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 02-Jul-2021 19:28:19 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/2_msa/Q00577_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577 --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/Q00577/2_msa/Q00577_trimmed_msa.fasta
[00:00:00] Loaded alignment with 406 taxa and 205 sites

WARNING: Sequences tr_R4GKR5_R4GKR5_CHICK_9031 and tr_A0A226MU76_A0A226MU76_CALSU_9009 are exactly identical!
WARNING: Sequences tr_R4GKR5_R4GKR5_CHICK_9031 and tr_A0A226P4I0_A0A226P4I0_COLVI_9014 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_M3YC66_M3YC66_MUSPF_9669 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_G3QIF9_G3QIF9_GORGO_9595 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_H2PGR4_H2PGR4_PONAB_9601 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_G1T0N5_G1T0N5_RABIT_9986 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_E2R2A4_E2R2A4_CANLF_9615 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_F7FSY5_F7FSY5_MONDO_13616 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_I3LVY7_I3LVY7_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_H0WMM7_H0WMM7_OTOGA_30611 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and sp_Q00577_PURA_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_F6T2C6_F6T2C6_MACMU_9544 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_G5BCQ6_G5BCQ6_HETGA_10181 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_G3WQB1_G3WQB1_SARHA_9305 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A2R8MMW8_A0A2R8MMW8_CALJA_9483 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_E1BMW9_E1BMW9_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A0D9S9H0_A0A0D9S9H0_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A1S2ZD82_A0A1S2ZD82_ERIEU_9365 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A1S3FI87_A0A1S3FI87_DIPOR_10020 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A3Q0D6Q5_A0A3Q0D6Q5_MESAU_10036 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A2U4AGJ4_A0A2U4AGJ4_TURTR_9739 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A2U3VRJ7_A0A2U3VRJ7_ODORO_9708 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A2Y9RI67_A0A2Y9RI67_TRIMA_127582 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A2Y9IT58_A0A2Y9IT58_ENHLU_391180 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A2Y9PHA3_A0A2Y9PHA3_DELLE_9749 are exactly identical!
WARNING: Sequences sp_P42669_PURA_MOUSE_10090 and tr_A0A2Y9SEJ6_A0A2Y9SEJ6_PHYCD_9755 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_A0A2I3H6G0_A0A2I3H6G0_NOMLE_61853 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_G3H626_G3H626_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_D3ZYS1_D3ZYS1_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and sp_Q9UJV8_PURG_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_I0FR81_I0FR81_MACMU_9544 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_G1MM22_G1MM22_AILME_9646 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_G7PD57_G7PD57_MACFA_9541 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_A0A2I3LS61_A0A2I3LS61_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_Q8R4E6_PURG_MOUSE_10090 and tr_A0A384BQF7_A0A384BQF7_URSMA_29073 are exactly identical!
WARNING: Sequences tr_W5JI09_W5JI09_ANODA_43151 and tr_Q7PPR8_Q7PPR8_ANOGA_7165 are exactly identical!
WARNING: Sequences tr_W5JI09_W5JI09_ANODA_43151 and tr_Q16N05_Q16N05_AEDAE_7159 are exactly identical!
WARNING: Sequences tr_W5JI09_W5JI09_ANODA_43151 and tr_A0A084VKX3_A0A084VKX3_ANOSI_74873 are exactly identical!
WARNING: Sequences tr_Q9V4D9_Q9V4D9_DROME_7227 and tr_B4IIX0_B4IIX0_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_H2QW00_H2QW00_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_I3NBV2_I3NBV2_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_F7IME5_F7IME5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A1U7T8K3_A0A1U7T8K3_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2K5NIA8_A0A2K5NIA8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2K6CUE0_A0A2K6CUE0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2K5XJR1_A0A2K5XJR1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2R9B1C9_A0A2R9B1C9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_H2PM71_H2PM71_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_G1U6F4_G1U6F4_RABIT_9986 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_H2RGZ5_H2RGZ5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and sp_Q68A21_PURB_RAT_10116 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_H0XWW9_H0XWW9_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_A0A286XVH5_A0A286XVH5_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and sp_Q96QR8_PURB_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_I2CY42_I2CY42_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_F6PGI5_F6PGI5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_A0A0D9SE08_A0A0D9SE08_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_A0A1U8CZB0_A0A1U8CZB0_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_A0A2K5L1U7_A0A2K5L1U7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_A0A2K6ATK1_A0A2K6ATK1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3SF88_G3SF88_GORGO_9595 and tr_A0A2R8ZA92_A0A2R8ZA92_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3ZZN1_M3ZZN1_XIPMA_8083 and tr_A0A087YR22_A0A087YR22_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M4B0T7_M4B0T7_XIPMA_8083 and tr_A0A087YLM3_A0A087YLM3_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A087ZNG2_A0A087ZNG2_APIME_7460 and tr_A0A0M9A712_A0A0M9A712_9HYME_166423 are exactly identical!
WARNING: Sequences tr_A0A087ZNG2_A0A087ZNG2_APIME_7460 and tr_A0A2A3E239_A0A2A3E239_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NMT9_A0A158NMT9_ATTCE_12957 and tr_A0A026WPX7_A0A026WPX7_OOCBI_2015173 are exactly identical!
WARNING: Sequences tr_A0A158NMT9_A0A158NMT9_ATTCE_12957 and tr_A0A151WVA1_A0A151WVA1_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A158NMT9_A0A158NMT9_ATTCE_12957 and tr_A0A151JBS4_A0A151JBS4_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158NMT9_A0A158NMT9_ATTCE_12957 and tr_A0A195BC11_A0A195BC11_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NMT9_A0A158NMT9_ATTCE_12957 and tr_A0A195EWT1_A0A195EWT1_9HYME_34720 are exactly identical!
WARNING: Sequences tr_I3KXW4_I3KXW4_ORENI_8128 and tr_A0A087YPR3_A0A087YPR3_POEFO_48698 are exactly identical!
WARNING: Sequences tr_I3KXW4_I3KXW4_ORENI_8128 and tr_A0A2I4CNE4_A0A2I4CNE4_9TELE_52670 are exactly identical!
WARNING: Sequences tr_I3KXW4_I3KXW4_ORENI_8128 and tr_A0A2U9C7D0_A0A2U9C7D0_SCOMX_52904 are exactly identical!
WARNING: Sequences tr_I3KYL7_I3KYL7_ORENI_8128 and tr_A0A2I4AHI4_A0A2I4AHI4_9TELE_52670 are exactly identical!
WARNING: Sequences tr_I3KZW7_I3KZW7_ORENI_8128 and tr_G3QBQ2_G3QBQ2_GASAC_69293 are exactly identical!
WARNING: Sequences tr_I3KZW7_I3KZW7_ORENI_8128 and tr_A0A087YPQ6_A0A087YPQ6_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A3B5KAS0_A0A3B5KAS0_TAKRU_31033 and tr_H3CXB5_H3CXB5_TETNG_99883 are exactly identical!
WARNING: Sequences tr_A0A286Y1B1_A0A286Y1B1_CAVPO_10141 and tr_G5C9Z0_G5C9Z0_HETGA_10181 are exactly identical!
WARNING: Sequences tr_A0A286Y1B1_A0A286Y1B1_CAVPO_10141 and tr_A0A091E4G4_A0A091E4G4_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_G3TSX8_G3TSX8_LOXAF_9785 and tr_A0A2Y9RE57_A0A2Y9RE57_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_A0A287A4H2_A0A287A4H2_PIG_9823 and tr_G3N0W8_G3N0W8_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A287A4H2_A0A287A4H2_PIG_9823 and tr_A0A2I2U5T1_A0A2I2U5T1_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A287A4H2_A0A287A4H2_PIG_9823 and tr_A0A2U4BN77_A0A2U4BN77_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A287A4H2_A0A287A4H2_PIG_9823 and tr_A0A2U3WX19_A0A2U3WX19_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A287A4H2_A0A287A4H2_PIG_9823 and tr_A0A2Y9KJB4_A0A2Y9KJB4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A287A4H2_A0A287A4H2_PIG_9823 and tr_A0A2Y9PUE8_A0A2Y9PUE8_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A287A4H2_A0A287A4H2_PIG_9823 and tr_A0A2Y9S4R1_A0A2Y9S4R1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_B3RKP5_B3RKP5_TRIAD_10228 and tr_A0A369SCN4_A0A369SCN4_9METZ_287889 are exactly identical!
WARNING: Sequences tr_M3WKB0_M3WKB0_FELCA_9685 and tr_A0A2U3ZNT6_A0A2U3ZNT6_ODORO_9708 are exactly identical!
WARNING: Sequences tr_W5LSR5_W5LSR5_ASTMX_7994 and tr_W5UAZ6_W5UAZ6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_W5NP59_W5NP59_LEPOC_7918 and tr_A0A1S3L1P4_A0A1S3L1P4_SALSA_8030 are exactly identical!
WARNING: Sequences tr_W5NP59_W5NP59_LEPOC_7918 and tr_A0A1S3RH74_A0A1S3RH74_SALSA_8030 are exactly identical!
WARNING: Sequences tr_W5NP59_W5NP59_LEPOC_7918 and tr_A0A060XIT1_A0A060XIT1_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_W5NP59_W5NP59_LEPOC_7918 and tr_A0A060Y9L0_A0A060Y9L0_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A091E2A4_A0A091E2A4_FUKDA_885580 and tr_A0A1U7T937_A0A1U7T937_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_A0A0Q3X6Z7_A0A0Q3X6Z7_AMAAE_12930 and tr_A0A218UPB4_A0A218UPB4_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A093PXU5_A0A093PXU5_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A091VGJ9_A0A091VGJ9_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A087R119_A0A087R119_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A0A0AIG8_A0A0A0AIG8_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0LMD3_A0A2I0LMD3_COLLI_8932 and tr_A0A1V4KZ58_A0A1V4KZ58_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1CYY4_A0A0V1CYY4_TRIBR_45882 and tr_A0A0V0V8K1_A0A0V0V8K1_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CYY4_A0A0V1CYY4_TRIBR_45882 and tr_A0A0V0ZXK0_A0A0V0ZXK0_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1CYY4_A0A0V1CYY4_TRIBR_45882 and tr_A0A0V1PBX8_A0A0V1PBX8_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CYY4_A0A0V1CYY4_TRIBR_45882 and tr_A0A0V0U9G0_A0A0V0U9G0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0WBC2_A0A0V0WBC2_9BILA_92179 and tr_A0A0V1KY99_A0A0V1KY99_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A1S3HVH5_A0A1S3HVH5_LINUN_7574 and tr_A0A1S3HVI1_A0A1S3HVI1_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3HVH5_A0A1S3HVH5_LINUN_7574 and tr_A0A1S3HVJ2_A0A1S3HVJ2_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3HVH5_A0A1S3HVH5_LINUN_7574 and tr_A0A1S3HY90_A0A1S3HY90_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3RQC6_A0A1S3RQC6_SALSA_8030 and tr_A0A060XIQ4_A0A060XIQ4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3SVX6_A0A1S3SVX6_SALSA_8030 and tr_A0A060Z1L3_A0A060Z1L3_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2U3XK48_A0A2U3XK48_LEPWE_9713 and tr_A0A2Y9J2F3_A0A2Y9J2F3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2Y9N135_A0A2Y9N135_DELLE_9749 and tr_A0A2Y9T8H8_A0A2Y9T8H8_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 113

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/Q00577/3_mltree/Q00577.raxml.reduced.phy

Alignment comprises 1 partitions and 205 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 205 / 205
Gaps: 8.28 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577.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 406 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 205 / 16400
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -87557.753096] Initial branch length optimization
[00:00:01 -66948.458375] Model parameter optimization (eps = 10.000000)
[00:00:24 -66484.197233] AUTODETECT spr round 1 (radius: 5)
[00:00:53 -42316.940306] AUTODETECT spr round 2 (radius: 10)
[00:01:25 -33604.797674] AUTODETECT spr round 3 (radius: 15)
[00:02:06 -27201.199116] AUTODETECT spr round 4 (radius: 20)
[00:02:52 -23306.627616] AUTODETECT spr round 5 (radius: 25)
[00:03:43 -22725.032723] SPR radius for FAST iterations: 25 (autodetect)
[00:03:43 -22725.032723] Model parameter optimization (eps = 3.000000)
[00:03:57 -22515.919026] FAST spr round 1 (radius: 25)
[00:04:29 -18993.912250] FAST spr round 2 (radius: 25)
[00:04:56 -18816.043147] FAST spr round 3 (radius: 25)
[00:05:21 -18802.570847] FAST spr round 4 (radius: 25)
[00:05:44 -18802.569169] Model parameter optimization (eps = 1.000000)
[00:05:55 -18778.152026] SLOW spr round 1 (radius: 5)
[00:06:26 -18769.306841] SLOW spr round 2 (radius: 5)
[00:06:57 -18769.267553] SLOW spr round 3 (radius: 10)
[00:07:29 -18768.022433] SLOW spr round 4 (radius: 5)
[00:08:12 -18768.021442] SLOW spr round 5 (radius: 10)
[00:08:48 -18768.021281] SLOW spr round 6 (radius: 15)
[00:09:35 -18767.736683] SLOW spr round 7 (radius: 5)
[00:10:18 -18767.735716] SLOW spr round 8 (radius: 10)
[00:10:55 -18767.735619] SLOW spr round 9 (radius: 15)
[00:11:31] [worker #3] ML tree search #4, logLikelihood: -18752.582684
[00:11:41 -18767.735597] SLOW spr round 10 (radius: 20)
[00:12:45 -18767.735591] SLOW spr round 11 (radius: 25)
[00:13:54 -18767.735589] Model parameter optimization (eps = 0.100000)

[00:14:01] [worker #0] ML tree search #1, logLikelihood: -18767.277767

[00:14:01 -87967.468005] Initial branch length optimization
[00:14:02] [worker #2] ML tree search #3, logLikelihood: -18753.611642
[00:14:03 -67386.567080] Model parameter optimization (eps = 10.000000)
[00:14:19 -66911.003036] AUTODETECT spr round 1 (radius: 5)
[00:14:34] [worker #1] ML tree search #2, logLikelihood: -18749.141846
[00:14:48 -41109.965366] AUTODETECT spr round 2 (radius: 10)
[00:15:21 -30525.113438] AUTODETECT spr round 3 (radius: 15)
[00:16:01 -22676.429079] AUTODETECT spr round 4 (radius: 20)
[00:16:45 -20851.580112] AUTODETECT spr round 5 (radius: 25)
[00:17:43 -20763.535106] SPR radius for FAST iterations: 25 (autodetect)
[00:17:43 -20763.535106] Model parameter optimization (eps = 3.000000)
[00:18:04 -20594.969466] FAST spr round 1 (radius: 25)
[00:18:37 -18862.211330] FAST spr round 2 (radius: 25)
[00:19:06 -18774.995122] FAST spr round 3 (radius: 25)
[00:19:31 -18766.458135] FAST spr round 4 (radius: 25)
[00:19:54 -18766.455657] Model parameter optimization (eps = 1.000000)
[00:20:07 -18755.945836] SLOW spr round 1 (radius: 5)
[00:20:37 -18753.428006] SLOW spr round 2 (radius: 5)
[00:21:08 -18753.105788] SLOW spr round 3 (radius: 5)
[00:21:38 -18753.105533] SLOW spr round 4 (radius: 10)
[00:22:09 -18752.604269] SLOW spr round 5 (radius: 5)
[00:22:52 -18752.604173] SLOW spr round 6 (radius: 10)
[00:23:05] [worker #3] ML tree search #8, logLikelihood: -18754.400893
[00:23:27 -18751.124571] SLOW spr round 7 (radius: 5)
[00:24:07 -18751.124529] SLOW spr round 8 (radius: 10)
[00:24:40 -18751.124519] SLOW spr round 9 (radius: 15)
[00:25:27 -18751.124475] SLOW spr round 10 (radius: 20)
[00:26:14] [worker #1] ML tree search #6, logLikelihood: -18747.431841
[00:26:34 -18751.124471] SLOW spr round 11 (radius: 25)
[00:27:55 -18751.124466] Model parameter optimization (eps = 0.100000)

[00:27:58] [worker #0] ML tree search #5, logLikelihood: -18751.100638

[00:27:58 -87914.707835] Initial branch length optimization
[00:27:59 -67764.096693] Model parameter optimization (eps = 10.000000)
[00:28:19 -67332.627075] AUTODETECT spr round 1 (radius: 5)
[00:28:48 -41174.307544] AUTODETECT spr round 2 (radius: 10)
[00:29:22 -28568.321026] AUTODETECT spr round 3 (radius: 15)
[00:30:04 -21741.514964] AUTODETECT spr round 4 (radius: 20)
[00:31:00 -20769.057532] AUTODETECT spr round 5 (radius: 25)
[00:31:37] [worker #2] ML tree search #7, logLikelihood: -18763.153841
[00:31:58 -20769.000122] SPR radius for FAST iterations: 20 (autodetect)
[00:31:58 -20769.000122] Model parameter optimization (eps = 3.000000)
[00:32:11 -20634.082585] FAST spr round 1 (radius: 20)
[00:32:42 -18917.616316] FAST spr round 2 (radius: 20)
[00:33:08 -18777.900286] FAST spr round 3 (radius: 20)
[00:33:34 -18770.170652] FAST spr round 4 (radius: 20)
[00:33:55 -18769.030112] FAST spr round 5 (radius: 20)
[00:34:16 -18767.971106] FAST spr round 6 (radius: 20)
[00:34:36 -18767.970145] Model parameter optimization (eps = 1.000000)
[00:34:45 -18759.829864] SLOW spr round 1 (radius: 5)
[00:35:16 -18759.486284] SLOW spr round 2 (radius: 5)
[00:35:46 -18759.033661] SLOW spr round 3 (radius: 5)
[00:36:16 -18759.032607] SLOW spr round 4 (radius: 10)
[00:36:48 -18757.909425] SLOW spr round 5 (radius: 5)
[00:37:33 -18754.147684] SLOW spr round 6 (radius: 5)
[00:38:09 -18754.011408] SLOW spr round 7 (radius: 5)
[00:38:41 -18754.011218] SLOW spr round 8 (radius: 10)
[00:39:12 -18754.011098] SLOW spr round 9 (radius: 15)
[00:39:24] [worker #1] ML tree search #10, logLikelihood: -18750.540945
[00:40:01 -18754.011087] SLOW spr round 10 (radius: 20)
[00:41:07 -18754.011077] SLOW spr round 11 (radius: 25)
[00:42:23 -18754.011067] Model parameter optimization (eps = 0.100000)

[00:42:29] [worker #0] ML tree search #9, logLikelihood: -18753.821982

[00:42:29 -85492.830495] Initial branch length optimization
[00:42:30 -66334.265559] Model parameter optimization (eps = 10.000000)
[00:42:49 -65868.200664] AUTODETECT spr round 1 (radius: 5)
[00:43:16 -40296.198021] AUTODETECT spr round 2 (radius: 10)
[00:43:48 -29503.030560] AUTODETECT spr round 3 (radius: 15)
[00:44:21] [worker #2] ML tree search #11, logLikelihood: -18753.781049
[00:44:32 -23256.295428] AUTODETECT spr round 4 (radius: 20)
[00:45:19 -22441.880611] AUTODETECT spr round 5 (radius: 25)
[00:45:50] [worker #3] ML tree search #12, logLikelihood: -18752.003910
[00:46:15 -21569.330883] SPR radius for FAST iterations: 25 (autodetect)
[00:46:15 -21569.330883] Model parameter optimization (eps = 3.000000)
[00:46:28 -21424.360291] FAST spr round 1 (radius: 25)
[00:47:04 -18935.002375] FAST spr round 2 (radius: 25)
[00:47:32 -18788.079092] FAST spr round 3 (radius: 25)
[00:47:56 -18782.285481] FAST spr round 4 (radius: 25)
[00:48:17 -18782.285275] Model parameter optimization (eps = 1.000000)
[00:48:29 -18774.216171] SLOW spr round 1 (radius: 5)
[00:49:02 -18769.668161] SLOW spr round 2 (radius: 5)
[00:49:33 -18768.949100] SLOW spr round 3 (radius: 5)
[00:50:05 -18768.948012] SLOW spr round 4 (radius: 10)
[00:50:35 -18768.741657] SLOW spr round 5 (radius: 5)
[00:50:51] [worker #1] ML tree search #14, logLikelihood: -18758.089402
[00:51:17 -18768.734176] SLOW spr round 6 (radius: 10)
[00:51:53 -18767.209944] SLOW spr round 7 (radius: 5)
[00:52:33 -18767.209787] SLOW spr round 8 (radius: 10)
[00:53:07 -18767.209744] SLOW spr round 9 (radius: 15)
[00:53:51 -18767.209711] SLOW spr round 10 (radius: 20)
[00:54:46 -18767.209680] SLOW spr round 11 (radius: 25)
[00:55:48 -18757.906431] SLOW spr round 12 (radius: 5)
[00:56:33 -18755.140127] SLOW spr round 13 (radius: 5)
[00:57:09 -18755.138100] SLOW spr round 14 (radius: 10)
[00:57:42 -18755.137716] SLOW spr round 15 (radius: 15)
[00:57:51] [worker #3] ML tree search #16, logLikelihood: -18756.552891
[00:58:26 -18755.137634] SLOW spr round 16 (radius: 20)
[00:59:10] [worker #2] ML tree search #15, logLikelihood: -18757.060260
[00:59:26 -18755.137598] SLOW spr round 17 (radius: 25)
[01:00:34 -18753.449700] SLOW spr round 18 (radius: 5)
[01:01:19 -18753.449589] SLOW spr round 19 (radius: 10)
[01:01:58 -18753.449542] SLOW spr round 20 (radius: 15)
[01:02:41 -18752.719208] SLOW spr round 21 (radius: 5)
[01:03:24 -18752.719006] SLOW spr round 22 (radius: 10)
[01:04:01 -18752.718965] SLOW spr round 23 (radius: 15)
[01:04:45 -18752.718927] SLOW spr round 24 (radius: 20)
[01:05:48 -18752.718888] SLOW spr round 25 (radius: 25)
[01:07:06 -18750.201404] SLOW spr round 26 (radius: 5)
[01:07:51 -18750.200755] SLOW spr round 27 (radius: 10)
[01:08:00] [worker #1] ML tree search #18, logLikelihood: -18753.961292
[01:08:30 -18750.200667] SLOW spr round 28 (radius: 15)
[01:08:42] [worker #3] ML tree search #20, logLikelihood: -18770.890533
[01:09:17 -18750.200616] SLOW spr round 29 (radius: 20)
[01:10:23 -18750.200570] SLOW spr round 30 (radius: 25)
[01:11:41 -18750.200526] Model parameter optimization (eps = 0.100000)

[01:11:48] [worker #0] ML tree search #13, logLikelihood: -18749.974963

[01:11:48 -87921.184628] Initial branch length optimization
[01:11:50 -67400.369900] Model parameter optimization (eps = 10.000000)
[01:12:08 -66921.369963] AUTODETECT spr round 1 (radius: 5)
[01:12:36 -39889.231195] AUTODETECT spr round 2 (radius: 10)
[01:12:42] [worker #2] ML tree search #19, logLikelihood: -18755.627364
[01:13:08 -29102.044678] AUTODETECT spr round 3 (radius: 15)
[01:13:47 -24019.799324] AUTODETECT spr round 4 (radius: 20)
[01:14:29 -22224.028314] AUTODETECT spr round 5 (radius: 25)
[01:15:29 -21564.293768] SPR radius for FAST iterations: 25 (autodetect)
[01:15:29 -21564.293768] Model parameter optimization (eps = 3.000000)
[01:15:43 -21404.404664] FAST spr round 1 (radius: 25)
[01:16:17 -19009.558197] FAST spr round 2 (radius: 25)
[01:16:42 -18782.058917] FAST spr round 3 (radius: 25)
[01:17:06 -18772.580431] FAST spr round 4 (radius: 25)
[01:17:27 -18772.481183] Model parameter optimization (eps = 1.000000)
[01:17:37 -18765.689734] SLOW spr round 1 (radius: 5)
[01:18:08 -18762.332392] SLOW spr round 2 (radius: 5)
[01:18:39 -18762.177743] SLOW spr round 3 (radius: 5)
[01:19:10 -18762.177462] SLOW spr round 4 (radius: 10)
[01:19:40 -18762.177397] SLOW spr round 5 (radius: 15)
[01:20:30 -18762.156269] SLOW spr round 6 (radius: 20)
[01:21:35 -18762.155701] SLOW spr round 7 (radius: 25)
[01:22:53 -18762.155640] Model parameter optimization (eps = 0.100000)

[01:23:00] [worker #0] ML tree search #17, logLikelihood: -18761.178029


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.270925,0.743584) (0.191707,1.336682) (0.417150,0.709745) (0.120218,2.048141) 
   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: -18747.431841

AIC score: 39124.863682 / AICc score: 1369204.863682 / BIC score: 41833.116815
Free parameters (model + branch lengths): 815

WARNING: Number of free parameters (K=815) is larger than alignment size (n=205).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 183 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577.raxml.log

Analysis started: 02-Jul-2021 19:28:19 / finished: 02-Jul-2021 20:51:20

Elapsed time: 4980.806 seconds

Consumed energy: 419.190 Wh (= 2 km in an electric car, or 10 km with an e-scooter!)