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 10-Jul-2021 23:51:28 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RP8/2_msa/Q96RP8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RP8/3_mltree/Q96RP8 --seed 2 --threads 6 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RP8/2_msa/Q96RP8_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 367 sites

WARNING: Sequences tr_A0A1D5PI60_A0A1D5PI60_CHICK_9031 and tr_G1NRG1_G1NRG1_MELGA_9103 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_R0M176_R0M176_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A091JQX9_A0A091JQX9_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A091VQM5_A0A091VQM5_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A087RJT1_A0A087RJT1_APTFO_9233 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A091XL48_A0A091XL48_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A099ZVZ5_A0A099ZVZ5_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A2I0MKC3_A0A2I0MKC3_COLLI_8932 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A1V4K8E8_A0A1V4K8E8_PATFA_372326 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A226MDZ7_A0A226MDZ7_CALSU_9009 are exactly identical!
WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A226PJZ6_A0A226PJZ6_COLVI_9014 are exactly identical!
WARNING: Sequences sp_Q7T199_KCA10_CHICK_9031 and tr_A0A226PYF8_A0A226PYF8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_G1NRG0_G1NRG0_MELGA_9103 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_U3KJP7_U3KJP7_FICAL_59894 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_R0L1C6_R0L1C6_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091F1M2_A0A091F1M2_CORBR_85066 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091JJF6_A0A091JJF6_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A093QHE1_A0A093QHE1_9PASS_328815 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091WS81_A0A091WS81_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A093HKM6_A0A093HKM6_STRCA_441894 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091V9H0_A0A091V9H0_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A099Z651_A0A099Z651_TINGU_94827 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091G9V4_A0A091G9V4_9AVES_55661 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A0A0AYN4_A0A0A0AYN4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A2I0M055_A0A2I0M055_COLLI_8932 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A093GIZ6_A0A093GIZ6_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091ID14_A0A091ID14_CALAN_9244 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A1V4KWW4_A0A1V4KWW4_PATFA_372326 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A218US50_A0A218US50_9PASE_299123 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A226NIE9_A0A226NIE9_CALSU_9009 are exactly identical!
WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A226PWN8_A0A226PWN8_COLVI_9014 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_M3Z617_M3Z617_MUSPF_9669 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_G1SB08_G1SB08_NOMLE_61853 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_G3GUL0_G3GUL0_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_G3S108_G3S108_GORGO_9595 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_H2NG69_H2NG69_PONAB_9601 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_F1PKN8_F1PKN8_CANLF_9615 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_H2Q593_H2Q593_PANTR_9598 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_F7DVF9_F7DVF9_HORSE_9796 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and sp_P10499_KCNA1_RAT_10116 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_H0V383_H0V383_CAVPO_10141 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and sp_Q09470_KCNA1_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_F7DS72_F7DS72_MACMU_9544 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_F1SL10_F1SL10_PIG_9823 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_M3W515_M3W515_FELCA_9685 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A096N578_A0A096N578_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A0D9SCZ1_A0A0D9SCZ1_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A1S3A1I4_A0A1S3A1I4_ERIEU_9365 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A1U7QZ53_A0A1U7QZ53_MESAU_10036 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A2K5KMH7_A0A2K5KMH7_CERAT_9531 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A2K6AM91_A0A2K6AM91_MACNE_9545 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A2K5XFR1_A0A2K5XFR1_MANLE_9568 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A2R8ZFZ7_A0A2R8ZFZ7_PANPA_9597 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A2U3WVM7_A0A2U3WVM7_ODORO_9708 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A2U3Z2P4_A0A2U3Z2P4_LEPWE_9713 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A2Y9KVN5_A0A2Y9KVN5_ENHLU_391180 are exactly identical!
WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_A0A384BI16_A0A384BI16_URSMA_29073 are exactly identical!
WARNING: Sequences sp_P16390_KCNA3_MOUSE_10090 and sp_P15384_KCNA3_RAT_10116 are exactly identical!
WARNING: Sequences sp_P16390_KCNA3_MOUSE_10090 and tr_A0A1U7QZY2_A0A1U7QZY2_MESAU_10036 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and tr_G1NZA6_G1NZA6_MYOLU_59463 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and sp_Q09081_KCNA2_RABIT_9986 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and tr_F6XE18_F6XE18_HORSE_9796 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and sp_P63142_KCNA2_RAT_10116 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and tr_I3NB95_I3NB95_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and tr_A0A286XTL3_A0A286XTL3_CAVPO_10141 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and tr_A0A1U7U342_A0A1U7U342_TARSY_1868482 are exactly identical!
WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and tr_A0A1U7QPQ5_A0A1U7QPQ5_MESAU_10036 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and sp_Q28527_KCNA4_MUSPF_9669 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_Q5REB6_Q5REB6_PONAB_9601 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and sp_P15385_KCNA4_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_H0XIB5_H0XIB5_OTOGA_30611 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and sp_P22459_KCNA4_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_F6QDP8_F6QDP8_MACMU_9544 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_F7IQA3_F7IQA3_CALJA_9483 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_G7PQH8_G7PQH8_MACFA_9541 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_F1MFZ3_F1MFZ3_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and sp_Q05037_KCNA4_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_M3XDS9_M3XDS9_FELCA_9685 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_A0A0D9SD86_A0A0D9SD86_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_A0A1S3A7D5_A0A1S3A7D5_ERIEU_9365 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_A0A1U7QF69_A0A1U7QF69_MESAU_10036 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_A0A2U3WU64_A0A2U3WU64_ODORO_9708 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_A0A2U3XCC4_A0A2U3XCC4_LEPWE_9713 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_A0A2Y9JQR5_A0A2Y9JQR5_ENHLU_391180 are exactly identical!
WARNING: Sequences sp_Q61423_KCNA4_MOUSE_10090 and tr_A0A384BSM9_A0A384BSM9_URSMA_29073 are exactly identical!
WARNING: Sequences tr_M3Z613_M3Z613_MUSPF_9669 and tr_J9P511_J9P511_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3Z613_M3Z613_MUSPF_9669 and tr_D2HEJ3_D2HEJ3_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3Z613_M3Z613_MUSPF_9669 and tr_A0A2U3X4T2_A0A2U3X4T2_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Z613_M3Z613_MUSPF_9669 and tr_A0A2U3Y7L2_A0A2U3Y7L2_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3Z613_M3Z613_MUSPF_9669 and tr_A0A2Y9KVM7_A0A2Y9KVM7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_F1PBP9_F1PBP9_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_W5PQ46_W5PQ46_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_H0XWH0_H0XWH0_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and sp_P16389_KCNA2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_G7MIG1_G7MIG1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_G3TLS6_G3TLS6_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_D2HZL7_D2HZL7_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_G7NW44_G7NW44_MACFA_9541 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_F1MKB0_F1MKB0_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A091DJ88_A0A091DJ88_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A0D9SAD5_A0A0D9SAD5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A1S3GEU1_A0A1S3GEU1_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2R8ZH38_A0A2R8ZH38_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2U3V2M1_A0A2U3V2M1_TURTR_9739 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2U3WF14_A0A2U3WF14_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2U3XN46_A0A2U3XN46_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2Y9IZ48_A0A2Y9IZ48_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2Y9P953_A0A2Y9P953_DELLE_9749 are exactly identical!
WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2Y9EPE4_A0A2Y9EPE4_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_M3Z868_M3Z868_MUSPF_9669 and tr_A0A2U3XN43_A0A2U3XN43_LEPWE_9713 are exactly identical!
WARNING: Sequences sp_P08510_KCNAS_DROME_7227 and tr_B4JJ88_B4JJ88_DROGR_7222 are exactly identical!
WARNING: Sequences sp_P08510_KCNAS_DROME_7227 and tr_B4I6L8_B4I6L8_DROSE_7238 are exactly identical!
WARNING: Sequences sp_P08510_KCNAS_DROME_7227 and tr_B4NPI1_B4NPI1_DROWI_7260 are exactly identical!
WARNING: Sequences sp_P08510_KCNAS_DROME_7227 and tr_A0A0P8ZSJ5_A0A0P8ZSJ5_DROAN_7217 are exactly identical!
WARNING: Sequences sp_P08510_KCNAS_DROME_7227 and tr_B4M6S3_B4M6S3_DROVI_7244 are exactly identical!
WARNING: Sequences sp_P08510_KCNAS_DROME_7227 and tr_B4L2A7_B4L2A7_DROMO_7230 are exactly identical!
WARNING: Sequences sp_P08510_KCNAS_DROME_7227 and tr_A0A1W4V0P7_A0A1W4V0P7_DROFC_30025 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_G3QEG2_G3QEG2_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_H2PZM6_H2PZM6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_H0XLY0_H0XLY0_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_H0VVP8_H0VVP8_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_F6ZSH4_F6ZSH4_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_G3TS00_G3TS00_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_F7GK19_F7GK19_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_G1MP37_G1MP37_AILME_9646 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_E1B7K3_E1B7K3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A096MPZ0_A0A096MPZ0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A2K5L382_A0A2K5L382_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A2K6B067_A0A2K6B067_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A2K5XYV8_A0A2K5XYV8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A2U3WF03_A0A2U3WF03_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A2Y9J1U9_A0A2Y9J1U9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A2Y9PBI8_A0A2Y9PBI8_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G1S9E4_G1S9E4_NOMLE_61853 and tr_A0A383Z480_A0A383Z480_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G1PAV8_G1PAV8_MYOLU_59463 and tr_F7DZR3_F7DZR3_HORSE_9796 are exactly identical!
WARNING: Sequences tr_G1PAV8_G1PAV8_MYOLU_59463 and tr_G3N1T8_G3N1T8_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G1PAV8_G1PAV8_MYOLU_59463 and tr_M3VYC4_M3VYC4_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A2I2YQ40_A0A2I2YQ40_GORGO_9595 and tr_H2NG68_H2NG68_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2YQ40_A0A2I2YQ40_GORGO_9595 and tr_H2R7L1_H2R7L1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YQ40_A0A2I2YQ40_GORGO_9595 and sp_P17658_KCNA6_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YQ40_A0A2I2YQ40_GORGO_9595 and tr_A0A2R8ZAS1_A0A2R8ZAS1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R8M9_G3R8M9_GORGO_9595 and tr_H2Q594_H2Q594_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R8M9_G3R8M9_GORGO_9595 and sp_P22460_KCNA5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R8M9_G3R8M9_GORGO_9595 and tr_F6WG11_F6WG11_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3R8M9_G3R8M9_GORGO_9595 and tr_A0A0D9SCZ2_A0A0D9SCZ2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1TAR8_G1TAR8_RABIT_9986 and tr_A0A2Y9NJI1_A0A2Y9NJI1_DELLE_9749 are exactly identical!
WARNING: Sequences tr_F7A2Q7_F7A2Q7_ORNAN_9258 and tr_A0A1S3A4Y5_A0A1S3A4Y5_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_F6UCV5_F6UCV5_MONDO_13616 and tr_G3VY70_G3VY70_SARHA_9305 are exactly identical!
WARNING: Sequences tr_M4AYG4_M4AYG4_XIPMA_8083 and tr_A0A087YQF0_A0A087YQF0_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M4AYG6_M4AYG6_XIPMA_8083 and tr_A0A087YQF2_A0A087YQF2_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M4B0C1_M4B0C1_XIPMA_8083 and tr_A0A087YSG6_A0A087YSG6_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M4B0C3_M4B0C3_XIPMA_8083 and tr_A0A087YCV4_A0A087YCV4_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A087ZXP3_A0A087ZXP3_APIME_7460 and tr_A0A2A3EI71_A0A2A3EI71_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A3B5KBV0_A0A3B5KBV0_TAKRU_31033 and tr_Q4RIH0_Q4RIH0_TETNG_99883 are exactly identical!
WARNING: Sequences tr_H2TUB9_H2TUB9_TAKRU_31033 and tr_H3DC31_H3DC31_TETNG_99883 are exactly identical!
WARNING: Sequences tr_H2UBT9_H2UBT9_TAKRU_31033 and tr_H3CA44_H3CA44_TETNG_99883 are exactly identical!
WARNING: Sequences tr_A0A0K0JTC3_A0A0K0JTC3_BRUMA_6279 and tr_A0A0R3QUS8_A0A0R3QUS8_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A096N545_A0A096N545_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A0D9SCZ0_A0A0D9SCZ0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A2K5KLX0_A0A2K5KLX0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A2K6B6G7_A0A2K6B6G7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A2K5ZHC2_A0A2K5ZHC2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1D5RG75_A0A1D5RG75_MACMU_9544 and tr_A0A0A0MWQ8_A0A0A0MWQ8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5RG75_A0A1D5RG75_MACMU_9544 and tr_A0A0D9S345_A0A0D9S345_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5RG75_A0A1D5RG75_MACMU_9544 and tr_A0A2K5L5C8_A0A2K5L5C8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5RG75_A0A1D5RG75_MACMU_9544 and tr_A0A2K6CQL3_A0A2K6CQL3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_G7NW43_G7NW43_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_A0A2K6B581_A0A2K6B581_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_A0A2K5XR20_A0A2K5XR20_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G5ARZ7_G5ARZ7_HETGA_10181 and tr_A0A091CQ76_A0A091CQ76_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0SI28_A0A0V0SI28_9BILA_6336 are exactly identical!
WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0X271_A0A0V0X271_9BILA_92179 are exactly identical!
WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0VUY8_A0A0V0VUY8_9BILA_181606 are exactly identical!
WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0ZLE5_A0A0V0ZLE5_9BILA_990121 are exactly identical!
WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V1P110_A0A0V1P110_9BILA_92180 are exactly identical!
WARNING: Sequences tr_E5SML7_E5SML7_TRISP_6334 and tr_A0A0V0UAJ5_A0A0V0UAJ5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_G3TB58_G3TB58_LOXAF_9785 and tr_A0A2Y9DU82_A0A2Y9DU82_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_H0YRL3_H0YRL3_TAEGU_59729 and tr_A0A087QMX2_A0A087QMX2_APTFO_9233 are exactly identical!
WARNING: Sequences tr_H0Z2W9_H0Z2W9_TAEGU_59729 and tr_U3KCM9_U3KCM9_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0Z2W9_H0Z2W9_TAEGU_59729 and tr_A0A091ECX3_A0A091ECX3_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0Z2W9_H0Z2W9_TAEGU_59729 and tr_A0A218UJ52_A0A218UJ52_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_U3KKD6_U3KKD6_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A091FNI5_A0A091FNI5_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A093GUI1_A0A093GUI1_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A091JAH5_A0A091JAH5_CALAN_9244 are exactly identical!
WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A218UFS4_A0A218UFS4_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A8WP18_A8WP18_CAEBR_6238 and tr_A0A2G5UUI2_A0A2G5UUI2_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_D2HEJ1_D2HEJ1_AILME_9646 and tr_A0A2I2U352_A0A2I2U352_FELCA_9685 are exactly identical!
WARNING: Sequences tr_D2HEJ1_D2HEJ1_AILME_9646 and tr_A0A2U3WVE0_A0A2U3WVE0_ODORO_9708 are exactly identical!
WARNING: Sequences tr_D2HEJ1_D2HEJ1_AILME_9646 and tr_A0A2U3Y7J7_A0A2U3Y7J7_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_U3JKF2_U3JKF2_FICAL_59894 and tr_A0A218URU7_A0A218URU7_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A096NBR8_A0A096NBR8_PAPAN_9555 and tr_A0A2K5M8R4_A0A2K5M8R4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NBR8_A0A096NBR8_PAPAN_9555 and tr_A0A2K6C9P5_A0A2K6C9P5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NBR8_A0A096NBR8_PAPAN_9555 and tr_A0A2K5XAS5_A0A2K5XAS5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3MQT4_A0A2I3MQT4_PAPAN_9555 and tr_A0A2K5KWS6_A0A2K5KWS6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A151MBP3_A0A151MBP3_ALLMI_8496 and tr_A0A1U7RN15_A0A1U7RN15_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151N8H7_A0A151N8H7_ALLMI_8496 and tr_A0A1U7RSW2_A0A1U7RSW2_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151NBE1_A0A151NBE1_ALLMI_8496 and tr_A0A3Q0G1U5_A0A3Q0G1U5_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151P6N5_A0A151P6N5_ALLMI_8496 and tr_A0A1U7RR93_A0A1U7RR93_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0Q3P3X0_A0A0Q3P3X0_AMAAE_12930 and tr_A0A087QMX3_A0A087QMX3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A0Q3P3X0_A0A0Q3P3X0_AMAAE_12930 and tr_A0A2I0M047_A0A2I0M047_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A0Q3P3X0_A0A0Q3P3X0_AMAAE_12930 and tr_A0A1V4KX76_A0A1V4KX76_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A091J2L1_A0A091J2L1_EGRGA_188379 and tr_A0A091UMT2_A0A091UMT2_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091J2L1_A0A091J2L1_EGRGA_188379 and tr_A0A093HIL2_A0A093HIL2_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091JLB9_A0A091JLB9_EGRGA_188379 and tr_A0A091VNW3_A0A091VNW3_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JLB9_A0A091JLB9_EGRGA_188379 and tr_A0A091V6V6_A0A091V6V6_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091JLB9_A0A091JLB9_EGRGA_188379 and tr_A0A0A0AVN4_A0A0A0AVN4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091KAD4_A0A091KAD4_EGRGA_188379 and tr_A0A093HE54_A0A093HE54_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091KAD4_A0A091KAD4_EGRGA_188379 and tr_A0A091GX91_A0A091GX91_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091KAD4_A0A091KAD4_EGRGA_188379 and tr_A0A091ICQ5_A0A091ICQ5_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A091KAD4_A0A091KAD4_EGRGA_188379 and tr_A0A1V4KX90_A0A1V4KX90_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A091KAD4_A0A091KAD4_EGRGA_188379 and tr_A0A226NI43_A0A226NI43_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A091KAD4_A0A091KAD4_EGRGA_188379 and tr_A0A226PWX2_A0A226PWX2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A093HQ36_A0A093HQ36_STRCA_441894 and tr_A0A099Z4G7_A0A099Z4G7_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A0V1MNF2_A0A0V1MNF2_9BILA_268474 and tr_A0A0V1H7J4_A0A0V1H7J4_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A151WRY2_A0A151WRY2_9HYME_64791 and tr_A0A195DUN5_A0A195DUN5_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A151WRY2_A0A151WRY2_9HYME_64791 and tr_A0A151I5G4_A0A151I5G4_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A151WRY2_A0A151WRY2_9HYME_64791 and tr_A0A151K1K0_A0A151K1K0_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A1S3LFL4_A0A1S3LFL4_SALSA_8030 and tr_A0A060VXH4_A0A060VXH4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3LFL4_A0A1S3LFL4_SALSA_8030 and tr_A0A060Y414_A0A060Y414_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3MK63_A0A1S3MK63_SALSA_8030 and tr_A0A060VYY0_A0A060VYY0_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3PTF9_A0A1S3PTF9_SALSA_8030 and tr_A0A060WYH4_A0A060WYH4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3QJC4_A0A1S3QJC4_SALSA_8030 and tr_A0A060YWI4_A0A060YWI4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226MEC7_A0A226MEC7_CALSU_9009 and tr_A0A226PLA0_A0A226PLA0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2K5KNT8_A0A2K5KNT8_CERAT_9531 and tr_A0A2K5XWN5_A0A2K5XWN5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U3V6H6_A0A2U3V6H6_TURTR_9739 and tr_A0A2Y9NP03_A0A2Y9NP03_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4APW7_A0A2U4APW7_TURTR_9739 and tr_A0A2Y9P5P2_A0A2Y9P5P2_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4CDF3_A0A2U4CDF3_TURTR_9739 and tr_A0A2Y9P2F2_A0A2Y9P2F2_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 228

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/Q96RP8/3_mltree/Q96RP8.raxml.reduced.phy

Alignment comprises 1 partitions and 367 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 367 / 367
Gaps: 2.78 %
Invariant sites: 0.54 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RP8/3_mltree/Q96RP8.raxml.rba

Parallelization scheme autoconfig: 6 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 367 / 29360
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -311958.551679] Initial branch length optimization
[00:00:14 -250165.608228] Model parameter optimization (eps = 10.000000)
[00:01:41 -248872.542928] AUTODETECT spr round 1 (radius: 5)
[00:05:52 -182659.252419] AUTODETECT spr round 2 (radius: 10)
[00:11:12 -137722.584008] AUTODETECT spr round 3 (radius: 15)
[00:16:56 -117359.726507] AUTODETECT spr round 4 (radius: 20)
[00:23:20 -104432.229831] AUTODETECT spr round 5 (radius: 25)
[00:31:58 -99428.680288] SPR radius for FAST iterations: 25 (autodetect)
[00:31:58 -99428.680288] Model parameter optimization (eps = 3.000000)
[00:32:53 -99100.026449] FAST spr round 1 (radius: 25)
[00:37:49 -85599.718049] FAST spr round 2 (radius: 25)
[00:41:13 -84496.212453] FAST spr round 3 (radius: 25)
[00:44:13 -84416.166944] FAST spr round 4 (radius: 25)
[00:46:58 -84411.849428] FAST spr round 5 (radius: 25)
[00:49:29 -84411.848912] Model parameter optimization (eps = 1.000000)
[00:49:51 -84407.482167] SLOW spr round 1 (radius: 5)
[00:53:08 -84394.090741] SLOW spr round 2 (radius: 5)
[00:56:26 -84393.377862] SLOW spr round 3 (radius: 5)
[00:59:43 -84388.293619] SLOW spr round 4 (radius: 5)
[01:02:51 -84388.293526] SLOW spr round 5 (radius: 10)
[01:06:30 -84386.069855] SLOW spr round 6 (radius: 5)
[01:10:50 -84385.965065] SLOW spr round 7 (radius: 5)
[01:14:29 -84385.964726] SLOW spr round 8 (radius: 10)
[01:18:09 -84384.598933] SLOW spr round 9 (radius: 5)
[01:22:21 -84384.083012] SLOW spr round 10 (radius: 5)
[01:26:00 -84384.082633] SLOW spr round 11 (radius: 10)
[01:29:34 -84384.082589] SLOW spr round 12 (radius: 15)
[01:35:12 -84384.082566] SLOW spr round 13 (radius: 20)
[01:45:59 -84384.082564] SLOW spr round 14 (radius: 25)
[01:46:40] [worker #4] ML tree search #5, logLikelihood: -84403.255971
[02:00:46 -84384.082562] Model parameter optimization (eps = 0.100000)

[02:00:55] [worker #0] ML tree search #1, logLikelihood: -84384.065640

[02:00:55 -313255.135043] Initial branch length optimization
[02:01:07 -250513.237543] Model parameter optimization (eps = 10.000000)
[02:02:16 -249256.434257] AUTODETECT spr round 1 (radius: 5)
[02:05:22] [worker #3] ML tree search #4, logLikelihood: -84423.342221
[02:06:06] [worker #1] ML tree search #2, logLikelihood: -84417.117955
[02:06:25 -182026.433132] AUTODETECT spr round 2 (radius: 10)
[02:07:45] [worker #5] ML tree search #6, logLikelihood: -84399.055261
[02:11:43 -139832.800459] AUTODETECT spr round 3 (radius: 15)
[02:17:49 -115439.297769] AUTODETECT spr round 4 (radius: 20)
[02:24:28 -99346.047538] AUTODETECT spr round 5 (radius: 25)
[02:30:08] [worker #2] ML tree search #3, logLikelihood: -84425.460493
[02:33:31 -97371.272181] SPR radius for FAST iterations: 25 (autodetect)
[02:33:31 -97371.272181] Model parameter optimization (eps = 3.000000)
[02:34:14 -97204.521913] FAST spr round 1 (radius: 25)
[02:38:56 -85314.145468] FAST spr round 2 (radius: 25)
[02:42:30 -84506.051450] FAST spr round 3 (radius: 25)
[02:45:32 -84440.398715] FAST spr round 4 (radius: 25)
[02:48:15 -84434.655296] FAST spr round 5 (radius: 25)
[02:50:44 -84432.374521] FAST spr round 6 (radius: 25)
[02:53:07 -84432.374154] Model parameter optimization (eps = 1.000000)
[02:53:31 -84416.702114] SLOW spr round 1 (radius: 5)
[02:56:46 -84405.547348] SLOW spr round 2 (radius: 5)
[02:59:55 -84405.326446] SLOW spr round 3 (radius: 5)
[03:02:59 -84405.326438] SLOW spr round 4 (radius: 10)
[03:06:30 -84404.384780] SLOW spr round 5 (radius: 5)
[03:10:44 -84404.383984] SLOW spr round 6 (radius: 10)
[03:14:37 -84403.090689] SLOW spr round 7 (radius: 5)
[03:18:46 -84403.090684] SLOW spr round 8 (radius: 10)
[03:22:35 -84403.090684] SLOW spr round 9 (radius: 15)
[03:28:23 -84401.148690] SLOW spr round 10 (radius: 5)
[03:32:55 -84401.146754] SLOW spr round 11 (radius: 10)
[03:37:04 -84401.146690] SLOW spr round 12 (radius: 15)
[03:42:23] [worker #4] ML tree search #11, logLikelihood: -84429.125163
[03:42:48 -84401.144298] SLOW spr round 13 (radius: 20)
[03:54:29 -84401.144100] SLOW spr round 14 (radius: 25)
[04:01:22] [worker #1] ML tree search #8, logLikelihood: -84416.920854
[04:10:24 -84400.942626] SLOW spr round 15 (radius: 5)
[04:15:09 -84398.655372] SLOW spr round 16 (radius: 5)
[04:19:08 -84398.648572] SLOW spr round 17 (radius: 10)
[04:22:53 -84398.648571] SLOW spr round 18 (radius: 15)
[04:28:42 -84398.648571] SLOW spr round 19 (radius: 20)
[04:36:43] [worker #3] ML tree search #10, logLikelihood: -84420.784412
[04:38:59] [worker #5] ML tree search #12, logLikelihood: -84402.854354
[04:40:16 -84398.648570] SLOW spr round 20 (radius: 25)
[04:56:11 -84398.648570] Model parameter optimization (eps = 0.100000)

[04:56:20] [worker #0] ML tree search #7, logLikelihood: -84398.629332

[04:56:20 -312869.588718] Initial branch length optimization
[04:56:34 -251071.360714] Model parameter optimization (eps = 10.000000)
[04:57:59 -249690.943965] AUTODETECT spr round 1 (radius: 5)
[05:02:15 -184446.402211] AUTODETECT spr round 2 (radius: 10)
[05:07:37 -133866.746797] AUTODETECT spr round 3 (radius: 15)
[05:13:15 -111443.595846] AUTODETECT spr round 4 (radius: 20)
[05:19:48 -100133.553485] AUTODETECT spr round 5 (radius: 25)
[05:27:06 -97208.436823] SPR radius for FAST iterations: 25 (autodetect)
[05:27:06 -97208.436823] Model parameter optimization (eps = 3.000000)
[05:28:12 -96886.984817] FAST spr round 1 (radius: 25)
[05:29:48] [worker #2] ML tree search #9, logLikelihood: -84418.183241
[05:33:14 -86442.852674] FAST spr round 2 (radius: 25)
[05:36:37 -84538.595999] FAST spr round 3 (radius: 25)
[05:39:32 -84494.779117] FAST spr round 4 (radius: 25)
[05:42:14 -84472.055340] FAST spr round 5 (radius: 25)
[05:44:45 -84472.055321] Model parameter optimization (eps = 1.000000)
[05:45:09 -84469.185266] SLOW spr round 1 (radius: 5)
[05:48:29 -84459.058090] SLOW spr round 2 (radius: 5)
[05:51:50 -84459.057025] SLOW spr round 3 (radius: 10)
[05:55:28 -84458.673018] SLOW spr round 4 (radius: 5)
[05:59:51 -84458.672668] SLOW spr round 5 (radius: 10)
[06:03:48 -84458.672478] SLOW spr round 6 (radius: 15)
[06:09:17 -84412.628228] SLOW spr round 7 (radius: 5)
[06:11:09] [worker #4] ML tree search #17, logLikelihood: -84404.892085
[06:13:56 -84412.625731] SLOW spr round 8 (radius: 10)
[06:18:10 -84402.070706] SLOW spr round 9 (radius: 5)
[06:22:22 -84401.940891] SLOW spr round 10 (radius: 5)
[06:25:58 -84401.940888] SLOW spr round 11 (radius: 10)
[06:29:35 -84401.940878] SLOW spr round 12 (radius: 15)
[06:34:55 -84401.940877] SLOW spr round 13 (radius: 20)
[06:38:02] [worker #1] ML tree search #14, logLikelihood: -84388.739237
[06:40:44] [worker #5] ML tree search #18, logLikelihood: -84392.048742
[06:44:53 -84401.940877] SLOW spr round 14 (radius: 25)
[06:59:14 -84401.940877] Model parameter optimization (eps = 0.100000)

[06:59:22] [worker #0] ML tree search #13, logLikelihood: -84401.925573

[06:59:22 -312940.123931] Initial branch length optimization
[06:59:34 -250120.770519] Model parameter optimization (eps = 10.000000)
[07:01:02 -248725.000680] AUTODETECT spr round 1 (radius: 5)
[07:05:19 -183127.264987] AUTODETECT spr round 2 (radius: 10)
[07:05:55] [worker #3] ML tree search #16, logLikelihood: -84413.140063
[07:10:41 -131432.508700] AUTODETECT spr round 3 (radius: 15)
[07:16:06 -109817.541038] AUTODETECT spr round 4 (radius: 20)
[07:23:05 -98513.272269] AUTODETECT spr round 5 (radius: 25)
[07:31:36 -96341.897688] SPR radius for FAST iterations: 25 (autodetect)
[07:31:36 -96341.897688] Model parameter optimization (eps = 3.000000)
[07:32:24 -96081.253883] FAST spr round 1 (radius: 25)
[07:37:23 -84970.932717] FAST spr round 2 (radius: 25)
[07:40:57 -84478.604428] FAST spr round 3 (radius: 25)
[07:43:55 -84453.245524] FAST spr round 4 (radius: 25)
[07:46:35 -84438.087910] FAST spr round 5 (radius: 25)
[07:49:03 -84436.609040] FAST spr round 6 (radius: 25)
[07:51:28 -84436.609039] Model parameter optimization (eps = 1.000000)
[07:51:57 -84433.104681] SLOW spr round 1 (radius: 5)
[07:55:16 -84420.827396] SLOW spr round 2 (radius: 5)
[07:58:36 -84419.406791] SLOW spr round 3 (radius: 5)
[08:01:54 -84419.406095] SLOW spr round 4 (radius: 10)
[08:05:36 -84414.072117] SLOW spr round 5 (radius: 5)
[08:06:01] [worker #2] ML tree search #15, logLikelihood: -84434.919381
[08:10:00 -84411.192273] SLOW spr round 6 (radius: 5)
[08:13:48 -84411.192025] SLOW spr round 7 (radius: 10)
[08:17:28 -84411.191944] SLOW spr round 8 (radius: 15)
[08:22:52 -84410.493389] SLOW spr round 9 (radius: 5)
[08:25:54] [worker #1] ML tree search #20, logLikelihood: -84415.603059
[08:27:24 -84410.493074] SLOW spr round 10 (radius: 10)
[08:31:33 -84410.492939] SLOW spr round 11 (radius: 15)
[08:36:51 -84409.877074] SLOW spr round 12 (radius: 5)
[08:41:23 -84409.877050] SLOW spr round 13 (radius: 10)
[08:45:27 -84409.877050] SLOW spr round 14 (radius: 15)
[08:50:44 -84409.877050] SLOW spr round 15 (radius: 20)
[09:00:25 -84409.877049] SLOW spr round 16 (radius: 25)
[09:13:01 -84409.877049] Model parameter optimization (eps = 0.100000)

[09:13:09] [worker #0] ML tree search #19, logLikelihood: -84409.861304


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.271039,0.355760) (0.293446,0.573767) (0.303732,1.106438) (0.131784,3.028791) 
   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: -84384.065640

AIC score: 172778.131280 / AICc score: 8216838.131280 / BIC score: 180608.381786
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=367).
         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/Q96RP8/3_mltree/Q96RP8.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RP8/3_mltree/Q96RP8.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RP8/3_mltree/Q96RP8.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RP8/3_mltree/Q96RP8.raxml.log

Analysis started: 10-Jul-2021 23:51:28 / finished: 11-Jul-2021 09:04:38

Elapsed time: 33190.176 seconds