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 04-Jul-2021 15:36:13 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/2_msa/Q96Q42_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/3_mltree/Q96Q42 --seed 2 --threads 5 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/2_msa/Q96Q42_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 228 sites

WARNING: Sequences tr_V7C2R0_V7C2R0_PHAVU_3885 and tr_A0A151S172_A0A151S172_CAJCA_3821 are exactly identical!
WARNING: Sequences tr_A0A2R8Q016_A0A2R8Q016_DANRE_7955 and tr_F1QS60_F1QS60_DANRE_7955 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_G1N136_G1N136_MELGA_9103 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_R0JV21_R0JV21_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_A0A087QQY5_A0A087QQY5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_A0A091FN84_A0A091FN84_9AVES_55661 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_A0A0A0B002_A0A0A0B002_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_A0A091HXY8_A0A091HXY8_CALAN_9244 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_A0A226MUE1_A0A226MUE1_CALSU_9009 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_A0A2I3GXI9_A0A2I3GXI9_NOMLE_61853 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_G3QYX9_G3QYX9_GORGO_9595 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_H2NAR8_H2NAR8_PONAB_9601 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_K7B173_K7B173_PANTR_9598 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and sp_Q5PQN1_HERC4_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_H0X7B7_H0X7B7_OTOGA_30611 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_F7H295_F7H295_CALJA_9483 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_A0A091DXT4_A0A091DXT4_FUKDA_885580 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_A0A1U7U5D7_A0A1U7U5D7_TARSY_1868482 are exactly identical!
WARNING: Sequences sp_Q6PAV2_HERC4_MOUSE_10090 and tr_A0A2R9BDZ0_A0A2R9BDZ0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3XML2_M3XML2_MUSPF_9669 and tr_E2RSG1_E2RSG1_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3XML2_M3XML2_MUSPF_9669 and tr_A0A2I2URF2_A0A2I2URF2_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3XML2_M3XML2_MUSPF_9669 and tr_A0A384BSM6_A0A384BSM6_URSMA_29073 are exactly identical!
WARNING: Sequences tr_D8R0H6_D8R0H6_SELML_88036 and tr_D8T1R8_D8T1R8_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A0F7VBC6_A0A0F7VBC6_TOXGV_432359 and tr_A0A074STU9_A0A074STU9_HAMHA_99158 are exactly identical!
WARNING: Sequences tr_A0A2J8PAD9_A0A2J8PAD9_PANTR_9598 and sp_Q60I27_AL2CL_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QJ88_H2QJ88_PANTR_9598 and sp_Q96Q42_ALS2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QJ88_H2QJ88_PANTR_9598 and tr_F7F2I1_F7F2I1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2QJ88_H2QJ88_PANTR_9598 and tr_A0A2R9BSL0_A0A2R9BSL0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3ZYZ3_M3ZYZ3_XIPMA_8083 and tr_A0A087XJJ0_A0A087XJJ0_POEFO_48698 are exactly identical!
WARNING: Sequences tr_Q9LFS0_Q9LFS0_ARATH_3702 and tr_D7M7I9_D7M7I9_ARALL_81972 are exactly identical!
WARNING: Sequences tr_Q9LFS0_Q9LFS0_ARATH_3702 and tr_R0FBV3_R0FBV3_9BRAS_81985 are exactly identical!
WARNING: Sequences sp_Q9SFB8_PI5K6_ARATH_3702 and tr_D7L735_D7L735_ARALL_81972 are exactly identical!
WARNING: Sequences tr_A0A0E0I561_A0A0E0I561_ORYNI_4536 and tr_B8B5I8_B8B5I8_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0IC62_A0A0E0IC62_ORYNI_4536 and tr_A0A0E0ELR8_A0A0E0ELR8_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0IC62_A0A0E0IC62_ORYNI_4536 and tr_A0A0E0QJC4_A0A0E0QJC4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0IC62_A0A0E0IC62_ORYNI_4536 and tr_A0A0D3H0H7_A0A0D3H0H7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0IC62_A0A0E0IC62_ORYNI_4536 and tr_A0A0E0AVM5_A0A0E0AVM5_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_F7HRI9_F7HRI9_MACMU_9544 and tr_A0A096MPY4_A0A096MPY4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HRI9_F7HRI9_MACMU_9544 and tr_A0A2K5N5W3_A0A2K5N5W3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HRI9_F7HRI9_MACMU_9544 and tr_A0A2K6ASP7_A0A2K6ASP7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_B8BB04_B8BB04_ORYSI_39946 and tr_I1QIV8_I1QIV8_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_B8BB04_B8BB04_ORYSI_39946 and tr_Q6ZKB8_Q6ZKB8_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1QE87_I1QE87_ORYGL_4538 and tr_A0A0E0EFJ7_A0A0E0EFJ7_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_B3RTM5_B3RTM5_TRIAD_10228 and tr_A0A369SC53_A0A369SC53_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PDD3_G7PDD3_MACFA_9541 and tr_A0A096P537_A0A096P537_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PDD3_G7PDD3_MACFA_9541 and tr_A0A0D9R593_A0A0D9R593_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7PDD3_G7PDD3_MACFA_9541 and tr_A0A2K5MP27_A0A2K5MP27_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7PDD3_G7PDD3_MACFA_9541 and tr_A0A2K6C0X7_A0A2K6C0X7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PDD3_G7PDD3_MACFA_9541 and tr_A0A2K5YV13_A0A2K5YV13_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7PL71_G7PL71_MACFA_9541 and tr_A0A096MS36_A0A096MS36_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PL71_G7PL71_MACFA_9541 and tr_A0A2K6BYF3_A0A2K6BYF3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PL71_G7PL71_MACFA_9541 and tr_A0A2K6A9A2_A0A2K6A9A2_MANLE_9568 are exactly identical!
WARNING: Sequences sp_A6QP75_AL2CL_BOVIN_9913 and tr_G3X7C3_G3X7C3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M4C7P1_M4C7P1_BRARP_51351 and tr_A0A078GAY0_A0A078GAY0_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4C7P1_M4C7P1_BRARP_51351 and tr_A0A078HF44_A0A078HF44_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4C7P1_M4C7P1_BRARP_51351 and tr_A0A0D3B671_A0A0D3B671_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4DY39_M4DY39_BRARP_51351 and tr_A0A0D3AG08_A0A0D3AG08_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4FG18_M4FG18_BRARP_51351 and tr_A0A078GAS7_A0A078GAS7_BRANA_3708 are exactly identical!
WARNING: Sequences tr_R1DGS9_R1DGS9_EMIHU_2903 and tr_R1FQH1_R1FQH1_EMIHU_2903 are exactly identical!
WARNING: Sequences tr_A0A3B6RJB9_A0A3B6RJB9_WHEAT_4565 and tr_A0A3B6SK16_A0A3B6SK16_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B6RJB9_A0A3B6RJB9_WHEAT_4565 and tr_A0A3B6TJQ2_A0A3B6TJQ2_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A0E0LV33_A0A0E0LV33_ORYPU_4537 and tr_A0A0D9X834_A0A0D9X834_9ORYZ_77586 are exactly identical!
WARNING: Sequences tr_A0A067EUT7_A0A067EUT7_CITSI_2711 and tr_A0A2H5PW43_A0A2H5PW43_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0A0LN82_A0A0A0LN82_CUCSA_3659 and tr_A0A1S3C5J5_A0A1S3C5J5_CUCME_3656 are exactly identical!
WARNING: Sequences tr_A0A091IYI5_A0A091IYI5_EGRGA_188379 and tr_A0A091VZJ4_A0A091VZJ4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JM03_A0A091JM03_EGRGA_188379 and tr_A0A091UZM0_A0A091UZM0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JM03_A0A091JM03_EGRGA_188379 and tr_A0A087QXW4_A0A087QXW4_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JM03_A0A091JM03_EGRGA_188379 and tr_A0A091XWB0_A0A091XWB0_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091JM03_A0A091JM03_EGRGA_188379 and tr_A0A091GIZ8_A0A091GIZ8_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091JM03_A0A091JM03_EGRGA_188379 and tr_A0A0A0AAM5_A0A0A0AAM5_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A1S3X5R0_A0A1S3X5R0_TOBAC_4097 and tr_A0A1U7WB42_A0A1U7WB42_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3XSS8_A0A1S3XSS8_TOBAC_4097 and tr_A0A1S3Z316_A0A1S3Z316_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3XSS8_A0A1S3XSS8_TOBAC_4097 and tr_A0A314L113_A0A314L113_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S3XSS8_A0A1S3XSS8_TOBAC_4097 and tr_A0A1U7XNG8_A0A1U7XNG8_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3YFY6_A0A1S3YFY6_TOBAC_4097 and tr_A0A1U7WUD7_A0A1U7WUD7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3YS04_A0A1S3YS04_TOBAC_4097 and tr_J7K3W0_J7K3W0_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3Z237_A0A1S3Z237_TOBAC_4097 and tr_A0A1U7YW74_A0A1U7YW74_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4A7F0_A0A1S4A7F0_TOBAC_4097 and tr_A0A1S4DJ91_A0A1S4DJ91_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S4A7F0_A0A1S4A7F0_TOBAC_4097 and tr_A0A1J6K042_A0A1J6K042_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S4A7F0_A0A1S4A7F0_TOBAC_4097 and tr_A0A1U7YFT1_A0A1U7YFT1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4DNX7_A0A1S4DNX7_TOBAC_4097 and tr_A0A1U7XMT0_A0A1U7XMT0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3U3Z0_A0A1S3U3Z0_VIGRR_3916 and tr_A0A3Q0EYW8_A0A3Q0EYW8_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A2D0QL78_A0A2D0QL78_ICTPU_7998 and tr_A0A2D0QN40_A0A2D0QN40_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S4V0_A0A2D0S4V0_ICTPU_7998 and tr_A0A2D0S6E2_A0A2D0S6E2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2G3AAA3_A0A2G3AAA3_CAPAN_4072 and tr_A0A2G3D7P9_A0A2G3D7P9_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2U4BNJ6_A0A2U4BNJ6_TURTR_9739 and tr_A0A2Y9SUZ7_A0A2Y9SUZ7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3VFM5_A0A2U3VFM5_ODORO_9708 and tr_A0A2Y9IY53_A0A2Y9IY53_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2Y9MVR6_A0A2Y9MVR6_DELLE_9749 and tr_A0A384AT90_A0A384AT90_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 88

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/Q96Q42/3_mltree/Q96Q42.raxml.reduced.phy

Alignment comprises 1 partitions and 228 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 228 / 228
Gaps: 19.17 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/3_mltree/Q96Q42.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 228 / 18240
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -416768.330786] Initial branch length optimization
[00:00:06 -349996.232526] Model parameter optimization (eps = 10.000000)
[00:01:44 -347969.937319] AUTODETECT spr round 1 (radius: 5)
[00:05:24 -266629.722312] AUTODETECT spr round 2 (radius: 10)
[00:09:25 -208655.874011] AUTODETECT spr round 3 (radius: 15)
[00:13:52 -176626.457867] AUTODETECT spr round 4 (radius: 20)
[00:18:44 -162004.291094] AUTODETECT spr round 5 (radius: 25)
[00:24:05 -159021.227919] SPR radius for FAST iterations: 25 (autodetect)
[00:24:05 -159021.227919] Model parameter optimization (eps = 3.000000)
[00:24:18 -159013.951817] FAST spr round 1 (radius: 25)
[00:30:07 -144700.574193] FAST spr round 2 (radius: 25)
[00:34:29 -143882.818845] FAST spr round 3 (radius: 25)
[00:38:08 -143818.708943] FAST spr round 4 (radius: 25)
[00:41:10 -143810.443163] FAST spr round 5 (radius: 25)
[00:43:57 -143810.139150] FAST spr round 6 (radius: 25)
[00:46:37 -143810.139131] Model parameter optimization (eps = 1.000000)
[00:47:04 -143661.931991] SLOW spr round 1 (radius: 5)
[00:50:43 -143618.508893] SLOW spr round 2 (radius: 5)
[00:54:08 -143618.035490] SLOW spr round 3 (radius: 5)
[00:57:26 -143618.035346] SLOW spr round 4 (radius: 10)
[01:01:00 -143613.148889] SLOW spr round 5 (radius: 5)
[01:05:05 -143608.346150] SLOW spr round 6 (radius: 5)
[01:08:43 -143607.432772] SLOW spr round 7 (radius: 5)
[01:12:09 -143607.432772] SLOW spr round 8 (radius: 10)
[01:15:48 -143598.380924] SLOW spr round 9 (radius: 5)
[01:20:01 -143588.298448] SLOW spr round 10 (radius: 5)
[01:23:38 -143588.235422] SLOW spr round 11 (radius: 10)
[01:27:19 -143588.235038] SLOW spr round 12 (radius: 15)
[01:33:31 -143585.376229] SLOW spr round 13 (radius: 5)
[01:37:42 -143585.375596] SLOW spr round 14 (radius: 10)
[01:42:07 -143585.375582] SLOW spr round 15 (radius: 15)
[01:48:04 -143584.894592] SLOW spr round 16 (radius: 5)
[01:52:18 -143582.711096] SLOW spr round 17 (radius: 5)
[01:56:06 -143579.120844] SLOW spr round 18 (radius: 5)
[01:59:36 -143575.713700] SLOW spr round 19 (radius: 5)
[02:02:57 -143575.712885] SLOW spr round 20 (radius: 10)
[02:04:37] [worker #1] ML tree search #2, logLikelihood: -143526.438729
[02:06:28 -143575.712849] SLOW spr round 21 (radius: 15)
[02:11:05] [worker #2] ML tree search #3, logLikelihood: -143524.426303
[02:13:01 -143567.077631] SLOW spr round 22 (radius: 5)
[02:17:22 -143562.356155] SLOW spr round 23 (radius: 5)
[02:21:14 -143561.095408] SLOW spr round 24 (radius: 5)
[02:24:49 -143558.909660] SLOW spr round 25 (radius: 5)
[02:28:10 -143558.908983] SLOW spr round 26 (radius: 10)
[02:31:39 -143558.908967] SLOW spr round 27 (radius: 15)
[02:34:01] [worker #3] ML tree search #4, logLikelihood: -143686.654270
[02:38:03 -143558.703230] SLOW spr round 28 (radius: 5)
[02:42:15 -143558.698146] SLOW spr round 29 (radius: 10)
[02:46:37 -143558.697893] SLOW spr round 30 (radius: 15)
[02:47:29] [worker #4] ML tree search #5, logLikelihood: -143560.798220
[02:52:40 -143556.921009] SLOW spr round 31 (radius: 5)
[02:56:58 -143553.194198] SLOW spr round 32 (radius: 5)
[03:00:45 -143552.102427] SLOW spr round 33 (radius: 5)
[03:04:13 -143552.102327] SLOW spr round 34 (radius: 10)
[03:07:51 -143551.277379] SLOW spr round 35 (radius: 5)
[03:11:51 -143550.948435] SLOW spr round 36 (radius: 5)
[03:15:27 -143550.948060] SLOW spr round 37 (radius: 10)
[03:19:03 -143550.948003] SLOW spr round 38 (radius: 15)
[03:24:11 -143550.344196] SLOW spr round 39 (radius: 5)
[03:27:37 -143550.343607] SLOW spr round 40 (radius: 10)
[03:31:11 -143550.343584] SLOW spr round 41 (radius: 15)
[03:36:11 -143550.343578] SLOW spr round 42 (radius: 20)
[03:39:24] [worker #2] ML tree search #8, logLikelihood: -143708.706509
[03:44:15 -143546.837351] SLOW spr round 43 (radius: 5)
[03:47:45 -143546.826488] SLOW spr round 44 (radius: 10)
[03:51:32 -143546.826405] SLOW spr round 45 (radius: 15)
[03:56:27 -143546.826404] SLOW spr round 46 (radius: 20)
[04:04:16 -143546.826403] SLOW spr round 47 (radius: 25)
[04:14:48 -143546.826403] Model parameter optimization (eps = 0.100000)

[04:15:05] [worker #0] ML tree search #1, logLikelihood: -143545.716382

[04:15:05 -420360.212967] Initial branch length optimization
[04:15:09 -351367.438679] Model parameter optimization (eps = 10.000000)
[04:15:57 -349317.319431] AUTODETECT spr round 1 (radius: 5)
[04:18:57 -264196.316830] AUTODETECT spr round 2 (radius: 10)
[04:22:05 -211617.689333] AUTODETECT spr round 3 (radius: 15)
[04:25:45] [worker #1] ML tree search #7, logLikelihood: -143530.110436
[04:25:47 -178318.774635] AUTODETECT spr round 4 (radius: 20)
[04:29:33 -161222.736812] AUTODETECT spr round 5 (radius: 25)
[04:31:09] [worker #3] ML tree search #9, logLikelihood: -143577.604958
[04:34:20 -158883.729330] SPR radius for FAST iterations: 25 (autodetect)
[04:34:20 -158883.729330] Model parameter optimization (eps = 3.000000)
[04:34:51 -158678.490339] FAST spr round 1 (radius: 25)
[04:34:53] [worker #4] ML tree search #10, logLikelihood: -143533.222726
[04:39:23 -144335.034921] FAST spr round 2 (radius: 25)
[04:42:51 -143697.907140] FAST spr round 3 (radius: 25)
[04:45:44 -143642.571634] FAST spr round 4 (radius: 25)
[04:48:12 -143628.097327] FAST spr round 5 (radius: 25)
[04:50:34 -143613.437261] FAST spr round 6 (radius: 25)
[04:52:46 -143610.135798] FAST spr round 7 (radius: 25)
[04:54:53 -143610.135247] Model parameter optimization (eps = 1.000000)
[04:55:10 -143607.544050] SLOW spr round 1 (radius: 5)
[04:58:04 -143587.141428] SLOW spr round 2 (radius: 5)
[05:00:57 -143582.035584] SLOW spr round 3 (radius: 5)
[05:03:42 -143581.677389] SLOW spr round 4 (radius: 5)
[05:06:24 -143581.677329] SLOW spr round 5 (radius: 10)
[05:09:17 -143581.313593] SLOW spr round 6 (radius: 5)
[05:12:35 -143581.312636] SLOW spr round 7 (radius: 10)
[05:16:21 -143581.312561] SLOW spr round 8 (radius: 15)
[05:21:49 -143581.051578] SLOW spr round 9 (radius: 5)
[05:25:41 -143578.511221] SLOW spr round 10 (radius: 5)
[05:28:05] [worker #2] ML tree search #13, logLikelihood: -143651.281422
[05:29:04 -143578.510826] SLOW spr round 11 (radius: 10)
[05:32:32 -143578.510787] SLOW spr round 12 (radius: 15)
[05:38:04 -143578.510758] SLOW spr round 13 (radius: 20)
[05:46:12 -143578.510730] SLOW spr round 14 (radius: 25)
[05:57:20 -143578.510702] Model parameter optimization (eps = 0.100000)

[05:57:27] [worker #0] ML tree search #6, logLikelihood: -143578.472700

[05:57:27 -419289.694854] Initial branch length optimization
[05:57:33 -349671.750753] Model parameter optimization (eps = 10.000000)
[05:58:45 -347824.703604] AUTODETECT spr round 1 (radius: 5)
[06:02:03 -270787.307708] AUTODETECT spr round 2 (radius: 10)
[06:05:38 -211287.065544] AUTODETECT spr round 3 (radius: 15)
[06:09:51 -177675.052885] AUTODETECT spr round 4 (radius: 20)
[06:11:54] [worker #3] ML tree search #14, logLikelihood: -143545.194251
[06:14:19 -162322.648783] AUTODETECT spr round 5 (radius: 25)
[06:19:13 -160112.253510] SPR radius for FAST iterations: 25 (autodetect)
[06:19:13 -160112.253510] Model parameter optimization (eps = 3.000000)
[06:19:43 -159902.599129] FAST spr round 1 (radius: 25)
[06:24:41 -144342.594844] FAST spr round 2 (radius: 25)
[06:27:23] [worker #1] ML tree search #12, logLikelihood: -143522.003594
[06:28:23 -143715.256237] FAST spr round 3 (radius: 25)
[06:31:26 -143647.860763] FAST spr round 4 (radius: 25)
[06:34:06 -143644.869997] FAST spr round 5 (radius: 25)
[06:36:34 -143644.869467] Model parameter optimization (eps = 1.000000)
[06:36:50 -143638.303042] SLOW spr round 1 (radius: 5)
[06:40:10 -143609.687568] SLOW spr round 2 (radius: 5)
[06:43:21 -143609.072037] SLOW spr round 3 (radius: 5)
[06:46:25 -143609.071900] SLOW spr round 4 (radius: 10)
[06:49:42 -143602.719361] SLOW spr round 5 (radius: 5)
[06:53:24 -143602.283781] SLOW spr round 6 (radius: 5)
[06:56:42 -143602.283748] SLOW spr round 7 (radius: 10)
[07:00:05 -143600.593512] SLOW spr round 8 (radius: 5)
[07:03:39 -143600.593505] SLOW spr round 9 (radius: 10)
[07:07:18 -143600.593505] SLOW spr round 10 (radius: 15)
[07:12:32 -143594.385435] SLOW spr round 11 (radius: 5)
[07:16:23 -143594.139930] SLOW spr round 12 (radius: 5)
[07:19:46 -143594.138439] SLOW spr round 13 (radius: 10)
[07:23:17 -143588.056416] SLOW spr round 14 (radius: 5)
[07:26:56 -143583.548475] SLOW spr round 15 (radius: 5)
[07:30:14 -143583.464701] SLOW spr round 16 (radius: 10)
[07:33:37 -143582.515838] SLOW spr round 17 (radius: 5)
[07:37:12 -143582.515643] SLOW spr round 18 (radius: 10)
[07:40:52 -143582.515635] SLOW spr round 19 (radius: 15)
[07:46:07 -143582.515635] SLOW spr round 20 (radius: 20)
[07:48:57] [worker #4] ML tree search #15, logLikelihood: -143552.415965
[07:53:51 -143579.518157] SLOW spr round 21 (radius: 5)
[07:57:54 -143573.936119] SLOW spr round 22 (radius: 5)
[08:01:05] [worker #2] ML tree search #18, logLikelihood: -143539.503735
[08:01:20 -143573.935997] SLOW spr round 23 (radius: 10)
[08:04:51 -143573.935995] SLOW spr round 24 (radius: 15)
[08:10:06 -143573.935993] SLOW spr round 25 (radius: 20)
[08:14:33] [worker #3] ML tree search #19, logLikelihood: -143573.086641
[08:17:47 -143573.935992] SLOW spr round 26 (radius: 25)
[08:27:59 -143573.935992] Model parameter optimization (eps = 0.100000)

[08:28:06] [worker #0] ML tree search #11, logLikelihood: -143573.840505

[08:28:07 -419396.805132] Initial branch length optimization
[08:28:13 -353854.289078] Model parameter optimization (eps = 10.000000)
[08:29:26 -351733.882859] AUTODETECT spr round 1 (radius: 5)
[08:32:44 -264193.833781] AUTODETECT spr round 2 (radius: 10)
[08:36:16 -211832.528352] AUTODETECT spr round 3 (radius: 15)
[08:40:04 -179838.068709] AUTODETECT spr round 4 (radius: 20)
[08:44:11 -168943.670004] AUTODETECT spr round 5 (radius: 25)
[08:48:59 -162696.646978] SPR radius for FAST iterations: 25 (autodetect)
[08:48:59 -162696.646978] Model parameter optimization (eps = 3.000000)
[08:49:10 -162687.940373] FAST spr round 1 (radius: 25)
[08:54:38 -144756.056391] FAST spr round 2 (radius: 25)
[08:58:39 -143915.933307] FAST spr round 3 (radius: 25)
[09:01:55 -143820.929644] FAST spr round 4 (radius: 25)
[09:04:35 -143811.364378] FAST spr round 5 (radius: 25)
[09:07:02 -143810.701837] FAST spr round 6 (radius: 25)
[09:09:22 -143810.701529] Model parameter optimization (eps = 1.000000)
[09:09:45 -143631.822543] SLOW spr round 1 (radius: 5)
[09:13:06 -143590.818913] SLOW spr round 2 (radius: 5)
[09:16:15 -143587.469225] SLOW spr round 3 (radius: 5)
[09:19:16 -143587.468358] SLOW spr round 4 (radius: 10)
[09:19:24] [worker #1] ML tree search #17, logLikelihood: -143515.765939
[09:22:32 -143576.693971] SLOW spr round 5 (radius: 5)
[09:26:17 -143569.582081] SLOW spr round 6 (radius: 5)
[09:29:39 -143562.915153] SLOW spr round 7 (radius: 5)
[09:32:44 -143562.914546] SLOW spr round 8 (radius: 10)
[09:35:59 -143561.959297] SLOW spr round 9 (radius: 5)
[09:39:35 -143561.573713] SLOW spr round 10 (radius: 5)
[09:42:52 -143561.384669] SLOW spr round 11 (radius: 5)
[09:45:57 -143561.383460] SLOW spr round 12 (radius: 10)
[09:49:09 -143561.383376] SLOW spr round 13 (radius: 15)
[09:54:41 -143559.188663] SLOW spr round 14 (radius: 5)
[09:58:38 -143552.755233] SLOW spr round 15 (radius: 5)
[10:02:05 -143550.652826] SLOW spr round 16 (radius: 5)
[10:05:12 -143550.652294] SLOW spr round 17 (radius: 10)
[10:08:25 -143550.652259] SLOW spr round 18 (radius: 15)
[10:13:45 -143549.796231] SLOW spr round 19 (radius: 5)
[10:17:35 -143548.875578] SLOW spr round 20 (radius: 5)
[10:20:59 -143544.267376] SLOW spr round 21 (radius: 5)
[10:24:10 -143542.940740] SLOW spr round 22 (radius: 5)
[10:27:12 -143542.939760] SLOW spr round 23 (radius: 10)
[10:30:22 -143541.170431] SLOW spr round 24 (radius: 5)
[10:33:57 -143541.168880] SLOW spr round 25 (radius: 10)
[10:37:35 -143541.168805] SLOW spr round 26 (radius: 15)
[10:42:37 -143540.281656] SLOW spr round 27 (radius: 5)
[10:43:39] [worker #4] ML tree search #20, logLikelihood: -143538.928644
[10:46:26 -143539.704008] SLOW spr round 28 (radius: 5)
[10:49:47 -143539.700523] SLOW spr round 29 (radius: 10)
[10:53:09 -143539.699057] SLOW spr round 30 (radius: 15)
[10:58:15 -143539.698428] SLOW spr round 31 (radius: 20)
[11:05:44 -143539.698156] SLOW spr round 32 (radius: 25)
[11:16:01 -143536.266052] SLOW spr round 33 (radius: 5)
[11:19:54 -143536.265997] SLOW spr round 34 (radius: 10)
[11:24:00 -143536.265970] SLOW spr round 35 (radius: 15)
[11:28:58 -143536.265955] SLOW spr round 36 (radius: 20)
[11:36:32 -143534.515333] SLOW spr round 37 (radius: 5)
[11:40:23 -143534.514584] SLOW spr round 38 (radius: 10)
[11:44:24 -143534.514560] SLOW spr round 39 (radius: 15)
[11:49:22 -143534.514553] SLOW spr round 40 (radius: 20)
[11:56:55 -143534.514546] SLOW spr round 41 (radius: 25)
[12:07:11 -143534.514539] Model parameter optimization (eps = 0.100000)

[12:07:21] [worker #0] ML tree search #16, logLikelihood: -143534.128576


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.051821,0.259736) (0.203019,0.966334) (0.500678,0.895871) (0.244482,1.398111) 
   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: -143515.765939

AIC score: 291041.531878 / AICc score: 8335101.531878 / BIC score: 297917.369864
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=228).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 117 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/3_mltree/Q96Q42.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/3_mltree/Q96Q42.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/3_mltree/Q96Q42.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/3_mltree/Q96Q42.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96Q42/3_mltree/Q96Q42.raxml.log

Analysis started: 04-Jul-2021 15:36:13 / finished: 05-Jul-2021 03:43:35

Elapsed time: 43642.198 seconds

Consumed energy: 3964.508 Wh (= 20 km in an electric car, or 99 km with an e-scooter!)