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 05-Jul-2021 04:41:18 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/2_msa/Q9H902_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/3_mltree/Q9H902 --seed 2 --threads 4 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/2_msa/Q9H902_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 201 sites

WARNING: Sequences sp_Q8BGH4_REEP1_MOUSE_10090 and tr_D4A193_D4A193_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3YD65_M3YD65_MUSPF_9669 and tr_G1MDP1_G1MDP1_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YD65_M3YD65_MUSPF_9669 and tr_M3XAD9_M3XAD9_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3YD65_M3YD65_MUSPF_9669 and tr_A0A2U3VRW9_A0A2U3VRW9_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YD65_M3YD65_MUSPF_9669 and tr_A0A2Y9IK63_A0A2Y9IK63_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2YAD9_A0A2I2YAD9_GORGO_9595 and sp_Q00765_REEP5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YAD9_A0A2I2YAD9_GORGO_9595 and tr_F6VJ89_F6VJ89_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I2YAD9_A0A2I2YAD9_GORGO_9595 and tr_A0A0D9RQZ8_A0A0D9RQZ8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I2YES5_A0A2I2YES5_GORGO_9595 and tr_A0A2K5XD57_A0A2K5XD57_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2YES5_A0A2I2YES5_GORGO_9595 and tr_A0A2R9BZ28_A0A2R9BZ28_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QPB5_G3QPB5_GORGO_9595 and sp_Q9H6H4_REEP4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NAS3_H2NAS3_PONAB_9601 and tr_A0A2Y9RTF6_A0A2Y9RTF6_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_B9PLF1_B9PLF1_TOXGV_432359 and tr_A0A074T4E9_A0A074T4E9_HAMHA_99158 are exactly identical!
WARNING: Sequences tr_A0A2I3TJX4_A0A2I3TJX4_PANTR_9598 and tr_A0A2I3MJV5_A0A2I3MJV5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3TJX4_A0A2I3TJX4_PANTR_9598 and tr_A0A2K5MTH8_A0A2K5MTH8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G2HFX9_G2HFX9_PANTR_9598 and tr_A0A2R9BBT2_A0A2R9BBT2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QRK6_H2QRK6_PANTR_9598 and tr_A0A2R9AKI9_A0A2R9AKI9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7CAY1_K7CAY1_PANTR_9598 and sp_Q6NUK4_REEP3_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q9H902_REEP1_HUMAN_9606 and tr_A0A0D9RUV5_A0A0D9RUV5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A0E0G0B3_A0A0E0G0B3_ORYNI_4536 and tr_B8AH15_B8AH15_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0G0B3_A0A0E0G0B3_ORYNI_4536 and tr_I1NWP6_I1NWP6_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0G0B3_A0A0E0G0B3_ORYNI_4536 and tr_A0A0E0N908_A0A0E0N908_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0G0B3_A0A0E0G0B3_ORYNI_4536 and tr_A0A0D3EZZ1_A0A0D3EZZ1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0G0B3_A0A0E0G0B3_ORYNI_4536 and tr_A0A0D9YLH4_A0A0D9YLH4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0GJR5_A0A0E0GJR5_ORYNI_4536 and tr_A0A0D3FG98_A0A0D3FG98_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_H9FVE8_H9FVE8_MACMU_9544 and tr_A0A096MZY9_A0A096MZY9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H9FVE8_H9FVE8_MACMU_9544 and tr_A0A2K5N8U6_A0A2K5N8U6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H9FVE8_H9FVE8_MACMU_9544 and tr_A0A2K6DU35_A0A2K6DU35_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A2XEL0_A2XEL0_ORYSI_39946 and tr_I1P9I4_I1P9I4_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_B8BDV3_B8BDV3_ORYSI_39946 and tr_I1QQQ3_I1QQQ3_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_F4PA41_F4PA41_BATDJ_684364 and tr_A0A177WWV0_A0A177WWV0_BATDE_403673 are exactly identical!
WARNING: Sequences tr_F2SJF7_F2SJF7_TRIRC_559305 and tr_A0A178EPR6_A0A178EPR6_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G7PCP4_G7PCP4_MACFA_9541 and tr_A0A0D9RVH8_A0A0D9RVH8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7PCP4_G7PCP4_MACFA_9541 and tr_A0A2K6B5B7_A0A2K6B5B7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PCP4_G7PCP4_MACFA_9541 and tr_A0A2K5Z1Y8_A0A2K5Z1Y8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F1MDM4_F1MDM4_BOVIN_9913 and sp_Q29RM3_REEP5_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M4DL86_M4DL86_BRARP_51351 and tr_A0A078I2C8_A0A078I2C8_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4DL86_M4DL86_BRARP_51351 and tr_A0A0D3C4H6_A0A0D3C4H6_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M8A6E8_M8A6E8_TRIUA_4572 and tr_A0A3B6HRE2_A0A3B6HRE2_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A015J1C1_A0A015J1C1_9GLOM_1432141 and tr_A0A2H5T405_A0A2H5T405_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015KT33_A0A015KT33_9GLOM_1432141 and tr_A0A2I1FVA9_A0A2I1FVA9_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015KT33_A0A015KT33_9GLOM_1432141 and tr_A0A2H5SXL6_A0A2H5SXL6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A044V472_A0A044V472_ONCVO_6282 and tr_A0A182E730_A0A182E730_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A067EJR8_A0A067EJR8_CITSI_2711 and tr_V4S7N8_V4S7N8_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067FWP9_A0A067FWP9_CITSI_2711 and tr_V4S775_V4S775_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A2I3MKK2_A0A2I3MKK2_PAPAN_9555 and tr_A0A2K5KP13_A0A2K5KP13_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3NEW5_A0A2I3NEW5_PAPAN_9555 and tr_A0A2K5P0U9_A0A2K5P0U9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3NEW5_A0A2I3NEW5_PAPAN_9555 and tr_A0A2K6E9S9_A0A2K6E9S9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A067D0L7_A0A067D0L7_SAPPC_695850 and tr_T0QUZ6_T0QUZ6_9STRA_1156394 are exactly identical!
WARNING: Sequences tr_A0A0W8CBA0_A0A0W8CBA0_PHYNI_4790 and tr_W2M6A0_W2M6A0_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A091IR46_A0A091IR46_EGRGA_188379 and tr_A0A091VMS9_A0A091VMS9_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091IR46_A0A091IR46_EGRGA_188379 and tr_A0A087QKJ6_A0A087QKJ6_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091IR46_A0A091IR46_EGRGA_188379 and tr_A0A0A0A9L2_A0A0A0A9L2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0L9V2K0_A0A0L9V2K0_PHAAN_3914 and tr_A0A1S3U931_A0A1S3U931_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A0L9V2K0_A0A0L9V2K0_PHAAN_3914 and tr_A0A3Q0F334_A0A3Q0F334_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A0V0RWL5_A0A0V0RWL5_9BILA_6336 and tr_A0A0V0WG93_A0A0V0WG93_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0RWL5_A0A0V0RWL5_9BILA_6336 and tr_A0A0V1LLJ1_A0A0V1LLJ1_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0RWL5_A0A0V0RWL5_9BILA_6336 and tr_A0A0V1NU01_A0A0V1NU01_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A1S4A883_A0A1S4A883_TOBAC_4097 and tr_A0A1U7VBQ7_A0A1U7VBQ7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BNI3_A0A1S4BNI3_TOBAC_4097 and tr_A0A1U7V684_A0A1U7V684_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BYK1_A0A1S4BYK1_TOBAC_4097 and tr_A0A1U7WCA1_A0A1U7WCA1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2D0SAF4_A0A2D0SAF4_ICTPU_7998 and tr_A0A2D0SB80_A0A2D0SB80_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3UZG8_A0A2U3UZG8_TURTR_9739 and tr_A0A2Y9PPA5_A0A2Y9PPA5_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3UZG8_A0A2U3UZG8_TURTR_9739 and tr_A0A2Y9STR1_A0A2Y9STR1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3UZG8_A0A2U3UZG8_TURTR_9739 and tr_A0A383ZB47_A0A383ZB47_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2U4BDV5_A0A2U4BDV5_TURTR_9739 and tr_A0A2Y9MGB8_A0A2Y9MGB8_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 66

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/Q9H902/3_mltree/Q9H902.raxml.reduced.phy

Alignment comprises 1 partitions and 201 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 201 / 201
Gaps: 15.07 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/3_mltree/Q9H902.raxml.rba

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

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 201 / 16080
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -332704.675681] Initial branch length optimization
[00:00:05 -269773.984956] Model parameter optimization (eps = 10.000000)
[00:01:02 -267157.155997] AUTODETECT spr round 1 (radius: 5)
[00:04:19 -191003.865189] AUTODETECT spr round 2 (radius: 10)
[00:07:55 -150005.465142] AUTODETECT spr round 3 (radius: 15)
[00:11:41 -135187.917050] AUTODETECT spr round 4 (radius: 20)
[00:16:20 -120562.839158] AUTODETECT spr round 5 (radius: 25)
[00:21:35 -108744.859748] SPR radius for FAST iterations: 25 (autodetect)
[00:21:35 -108744.859748] Model parameter optimization (eps = 3.000000)
[00:22:06 -108676.456238] FAST spr round 1 (radius: 25)
[00:26:01 -90656.992929] FAST spr round 2 (radius: 25)
[00:28:57 -87910.268680] FAST spr round 3 (radius: 25)
[00:31:30 -87705.794144] FAST spr round 4 (radius: 25)
[00:33:56 -87682.965586] FAST spr round 5 (radius: 25)
[00:36:09 -87682.965312] Model parameter optimization (eps = 1.000000)
[00:36:31 -87662.187571] SLOW spr round 1 (radius: 5)
[00:39:32 -87618.696441] SLOW spr round 2 (radius: 5)
[00:42:29 -87609.598332] SLOW spr round 3 (radius: 5)
[00:45:18 -87608.865080] SLOW spr round 4 (radius: 5)
[00:48:04 -87608.864918] SLOW spr round 5 (radius: 10)
[00:50:56 -87604.910949] SLOW spr round 6 (radius: 5)
[00:54:23 -87604.910893] SLOW spr round 7 (radius: 10)
[00:57:36 -87604.910890] SLOW spr round 8 (radius: 15)
[01:01:52 -87601.501647] SLOW spr round 9 (radius: 5)
[01:05:31 -87601.171783] SLOW spr round 10 (radius: 5)
[01:08:41 -87601.171683] SLOW spr round 11 (radius: 10)
[01:11:41 -87600.442877] SLOW spr round 12 (radius: 5)
[01:15:05 -87600.127061] SLOW spr round 13 (radius: 5)
[01:18:09 -87600.127001] SLOW spr round 14 (radius: 10)
[01:21:04 -87600.126999] SLOW spr round 15 (radius: 15)
[01:25:29 -87599.941381] SLOW spr round 16 (radius: 5)
[01:29:06 -87599.586667] SLOW spr round 17 (radius: 5)
[01:31:55] [worker #3] ML tree search #4, logLikelihood: -87590.825226
[01:32:17 -87599.586546] SLOW spr round 18 (radius: 10)
[01:35:17 -87599.586467] SLOW spr round 19 (radius: 15)
[01:39:43 -87599.586401] SLOW spr round 20 (radius: 20)
[01:45:41 -87599.552082] SLOW spr round 21 (radius: 25)
[01:51:46] [worker #2] ML tree search #3, logLikelihood: -87575.205212
[01:52:56 -87599.551758] Model parameter optimization (eps = 0.100000)

[01:53:13] [worker #0] ML tree search #1, logLikelihood: -87598.245639

[01:53:14 -331930.065089] Initial branch length optimization
[01:53:18 -270577.347414] Model parameter optimization (eps = 10.000000)
[01:54:35 -267989.462271] AUTODETECT spr round 1 (radius: 5)
[01:57:51 -191773.529033] AUTODETECT spr round 2 (radius: 10)
[02:00:33] [worker #1] ML tree search #2, logLikelihood: -87612.045000
[02:01:25 -147952.383012] AUTODETECT spr round 3 (radius: 15)
[02:05:28 -122952.056913] AUTODETECT spr round 4 (radius: 20)
[02:10:03 -107158.275444] AUTODETECT spr round 5 (radius: 25)
[02:15:25 -103307.210279] SPR radius for FAST iterations: 25 (autodetect)
[02:15:25 -103307.210279] Model parameter optimization (eps = 3.000000)
[02:16:05 -103235.254841] FAST spr round 1 (radius: 25)
[02:20:13 -88457.941421] FAST spr round 2 (radius: 25)
[02:23:15 -87722.954728] FAST spr round 3 (radius: 25)
[02:25:52 -87652.276353] FAST spr round 4 (radius: 25)
[02:28:19 -87640.174901] FAST spr round 5 (radius: 25)
[02:30:34 -87639.768679] FAST spr round 6 (radius: 25)
[02:32:46 -87639.767223] Model parameter optimization (eps = 1.000000)
[02:33:08 -87625.486023] SLOW spr round 1 (radius: 5)
[02:36:11 -87600.100822] SLOW spr round 2 (radius: 5)
[02:39:06 -87597.996898] SLOW spr round 3 (radius: 5)
[02:41:54 -87597.996702] SLOW spr round 4 (radius: 10)
[02:44:43 -87596.905575] SLOW spr round 5 (radius: 5)
[02:48:10 -87596.548954] SLOW spr round 6 (radius: 5)
[02:51:15 -87596.547314] SLOW spr round 7 (radius: 10)
[02:54:12 -87596.547127] SLOW spr round 8 (radius: 15)
[02:58:29 -87595.813573] SLOW spr round 9 (radius: 5)
[03:02:06 -87591.396112] SLOW spr round 10 (radius: 5)
[03:05:17 -87589.110792] SLOW spr round 11 (radius: 5)
[03:08:15 -87588.745789] SLOW spr round 12 (radius: 5)
[03:11:06 -87588.745788] SLOW spr round 13 (radius: 10)
[03:13:55 -87588.745788] SLOW spr round 14 (radius: 15)
[03:18:18 -87588.745787] SLOW spr round 15 (radius: 20)
[03:23:51 -87588.745787] SLOW spr round 16 (radius: 25)
[03:30:02] [worker #1] ML tree search #6, logLikelihood: -87597.934152
[03:30:43 -87588.745787] Model parameter optimization (eps = 0.100000)

[03:30:53] [worker #0] ML tree search #5, logLikelihood: -87588.548961

[03:30:53 -331322.861585] Initial branch length optimization
[03:30:57 -269890.256546] Model parameter optimization (eps = 10.000000)
[03:31:57 -267413.162887] AUTODETECT spr round 1 (radius: 5)
[03:35:09 -188055.296086] AUTODETECT spr round 2 (radius: 10)
[03:38:39 -143334.422846] AUTODETECT spr round 3 (radius: 15)
[03:42:27 -119279.427808] AUTODETECT spr round 4 (radius: 20)
[03:46:22 -110162.394297] AUTODETECT spr round 5 (radius: 25)
[03:51:11 -106391.317680] SPR radius for FAST iterations: 25 (autodetect)
[03:51:11 -106391.317680] Model parameter optimization (eps = 3.000000)
[03:51:34 -106323.235724] FAST spr round 1 (radius: 25)
[03:55:44 -88623.156822] FAST spr round 2 (radius: 25)
[03:58:51 -87710.011433] FAST spr round 3 (radius: 25)
[04:01:30 -87656.971273] FAST spr round 4 (radius: 25)
[04:03:52 -87651.254728] FAST spr round 5 (radius: 25)
[04:04:37] [worker #2] ML tree search #7, logLikelihood: -87579.888921
[04:06:05 -87651.254430] Model parameter optimization (eps = 1.000000)
[04:06:23 -87647.870051] SLOW spr round 1 (radius: 5)
[04:09:26 -87613.458715] SLOW spr round 2 (radius: 5)
[04:12:25 -87609.334785] SLOW spr round 3 (radius: 5)
[04:15:13 -87609.333801] SLOW spr round 4 (radius: 10)
[04:18:09 -87604.948204] SLOW spr round 5 (radius: 5)
[04:21:44 -87600.962761] SLOW spr round 6 (radius: 5)
[04:24:55 -87597.698979] SLOW spr round 7 (radius: 5)
[04:27:43] [worker #3] ML tree search #8, logLikelihood: -87592.025959
[04:27:52 -87595.266396] SLOW spr round 8 (radius: 5)
[04:30:46 -87591.680358] SLOW spr round 9 (radius: 5)
[04:33:33 -87591.679918] SLOW spr round 10 (radius: 10)
[04:36:24 -87591.679904] SLOW spr round 11 (radius: 15)
[04:41:05 -87591.679899] SLOW spr round 12 (radius: 20)
[04:47:09 -87591.679895] SLOW spr round 13 (radius: 25)
[04:52:49] [worker #1] ML tree search #10, logLikelihood: -87572.274844
[04:54:38 -87591.679890] Model parameter optimization (eps = 0.100000)

[04:54:49] [worker #0] ML tree search #9, logLikelihood: -87591.577636

[04:54:49 -333490.706457] Initial branch length optimization
[04:54:54 -270297.418121] Model parameter optimization (eps = 10.000000)
[04:56:01 -267665.055597] AUTODETECT spr round 1 (radius: 5)
[04:59:15 -186349.818294] AUTODETECT spr round 2 (radius: 10)
[05:02:42 -146797.829885] AUTODETECT spr round 3 (radius: 15)
[05:06:31 -123688.828160] AUTODETECT spr round 4 (radius: 20)
[05:10:59 -108827.664093] AUTODETECT spr round 5 (radius: 25)
[05:16:11 -103866.708217] SPR radius for FAST iterations: 25 (autodetect)
[05:16:11 -103866.708217] Model parameter optimization (eps = 3.000000)
[05:16:55 -103777.222181] FAST spr round 1 (radius: 25)
[05:21:14 -88615.891795] FAST spr round 2 (radius: 25)
[05:24:24 -87725.050175] FAST spr round 3 (radius: 25)
[05:27:01 -87666.900459] FAST spr round 4 (radius: 25)
[05:29:34 -87647.844840] FAST spr round 5 (radius: 25)
[05:31:50 -87644.337326] FAST spr round 6 (radius: 25)
[05:33:59 -87644.335423] Model parameter optimization (eps = 1.000000)
[05:34:20 -87630.494132] SLOW spr round 1 (radius: 5)
[05:37:30 -87604.330274] SLOW spr round 2 (radius: 5)
[05:40:28 -87602.101838] SLOW spr round 3 (radius: 5)
[05:43:18 -87599.410811] SLOW spr round 4 (radius: 5)
[05:46:05 -87599.410677] SLOW spr round 5 (radius: 10)
[05:48:58 -87597.613839] SLOW spr round 6 (radius: 5)
[05:50:17] [worker #2] ML tree search #11, logLikelihood: -87606.992503
[05:52:27 -87597.613650] SLOW spr round 7 (radius: 10)
[05:55:43 -87597.613638] SLOW spr round 8 (radius: 15)
[05:57:12] [worker #3] ML tree search #12, logLikelihood: -87586.834967
[06:00:01 -87597.234047] SLOW spr round 9 (radius: 5)
[06:03:38 -87597.232195] SLOW spr round 10 (radius: 10)
[06:07:04 -87597.232117] SLOW spr round 11 (radius: 15)
[06:11:16 -87597.162417] SLOW spr round 12 (radius: 20)
[06:17:21] [worker #1] ML tree search #14, logLikelihood: -87598.501220
[06:17:21 -87597.162377] SLOW spr round 13 (radius: 25)
[06:25:02 -87595.532634] SLOW spr round 14 (radius: 5)
[06:28:48 -87594.302017] SLOW spr round 15 (radius: 5)
[06:32:03 -87594.169913] SLOW spr round 16 (radius: 5)
[06:35:02 -87594.169887] SLOW spr round 17 (radius: 10)
[06:37:58 -87593.726064] SLOW spr round 18 (radius: 5)
[06:41:24 -87593.726014] SLOW spr round 19 (radius: 10)
[06:44:39 -87593.726008] SLOW spr round 20 (radius: 15)
[06:48:55 -87593.726002] SLOW spr round 21 (radius: 20)
[06:55:04 -87593.725997] SLOW spr round 22 (radius: 25)
[07:02:47 -87593.725991] Model parameter optimization (eps = 0.100000)

[07:03:00] [worker #0] ML tree search #13, logLikelihood: -87593.466217

[07:03:00 -328937.213148] Initial branch length optimization
[07:03:05 -268942.077993] Model parameter optimization (eps = 10.000000)
[07:03:56 -266531.634637] AUTODETECT spr round 1 (radius: 5)
[07:07:10 -188326.036894] AUTODETECT spr round 2 (radius: 10)
[07:10:40 -143226.833634] AUTODETECT spr round 3 (radius: 15)
[07:12:36] [worker #2] ML tree search #15, logLikelihood: -87610.665294
[07:14:28 -121779.158688] AUTODETECT spr round 4 (radius: 20)
[07:18:23 -113430.015390] AUTODETECT spr round 5 (radius: 25)
[07:22:47 -111964.400341] SPR radius for FAST iterations: 25 (autodetect)
[07:22:47 -111964.400341] Model parameter optimization (eps = 3.000000)
[07:23:18 -111886.245468] FAST spr round 1 (radius: 25)
[07:26:46] [worker #1] ML tree search #18, logLikelihood: -87627.748024
[07:27:17 -96334.541626] FAST spr round 2 (radius: 25)
[07:30:16 -95768.569960] FAST spr round 3 (radius: 25)
[07:30:40] [worker #3] ML tree search #16, logLikelihood: -87590.526182
[07:32:59 -89843.601409] FAST spr round 4 (radius: 25)
[07:35:25 -87729.040942] FAST spr round 5 (radius: 25)
[07:37:48 -87669.946652] FAST spr round 6 (radius: 25)
[07:40:04 -87656.818910] FAST spr round 7 (radius: 25)
[07:42:17 -87645.513196] FAST spr round 8 (radius: 25)
[07:44:25 -87645.512262] Model parameter optimization (eps = 1.000000)
[07:44:56 -87629.686446] SLOW spr round 1 (radius: 5)
[07:47:51 -87606.572671] SLOW spr round 2 (radius: 5)
[07:50:44 -87605.139877] SLOW spr round 3 (radius: 5)
[07:53:32 -87605.139818] SLOW spr round 4 (radius: 10)
[07:56:24 -87598.643400] SLOW spr round 5 (radius: 5)
[08:00:03 -87592.793945] SLOW spr round 6 (radius: 5)
[08:03:13 -87592.445376] SLOW spr round 7 (radius: 5)
[08:06:11 -87592.443761] SLOW spr round 8 (radius: 10)
[08:09:09 -87589.190631] SLOW spr round 9 (radius: 5)
[08:12:37 -87589.133716] SLOW spr round 10 (radius: 10)
[08:15:47 -87589.133691] SLOW spr round 11 (radius: 15)
[08:19:59 -87582.145318] SLOW spr round 12 (radius: 5)
[08:23:38 -87582.145200] SLOW spr round 13 (radius: 10)
[08:26:57 -87581.505762] SLOW spr round 14 (radius: 5)
[08:30:18 -87581.505622] SLOW spr round 15 (radius: 10)
[08:33:23 -87581.505565] SLOW spr round 16 (radius: 15)
[08:37:21 -87581.505504] SLOW spr round 17 (radius: 20)
[08:42:53 -87581.505440] SLOW spr round 18 (radius: 25)
[08:49:36 -87581.505375] Model parameter optimization (eps = 0.100000)

[08:49:43] [worker #0] ML tree search #17, logLikelihood: -87581.419505

[09:18:22] [worker #2] ML tree search #19, logLikelihood: -87577.133494
[09:29:37] [worker #3] ML tree search #20, logLikelihood: -87594.827296

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.140768,0.424170) (0.226251,0.574866) (0.378087,0.830408) (0.254895,1.946921) 
   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: -87572.274844

AIC score: 179154.549687 / AICc score: 8223214.549687 / BIC score: 185777.676028
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=201).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/3_mltree/Q9H902.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/3_mltree/Q9H902.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/3_mltree/Q9H902.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H902/3_mltree/Q9H902.raxml.log

Analysis started: 05-Jul-2021 04:41:18 / finished: 05-Jul-2021 14:10:56

Elapsed time: 34178.111 seconds

Consumed energy: 3054.474 Wh (= 15 km in an electric car, or 76 km with an e-scooter!)