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 05-Jul-2021 19:47:37 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/2_msa/Q96Q27_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/3_mltree/Q96Q27 --seed 2 --threads 4 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/2_msa/Q96Q27_trimmed_msa.fasta
[00:00:00] Loaded alignment with 998 taxa and 216 sites

WARNING: Sequences tr_B4QLS7_B4QLS7_DROSI_7240 and sp_Q9VUX2_MIB_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QLS7_B4QLS7_DROSI_7240 and tr_B4HIM6_B4HIM6_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2R8PZ70_A0A2R8PZ70_DANRE_7955 and tr_A0A2R8Q1K5_A0A2R8Q1K5_DANRE_7955 are exactly identical!
WARNING: Sequences tr_A0A2R8RUP4_A0A2R8RUP4_DANRE_7955 and tr_F1QNB1_F1QNB1_DANRE_7955 are exactly identical!
WARNING: Sequences tr_D3YVV3_D3YVV3_MOUSE_10090 and tr_F1M3B1_F1M3B1_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3XSX4_M3XSX4_MUSPF_9669 and tr_A0A2Y9K9H8_A0A2Y9K9H8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XSX4_M3XSX4_MUSPF_9669 and tr_A0A384DTB0_A0A384DTB0_URSMA_29073 are exactly identical!
WARNING: Sequences tr_M3Y353_M3Y353_MUSPF_9669 and tr_A0A2Y9ISF0_A0A2Y9ISF0_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1S5Y7_G1S5Y7_NOMLE_61853 and tr_H2NM43_H2NM43_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2YF64_A0A2I2YF64_GORGO_9595 and sp_Q8N6D5_ANR29_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YF64_A0A2I2YF64_GORGO_9595 and tr_U3E4P1_U3E4P1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3QZR9_G3QZR9_GORGO_9595 and sp_Q8WXK1_ASB15_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RHC1_G3RHC1_GORGO_9595 and tr_H2Q8U5_H2Q8U5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RHC1_G3RHC1_GORGO_9595 and sp_Q96Q27_ASB2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RHC1_G3RHC1_GORGO_9595 and tr_A0A2R9BWP8_A0A2R9BWP8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0R3NLH3_A0A0R3NLH3_DROPS_46245 and tr_B4GA84_B4GA84_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3RVR1_A0A2I3RVR1_PANTR_9598 and tr_A0A2R9C1K6_A0A2R9C1K6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8QX46_A0A2J8QX46_PANTR_9598 and tr_A0A2R9AAB1_A0A2R9AAB1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QEC6_H2QEC6_PANTR_9598 and tr_A0A2R9AHP1_A0A2R9AHP1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R0V4_H2R0V4_PANTR_9598 and tr_A0A2R9BFU1_A0A2R9BFU1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5R3A1_A0A1D5R3A1_MACMU_9544 and tr_A0A0D9RJX8_A0A0D9RJX8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5R3A1_A0A1D5R3A1_MACMU_9544 and tr_A0A2K5YXS8_A0A2K5YXS8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1D5R579_A0A1D5R579_MACMU_9544 and tr_G7P0J8_G7P0J8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R579_A0A1D5R579_MACMU_9544 and tr_A0A2K5NB80_A0A2K5NB80_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R579_A0A1D5R579_MACMU_9544 and tr_A0A2K6DM88_A0A2K6DM88_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R579_A0A1D5R579_MACMU_9544 and tr_A0A2K5Y9P3_A0A2K5Y9P3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1D5RJR8_A0A1D5RJR8_MACMU_9544 and tr_G7PSM8_G7PSM8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5RJR8_A0A1D5RJR8_MACMU_9544 and tr_A0A2K6E5N0_A0A2K6E5N0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7EA98_F7EA98_MACMU_9544 and tr_A0A0D9RF35_A0A0D9RF35_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9ETU3_H9ETU3_MACMU_9544 and tr_A0A2I3MHH3_A0A2I3MHH3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H9ETU3_H9ETU3_MACMU_9544 and tr_A0A0D9RYN3_A0A0D9RYN3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9ETU3_H9ETU3_MACMU_9544 and tr_A0A2K5ZKR2_A0A2K5ZKR2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0YUA6_H0YUA6_TAEGU_59729 and tr_A0A218UPI7_A0A218UPI7_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0ZJN7_H0ZJN7_TAEGU_59729 and tr_U3JUE1_U3JUE1_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0ZQ84_H0ZQ84_TAEGU_59729 and tr_A0A218VCK3_A0A218VCK3_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0ZQW2_H0ZQW2_TAEGU_59729 and tr_A0A218UFR6_A0A218UFR6_9PASE_299123 are exactly identical!
WARNING: Sequences tr_B4MF25_B4MF25_DROVI_7244 and tr_D0Z7C6_D0Z7C6_DROVI_7244 are exactly identical!
WARNING: Sequences tr_G7NZD0_G7NZD0_MACFA_9541 and tr_A0A2K5MIF6_A0A2K5MIF6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7NZD0_G7NZD0_MACFA_9541 and tr_A0A2K6EBV3_A0A2K6EBV3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F1MN41_F1MN41_BOVIN_9913 and sp_Q08DV6_ASB3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F1N2S1_F1N2S1_BOVIN_9913 and sp_Q3SX45_ASB2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A2I3MFY9_A0A2I3MFY9_PAPAN_9555 and tr_A0A2K5KKA1_A0A2K5KKA1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MFY9_A0A2I3MFY9_PAPAN_9555 and tr_A0A2K6DRE3_A0A2K6DRE3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MFY9_A0A2I3MFY9_PAPAN_9555 and tr_A0A2K5YJ26_A0A2K5YJ26_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151PGN5_A0A151PGN5_ALLMI_8496 and tr_A0A3Q0FSN4_A0A3Q0FSN4_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091FJL2_A0A091FJL2_CORBR_85066 and tr_A0A218V144_A0A218V144_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A091JTW0_A0A091JTW0_EGRGA_188379 and tr_A0A1V4KFX3_A0A1V4KFX3_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2I0MNC9_A0A2I0MNC9_COLLI_8932 and tr_A0A1V4KAK8_A0A1V4KAK8_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3PBU6_A0A1S3PBU6_SALSA_8030 and tr_B5DGA6_B5DGA6_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3PBU6_A0A1S3PBU6_SALSA_8030 and tr_A0A060WL95_A0A060WL95_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226NKX9_A0A226NKX9_CALSU_9009 and tr_A0A226PXS3_A0A226PXS3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NL03_A0A226NL03_CALSU_9009 and tr_A0A226P058_A0A226P058_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PZQ0_A0A2D0PZQ0_ICTPU_7998 and tr_A0A2D0Q0Z0_A0A2D0Q0Z0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PZQ0_A0A2D0PZQ0_ICTPU_7998 and tr_A0A2D0Q0Z4_A0A2D0Q0Z4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PZQ0_A0A2D0PZQ0_ICTPU_7998 and tr_A0A2D0Q106_A0A2D0Q106_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RQA5_A0A2D0RQA5_ICTPU_7998 and tr_A0A2D0RR81_A0A2D0RR81_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4BRY4_A0A2U4BRY4_TURTR_9739 and tr_A0A2Y9TIG9_A0A2Y9TIG9_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3VIL4_A0A2U3VIL4_ODORO_9708 and tr_A0A2U3YWG4_A0A2U3YWG4_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9S6M9_A0A2Y9S6M9_PHYCD_9755 and tr_A0A384B8X0_A0A384B8X0_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 59

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/3_mltree/Q96Q27.raxml.reduced.phy

Alignment comprises 1 partitions and 216 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 216 / 216
Gaps: 4.57 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/3_mltree/Q96Q27.raxml.rba

Parallelization scheme autoconfig: 4 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 998 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 216 / 17280
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -440771.227907] Initial branch length optimization
[00:00:06 -376904.376154] Model parameter optimization (eps = 10.000000)
[00:01:14 -375445.009304] AUTODETECT spr round 1 (radius: 5)
[00:04:37 -271098.057070] AUTODETECT spr round 2 (radius: 10)
[00:08:21 -209542.988174] AUTODETECT spr round 3 (radius: 15)
[00:12:23 -178131.127002] AUTODETECT spr round 4 (radius: 20)
[00:16:53 -165749.528209] AUTODETECT spr round 5 (radius: 25)
[00:22:02 -164720.698596] SPR radius for FAST iterations: 25 (autodetect)
[00:22:02 -164720.698596] Model parameter optimization (eps = 3.000000)
[00:22:09 -164718.626671] FAST spr round 1 (radius: 25)
[00:27:12 -150959.761296] FAST spr round 2 (radius: 25)
[00:30:56 -149634.715960] FAST spr round 3 (radius: 25)
[00:34:06 -149483.907935] FAST spr round 4 (radius: 25)
[00:36:59 -149469.997720] FAST spr round 5 (radius: 25)
[00:39:38 -149463.629998] FAST spr round 6 (radius: 25)
[00:42:12 -149463.124619] FAST spr round 7 (radius: 25)
[00:44:42 -149463.124156] Model parameter optimization (eps = 1.000000)
[00:45:03 -149355.220551] SLOW spr round 1 (radius: 5)
[00:48:28 -149292.561091] SLOW spr round 2 (radius: 5)
[00:51:45 -149271.722046] SLOW spr round 3 (radius: 5)
[00:55:00 -149265.460858] SLOW spr round 4 (radius: 5)
[00:58:11 -149261.888993] SLOW spr round 5 (radius: 5)
[01:01:17 -149261.888352] SLOW spr round 6 (radius: 10)
[01:04:29 -149248.340591] SLOW spr round 7 (radius: 5)
[01:08:20 -149238.827400] SLOW spr round 8 (radius: 5)
[01:11:47 -149236.656890] SLOW spr round 9 (radius: 5)
[01:15:00 -149233.505770] SLOW spr round 10 (radius: 5)
[01:18:07 -149233.410915] SLOW spr round 11 (radius: 10)
[01:21:18 -149227.736077] SLOW spr round 12 (radius: 5)
[01:25:10 -149222.620114] SLOW spr round 13 (radius: 5)
[01:28:36 -149220.716559] SLOW spr round 14 (radius: 5)
[01:31:54 -149220.104642] SLOW spr round 15 (radius: 5)
[01:35:02 -149219.770241] SLOW spr round 16 (radius: 5)
[01:38:10 -149219.770087] SLOW spr round 17 (radius: 10)
[01:41:19 -149219.770083] SLOW spr round 18 (radius: 15)
[01:46:41 -149211.018973] SLOW spr round 19 (radius: 5)
[01:50:34 -149211.013912] SLOW spr round 20 (radius: 10)
[01:54:22 -149211.013398] SLOW spr round 21 (radius: 15)
[01:59:18 -149208.929561] SLOW spr round 22 (radius: 5)
[02:03:13 -149208.029405] SLOW spr round 23 (radius: 5)
[02:06:42 -149208.029396] SLOW spr round 24 (radius: 10)
[02:10:02 -149207.504985] SLOW spr round 25 (radius: 5)
[02:13:46 -149205.921459] SLOW spr round 26 (radius: 5)
[02:17:08 -149205.921403] SLOW spr round 27 (radius: 10)
[02:20:25 -149205.921403] SLOW spr round 28 (radius: 15)
[02:25:35 -149205.462797] SLOW spr round 29 (radius: 5)
[02:29:30 -149204.476604] SLOW spr round 30 (radius: 5)
[02:32:58 -149204.476526] SLOW spr round 31 (radius: 10)
[02:36:18 -149204.476526] SLOW spr round 32 (radius: 15)
[02:41:22 -149204.476526] SLOW spr round 33 (radius: 20)
[02:48:37 -149201.479560] SLOW spr round 34 (radius: 5)
[02:52:37 -149200.638225] SLOW spr round 35 (radius: 5)
[02:56:09 -149200.638189] SLOW spr round 36 (radius: 10)
[02:59:32 -149200.638189] SLOW spr round 37 (radius: 15)
[03:04:34 -149200.638189] SLOW spr round 38 (radius: 20)
[03:09:56] [worker #2] ML tree search #3, logLikelihood: -149285.597818
[03:11:49 -149200.638189] SLOW spr round 39 (radius: 25)
[03:21:31 -149200.638189] Model parameter optimization (eps = 0.100000)

[03:21:42] [worker #0] ML tree search #1, logLikelihood: -149200.379161

[03:21:42 -441270.586074] Initial branch length optimization
[03:21:49 -377709.543055] Model parameter optimization (eps = 10.000000)
[03:22:52 -376108.363826] AUTODETECT spr round 1 (radius: 5)
[03:26:15 -270096.864940] AUTODETECT spr round 2 (radius: 10)
[03:29:57 -214398.955588] AUTODETECT spr round 3 (radius: 15)
[03:33:56 -188340.505532] AUTODETECT spr round 4 (radius: 20)
[03:37:25] [worker #1] ML tree search #2, logLikelihood: -149328.812927
[03:38:54 -170679.945344] AUTODETECT spr round 5 (radius: 25)
[03:44:53 -166070.587944] SPR radius for FAST iterations: 25 (autodetect)
[03:44:53 -166070.587944] Model parameter optimization (eps = 3.000000)
[03:45:21 -165968.611424] FAST spr round 1 (radius: 25)
[03:50:26 -150054.479662] FAST spr round 2 (radius: 25)
[03:54:15 -149532.065442] FAST spr round 3 (radius: 25)
[03:57:29 -149424.229432] FAST spr round 4 (radius: 25)
[04:00:27 -149406.085594] FAST spr round 5 (radius: 25)
[04:03:11 -149401.668430] FAST spr round 6 (radius: 25)
[04:05:48 -149394.715680] FAST spr round 7 (radius: 25)
[04:08:20 -149394.713414] Model parameter optimization (eps = 1.000000)
[04:08:32 -149390.355147] SLOW spr round 1 (radius: 5)
[04:11:58 -149299.885149] SLOW spr round 2 (radius: 5)
[04:15:17 -149290.073590] SLOW spr round 3 (radius: 5)
[04:18:33 -149284.132094] SLOW spr round 4 (radius: 5)
[04:21:46 -149281.179696] SLOW spr round 5 (radius: 5)
[04:24:52 -149281.179499] SLOW spr round 6 (radius: 10)
[04:28:09 -149272.310436] SLOW spr round 7 (radius: 5)
[04:32:03 -149251.791745] SLOW spr round 8 (radius: 5)
[04:35:30 -149249.515956] SLOW spr round 9 (radius: 5)
[04:38:51 -149248.533220] SLOW spr round 10 (radius: 5)
[04:42:00 -149248.533075] SLOW spr round 11 (radius: 10)
[04:45:13 -149247.702787] SLOW spr round 12 (radius: 5)
[04:49:00 -149247.702537] SLOW spr round 13 (radius: 10)
[04:52:41 -149247.494366] SLOW spr round 14 (radius: 5)
[04:56:22 -149247.494013] SLOW spr round 15 (radius: 10)
[04:59:38] [worker #3] ML tree search #4, logLikelihood: -149263.809674
[04:59:59 -149247.494011] SLOW spr round 16 (radius: 15)
[05:05:04 -149240.728652] SLOW spr round 17 (radius: 5)
[05:09:05 -149237.375279] SLOW spr round 18 (radius: 5)
[05:12:34 -149237.375179] SLOW spr round 19 (radius: 10)
[05:13:15] [worker #2] ML tree search #7, logLikelihood: -149260.196336
[05:16:03 -149237.375177] SLOW spr round 20 (radius: 15)
[05:21:16 -149236.693408] SLOW spr round 21 (radius: 5)
[05:25:13 -149234.268161] SLOW spr round 22 (radius: 5)
[05:28:43 -149234.268139] SLOW spr round 23 (radius: 10)
[05:32:12 -149232.496675] SLOW spr round 24 (radius: 5)
[05:35:56 -149232.477150] SLOW spr round 25 (radius: 10)
[05:39:36 -149232.477032] SLOW spr round 26 (radius: 15)
[05:44:42 -149232.477031] SLOW spr round 27 (radius: 20)
[05:52:22 -149231.671765] SLOW spr round 28 (radius: 5)
[05:56:27 -149229.805226] SLOW spr round 29 (radius: 5)
[06:00:01 -149229.804848] SLOW spr round 30 (radius: 10)
[06:02:38] [worker #1] ML tree search #6, logLikelihood: -149293.745479
[06:03:34 -149228.483939] SLOW spr round 31 (radius: 5)
[06:07:16 -149228.482841] SLOW spr round 32 (radius: 10)
[06:10:58 -149228.482801] SLOW spr round 33 (radius: 15)
[06:16:04 -149228.482799] SLOW spr round 34 (radius: 20)
[06:23:50 -149228.482799] SLOW spr round 35 (radius: 25)
[06:34:01 -149228.482799] Model parameter optimization (eps = 0.100000)

[06:34:24] [worker #0] ML tree search #5, logLikelihood: -149226.346069

[06:34:25 -440498.650398] Initial branch length optimization
[06:34:32 -376478.604585] Model parameter optimization (eps = 10.000000)
[06:35:37 -374916.985762] AUTODETECT spr round 1 (radius: 5)
[06:39:03 -267851.853167] AUTODETECT spr round 2 (radius: 10)
[06:42:49 -203718.560367] AUTODETECT spr round 3 (radius: 15)
[06:46:54 -180240.473169] AUTODETECT spr round 4 (radius: 20)
[06:51:18 -168046.630803] AUTODETECT spr round 5 (radius: 25)
[06:56:42 -166048.510866] SPR radius for FAST iterations: 25 (autodetect)
[06:56:42 -166048.510866] Model parameter optimization (eps = 3.000000)
[06:56:51 -166047.573967] FAST spr round 1 (radius: 25)
[07:01:51 -150971.890413] FAST spr round 2 (radius: 25)
[07:05:50 -149713.520591] FAST spr round 3 (radius: 25)
[07:09:19 -149529.756148] FAST spr round 4 (radius: 25)
[07:12:29 -149496.703779] FAST spr round 5 (radius: 25)
[07:15:32 -149465.182565] FAST spr round 6 (radius: 25)
[07:18:10 -149455.294600] FAST spr round 7 (radius: 25)
[07:20:44 -149453.078231] FAST spr round 8 (radius: 25)
[07:23:15 -149453.078224] Model parameter optimization (eps = 1.000000)
[07:23:39 -149347.110734] SLOW spr round 1 (radius: 5)
[07:27:10 -149324.570966] SLOW spr round 2 (radius: 5)
[07:30:32 -149315.695205] SLOW spr round 3 (radius: 5)
[07:33:51 -149313.209161] SLOW spr round 4 (radius: 5)
[07:37:03 -149313.019454] SLOW spr round 5 (radius: 5)
[07:40:12 -149313.019432] SLOW spr round 6 (radius: 10)
[07:43:31 -149303.483174] SLOW spr round 7 (radius: 5)
[07:47:31 -149298.737248] SLOW spr round 8 (radius: 5)
[07:50:56 -149298.737094] SLOW spr round 9 (radius: 10)
[07:54:18 -149297.916627] SLOW spr round 10 (radius: 5)
[07:58:02 -149297.916242] SLOW spr round 11 (radius: 10)
[08:01:42 -149297.488571] SLOW spr round 12 (radius: 5)
[08:04:14] [worker #3] ML tree search #8, logLikelihood: -149205.023201
[08:05:24 -149297.488571] SLOW spr round 13 (radius: 10)
[08:09:01 -149297.423642] SLOW spr round 14 (radius: 15)
[08:14:07 -149292.583816] SLOW spr round 15 (radius: 5)
[08:18:11 -149288.049253] SLOW spr round 16 (radius: 5)
[08:21:45 -149285.756956] SLOW spr round 17 (radius: 5)
[08:25:02 -149285.406046] SLOW spr round 18 (radius: 5)
[08:28:14 -149284.401978] SLOW spr round 19 (radius: 5)
[08:31:24 -149282.925620] SLOW spr round 20 (radius: 5)
[08:34:31 -149282.924439] SLOW spr round 21 (radius: 10)
[08:37:42 -149282.924401] SLOW spr round 22 (radius: 15)
[08:43:04 -149282.532344] SLOW spr round 23 (radius: 5)
[08:46:58 -149282.531391] SLOW spr round 24 (radius: 10)
[08:50:53 -149279.852049] SLOW spr round 25 (radius: 5)
[08:54:38 -149276.398609] SLOW spr round 26 (radius: 5)
[08:57:59 -149276.397858] SLOW spr round 27 (radius: 10)
[09:01:17 -149276.340049] SLOW spr round 28 (radius: 15)
[09:05:17] [worker #2] ML tree search #11, logLikelihood: -149336.721924
[09:06:24 -149275.830088] SLOW spr round 29 (radius: 5)
[09:10:20 -149274.643240] SLOW spr round 30 (radius: 5)
[09:13:50 -149274.505352] SLOW spr round 31 (radius: 5)
[09:17:06 -149274.505326] SLOW spr round 32 (radius: 10)
[09:20:21 -149274.505326] SLOW spr round 33 (radius: 15)
[09:25:31 -149274.505326] SLOW spr round 34 (radius: 20)
[09:32:45 -149272.847818] SLOW spr round 35 (radius: 5)
[09:36:47 -149272.414376] SLOW spr round 36 (radius: 5)
[09:40:19 -149272.414229] SLOW spr round 37 (radius: 10)
[09:43:47 -149272.414226] SLOW spr round 38 (radius: 15)
[09:48:47 -149272.414226] SLOW spr round 39 (radius: 20)
[09:56:04 -149272.414226] SLOW spr round 40 (radius: 25)
[09:59:45] [worker #1] ML tree search #10, logLikelihood: -149257.854028
[10:06:22 -149272.414226] Model parameter optimization (eps = 0.100000)

[10:06:41] [worker #0] ML tree search #9, logLikelihood: -149272.048574

[10:06:41 -441827.995506] Initial branch length optimization
[10:06:48 -378339.030800] Model parameter optimization (eps = 10.000000)
[10:08:01 -376576.208711] AUTODETECT spr round 1 (radius: 5)
[10:11:29 -274458.985763] AUTODETECT spr round 2 (radius: 10)
[10:15:19 -210476.681706] AUTODETECT spr round 3 (radius: 15)
[10:19:29 -187163.143585] AUTODETECT spr round 4 (radius: 20)
[10:24:03 -174187.571715] AUTODETECT spr round 5 (radius: 25)
[10:29:38 -172616.575861] SPR radius for FAST iterations: 25 (autodetect)
[10:29:38 -172616.575861] Model parameter optimization (eps = 3.000000)
[10:29:47 -172615.318761] FAST spr round 1 (radius: 25)
[10:35:17 -154001.251201] FAST spr round 2 (radius: 25)
[10:39:27 -150549.477288] FAST spr round 3 (radius: 25)
[10:42:54 -149569.976289] FAST spr round 4 (radius: 25)
[10:46:07 -149460.290593] FAST spr round 5 (radius: 25)
[10:48:57 -149444.965424] FAST spr round 6 (radius: 25)
[10:51:41 -149432.657474] FAST spr round 7 (radius: 25)
[10:54:17 -149432.657434] Model parameter optimization (eps = 1.000000)
[10:54:23 -149432.466030] SLOW spr round 1 (radius: 5)
[10:58:02 -149395.458403] SLOW spr round 2 (radius: 5)
[11:01:25 -149391.915116] SLOW spr round 3 (radius: 5)
[11:04:41 -149388.460519] SLOW spr round 4 (radius: 5)
[11:07:55 -149387.697169] SLOW spr round 5 (radius: 5)
[11:11:08 -149387.486131] SLOW spr round 6 (radius: 5)
[11:14:20 -149387.195992] SLOW spr round 7 (radius: 5)
[11:17:29 -149385.523874] SLOW spr round 8 (radius: 5)
[11:20:37 -149385.522822] SLOW spr round 9 (radius: 10)
[11:23:54 -149379.632248] SLOW spr round 10 (radius: 5)
[11:27:44 -149378.544817] SLOW spr round 11 (radius: 5)
[11:31:12 -149378.544786] SLOW spr round 12 (radius: 10)
[11:34:38 -149376.862213] SLOW spr round 13 (radius: 5)
[11:38:28 -149373.498346] SLOW spr round 14 (radius: 5)
[11:41:55 -149373.498003] SLOW spr round 15 (radius: 10)
[11:45:17 -149373.497999] SLOW spr round 16 (radius: 15)
[11:49:21] [worker #3] ML tree search #12, logLikelihood: -149250.212062
[11:50:43 -149360.515504] SLOW spr round 17 (radius: 5)
[11:54:47 -149352.049554] SLOW spr round 18 (radius: 5)
[11:58:21 -149351.740065] SLOW spr round 19 (radius: 5)
[12:01:41 -149351.740027] SLOW spr round 20 (radius: 10)
[12:05:00 -149351.740026] SLOW spr round 21 (radius: 15)
[12:10:30 -149351.740026] SLOW spr round 22 (radius: 20)
[12:17:52 -149351.740026] SLOW spr round 23 (radius: 25)
[12:27:58 -149351.740026] Model parameter optimization (eps = 0.100000)

[12:28:04] [worker #0] ML tree search #13, logLikelihood: -149351.735905

[12:28:04 -442896.986964] Initial branch length optimization
[12:28:09 -378020.576350] Model parameter optimization (eps = 10.000000)
[12:29:12 -376415.732219] AUTODETECT spr round 1 (radius: 5)
[12:32:14] [worker #1] ML tree search #14, logLikelihood: -149275.835768
[12:32:41 -270597.536390] AUTODETECT spr round 2 (radius: 10)
[12:36:29 -204133.976408] AUTODETECT spr round 3 (radius: 15)
[12:40:21 -186016.175035] AUTODETECT spr round 4 (radius: 20)
[12:44:40 -177499.950172] AUTODETECT spr round 5 (radius: 25)
[12:49:42 -169484.425210] SPR radius for FAST iterations: 25 (autodetect)
[12:49:42 -169484.425210] Model parameter optimization (eps = 3.000000)
[12:50:02 -169382.952531] FAST spr round 1 (radius: 25)
[12:55:22 -150467.951841] FAST spr round 2 (radius: 25)
[12:59:18 -149483.083996] FAST spr round 3 (radius: 25)
[13:02:39 -149351.489042] FAST spr round 4 (radius: 25)
[13:05:37 -149344.357213] FAST spr round 5 (radius: 25)
[13:08:19 -149336.698226] FAST spr round 6 (radius: 25)
[13:10:54 -149336.686984] Model parameter optimization (eps = 1.000000)
[13:11:02 -149336.374483] SLOW spr round 1 (radius: 5)
[13:14:37 -149276.347948] SLOW spr round 2 (radius: 5)
[13:15:44] [worker #2] ML tree search #15, logLikelihood: -149223.624584
[13:18:01 -149269.713963] SLOW spr round 3 (radius: 5)
[13:21:16 -149267.008898] SLOW spr round 4 (radius: 5)
[13:24:26 -149267.008639] SLOW spr round 5 (radius: 10)
[13:27:43 -149259.610164] SLOW spr round 6 (radius: 5)
[13:31:35 -149256.536488] SLOW spr round 7 (radius: 5)
[13:35:02 -149256.535859] SLOW spr round 8 (radius: 10)
[13:38:29 -149255.976947] SLOW spr round 9 (radius: 5)
[13:42:23 -149254.088254] SLOW spr round 10 (radius: 5)
[13:45:49 -149254.087820] SLOW spr round 11 (radius: 10)
[13:49:18 -149254.087809] SLOW spr round 12 (radius: 15)
[13:54:33 -149252.917187] SLOW spr round 13 (radius: 5)
[13:58:32 -149249.562100] SLOW spr round 14 (radius: 5)
[14:02:05 -149249.562097] SLOW spr round 15 (radius: 10)
[14:05:36 -149249.562097] SLOW spr round 16 (radius: 15)
[14:10:45 -149248.839400] SLOW spr round 17 (radius: 5)
[14:14:42 -149248.718405] SLOW spr round 18 (radius: 5)
[14:18:14 -149248.717661] SLOW spr round 19 (radius: 10)
[14:21:41 -149248.525888] SLOW spr round 20 (radius: 5)
[14:25:30 -149247.044195] SLOW spr round 21 (radius: 5)
[14:28:53 -149247.044161] SLOW spr round 22 (radius: 10)
[14:32:15 -149247.044160] SLOW spr round 23 (radius: 15)
[14:37:27 -149245.224676] SLOW spr round 24 (radius: 5)
[14:41:35 -149239.114049] SLOW spr round 25 (radius: 5)
[14:45:08 -149238.603582] SLOW spr round 26 (radius: 5)
[14:48:27 -149238.603371] SLOW spr round 27 (radius: 10)
[14:51:47 -149236.566449] SLOW spr round 28 (radius: 5)
[14:55:37 -149236.299505] SLOW spr round 29 (radius: 5)
[14:56:18] [worker #3] ML tree search #16, logLikelihood: -149209.217312
[14:59:05 -149233.872367] SLOW spr round 30 (radius: 5)
[15:02:20 -149233.872294] SLOW spr round 31 (radius: 10)
[15:05:38 -149233.625565] SLOW spr round 32 (radius: 5)
[15:09:31 -149229.894810] SLOW spr round 33 (radius: 5)
[15:13:00 -149220.860789] SLOW spr round 34 (radius: 5)
[15:16:13 -149220.860753] SLOW spr round 35 (radius: 10)
[15:19:28 -149220.860753] SLOW spr round 36 (radius: 15)
[15:24:42 -149215.615319] SLOW spr round 37 (radius: 5)
[15:28:43 -149215.078480] SLOW spr round 38 (radius: 5)
[15:32:14 -149215.078318] SLOW spr round 39 (radius: 10)
[15:35:43 -149215.078315] SLOW spr round 40 (radius: 15)
[15:40:49 -149215.078315] SLOW spr round 41 (radius: 20)
[15:42:24] [worker #1] ML tree search #18, logLikelihood: -149391.175975
[15:48:05 -149213.103596] SLOW spr round 42 (radius: 5)
[15:52:10 -149212.488927] SLOW spr round 43 (radius: 5)
[15:55:45 -149212.488669] SLOW spr round 44 (radius: 10)
[15:59:16 -149212.488666] SLOW spr round 45 (radius: 15)
[16:04:17 -149212.488666] SLOW spr round 46 (radius: 20)
[16:11:30 -149212.488666] SLOW spr round 47 (radius: 25)
[16:21:27 -149212.488666] Model parameter optimization (eps = 0.100000)

[16:21:33] [worker #0] ML tree search #17, logLikelihood: -149212.485374

[16:43:02] [worker #2] ML tree search #19, logLikelihood: -149270.400464
[20:38:37] [worker #3] ML tree search #20, logLikelihood: -149209.924618

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.176312,0.382621) (0.193784,0.453008) (0.398265,1.078051) (0.231638,1.793327) 
   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: -149200.379161

AIC score: 302398.758323 / AICc score: 8298398.758323 / BIC score: 309145.939860
Free parameters (model + branch lengths): 1999

WARNING: Number of free parameters (K=1999) is larger than alignment size (n=216).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/3_mltree/Q96Q27.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/3_mltree/Q96Q27.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/3_mltree/Q96Q27.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96Q27/3_mltree/Q96Q27.raxml.log

Analysis started: 05-Jul-2021 19:47:37 / finished: 06-Jul-2021 16:26:14

Elapsed time: 74317.489 seconds