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 09-Jul-2021 04:26:36 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P35398/2_msa/P35398_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P35398/3_mltree/P35398 --seed 2 --threads 5 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P35398/2_msa/P35398_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 318 sites

WARNING: Sequences tr_A0A1D5P5J4_A0A1D5P5J4_CHICK_9031 and sp_Q90966_RARA_CHICK_9031 are exactly identical!
WARNING: Sequences sp_P22448_RARB_CHICK_9031 and tr_G3UUU2_G3UUU2_MELGA_9103 are exactly identical!
WARNING: Sequences tr_Q98934_Q98934_CHICK_9031 and tr_A0A151M8D6_A0A151M8D6_ALLMI_8496 are exactly identical!
WARNING: Sequences tr_Q98934_Q98934_CHICK_9031 and tr_A0A091J1X3_A0A091J1X3_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_Q98934_Q98934_CHICK_9031 and tr_A0A091UYY8_A0A091UYY8_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_Q98934_Q98934_CHICK_9031 and tr_A0A087RDR3_A0A087RDR3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_Q98934_Q98934_CHICK_9031 and tr_A0A093HN20_A0A093HN20_STRCA_441894 are exactly identical!
WARNING: Sequences tr_Q98934_Q98934_CHICK_9031 and tr_A0A091WGZ1_A0A091WGZ1_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_Q98934_Q98934_CHICK_9031 and tr_A0A093GNG6_A0A093GNG6_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_Q9I878_Q9I878_CHICK_9031 and tr_G1N0E5_G1N0E5_MELGA_9103 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_H2NNE5_H2NNE5_PONAB_9601 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_W5QI24_W5QI24_SHEEP_9940 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_I3MJ32_I3MJ32_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and sp_P35398_RORA_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_F1N7R0_F1N7R0_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_A0A0D9RI27_A0A0D9RI27_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_A0A1U8C091_A0A1U8C091_MESAU_10036 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_A0A2U4CCG6_A0A2U4CCG6_TURTR_9739 are exactly identical!
WARNING: Sequences sp_P51448_RORA_MOUSE_10090 and tr_A0A383YTG6_A0A383YTG6_BALAS_310752 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_G3I5M5_G3I5M5_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_G1SXT3_G1SXT3_RABIT_9986 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_E2R4U0_E2R4U0_CANLF_9615 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and sp_B3SV56_NR1D1_SHEEP_9940 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_W5PU23_W5PU23_SHEEP_9940 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_I3M7Q0_I3M7Q0_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_U3B5W3_U3B5W3_CALJA_9483 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_A0A286ZW94_A0A286ZW94_PIG_9823 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and sp_Q08E02_NR1D1_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_L5JQB5_L5JQB5_PTEAL_9402 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_M3WLR4_M3WLR4_FELCA_9685 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_A0A0D9S337_A0A0D9S337_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_A0A1S3GXA6_A0A1S3GXA6_DIPOR_10020 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_A0A1U8C0X5_A0A1U8C0X5_MESAU_10036 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_A0A2Y9F083_A0A2Y9F083_PHYCD_9755 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_A0A384BYD4_A0A384BYD4_URSMA_29073 are exactly identical!
WARNING: Sequences sp_Q3UV55_NR1D1_MOUSE_10090 and tr_A0A383ZR92_A0A383ZR92_BALAS_310752 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_M3YBV6_M3YBV6_MUSPF_9669 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2I3H0P5_A0A2I3H0P5_NOMLE_61853 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_G3R8H4_G3R8H4_GORGO_9595 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_F1PET8_F1PET8_CANLF_9615 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_F6XEI8_F6XEI8_HORSE_9796 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_B3F205_B3F205_SHEEP_9940 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A287CZL9_A0A287CZL9_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A286XYB5_A0A286XYB5_CAVPO_10141 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and sp_Q92753_RORB_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_F7FEQ5_F7FEQ5_MACMU_9544 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_G3TA11_G3TA11_LOXAF_9785 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_F7IE81_F7IE81_CALJA_9483 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A287ALC9_A0A287ALC9_PIG_9823 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_G7PSJ8_G7PSJ8_MACFA_9541 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_F1MWS0_F1MWS0_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_L5K8H4_L5K8H4_PTEAL_9402 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2I3LCF1_A0A2I3LCF1_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A0D9R731_A0A0D9R731_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A1S3FBG5_A0A1S3FBG5_DIPOR_10020 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A3Q0DM44_A0A3Q0DM44_TARSY_1868482 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A1U7Q2R8_A0A1U7Q2R8_MESAU_10036 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2K6DSS4_A0A2K6DSS4_MACNE_9545 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2K5ZNM4_A0A2K5ZNM4_MANLE_9568 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2R8ZST3_A0A2R8ZST3_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2U4BAI3_A0A2U4BAI3_TURTR_9739 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2U3VNW1_A0A2U3VNW1_ODORO_9708 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2U3XIK1_A0A2U3XIK1_LEPWE_9713 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2Y9RDX3_A0A2Y9RDX3_TRIMA_127582 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2Y9K419_A0A2Y9K419_ENHLU_391180 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A2Y9NCP0_A0A2Y9NCP0_DELLE_9749 are exactly identical!
WARNING: Sequences sp_Q8R1B8_RORB_MOUSE_10090 and tr_A0A384A4Q7_A0A384A4Q7_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_G1TI43_G1TI43_RABIT_9986 are exactly identical!
WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_I3M4V2_I3M4V2_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_G1LMX4_G1LMX4_AILME_9646 are exactly identical!
WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_A0A2U3VJK3_A0A2U3VJK3_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_A0A383ZRW1_A0A383ZRW1_BALAS_310752 are exactly identical!
WARNING: Sequences tr_M3YTZ8_M3YTZ8_MUSPF_9669 and tr_G3R2J1_G3R2J1_GORGO_9595 are exactly identical!
WARNING: Sequences tr_M3YTZ8_M3YTZ8_MUSPF_9669 and tr_H2QCV8_H2QCV8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3YTZ8_M3YTZ8_MUSPF_9669 and sp_P20393_NR1D1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3YTZ8_M3YTZ8_MUSPF_9669 and tr_A0A2R9CEW1_A0A2R9CEW1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3Z0G0_M3Z0G0_MUSPF_9669 and tr_A0A2Y9J2B4_A0A2Y9J2B4_ENHLU_391180 are exactly identical!
WARNING: Sequences sp_P13055_E75BB_DROME_7227 and tr_A0A0P9AJG7_A0A0P9AJG7_DROAN_7217 are exactly identical!
WARNING: Sequences sp_P31396_HR3_DROME_7227 and tr_B4GBS9_B4GBS9_DROPE_7234 are exactly identical!
WARNING: Sequences sp_P31396_HR3_DROME_7227 and tr_A0A1W4VCQ0_A0A1W4VCQ0_DROFC_30025 are exactly identical!
WARNING: Sequences sp_P45447_E78C_DROME_7227 and tr_B4IAL4_B4IAL4_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_H2PBB8_H2PBB8_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_F7C3L4_F7C3L4_HORSE_9796 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_F6Z1J2_F6Z1J2_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_U3D5Q9_U3D5Q9_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_I3LL46_I3LL46_PIG_9823 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_G7NY91_G7NY91_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_A0A2I3LYC8_A0A2I3LYC8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_A0A0D9RBL7_A0A0D9RBL7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_A0A1S2ZCH6_A0A1S2ZCH6_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_A0A2K5KI47_A0A2K5KI47_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_A0A2K6BM26_A0A2K6BM26_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_A0A2K5YIH9_A0A2K5YIH9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3GXG2_A0A2I3GXG2_NOMLE_61853 and tr_A0A2Y9R8U6_A0A2Y9R8U6_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_G1NXZ8_G1NXZ8_MYOLU_59463 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_G3QE47_G3QE47_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A2I3TCT2_A0A2I3TCT2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_F1LZZ3_F1LZZ3_RAT_10116 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_H0WW54_H0WW54_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A1D5QF05_A0A1D5QF05_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_F1S075_F1S075_PIG_9823 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A2I3MFB3_A0A2I3MFB3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A091D6A3_A0A091D6A3_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A1S3AEW6_A0A1S3AEW6_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A1S3EMU1_A0A1S3EMU1_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A2K5NL77_A0A2K5NL77_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A2K6AZL1_A0A2K6AZL1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A2K5XYK6_A0A2K5XYK6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A2R9BLX0_A0A2R9BLX0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3GYF3_A0A2I3GYF3_NOMLE_61853 and tr_A0A2Y9T725_A0A2Y9T725_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2I2YCE9_A0A2I2YCE9_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A0A0MPB6_A0A0A0MPB6_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and sp_Q4U3Q4_PPARG_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2I3SI31_A0A2I3SI31_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and sp_P37231_PPARG_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_G1K373_G1K373_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and sp_O18924_PPARG_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_F6T9U1_F6T9U1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_G1LDR7_G1LDR7_AILME_9646 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_G7NYH4_G7NYH4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_M3W5I7_M3W5I7_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A0D9RBU3_A0A0D9RBU3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A1U7TT84_A0A1U7TT84_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2K5L4H2_A0A2K5L4H2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2K6B7D4_A0A2K6B7D4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2K6AFG8_A0A2K6AFG8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2R9A8K3_A0A2R9A8K3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2U3VLH3_A0A2U3VLH3_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1QML8_G1QML8_NOMLE_61853 and tr_W5PXH0_W5PXH0_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_G1QML8_G1QML8_NOMLE_61853 and sp_P10276_RARA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QML8_G1QML8_NOMLE_61853 and tr_F1MWQ3_F1MWQ3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G1QML8_G1QML8_NOMLE_61853 and tr_A0A0D9S321_A0A0D9S321_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1QML8_G1QML8_NOMLE_61853 and tr_A0A1U7UH95_A0A1U7UH95_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_G3S8K4_G3S8K4_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_A0A2I3T0W6_A0A2I3T0W6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and sp_P10826_RARB_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_A0A1D5QJY1_A0A1D5QJY1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_A0A2I3MGX5_A0A2I3MGX5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_A0A2K5NBP9_A0A2K5NBP9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_A0A2K6DR22_A0A2K6DR22_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_A0A2K5Z0E7_A0A2K5Z0E7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1QU20_G1QU20_NOMLE_61853 and tr_A0A2R9BQB5_A0A2R9BQB5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2ZPR1_A0A2I2ZPR1_GORGO_9595 and tr_A0A2I3S658_A0A2I3S658_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZPR1_A0A2I2ZPR1_GORGO_9595 and tr_A0A2R9AUD5_A0A2R9AUD5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1MZ62_G1MZ62_MELGA_9103 and tr_A0A226MSS4_A0A226MSS4_CALSU_9009 are exactly identical!
WARNING: Sequences tr_G1SDW7_G1SDW7_RABIT_9986 and tr_E2R2A6_E2R2A6_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G1SDW7_G1SDW7_RABIT_9986 and tr_I3MAT4_I3MAT4_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G1SDW7_G1SDW7_RABIT_9986 and tr_G1L1L8_G1L1L8_AILME_9646 are exactly identical!
WARNING: Sequences tr_G1SDW7_G1SDW7_RABIT_9986 and tr_M3WD77_M3WD77_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1SDW7_G1SDW7_RABIT_9986 and tr_A0A1U7TWI3_A0A1U7TWI3_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_E2QXI5_E2QXI5_CANLF_9615 and tr_D2I6L8_D2I6L8_AILME_9646 are exactly identical!
WARNING: Sequences tr_E2QXI5_E2QXI5_CANLF_9615 and tr_M3XD13_M3XD13_FELCA_9685 are exactly identical!
WARNING: Sequences tr_E2QXI5_E2QXI5_CANLF_9615 and tr_A0A2U3X0X1_A0A2U3X0X1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_E2QXI5_E2QXI5_CANLF_9615 and tr_A0A2U3YN11_A0A2U3YN11_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_E2QXI5_E2QXI5_CANLF_9615 and tr_A0A384DKD7_A0A384DKD7_URSMA_29073 are exactly identical!
WARNING: Sequences tr_F1P607_F1P607_CANLF_9615 and tr_G1LN19_G1LN19_AILME_9646 are exactly identical!
WARNING: Sequences tr_F1P607_F1P607_CANLF_9615 and tr_A0A337SJC1_A0A337SJC1_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A2I3T288_A0A2I3T288_PANTR_9598 and tr_A0A2R8ZTG3_A0A2R8ZTG3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7FND5_F7FND5_ORNAN_9258 and tr_A0A3Q0GAS5_A0A3Q0GAS5_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_F6QXD7_F6QXD7_MONDO_13616 and tr_K7FX40_K7FX40_PELSI_13735 are exactly identical!
WARNING: Sequences tr_F6QXD7_F6QXD7_MONDO_13616 and tr_A0A151MA31_A0A151MA31_ALLMI_8496 are exactly identical!
WARNING: Sequences tr_W5Q4M7_W5Q4M7_SHEEP_9940 and sp_O18971_PPARG_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5QWS9_A0A3B5QWS9_XIPMA_8083 and tr_H2TPM7_H2TPM7_TAKRU_31033 are exactly identical!
WARNING: Sequences tr_A0A3B5QWS9_A0A3B5QWS9_XIPMA_8083 and tr_A0A2I4AU91_A0A2I4AU91_9TELE_52670 are exactly identical!
WARNING: Sequences tr_A0A088A832_A0A088A832_APIME_7460 and tr_A0A2A3EQM4_A0A2A3EQM4_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NJW5_A0A158NJW5_ATTCE_12957 and tr_F4WIM8_F4WIM8_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NPD0_A0A158NPD0_ATTCE_12957 and tr_A0A151X6D8_A0A151X6D8_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A158NPD0_A0A158NPD0_ATTCE_12957 and tr_A0A195E4Z2_A0A195E4Z2_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158NPD0_A0A158NPD0_ATTCE_12957 and tr_A0A195BAA0_A0A195BAA0_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NPD0_A0A158NPD0_ATTCE_12957 and tr_A0A195F3J9_A0A195F3J9_9HYME_34720 are exactly identical!
WARNING: Sequences tr_H0VTA6_H0VTA6_CAVPO_10141 and tr_A0A091D601_A0A091D601_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_H0VTA6_H0VTA6_CAVPO_10141 and tr_A0A3Q0D8A4_A0A3Q0D8A4_MESAU_10036 are exactly identical!
WARNING: Sequences tr_F7GZS9_F7GZS9_MACMU_9544 and tr_G7NTT8_G7NTT8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GZS9_F7GZS9_MACMU_9544 and tr_A0A2K5M6K7_A0A2K5M6K7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GZS9_F7GZS9_MACMU_9544 and tr_A0A2K6DJX2_A0A2K6DJX2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GZS9_F7GZS9_MACMU_9544 and tr_A0A2K6A2E8_A0A2K6A2E8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_I2CUB0_I2CUB0_MACMU_9544 and tr_G8F5X4_G8F5X4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_I2CUB0_I2CUB0_MACMU_9544 and tr_A0A2I3MXD6_A0A2I3MXD6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_I2CUB0_I2CUB0_MACMU_9544 and tr_A0A2K5NFM9_A0A2K5NFM9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_I2CUB0_I2CUB0_MACMU_9544 and tr_A0A2K6ASZ8_A0A2K6ASZ8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_I2CUB0_I2CUB0_MACMU_9544 and tr_A0A2K5ZA35_A0A2K5ZA35_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H3CSJ1_H3CSJ1_TETNG_99883 and tr_A0A087XD51_A0A087XD51_POEFO_48698 are exactly identical!
WARNING: Sequences tr_G3W3E2_G3W3E2_SARHA_9305 and sp_O62807_PPARG_PIG_9823 are exactly identical!
WARNING: Sequences tr_G3WSX9_G3WSX9_SARHA_9305 and tr_A0A2I0M6Z1_A0A2I0M6Z1_COLLI_8932 are exactly identical!
WARNING: Sequences tr_G3WSX9_G3WSX9_SARHA_9305 and tr_A0A218UYJ1_A0A218UYJ1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0YPS1_H0YPS1_TAEGU_59729 and tr_A0A091E612_A0A091E612_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0YPS1_H0YPS1_TAEGU_59729 and tr_A0A091UTR0_A0A091UTR0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_H0YPS1_H0YPS1_TAEGU_59729 and tr_A0A0A0A148_A0A0A0A148_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_H0YR96_H0YR96_TAEGU_59729 and tr_U3KE76_U3KE76_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0YYW9_H0YYW9_TAEGU_59729 and tr_U3K3J3_U3K3J3_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0YYW9_H0YYW9_TAEGU_59729 and tr_U3IFR1_U3IFR1_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_H0YYW9_H0YYW9_TAEGU_59729 and tr_A0A218VEB2_A0A218VEB2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0Z0W7_H0Z0W7_TAEGU_59729 and tr_A0A087RH46_A0A087RH46_APTFO_9233 are exactly identical!
WARNING: Sequences tr_H0Z0W7_H0Z0W7_TAEGU_59729 and tr_A0A093GPP6_A0A093GPP6_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_H0Z0W7_H0Z0W7_TAEGU_59729 and tr_A0A218UPA3_A0A218UPA3_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_U3KDN1_U3KDN1_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_U3IDX3_U3IDX3_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A0Q3UUC1_A0A0Q3UUC1_AMAAE_12930 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A091E871_A0A091E871_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A091JHS2_A0A091JHS2_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A093Q6T0_A0A093Q6T0_9PASS_328815 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A091WKM4_A0A091WKM4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A087QRV8_A0A087QRV8_APTFO_9233 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A093HQ19_A0A093HQ19_STRCA_441894 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A091XXK0_A0A091XXK0_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A093G2S4_A0A093G2S4_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_H0Z4K8_H0Z4K8_TAEGU_59729 and tr_A0A091IAB5_A0A091IAB5_CALAN_9244 are exactly identical!
WARNING: Sequences tr_E3N2P9_E3N2P9_CAERE_31234 and tr_A0A261AEQ7_A0A261AEQ7_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8X5D8_A8X5D8_CAEBR_6238 and tr_A0A2G5VR68_A0A2G5VR68_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_A8Y172_A8Y172_CAEBR_6238 and tr_A0A2G5VH33_A0A2G5VH33_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_U3IDQ5_U3IDQ5_ANAPL_8839 and tr_A0A091V572_A0A091V572_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_U3IDQ5_U3IDQ5_ANAPL_8839 and tr_A0A087RJZ8_A0A087RJZ8_APTFO_9233 are exactly identical!
WARNING: Sequences tr_U3IDQ5_U3IDQ5_ANAPL_8839 and tr_A0A091XLW3_A0A091XLW3_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_U3IDQ5_U3IDQ5_ANAPL_8839 and tr_A0A091FNN5_A0A091FNN5_9AVES_55661 are exactly identical!
WARNING: Sequences tr_U3IDQ5_U3IDQ5_ANAPL_8839 and tr_A0A0A0ATM1_A0A0A0ATM1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_U3IDQ5_U3IDQ5_ANAPL_8839 and tr_A0A091JA75_A0A091JA75_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A151MRA2_A0A151MRA2_ALLMI_8496 and tr_A0A1U7RNG1_A0A1U7RNG1_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151PJ63_A0A151PJ63_ALLMI_8496 and tr_A0A1U7RQ42_A0A1U7RQ42_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091EVB0_A0A091EVB0_CORBR_85066 and tr_A0A091JR95_A0A091JR95_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A091EVB0_A0A091EVB0_CORBR_85066 and tr_A0A091UPZ7_A0A091UPZ7_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091EVB0_A0A091EVB0_CORBR_85066 and tr_A0A091GHI5_A0A091GHI5_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091EVB0_A0A091EVB0_CORBR_85066 and tr_A0A0A0ARI2_A0A0A0ARI2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A194R532_A0A194R532_PAPMA_76193 and tr_A0A194PU94_A0A194PU94_PAPXU_66420 are exactly identical!
WARNING: Sequences tr_A0A093QL49_A0A093QL49_9PASS_328815 and tr_A0A091WKS3_A0A091WKS3_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A2I0LTY3_A0A2I0LTY3_COLLI_8932 and tr_A0A1V4K348_A0A1V4K348_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2I0MQP2_A0A2I0MQP2_COLLI_8932 and tr_A0A1V4KDS9_A0A1V4KDS9_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1CSX1_A0A0V1CSX1_TRIBR_45882 and tr_A0A0V0U9D4_A0A0V0U9D4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1CVV0_A0A0V1CVV0_TRIBR_45882 and tr_A0A0V0VAB2_A0A0V0VAB2_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CVV0_A0A0V1CVV0_TRIBR_45882 and tr_A0A0V1PB73_A0A0V1PB73_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CVV0_A0A0V1CVV0_TRIBR_45882 and tr_A0A0V0TM25_A0A0V0TM25_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1D4X9_A0A0V1D4X9_TRIBR_45882 and tr_A0A0V0VJE8_A0A0V0VJE8_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1D4X9_A0A0V1D4X9_TRIBR_45882 and tr_A0A0V1A020_A0A0V1A020_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1D4X9_A0A0V1D4X9_TRIBR_45882 and tr_A0A0V1P7W6_A0A0V1P7W6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1D4X9_A0A0V1D4X9_TRIBR_45882 and tr_A0A0V0TQG9_A0A0V0TQG9_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0WSV5_A0A0V0WSV5_9BILA_92179 and tr_A0A0V1L9E0_A0A0V1L9E0_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1MB95_A0A0V1MB95_9BILA_268474 and tr_A0A0V1HYS5_A0A0V1HYS5_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A0V1MSU3_A0A0V1MSU3_9BILA_268474 and tr_A0A0V1HA56_A0A0V1HA56_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1S3JVH9_A0A1S3JVH9_LINUN_7574 and tr_A0A1S3JVI3_A0A1S3JVI3_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3JVH9_A0A1S3JVH9_LINUN_7574 and tr_A0A1S3JVP8_A0A1S3JVP8_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3JVH9_A0A1S3JVH9_LINUN_7574 and tr_A0A1S3JWD1_A0A1S3JWD1_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3KNS5_A0A1S3KNS5_SALSA_8030 and tr_A0A1S3MLU8_A0A1S3MLU8_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3KNS5_A0A1S3KNS5_SALSA_8030 and tr_A0A060WFH1_A0A060WFH1_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226MJ39_A0A226MJ39_CALSU_9009 and tr_A0A226PNS3_A0A226PNS3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226N242_A0A226N242_CALSU_9009 and tr_A0A226NQ93_A0A226NQ93_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PUW4_A0A2D0PUW4_ICTPU_7998 and tr_W5UJU1_W5UJU1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S2L5_A0A2D0S2L5_ICTPU_7998 and tr_A0A2D0S2N1_A0A2D0S2N1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S2L5_A0A2D0S2L5_ICTPU_7998 and tr_A0A2D0S2N7_A0A2D0S2N7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0TAJ9_A0A2D0TAJ9_ICTPU_7998 and tr_A0A2D0TB55_A0A2D0TB55_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4CFH0_A0A2U4CFH0_TURTR_9739 and tr_A0A2Y9LNQ6_A0A2Y9LNQ6_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3W7Y2_A0A2U3W7Y2_ODORO_9708 and tr_A0A2U3XAH9_A0A2U3XAH9_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2U3WEC0_A0A2U3WEC0_ODORO_9708 and tr_A0A2U3XLM9_A0A2U3XLM9_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2U3WEC0_A0A2U3WEC0_ODORO_9708 and tr_A0A2Y9KEG6_A0A2Y9KEG6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2Y9FLF7_A0A2Y9FLF7_PHYCD_9755 and tr_A0A384AZB2_A0A384AZB2_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 253

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/P35398/3_mltree/P35398.raxml.reduced.phy

Alignment comprises 1 partitions and 318 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 318 / 318
Gaps: 8.08 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P35398/3_mltree/P35398.raxml.rba

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

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 318 / 25440
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -497546.915527] Initial branch length optimization
[00:00:09 -407189.252557] Model parameter optimization (eps = 10.000000)
[00:01:07 -406910.914996] AUTODETECT spr round 1 (radius: 5)
[00:05:26 -239226.782541] AUTODETECT spr round 2 (radius: 10)
[00:09:51 -154868.878681] AUTODETECT spr round 3 (radius: 15)
[00:14:20 -125053.003371] AUTODETECT spr round 4 (radius: 20)
[00:19:13 -110715.208870] AUTODETECT spr round 5 (radius: 25)
[00:24:47 -104604.979254] SPR radius for FAST iterations: 25 (autodetect)
[00:24:47 -104604.979254] Model parameter optimization (eps = 3.000000)
[00:25:14 -104577.335009] FAST spr round 1 (radius: 25)
[00:29:56 -78375.423762] FAST spr round 2 (radius: 25)
[00:33:30 -76391.584207] FAST spr round 3 (radius: 25)
[00:36:26 -76042.256755] FAST spr round 4 (radius: 25)
[00:39:09 -76022.870859] FAST spr round 5 (radius: 25)
[00:41:28 -76022.606146] FAST spr round 6 (radius: 25)
[00:43:44 -76022.606125] Model parameter optimization (eps = 1.000000)
[00:44:04 -76008.715089] SLOW spr round 1 (radius: 5)
[00:47:11 -76001.274216] SLOW spr round 2 (radius: 5)
[00:50:11 -76001.273700] SLOW spr round 3 (radius: 10)
[00:53:32 -76000.381221] SLOW spr round 4 (radius: 5)
[00:57:25 -76000.380962] SLOW spr round 5 (radius: 10)
[01:01:11 -76000.380763] SLOW spr round 6 (radius: 15)
[01:06:23 -75999.977811] SLOW spr round 7 (radius: 5)
[01:10:33 -75999.976557] SLOW spr round 8 (radius: 10)
[01:14:29 -75999.976285] SLOW spr round 9 (radius: 15)
[01:19:36 -75999.976191] SLOW spr round 10 (radius: 20)
[01:27:40 -75999.976139] SLOW spr round 11 (radius: 25)
[01:28:08] [worker #3] ML tree search #4, logLikelihood: -75996.886434
[01:34:57] [worker #2] ML tree search #3, logLikelihood: -75999.511023
[01:38:39 -75999.976104] Model parameter optimization (eps = 0.100000)

[01:38:46] [worker #0] ML tree search #1, logLikelihood: -75999.963353

[01:38:46 -493928.737896] Initial branch length optimization
[01:38:53 -403408.462807] Model parameter optimization (eps = 10.000000)
[01:39:55 -403106.348581] AUTODETECT spr round 1 (radius: 5)
[01:44:16 -233388.716455] AUTODETECT spr round 2 (radius: 10)
[01:48:37 -154476.194765] AUTODETECT spr round 3 (radius: 15)
[01:53:20 -117661.658914] AUTODETECT spr round 4 (radius: 20)
[01:58:19 -107043.821321] AUTODETECT spr round 5 (radius: 25)
[02:03:21] [worker #1] ML tree search #2, logLikelihood: -75993.751689
[02:04:18 -97595.009110] SPR radius for FAST iterations: 25 (autodetect)
[02:04:18 -97595.009110] Model parameter optimization (eps = 3.000000)
[02:04:43 -97569.686396] FAST spr round 1 (radius: 25)
[02:08:57 -77070.267899] FAST spr round 2 (radius: 25)
[02:12:19 -76103.663848] FAST spr round 3 (radius: 25)
[02:15:04 -76034.361996] FAST spr round 4 (radius: 25)
[02:17:39 -76021.108086] FAST spr round 5 (radius: 25)
[02:19:58 -76021.107347] Model parameter optimization (eps = 1.000000)
[02:20:21 -76015.310851] SLOW spr round 1 (radius: 5)
[02:23:29 -75991.555329] SLOW spr round 2 (radius: 5)
[02:24:31] [worker #4] ML tree search #5, logLikelihood: -76001.152744
[02:26:36 -75991.075694] SLOW spr round 3 (radius: 5)
[02:29:37 -75991.075048] SLOW spr round 4 (radius: 10)
[02:33:00 -75988.660993] SLOW spr round 5 (radius: 5)
[02:36:55 -75988.585686] SLOW spr round 6 (radius: 10)
[02:40:44 -75988.585657] SLOW spr round 7 (radius: 15)
[02:46:01 -75988.416824] SLOW spr round 8 (radius: 5)
[02:50:10 -75987.718462] SLOW spr round 9 (radius: 5)
[02:53:43 -75987.718456] SLOW spr round 10 (radius: 10)
[02:54:35] [worker #3] ML tree search #9, logLikelihood: -75989.773607
[02:57:22 -75987.718452] SLOW spr round 11 (radius: 15)
[03:02:41 -75987.718449] SLOW spr round 12 (radius: 20)
[03:10:55 -75987.718447] SLOW spr round 13 (radius: 25)
[03:22:17 -75987.718446] Model parameter optimization (eps = 0.100000)

[03:22:35] [worker #0] ML tree search #6, logLikelihood: -75987.346335

[03:22:35 -494555.328955] Initial branch length optimization
[03:22:43 -406613.109975] Model parameter optimization (eps = 10.000000)
[03:24:21 -406204.719856] AUTODETECT spr round 1 (radius: 5)
[03:28:41 -238213.909000] AUTODETECT spr round 2 (radius: 10)
[03:32:58 -160680.048038] AUTODETECT spr round 3 (radius: 15)
[03:37:35 -134058.477200] AUTODETECT spr round 4 (radius: 20)
[03:43:23 -111015.243473] AUTODETECT spr round 5 (radius: 25)
[03:45:50] [worker #2] ML tree search #8, logLikelihood: -75999.183943
[03:49:50 -102575.312791] SPR radius for FAST iterations: 25 (autodetect)
[03:49:50 -102575.312791] Model parameter optimization (eps = 3.000000)
[03:50:25 -102551.191554] FAST spr round 1 (radius: 25)
[03:54:25 -84336.522690] FAST spr round 2 (radius: 25)
[03:56:24] [worker #1] ML tree search #7, logLikelihood: -76003.551231
[03:57:31 -77401.905291] FAST spr round 3 (radius: 25)
[04:00:17 -76141.867475] FAST spr round 4 (radius: 25)
[04:02:54 -76028.353475] FAST spr round 5 (radius: 25)
[04:05:24 -76024.164985] FAST spr round 6 (radius: 25)
[04:07:44 -76023.758265] FAST spr round 7 (radius: 25)
[04:10:01 -76023.758091] Model parameter optimization (eps = 1.000000)
[04:10:22 -76013.256388] SLOW spr round 1 (radius: 5)
[04:13:32 -75999.115566] SLOW spr round 2 (radius: 5)
[04:16:39 -75998.427627] SLOW spr round 3 (radius: 5)
[04:19:41 -75998.427560] SLOW spr round 4 (radius: 10)
[04:23:02 -75998.427544] SLOW spr round 5 (radius: 15)
[04:28:30 -75998.256972] SLOW spr round 6 (radius: 5)
[04:32:40 -75998.256967] SLOW spr round 7 (radius: 10)
[04:36:40 -75998.256964] SLOW spr round 8 (radius: 15)
[04:37:21] [worker #4] ML tree search #10, logLikelihood: -75997.696050
[04:41:54 -75998.256961] SLOW spr round 9 (radius: 20)
[04:46:10] [worker #3] ML tree search #14, logLikelihood: -75986.644558
[04:50:07 -75998.256959] SLOW spr round 10 (radius: 25)
[05:01:24 -75998.256957] Model parameter optimization (eps = 0.100000)

[05:01:30] [worker #0] ML tree search #11, logLikelihood: -75998.254878

[05:01:30 -495873.559499] Initial branch length optimization
[05:01:38 -406337.246719] Model parameter optimization (eps = 10.000000)
[05:02:32 -406002.801350] AUTODETECT spr round 1 (radius: 5)
[05:06:52 -239219.317318] AUTODETECT spr round 2 (radius: 10)
[05:11:10 -157012.238291] AUTODETECT spr round 3 (radius: 15)
[05:15:42 -123897.572167] AUTODETECT spr round 4 (radius: 20)
[05:20:45 -111989.014260] AUTODETECT spr round 5 (radius: 25)
[05:27:09 -96440.661470] SPR radius for FAST iterations: 25 (autodetect)
[05:27:09 -96440.661470] Model parameter optimization (eps = 3.000000)
[05:27:38 -96409.562649] FAST spr round 1 (radius: 25)
[05:28:12] [worker #2] ML tree search #13, logLikelihood: -76003.748183
[05:32:02 -77917.434484] FAST spr round 2 (radius: 25)
[05:35:36 -76087.662259] FAST spr round 3 (radius: 25)
[05:38:31 -76031.255989] FAST spr round 4 (radius: 25)
[05:38:41] [worker #1] ML tree search #12, logLikelihood: -75996.000488
[05:41:13 -76019.411214] FAST spr round 5 (radius: 25)
[05:43:31 -76019.410697] Model parameter optimization (eps = 1.000000)
[05:43:50 -76010.447708] SLOW spr round 1 (radius: 5)
[05:47:00 -75998.869722] SLOW spr round 2 (radius: 5)
[05:50:04 -75997.961833] SLOW spr round 3 (radius: 5)
[05:53:04 -75997.961807] SLOW spr round 4 (radius: 10)
[05:56:27 -75997.824211] SLOW spr round 5 (radius: 5)
[06:00:18 -75997.741751] SLOW spr round 6 (radius: 10)
[06:04:08 -75997.043355] SLOW spr round 7 (radius: 5)
[06:07:53 -75997.043352] SLOW spr round 8 (radius: 10)
[06:09:15] [worker #3] ML tree search #19, logLikelihood: -75993.046076
[06:11:38 -75997.043350] SLOW spr round 9 (radius: 15)
[06:15:27] [worker #4] ML tree search #15, logLikelihood: -75997.904525
[06:16:51 -75996.759609] SLOW spr round 10 (radius: 5)
[06:20:59 -75996.759608] SLOW spr round 11 (radius: 10)
[06:25:01 -75996.759606] SLOW spr round 12 (radius: 15)
[06:30:12 -75996.759605] SLOW spr round 13 (radius: 20)
[06:38:25 -75996.759598] SLOW spr round 14 (radius: 25)
[06:49:10 -75996.759598] Model parameter optimization (eps = 0.100000)

[06:49:17] [worker #0] ML tree search #16, logLikelihood: -75996.737938

[07:06:21] [worker #1] ML tree search #17, logLikelihood: -76002.188447
[07:55:26] [worker #4] ML tree search #20, logLikelihood: -75986.203882
[08:34:31] [worker #2] ML tree search #18, logLikelihood: -75995.199271

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.198493,0.277556) (0.230123,0.545198) (0.332618,0.960147) (0.238766,2.094447) 
   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: -75986.203882

AIC score: 155982.407765 / AICc score: 8200042.407765 / BIC score: 163525.320787
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=318).
         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/P35398/3_mltree/P35398.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P35398/3_mltree/P35398.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P35398/3_mltree/P35398.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P35398/3_mltree/P35398.raxml.log

Analysis started: 09-Jul-2021 04:26:36 / finished: 09-Jul-2021 13:01:09

Elapsed time: 30872.177 seconds