RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 05-Jul-2021 21:21:10 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/2_msa/Q9NR09_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/3_mltree/Q9NR09 --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/Q9NR09/2_msa/Q9NR09_trimmed_msa.fasta
[00:00:00] Loaded alignment with 986 taxa and 284 sites

WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_U3J3N3_U3J3N3_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A087RAT5_A0A087RAT5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A093I0F2_A0A093I0F2_STRCA_441894 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A091W6U4_A0A091W6U4_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A099Z349_A0A099Z349_TINGU_94827 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A0A0A971_A0A0A0A971_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A2I0LYE0_A0A2I0LYE0_COLLI_8932 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A091I0M1_A0A091I0M1_CALAN_9244 are exactly identical!
WARNING: Sequences tr_F1NLF6_F1NLF6_CHICK_9031 and tr_A0A1V4JJX5_A0A1V4JJX5_PATFA_372326 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2I3GX44_A0A2I3GX44_NOMLE_61853 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2I2ZP94_A0A2I2ZP94_GORGO_9595 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_H2P6J0_H2P6J0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_G1SRC9_G1SRC9_RABIT_9986 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2I3TAY7_A0A2I3TAY7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_W5PLH4_W5PLH4_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and sp_Q9NR09_BIRC6_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_F7HH34_F7HH34_MACMU_9544 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_G3T2L1_G3T2L1_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_F1S402_F1S402_PIG_9823 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_G1LN83_G1LN83_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_E1BE13_E1BE13_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_L5KSA9_L5KSA9_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_M3W539_M3W539_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A096NGW4_A0A096NGW4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A0D9RGP2_A0A0D9RGP2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2K5P209_A0A2K5P209_CERAT_9531 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2K6AQ69_A0A2K6AQ69_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2K5YE92_A0A2K5YE92_MANLE_9568 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2R9BAM9_A0A2R9BAM9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2U3W6D1_A0A2U3W6D1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2Y9RJ36_A0A2Y9RJ36_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A2Y9KIZ0_A0A2Y9KIZ0_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Y1N8_M3Y1N8_MUSPF_9669 and tr_A0A384CV99_A0A384CV99_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G3HEV6_G3HEV6_CRIGR_10029 and tr_A0A1U7QV43_A0A1U7QV43_MESAU_10036 are exactly identical!
WARNING: Sequences tr_B2WB14_B2WB14_PYRTR_426418 and tr_A0A317B2Z3_A0A317B2Z3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3URH8_G3URH8_MELGA_9103 and tr_F6YZT2_F6YZT2_ORNAN_9258 are exactly identical!
WARNING: Sequences tr_B8P1K6_B8P1K6_POSPM_561896 and tr_A0A1X6NEW9_A0A1X6NEW9_9APHY_670580 are exactly identical!
WARNING: Sequences tr_F6S3J4_F6S3J4_MONDO_13616 and tr_G3VRK2_G3VRK2_SARHA_9305 are exactly identical!
WARNING: Sequences tr_A0A368QLS9_A0A368QLS9_SETIT_4555 and tr_A0A368QM08_A0A368QM08_SETIT_4555 are exactly identical!
WARNING: Sequences tr_A0A088A067_A0A088A067_APIME_7460 and tr_A0A2A3E5U2_A0A2A3E5U2_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NKP4_A0A158NKP4_ATTCE_12957 and tr_F4X3E7_F4X3E7_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NKP4_A0A158NKP4_ATTCE_12957 and tr_A0A195BLW9_A0A195BLW9_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0FFM8_A0A0E0FFM8_ORYNI_4536 and tr_A0A0E0MQU3_A0A0E0MQU3_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0FFM8_A0A0E0FFM8_ORYNI_4536 and tr_A0A0D3EJ48_A0A0D3EJ48_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0FJ34_A0A0E0FJ34_ORYNI_4536 and tr_A0A0D9Y5N7_A0A0D9Y5N7_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0FJ48_A0A0E0FJ48_ORYNI_4536 and tr_A0A0E0BZK9_A0A0E0BZK9_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0HI13_A0A0E0HI13_ORYNI_4536 and tr_A2Y7C1_A2Y7C1_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HI13_A0A0E0HI13_ORYNI_4536 and tr_I1PXU5_I1PXU5_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HI13_A0A0E0HI13_ORYNI_4536 and tr_A0A0E0PR28_A0A0E0PR28_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HI13_A0A0E0HI13_ORYNI_4536 and tr_A0A0D3GAN9_A0A0D3GAN9_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0HI13_A0A0E0HI13_ORYNI_4536 and tr_A0A0E0A2M6_A0A0E0A2M6_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0HI13_A0A0E0HI13_ORYNI_4536 and tr_Q6I602_Q6I602_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0K0INH8_A0A0K0INH8_BRUMA_6279 and tr_A0A0R3QJP8_A0A0R3QJP8_9BILA_42155 are exactly identical!
WARNING: Sequences tr_I1NJW2_I1NJW2_ORYGL_4538 and tr_Q5ZCB9_Q5ZCB9_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1NLL4_I1NLL4_ORYGL_4538 and tr_Q5NAY5_Q5NAY5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1PTJ9_I1PTJ9_ORYGL_4538 and tr_A0A0D3G4T0_A0A0D3G4T0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1QMQ0_I1QMQ0_ORYGL_4538 and tr_Q69LG5_Q69LG5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_H0ZEY7_H0ZEY7_TAEGU_59729 and tr_U3KBV1_U3KBV1_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0ZEY7_H0ZEY7_TAEGU_59729 and tr_A0A091EA08_A0A091EA08_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0ZEY7_H0ZEY7_TAEGU_59729 and tr_A0A218U980_A0A218U980_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A0E0PJA5_A0A0E0PJA5_ORYRU_4529 and tr_Q0DJS7_Q0DJS7_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0QPB3_A0A0E0QPB3_ORYRU_4529 and tr_A0A0D3H4U0_A0A0D3H4U0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0QPB3_A0A0E0QPB3_ORYRU_4529 and tr_A0A0E0B0Y8_A0A0E0B0Y8_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_E3LD66_E3LD66_CAERE_31234 and tr_A0A261CP09_A0A261CP09_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_M4FI85_M4FI85_BRARP_51351 and tr_A0A078GKG1_A0A078GKG1_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M7ZJK8_M7ZJK8_TRIUA_4572 and tr_A0A3B6EFP3_A0A3B6EFP3_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_V2X3T8_V2X3T8_MONRO_1381753 and tr_A0A0W0G9C7_A0A0W0G9C7_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A3B6FEG7_A0A3B6FEG7_WHEAT_4565 and tr_A0A3B6GM01_A0A3B6GM01_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A044UAU0_A0A044UAU0_ONCVO_6282 and tr_A0A182DXR6_A0A182DXR6_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A067GKJ2_A0A067GKJ2_CITSI_2711 and tr_V4U9B3_V4U9B3_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A078IBR9_A0A078IBR9_BRANA_3708 and tr_A0A0D3BMS7_A0A0D3BMS7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078IXN2_A0A078IXN2_BRANA_3708 and tr_A0A0D3C3Z9_A0A0D3C3Z9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078IZD0_A0A078IZD0_BRANA_3708 and tr_A0A0D3CR90_A0A0D3CR90_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0D2T1J6_A0A0D2T1J6_GOSRA_29730 and tr_A0A1U8N3L7_A0A1U8N3L7_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A151MHA8_A0A151MHA8_ALLMI_8496 and tr_A0A3Q0G1A0_A0A3Q0G1A0_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0V0WRD4_A0A0V0WRD4_9BILA_92179 and tr_A0A0V0VJE3_A0A0V0VJE3_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0WRD4_A0A0V0WRD4_9BILA_92179 and tr_A0A0V1KZS0_A0A0V1KZS0_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0WRD4_A0A0V0WRD4_9BILA_92179 and tr_A0A0V0ZMF1_A0A0V0ZMF1_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0WRD4_A0A0V0WRD4_9BILA_92179 and tr_A0A0V1NMJ6_A0A0V1NMJ6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0WRD4_A0A0V0WRD4_9BILA_92179 and tr_A0A0V0TPV3_A0A0V0TPV3_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A151WRQ9_A0A151WRQ9_9HYME_64791 and tr_A0A195DG35_A0A195DG35_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A151WRQ9_A0A151WRQ9_9HYME_64791 and tr_A0A195CJV5_A0A195CJV5_9HYME_456900 are exactly identical!
WARNING: Sequences tr_A0A1S3YEW4_A0A1S3YEW4_TOBAC_4097 and tr_A0A1U7WH42_A0A1U7WH42_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3ZSQ8_A0A1S3ZSQ8_TOBAC_4097 and tr_A0A1U7X8I5_A0A1U7X8I5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4AVB0_A0A1S4AVB0_TOBAC_4097 and tr_A0A1U7V4S6_A0A1U7V4S6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BSZ2_A0A1S4BSZ2_TOBAC_4097 and tr_A0A1U7VZX1_A0A1U7VZX1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BX07_A0A1S4BX07_TOBAC_4097 and tr_A0A1U7WM82_A0A1U7WM82_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4DRX4_A0A1S4DRX4_TOBAC_4097 and tr_A0A1U7VWR6_A0A1U7VWR6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3S2B1_A0A1S3S2B1_SALSA_8030 and tr_A0A060X4B4_A0A060X4B4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1I7TC69_A0A1I7TC69_9PELO_1561998 and tr_A0A1I7TC70_A0A1I7TC70_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1U8IN38_A0A1U8IN38_GOSHI_3635 and tr_A0A1U8NJN6_A0A1U8NJN6_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A2I4ASL4_A0A2I4ASL4_9TELE_52670 and tr_A0A2I4D669_A0A2I4D669_9TELE_52670 are exactly identical!
WARNING: Sequences tr_A0A2H3CBC3_A0A2H3CBC3_9AGAR_1076256 and tr_A0A284QZR4_A0A284QZR4_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2Y9NA76_A0A2Y9NA76_DELLE_9749 and tr_A0A2Y9S763_A0A2Y9S763_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 94

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/Q9NR09/3_mltree/Q9NR09.raxml.reduced.phy

Alignment comprises 1 partitions and 284 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 284 / 284
Gaps: 10.42 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/3_mltree/Q9NR09.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 986 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 284 / 22720
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -465532.472160] Initial branch length optimization
[00:00:10 -394376.062720] Model parameter optimization (eps = 10.000000)
[00:01:52 -393723.140631] AUTODETECT spr round 1 (radius: 5)
[00:05:58 -283435.100648] AUTODETECT spr round 2 (radius: 10)
[00:10:40 -211989.962505] AUTODETECT spr round 3 (radius: 15)
[00:15:43 -178819.767161] AUTODETECT spr round 4 (radius: 20)
[00:21:37 -169386.041305] AUTODETECT spr round 5 (radius: 25)
[00:29:21 -166574.558555] SPR radius for FAST iterations: 25 (autodetect)
[00:29:21 -166574.558555] Model parameter optimization (eps = 3.000000)
[00:29:57 -166470.033102] FAST spr round 1 (radius: 25)
[00:35:40 -148310.843736] FAST spr round 2 (radius: 25)
[00:39:50 -147591.707553] FAST spr round 3 (radius: 25)
[00:43:24 -147514.278895] FAST spr round 4 (radius: 25)
[00:46:23 -147508.384785] FAST spr round 5 (radius: 25)
[00:49:06 -147508.384371] Model parameter optimization (eps = 1.000000)
[00:49:32 -147505.644199] SLOW spr round 1 (radius: 5)
[00:53:03 -147456.498434] SLOW spr round 2 (radius: 5)
[00:56:36 -147454.423210] SLOW spr round 3 (radius: 5)
[01:00:15 -147451.492981] SLOW spr round 4 (radius: 5)
[01:03:51 -147445.396659] SLOW spr round 5 (radius: 5)
[01:07:22 -147444.967406] SLOW spr round 6 (radius: 5)
[01:10:51 -147444.966922] SLOW spr round 7 (radius: 10)
[01:14:29 -147444.966533] SLOW spr round 8 (radius: 15)
[01:21:20 -147443.815413] SLOW spr round 9 (radius: 5)
[01:25:58 -147443.815079] SLOW spr round 10 (radius: 10)
[01:30:18 -147443.814788] SLOW spr round 11 (radius: 15)
[01:36:39 -147443.814521] SLOW spr round 12 (radius: 20)
[01:38:21] [worker #2] ML tree search #3, logLikelihood: -147462.967541
[01:45:31] [worker #4] ML tree search #5, logLikelihood: -147447.454812
[01:47:38 -147443.814276] SLOW spr round 13 (radius: 25)
[02:02:26 -147443.472353] SLOW spr round 14 (radius: 5)
[02:07:16 -147443.472143] SLOW spr round 15 (radius: 10)
[02:11:52 -147443.471960] SLOW spr round 16 (radius: 15)
[02:14:59] [worker #5] ML tree search #6, logLikelihood: -147436.855268
[02:18:12 -147443.471792] SLOW spr round 17 (radius: 20)
[02:22:20] [worker #3] ML tree search #4, logLikelihood: -147431.217037
[02:22:41] [worker #1] ML tree search #2, logLikelihood: -147439.970879
[02:29:14 -147443.471638] SLOW spr round 18 (radius: 25)
[02:44:01 -147443.471496] Model parameter optimization (eps = 0.100000)

[02:44:08] [worker #0] ML tree search #1, logLikelihood: -147443.458409

[02:44:08 -466945.263592] Initial branch length optimization
[02:44:15 -397249.431329] Model parameter optimization (eps = 10.000000)
[02:45:10 -396497.557839] AUTODETECT spr round 1 (radius: 5)
[02:49:19 -287419.057204] AUTODETECT spr round 2 (radius: 10)
[02:53:56 -225350.057976] AUTODETECT spr round 3 (radius: 15)
[02:59:17 -194962.783574] AUTODETECT spr round 4 (radius: 20)
[03:05:50 -182851.759883] AUTODETECT spr round 5 (radius: 25)
[03:13:34 -174573.055515] SPR radius for FAST iterations: 25 (autodetect)
[03:13:34 -174573.055515] Model parameter optimization (eps = 3.000000)
[03:14:17 -174464.583946] FAST spr round 1 (radius: 25)
[03:20:22 -148710.853104] FAST spr round 2 (radius: 25)
[03:24:37 -147573.556530] FAST spr round 3 (radius: 25)
[03:27:06] [worker #4] ML tree search #11, logLikelihood: -147442.945249
[03:28:01 -147502.156294] FAST spr round 4 (radius: 25)
[03:31:01 -147491.627926] FAST spr round 5 (radius: 25)
[03:33:45 -147491.627522] Model parameter optimization (eps = 1.000000)
[03:34:08 -147488.608921] SLOW spr round 1 (radius: 5)
[03:37:46 -147454.202714] SLOW spr round 2 (radius: 5)
[03:41:20 -147451.534126] SLOW spr round 3 (radius: 5)
[03:44:53 -147451.531870] SLOW spr round 4 (radius: 10)
[03:48:37 -147451.531020] SLOW spr round 5 (radius: 15)
[03:55:45 -147451.530672] SLOW spr round 6 (radius: 20)
[04:07:30 -147451.530521] SLOW spr round 7 (radius: 25)
[04:23:28 -147451.530438] Model parameter optimization (eps = 0.100000)

[04:23:35] [worker #0] ML tree search #7, logLikelihood: -147451.488490

[04:23:35 -467102.860287] Initial branch length optimization
[04:23:42 -396048.332504] Model parameter optimization (eps = 10.000000)
[04:24:48 -395203.776538] AUTODETECT spr round 1 (radius: 5)
[04:28:52 -280544.330409] AUTODETECT spr round 2 (radius: 10)
[04:33:04] [worker #2] ML tree search #9, logLikelihood: -147468.877361
[04:33:28 -213249.977359] AUTODETECT spr round 3 (radius: 15)
[04:37:24] [worker #3] ML tree search #10, logLikelihood: -147435.019064
[04:38:45 -189278.059132] AUTODETECT spr round 4 (radius: 20)
[04:39:34] [worker #5] ML tree search #12, logLikelihood: -147437.674672
[04:44:45 -172389.663507] AUTODETECT spr round 5 (radius: 25)
[04:52:15 -169595.620879] SPR radius for FAST iterations: 25 (autodetect)
[04:52:15 -169595.620879] Model parameter optimization (eps = 3.000000)
[04:52:54 -169500.891738] FAST spr round 1 (radius: 25)
[04:58:42 -148923.151258] FAST spr round 2 (radius: 25)
[05:02:57 -148300.884902] FAST spr round 3 (radius: 25)
[05:06:44 -147611.597521] FAST spr round 4 (radius: 25)
[05:09:47] [worker #1] ML tree search #8, logLikelihood: -147451.175466
[05:10:12 -147566.020086] FAST spr round 5 (radius: 25)
[05:13:06 -147565.308099] FAST spr round 6 (radius: 25)
[05:15:51 -147565.068591] FAST spr round 7 (radius: 25)
[05:18:33 -147565.068362] Model parameter optimization (eps = 1.000000)
[05:18:56 -147553.167230] SLOW spr round 1 (radius: 5)
[05:22:22] [worker #4] ML tree search #17, logLikelihood: -147430.645140
[05:22:27 -147510.982707] SLOW spr round 2 (radius: 5)
[05:26:01 -147506.053213] SLOW spr round 3 (radius: 5)
[05:29:31 -147505.762908] SLOW spr round 4 (radius: 5)
[05:33:02 -147505.762630] SLOW spr round 5 (radius: 10)
[05:36:42 -147505.762586] SLOW spr round 6 (radius: 15)
[05:43:34 -147505.762584] SLOW spr round 7 (radius: 20)
[05:54:08 -147505.762582] SLOW spr round 8 (radius: 25)
[06:08:27 -147504.575063] SLOW spr round 9 (radius: 5)
[06:13:19 -147501.635368] SLOW spr round 10 (radius: 5)
[06:16:04] [worker #5] ML tree search #18, logLikelihood: -147511.450318
[06:17:28 -147501.632169] SLOW spr round 11 (radius: 10)
[06:21:24 -147474.639020] SLOW spr round 12 (radius: 5)
[06:25:49 -147465.609112] SLOW spr round 13 (radius: 5)
[06:29:40 -147465.607981] SLOW spr round 14 (radius: 10)
[06:33:23 -147465.607976] SLOW spr round 15 (radius: 15)
[06:40:00 -147465.607974] SLOW spr round 16 (radius: 20)
[06:50:34 -147465.607972] SLOW spr round 17 (radius: 25)
[06:52:08] [worker #2] ML tree search #15, logLikelihood: -147452.529523
[06:55:42] [worker #1] ML tree search #14, logLikelihood: -147461.997777
[07:04:49 -147465.607970] Model parameter optimization (eps = 0.100000)

[07:04:56] [worker #0] ML tree search #13, logLikelihood: -147465.588050

[07:04:56 -465852.883323] Initial branch length optimization
[07:05:02 -395388.886332] Model parameter optimization (eps = 10.000000)
[07:06:34 -394599.688966] AUTODETECT spr round 1 (radius: 5)
[07:10:41 -283721.760879] AUTODETECT spr round 2 (radius: 10)
[07:15:12 -225321.492369] AUTODETECT spr round 3 (radius: 15)
[07:20:22 -188116.576824] AUTODETECT spr round 4 (radius: 20)
[07:25:42 -174690.954241] AUTODETECT spr round 5 (radius: 25)
[07:33:00 -172243.178498] SPR radius for FAST iterations: 25 (autodetect)
[07:33:00 -172243.178498] Model parameter optimization (eps = 3.000000)
[07:33:43 -172093.477069] FAST spr round 1 (radius: 25)
[07:39:39 -148725.848986] FAST spr round 2 (radius: 25)
[07:43:47 -147730.110039] FAST spr round 3 (radius: 25)
[07:47:28 -147538.186013] FAST spr round 4 (radius: 25)
[07:50:42 -147519.683717] FAST spr round 5 (radius: 25)
[07:53:33 -147507.180404] FAST spr round 6 (radius: 25)
[07:56:10 -147507.179555] Model parameter optimization (eps = 1.000000)
[07:56:35 -147501.261386] SLOW spr round 1 (radius: 5)
[08:00:06 -147460.109432] SLOW spr round 2 (radius: 5)
[08:03:42 -147450.250114] SLOW spr round 3 (radius: 5)
[08:07:16 -147449.440108] SLOW spr round 4 (radius: 5)
[08:10:39] [worker #3] ML tree search #16, logLikelihood: -148021.340363
[08:10:44 -147449.296672] SLOW spr round 5 (radius: 5)
[08:14:09 -147449.296061] SLOW spr round 6 (radius: 10)
[08:17:50 -147449.295667] SLOW spr round 7 (radius: 15)
[08:24:40 -147449.295389] SLOW spr round 8 (radius: 20)
[08:35:38 -147449.295374] SLOW spr round 9 (radius: 25)
[08:50:39 -147449.295370] Model parameter optimization (eps = 0.100000)

[08:50:47] [worker #0] ML tree search #19, logLikelihood: -147449.205500

[08:51:49] [worker #1] ML tree search #20, logLikelihood: -147462.052194

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.154738,0.218387) (0.163249,0.358424) (0.317550,0.792670) (0.364464,1.799859) 
   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: -147430.645140

AIC score: 298811.290280 / AICc score: 8104011.290280 / BIC score: 306018.014400
Free parameters (model + branch lengths): 1975

WARNING: Number of free parameters (K=1975) is larger than alignment size (n=284).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 118 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/3_mltree/Q9NR09.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/3_mltree/Q9NR09.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/3_mltree/Q9NR09.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/3_mltree/Q9NR09.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NR09/3_mltree/Q9NR09.raxml.log

Analysis started: 05-Jul-2021 21:21:10 / finished: 06-Jul-2021 06:13:00

Elapsed time: 31909.723 seconds