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

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 23-Jun-2021 08:47:21 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/2_msa/Q6A162_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/3_mltree/Q6A162 --seed 2 --threads 6 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/2_msa/Q6A162_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 297 sites

WARNING: Sequences tr_A0A1D5PZ89_A0A1D5PZ89_CHICK_9031 and sp_Q6PVZ1_K1C14_CHICK_9031 are exactly identical!
WARNING: Sequences tr_G1RIS7_G1RIS7_NOMLE_61853 and tr_H2NU31_H2NU31_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RIS7_G1RIS7_NOMLE_61853 and sp_P08727_K1C19_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z0J1_A0A2I2Z0J1_GORGO_9595 and sp_P19012_K1C15_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RL08_G3RL08_GORGO_9595 and tr_H2NU40_H2NU40_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RL08_G3RL08_GORGO_9595 and sp_A5A6M5_K1H1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RL08_G3RL08_GORGO_9595 and sp_Q15323_K1H1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RL08_G3RL08_GORGO_9595 and tr_A0A2R9CQW6_A0A2R9CQW6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_H2QCZ7_H2QCZ7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and sp_P02533_K1C14_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_F7H312_F7H312_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A096P5N3_A0A096P5N3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A0D9S2F0_A0A0D9S2F0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2K5NH02_A0A2K5NH02_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2K6E2S6_A0A2K6E2S6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2K5ZWJ8_A0A2K5ZWJ8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2R9CHA8_A0A2R9CHA8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8KGG8_A0A2J8KGG8_PANTR_9598 and tr_A0A2R9AGR7_A0A2R9AGR7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCC4_H2QCC4_PANTR_9598 and tr_A0A2R9BI07_A0A2R9BI07_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCX4_H2QCX4_PANTR_9598 and sp_Q99456_K1C12_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QCX4_H2QCX4_PANTR_9598 and tr_A0A2R9B0H7_A0A2R9B0H7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCX5_H2QCX5_PANTR_9598 and tr_A0A2R9AN97_A0A2R9AN97_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCY7_H2QCY7_PANTR_9598 and tr_A0A2R8Z5Q7_A0A2R8Z5Q7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCY9_H2QCY9_PANTR_9598 and sp_Q14532_K1H2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QCY9_H2QCY9_PANTR_9598 and tr_A0A2R8ZEN7_A0A2R8ZEN7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCZ0_H2QCZ0_PANTR_9598 and tr_A0A2R9BRN9_A0A2R9BRN9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCZ2_H2QCZ2_PANTR_9598 and tr_A0A2R9ATZ6_A0A2R9ATZ6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCZ4_H2QCZ4_PANTR_9598 and tr_A0A2R8ZHV6_A0A2R8ZHV6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCZ8_H2QCZ8_PANTR_9598 and sp_Q04695_K1C17_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QCZ8_H2QCZ8_PANTR_9598 and tr_A0A2R9BML2_A0A2R9BML2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R114_H2R114_PANTR_9598 and tr_A0A2R9ALU5_A0A2R9ALU5_PANPA_9597 are exactly identical!
WARNING: Sequences sp_B0LKP1_KRT35_SHEEP_9940 and tr_W5Q5N5_W5Q5N5_SHEEP_9940 are exactly identical!
WARNING: Sequences sp_P02534_K1M1_SHEEP_9940 and tr_W5Q4Q4_W5Q4Q4_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_A0A1D5Q3N1_A0A1D5Q3N1_MACMU_9544 and tr_G7PUS3_G7PUS3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6YKA7_F6YKA7_MACMU_9544 and tr_A0A2K6C8U3_A0A2K6C8U3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A2I3MA29_A0A2I3MA29_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A0D9S2G2_A0A0D9S2G2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7A670_F7A670_MACMU_9544 and tr_G7PUS4_G7PUS4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7ACB4_F7ACB4_MACMU_9544 and tr_G7PUS1_G7PUS1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7ACC2_F7ACC2_MACMU_9544 and tr_A0A096P5M0_A0A096P5M0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7ACE0_F7ACE0_MACMU_9544 and tr_G7PUR8_G7PUR8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7ACE0_F7ACE0_MACMU_9544 and tr_G7PUR9_G7PUR9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7ACE0_F7ACE0_MACMU_9544 and tr_A0A2K5NI97_A0A2K5NI97_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7ACE0_F7ACE0_MACMU_9544 and tr_A0A2K6ALH3_A0A2K6ALH3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7B5A6_F7B5A6_MACMU_9544 and tr_G7PUQ1_G7PUQ1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_G7PUQ0_G7PUQ0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A096P5J0_A0A096P5J0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A0D9S2W8_A0A0D9S2W8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A2K6AP56_A0A2K6AP56_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FXM2_F7FXM2_MACMU_9544 and tr_A0A0D9S2N0_A0A0D9S2N0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7FXY8_F7FXY8_MACMU_9544 and tr_G7PUR6_G7PUR6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FXZ5_F7FXZ5_MACMU_9544 and tr_A0A2K5N545_A0A2K5N545_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7FXZ5_F7FXZ5_MACMU_9544 and tr_A0A2K5ZDS4_A0A2K5ZDS4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7FXZ9_F7FXZ9_MACMU_9544 and tr_G7PUR5_G7PUR5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GFM5_F7GFM5_MACMU_9544 and tr_G7PUQ3_G7PUQ3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GFM5_F7GFM5_MACMU_9544 and tr_A0A2K5MNH4_A0A2K5MNH4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H0YVX6_H0YVX6_TAEGU_59729 and tr_A0A218UN40_A0A218UN40_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H1A2Y8_H1A2Y8_TAEGU_59729 and tr_U3JC30_U3JC30_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H1A2Y8_H1A2Y8_TAEGU_59729 and tr_A0A091ESI5_A0A091ESI5_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H1A2Y8_H1A2Y8_TAEGU_59729 and tr_A0A093PX43_A0A093PX43_9PASS_328815 are exactly identical!
WARNING: Sequences tr_B0BMI8_B0BMI8_XENTR_8364 and tr_F6RGW5_F6RGW5_XENTR_8364 are exactly identical!
WARNING: Sequences tr_A0A140T867_A0A140T867_BOVIN_9913 and sp_A1L595_K1C17_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A096P5L8_A0A096P5L8_PAPAN_9555 and tr_A0A2K5NYF9_A0A2K5NYF9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P5L8_A0A096P5L8_PAPAN_9555 and tr_A0A2K5YF21_A0A2K5YF21_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P5L8_A0A096P5L8_PAPAN_9555 and tr_A0A2K5Z3H7_A0A2K5Z3H7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P5M5_A0A096P5M5_PAPAN_9555 and tr_A0A0D9S2H7_A0A0D9S2H7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096P5M5_A0A096P5M5_PAPAN_9555 and tr_A0A2K6E6P7_A0A2K6E6P7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3LFF0_A0A2I3LFF0_PAPAN_9555 and tr_A0A2K5YQY4_A0A2K5YQY4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D9S2G3_A0A0D9S2G3_CHLSB_60711 and tr_A0A2K6A0P8_A0A2K6A0P8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151PC58_A0A151PC58_ALLMI_8496 and tr_A0A1U7S127_A0A1U7S127_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151PC64_A0A151PC64_ALLMI_8496 and tr_A0A1U7RR64_A0A1U7RR64_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151PC95_A0A151PC95_ALLMI_8496 and tr_A0A1U7RME3_A0A1U7RME3_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091UVR9_A0A091UVR9_NIPNI_128390 and tr_A0A0A0ASS1_A0A0A0ASS1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A226N7Z7_A0A226N7Z7_CALSU_9009 and tr_A0A226NRM3_A0A226NRM3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2K5KJ84_A0A2K5KJ84_CERAT_9531 and tr_A0A2K6A2M2_A0A2K6A2M2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5NH06_A0A2K5NH06_CERAT_9531 and tr_A0A2K6AK51_A0A2K6AK51_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5P1B1_A0A2K5P1B1_CERAT_9531 and tr_A0A2K5ZJV4_A0A2K5ZJV4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5P1P6_A0A2K5P1P6_CERAT_9531 and tr_A0A2K5Y3D0_A0A2K5Y3D0_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 78

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/3_mltree/Q6A162.raxml.reduced.phy

Alignment comprises 1 partitions and 297 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 297 / 297
Gaps: 0.41 %
Invariant sites: 0.34 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/3_mltree/Q6A162.raxml.rba

Parallelization scheme autoconfig: 6 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 / 297 / 23760
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -329702.159389] Initial branch length optimization
[00:00:10 -284663.437990] Model parameter optimization (eps = 10.000000)
[00:01:16 -282408.850687] AUTODETECT spr round 1 (radius: 5)
[00:05:00 -183362.806779] AUTODETECT spr round 2 (radius: 10)
[00:08:41 -130335.997781] AUTODETECT spr round 3 (radius: 15)
[00:13:01 -107989.258905] AUTODETECT spr round 4 (radius: 20)
[00:18:17 -93480.749369] AUTODETECT spr round 5 (radius: 25)
[00:24:12 -91341.004854] SPR radius for FAST iterations: 25 (autodetect)
[00:24:12 -91341.004854] Model parameter optimization (eps = 3.000000)
[00:24:50 -91225.205269] FAST spr round 1 (radius: 25)
[00:28:40 -76246.443227] FAST spr round 2 (radius: 25)
[00:31:34 -75400.641808] FAST spr round 3 (radius: 25)
[00:34:06 -75362.345163] FAST spr round 4 (radius: 25)
[00:36:29 -75331.962984] FAST spr round 5 (radius: 25)
[00:38:39 -75327.639940] FAST spr round 6 (radius: 25)
[00:40:46 -75327.639888] Model parameter optimization (eps = 1.000000)
[00:40:59 -75324.737620] SLOW spr round 1 (radius: 5)
[00:44:16 -75303.039995] SLOW spr round 2 (radius: 5)
[00:47:24 -75298.936548] SLOW spr round 3 (radius: 5)
[00:50:20 -75298.936338] SLOW spr round 4 (radius: 10)
[00:53:10 -75298.936336] SLOW spr round 5 (radius: 15)
[00:58:09 -75298.936335] SLOW spr round 6 (radius: 20)
[01:06:06 -75298.936335] SLOW spr round 7 (radius: 25)
[01:17:57 -75298.936335] Model parameter optimization (eps = 0.100000)

[01:18:05] [worker #0] ML tree search #1, logLikelihood: -75298.879012

[01:18:05 -330257.640116] Initial branch length optimization
[01:18:13 -283813.368467] Model parameter optimization (eps = 10.000000)
[01:19:14 -281479.152838] AUTODETECT spr round 1 (radius: 5)
[01:22:53 -187198.585797] AUTODETECT spr round 2 (radius: 10)
[01:24:23] [worker #5] ML tree search #6, logLikelihood: -75272.896615
[01:26:34 -125985.200798] AUTODETECT spr round 3 (radius: 15)
[01:29:08] [worker #1] ML tree search #2, logLikelihood: -75273.236088
[01:31:04 -97888.714568] AUTODETECT spr round 4 (radius: 20)
[01:31:50] [worker #2] ML tree search #3, logLikelihood: -75266.238455
[01:32:17] [worker #3] ML tree search #4, logLikelihood: -75273.301339
[01:36:27 -90639.074592] AUTODETECT spr round 5 (radius: 25)
[01:37:21] [worker #4] ML tree search #5, logLikelihood: -75264.101590
[01:43:58 -88755.570554] SPR radius for FAST iterations: 25 (autodetect)
[01:43:58 -88755.570554] Model parameter optimization (eps = 3.000000)
[01:44:27 -88684.223415] FAST spr round 1 (radius: 25)
[01:48:14 -76175.689772] FAST spr round 2 (radius: 25)
[01:51:10 -75492.656894] FAST spr round 3 (radius: 25)
[01:53:42 -75438.276085] FAST spr round 4 (radius: 25)
[01:56:02 -75423.054726] FAST spr round 5 (radius: 25)
[01:58:13 -75422.453513] FAST spr round 6 (radius: 25)
[02:00:22 -75422.453489] Model parameter optimization (eps = 1.000000)
[02:00:41 -75407.361211] SLOW spr round 1 (radius: 5)
[02:04:07 -75377.489880] SLOW spr round 2 (radius: 5)
[02:07:19 -75365.896247] SLOW spr round 3 (radius: 5)
[02:10:21 -75365.896101] SLOW spr round 4 (radius: 10)
[02:13:22 -75356.230685] SLOW spr round 5 (radius: 5)
[02:17:23 -75353.192543] SLOW spr round 6 (radius: 5)
[02:20:51 -75353.192541] SLOW spr round 7 (radius: 10)
[02:23:54 -75349.588529] SLOW spr round 8 (radius: 5)
[02:27:53 -75345.567672] SLOW spr round 9 (radius: 5)
[02:31:28 -75249.797259] SLOW spr round 10 (radius: 5)
[02:34:36 -75249.797254] SLOW spr round 11 (radius: 10)
[02:37:35 -75247.002178] SLOW spr round 12 (radius: 5)
[02:41:33 -75247.002000] SLOW spr round 13 (radius: 10)
[02:44:50 -75247.002000] SLOW spr round 14 (radius: 15)
[02:49:23 -75245.164210] SLOW spr round 15 (radius: 5)
[02:53:34 -75244.398135] SLOW spr round 16 (radius: 5)
[02:57:08 -75244.398110] SLOW spr round 17 (radius: 10)
[03:00:12 -75244.398109] SLOW spr round 18 (radius: 15)
[03:00:32] [worker #5] ML tree search #12, logLikelihood: -75255.539214
[03:01:36] [worker #3] ML tree search #10, logLikelihood: -75249.091832
[03:03:08] [worker #1] ML tree search #8, logLikelihood: -75272.026137
[03:04:24] [worker #2] ML tree search #9, logLikelihood: -75267.912247
[03:04:55 -75244.398109] SLOW spr round 19 (radius: 20)
[03:13:06 -75244.398109] SLOW spr round 20 (radius: 25)
[03:25:08 -75244.398109] Model parameter optimization (eps = 0.100000)

[03:25:24] [worker #0] ML tree search #7, logLikelihood: -75243.430272

[03:25:24 -331636.217863] Initial branch length optimization
[03:25:34 -286329.205465] Model parameter optimization (eps = 10.000000)
[03:26:21] [worker #4] ML tree search #11, logLikelihood: -75280.286851
[03:26:38 -283900.423474] AUTODETECT spr round 1 (radius: 5)
[03:30:26 -183392.986021] AUTODETECT spr round 2 (radius: 10)
[03:34:10 -132019.234538] AUTODETECT spr round 3 (radius: 15)
[03:38:30 -99787.170776] AUTODETECT spr round 4 (radius: 20)
[03:44:05 -90435.956140] AUTODETECT spr round 5 (radius: 25)
[03:50:36 -89644.773344] SPR radius for FAST iterations: 25 (autodetect)
[03:50:36 -89644.773344] Model parameter optimization (eps = 3.000000)
[03:51:12 -89563.684524] FAST spr round 1 (radius: 25)
[03:54:48 -75752.343139] FAST spr round 2 (radius: 25)
[03:57:39 -75399.031752] FAST spr round 3 (radius: 25)
[04:00:06 -75377.954268] FAST spr round 4 (radius: 25)
[04:02:20 -75369.411171] FAST spr round 5 (radius: 25)
[04:04:32 -75367.198362] FAST spr round 6 (radius: 25)
[04:06:37 -75367.198317] Model parameter optimization (eps = 1.000000)
[04:06:52 -75363.730160] SLOW spr round 1 (radius: 5)
[04:10:07 -75319.315645] SLOW spr round 2 (radius: 5)
[04:13:17 -75306.599173] SLOW spr round 3 (radius: 5)
[04:16:21 -75305.723723] SLOW spr round 4 (radius: 5)
[04:19:17 -75305.723722] SLOW spr round 5 (radius: 10)
[04:22:13 -75300.730650] SLOW spr round 6 (radius: 5)
[04:26:12 -75300.730646] SLOW spr round 7 (radius: 10)
[04:29:24 -75300.730646] SLOW spr round 8 (radius: 15)
[04:34:05 -75300.730646] SLOW spr round 9 (radius: 20)
[04:34:24] [worker #2] ML tree search #15, logLikelihood: -75286.092757
[04:42:35] [worker #4] ML tree search #17, logLikelihood: -75279.449395
[04:43:10 -75300.730646] SLOW spr round 10 (radius: 25)
[04:48:14] [worker #3] ML tree search #16, logLikelihood: -75273.577629
[04:49:38] [worker #5] ML tree search #18, logLikelihood: -75261.833450
[04:55:11 -75300.730646] Model parameter optimization (eps = 0.100000)

[04:55:25] [worker #0] ML tree search #13, logLikelihood: -75300.080444

[04:55:25 -332030.390692] Initial branch length optimization
[04:55:33 -285749.869159] Model parameter optimization (eps = 10.000000)
[04:56:36 -283468.420971] AUTODETECT spr round 1 (radius: 5)
[05:00:17 -181460.808901] AUTODETECT spr round 2 (radius: 10)
[05:03:53] [worker #1] ML tree search #14, logLikelihood: -75258.041225
[05:03:55 -125038.072013] AUTODETECT spr round 3 (radius: 15)
[05:08:08 -96942.578965] AUTODETECT spr round 4 (radius: 20)
[05:13:34 -89041.821374] AUTODETECT spr round 5 (radius: 25)
[05:20:04 -88170.870172] SPR radius for FAST iterations: 25 (autodetect)
[05:20:04 -88170.870172] Model parameter optimization (eps = 3.000000)
[05:20:31 -88045.567904] FAST spr round 1 (radius: 25)
[05:24:07 -75940.205227] FAST spr round 2 (radius: 25)
[05:26:54 -75372.373546] FAST spr round 3 (radius: 25)
[05:29:18 -75315.162135] FAST spr round 4 (radius: 25)
[05:31:30 -75305.733417] FAST spr round 5 (radius: 25)
[05:33:35 -75305.731342] Model parameter optimization (eps = 1.000000)
[05:33:49 -75303.126594] SLOW spr round 1 (radius: 5)
[05:37:03 -75283.015361] SLOW spr round 2 (radius: 5)
[05:40:12 -75278.004438] SLOW spr round 3 (radius: 5)
[05:43:07 -75278.004425] SLOW spr round 4 (radius: 10)
[05:45:55 -75278.004425] SLOW spr round 5 (radius: 15)
[05:50:40 -75278.004425] SLOW spr round 6 (radius: 20)
[05:58:23 -75278.004425] SLOW spr round 7 (radius: 25)
[06:09:44 -75278.004425] Model parameter optimization (eps = 0.100000)

[06:09:51] [worker #0] ML tree search #19, logLikelihood: -75277.982493

[06:35:39] [worker #1] ML tree search #20, logLikelihood: -75267.119893

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.282694,0.466664) (0.189490,1.122000) (0.366023,0.913189) (0.161793,1.985382) 
   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: -75243.430272

AIC score: 154496.860544 / AICc score: 8198556.860544 / BIC score: 161902.793483
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=297).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/3_mltree/Q6A162.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/3_mltree/Q6A162.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/3_mltree/Q6A162.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6A162/3_mltree/Q6A162.raxml.log

Analysis started: 23-Jun-2021 08:47:21 / finished: 23-Jun-2021 15:23:01

Elapsed time: 23739.990 seconds