:21 -8917.963583] Model parameter optimization (eps = 0.100000)

[00:24:22] [worker #0] ML tree search #11, logLikelihood: -8917.852813

[00:24:22 -43498.879196] Initial branch length optimization
[00:24:23 -34650.508911] Model parameter optimization (eps = 10.000000)
[00:24:29 -34571.246059] AUTODETECT spr round 1 (radius: 5)
[00:24:37 -17296.177408] AUTODETECT spr round 2 (radius: 10)
[00:24:47 -11725.909721] AUTODETECT spr round 3 (radius: 15)
[00:25:00 -10082.458945] AUTODETECT spr round 4 (radius: 20)
[00:25:15 -10015.740806] AUTODETECT spr round 5 (radius: 25)
[00:25:33 -9960.156862] SPR radius for FAST iterations: 25 (autodetect)
[00:25:33 -9960.156862] Model parameter optimization (eps = 3.000000)
[00:25:43 -9912.872007] FAST spr round 1 (radius: 25)
[00:25:52 -9001.216316] FAST spr round 2 (radius: 25)
[00:26:00 -8948.670931] FAST spr round 3 (radius: 25)
[00:26:08 -8935.567435] FAST spr round 4 (radius: 25)
[00:26:15 -8934.816900] FAST spr round 5 (radius: 25)
[00:26:21 -8934.816840] Model parameter optimization (eps = 1.000000)
[00:26:26 -8931.020813] SLOW spr round 1 (radius: 5)
[00:26:37 -8929.019477] SLOW spr round 2 (radius: 5)
[00:26:48 -8929.019180] SLOW spr round 3 (radius: 10)
[00:26:56] [worker #1] ML tree search #14, logLikelihood: -8921.289186
[00:27:00 -8927.803377] SLOW spr round 4 (radius: 5)
[00:27:15 -8927.803272] SLOW spr round 5 (radius: 10)
[00:27:28 -8927.803270] SLOW spr round 6 (radius: 15)
[00:27:42 -8927.803250] SLOW spr round 7 (radius: 20)
[00:27:57 -8922.643694] SLOW spr round 8 (radius: 5)
[00:28:16 -8916.861992] SLOW spr round 9 (radius: 5)
[00:28:31 -8916.861954] SLOW spr round 10 (radius: 10)
[00:28:43 -8916.861950] SLOW spr round 11 (radius: 15)
[00:28:57 -8916.861949] SLOW spr round 12 (radius: 20)
[00:29:11 -8916.861949] SLOW spr round 13 (radius: 25)
[00:29:27 -8916.861949] Model parameter optimization (eps = 0.100000)

[00:29:28] [worker #0] ML tree search #13, logLikelihood: -8916.819085

[00:29:28 -44785.869351] Initial branch length optimization
[00:29:29 -35326.485456] Model parameter optimization (eps = 10.000000)
[00:29:35 -35288.120770] AUTODETECT spr round 1 (radius: 5)
[00:29:44 -17672.148193] AUTODETECT spr round 2 (radius: 10)
[00:29:54 -12618.043651] AUTODETECT spr round 3 (radius: 15)
[00:30:06 -10652.136057] AUTODETECT spr round 4 (radius: 20)
[00:30:19 -10170.505866] AUTODETECT spr round 5 (radius: 25)
[00:30:31 -10169.944456] SPR radius for FAST iterations: 25 (autodetect)
[00:30:31 -10169.944456] Model parameter optimization (eps = 3.000000)
[00:30:35 -10149.104943] FAST spr round 1 (radius: 25)
[00:30:44 -8984.272196] FAST spr round 2 (radius: 25)
[00:30:47] [worker #1] ML tree search #16, logLikelihood: -8918.785720
[00:30:52 -8926.199309] FAST spr round 3 (radius: 25)
[00:30:58 -8920.784580] FAST spr round 4 (radius: 25)
[00:31:05 -8920.298161] FAST spr round 5 (radius: 25)
[00:31:11 -8920.298160] Model parameter optimization (eps = 1.000000)
[00:31:14 -8919.369526] SLOW spr round 1 (radius: 5)
[00:31:25 -8916.309655] SLOW spr round 2 (radius: 5)
[00:31:37 -8916.117293] SLOW spr round 3 (radius: 5)
[00:31:48 -8916.115128] SLOW spr round 4 (radius: 10)
[00:31:59 -8916.114727] SLOW spr round 5 (radius: 15)
[00:32:14 -8916.114675] SLOW spr round 6 (radius: 20)
[00:32:30 -8916.114667] SLOW spr round 7 (radius: 25)
[00:32:46 -8916.114666] Model parameter optimization (eps = 0.100000)

[00:32:48] [worker #0] ML tree search #15, logLikelihood: -8916.077180

[00:32:48 -43341.903060] Initial branch length optimization
[00:32:49 -34771.880844] Model parameter optimization (eps = 10.000000)
[00:32:54 -34725.590191] AUTODETECT spr round 1 (radius: 5)
[00:33:02 -16424.778020] AUTODETECT spr round 2 (radius: 10)
[00:33:12 -12431.561119] AUTODETECT spr round 3 (radius: 15)
[00:33:23 -10577.189115] AUTODETECT spr round 4 (radius: 20)
[00:33:37 -10298.935711] AUTODETECT spr round 5 (radius: 25)
[00:33:49 -10298.929581] SPR radius for FAST iterations: 20 (autodetect)
[00:33:49 -10298.929581] Model parameter optimization (eps = 3.000000)
[00:33:53 -10254.114026] FAST spr round 1 (radius: 20)
[00:34:04 -8981.661978] FAST spr round 2 (radius: 20)
[00:34:13 -8937.862663] FAST spr round 3 (radius: 20)
[00:34:21 -8930.429981] FAST spr round 4 (radius: 20)
[00:34:27 -8929.826318] FAST spr round 5 (radius: 20)
[00:34:34 -8929.826308] Model parameter optimization (eps = 1.000000)
[00:34:37 -8928.394854] SLOW spr round 1 (radius: 5)
[00:34:48 -8927.023363] SLOW spr round 2 (radius: 5)
[00:35:00 -8927.022587] SLOW spr round 3 (radius: 10)
[00:35:11 -8927.022496] SLOW spr round 4 (radius: 15)
[00:35:25 -8927.022482] SLOW spr round 5 (radius: 20)
[00:35:40 -8923.567901] SLOW spr round 6 (radius: 5)
[00:35:51] [worker #1] ML tree search #18, logLikelihood: -8912.826284
[00:35:58 -8923.567761] SLOW spr round 7 (radius: 10)
[00:36:13 -8922.639244] SLOW spr round 8 (radius: 5)
[00:36:28 -8922.639241] SLOW spr round 9 (radius: 10)
[00:36:41 -8922.639241] SLOW spr round 10 (radius: 15)
[00:36:54 -8922.639241] SLOW spr round 11 (radius: 20)
[00:37:09 -8922.639241] SLOW spr round 12 (radius: 25)
[00:37:25 -8922.639241] Model parameter optimization (eps = 0.100000)

[00:37:28] [worker #0] ML tree search #17, logLikelihood: -8922.546641

[00:37:28 -43044.333482] Initial branch length optimization
[00:37:28 -34401.978578] Model parameter optimization (eps = 10.000000)
[00:37:35 -34376.877963] AUTODETECT spr round 1 (radius: 5)
[00:37:44 -15749.422733] AUTODETECT spr round 2 (radius: 10)
[00:37:54 -11799.877799] AUTODETECT spr round 3 (radius: 15)
[00:38:06 -10669.555938] AUTODETECT spr round 4 (radius: 20)
[00:38:22 -10421.565576] AUTODETECT spr round 5 (radius: 25)
[00:38:34 -10331.677323] SPR radius for FAST iterations: 25 (autodetect)
[00:38:34 -10331.677323] Model parameter optimization (eps = 3.000000)
[00:38:42 -10315.024071] FAST spr round 1 (radius: 25)
[00:38:51 -9016.139982] FAST spr round 2 (radius: 25)
[00:38:59 -8928.017206] FAST spr round 3 (radius: 25)
[00:39:06 -8926.134351] FAST spr round 4 (radius: 25)
[00:39:12 -8925.494489] FAST spr round 5 (radius: 25)
[00:39:19 -8925.494461] Model parameter optimization (eps = 1.000000)
[00:39:22] [worker #1] ML tree search #20, logLikelihood: -8924.004598
[00:39:26 -8921.227243] SLOW spr round 1 (radius: 5)
[00:39:37 -8919.910637] SLOW spr round 2 (radius: 5)
[00:39:48 -8919.910165] SLOW spr round 3 (radius: 10)
[00:39:57 -8919.910151] SLOW spr round 4 (radius: 15)
[00:40:11 -8919.910151] SLOW spr round 5 (radius: 20)
[00:40:25 -8919.910151] SLOW spr round 6 (radius: 25)
[00:40:39 -8919.910151] Model parameter optimization (eps = 0.100000)

[00:40:40] [worker #0] ML tree search #19, logLikelihood: -8919.895195


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.194843,0.337169) (0.344975,0.579398) (0.297730,1.372682) (0.162452,2.005140) 
   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: -8911.021394

AIC score: 18816.042788 / AICc score: 513828.042788 / BIC score: 20217.722726
Free parameters (model + branch lengths): 497

WARNING: Number of free parameters (K=497) is larger than alignment size (n=124).
         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/Q86SU0/3_mltree/Q86SU0.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86SU0/3_mltree/Q86SU0.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86SU0/3_mltree/Q86SU0.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q86SU0/3_mltree/Q86SU0.raxml.log

Analysis started: 06-Jul-2021 17:09:52 / finished: 06-Jul-2021 17:50:32

Elapsed time: 2440.693 seconds

Consumed energy: 216.924 Wh (= 1 km in an electric car, or 5 km with an e-scooter!)