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 08-Jul-2021 18:31:12 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/2_msa/Q96RY5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/3_mltree/Q96RY5 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/2_msa/Q96RY5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 186 taxa and 162 sites

WARNING: Sequences tr_B4R3U4_B4R3U4_DROSI_7240 and tr_B4I9Z9_B4I9Z9_DROSE_7238 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_G1NCV0_G1NCV0_MELGA_9103 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_U3IV16_U3IV16_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A091ITY9_A0A091ITY9_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A093PLV2_A0A093PLV2_9PASS_328815 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A091VLR0_A0A091VLR0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A093HDK5_A0A093HDK5_STRCA_441894 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A091GAR3_A0A091GAR3_9AVES_55661 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A0A0AKF7_A0A0A0AKF7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A2I0LWS3_A0A2I0LWS3_COLLI_8932 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A093GKA6_A0A093GKA6_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A091IH96_A0A091IH96_CALAN_9244 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A226MVE5_A0A226MVE5_CALSU_9009 are exactly identical!
WARNING: Sequences tr_F1P2P0_F1P2P0_CHICK_9031 and tr_A0A226NZ41_A0A226NZ41_COLVI_9014 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_G1SMY0_G1SMY0_RABIT_9986 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_F7D6I3_F7D6I3_MONDO_13616 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_D3ZNU3_D3ZNU3_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_I3M2T6_I3M2T6_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_H0V581_H0V581_CAVPO_10141 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_G5BY72_G5BY72_HETGA_10181 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_G3WFG6_G3WFG6_SARHA_9305 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_A0A091DRJ5_A0A091DRJ5_FUKDA_885580 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_A0A1S3EQP4_A0A1S3EQP4_DIPOR_10020 are exactly identical!
WARNING: Sequences sp_Q6PG95_CRML_MOUSE_10090 and tr_A0A1U8CCM9_A0A1U8CCM9_MESAU_10036 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_A0A2J8J7V5_A0A2J8J7V5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and sp_Q96RY5_CRML_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_F6SRW3_F6SRW3_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_U3FRU0_U3FRU0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_G7Q056_G7Q056_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_A0A096NKT1_A0A096NKT1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_A0A0D9RGH6_A0A0D9RGH6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_A0A2K5N7A0_A0A2K5N7A0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_A0A2K6BYT8_A0A2K6BYT8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_A0A2K5ZVG8_A0A2K5ZVG8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2NPQ1_H2NPQ1_PONAB_9601 and tr_A0A2R9BCG0_A0A2R9BCG0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q29HQ6_Q29HQ6_DROPS_46245 and tr_B4GYG9_B4GYG9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_W5Q3D9_W5Q3D9_SHEEP_9940 and tr_E1BN92_E1BN92_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5PTY7_A0A3B5PTY7_XIPMA_8083 and tr_A0A087XM18_A0A087XM18_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A088A354_A0A088A354_APIME_7460 and tr_A0A2A3E8W4_A0A2A3E8W4_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NL73_A0A158NL73_ATTCE_12957 and tr_F4WFU4_F4WFU4_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NL73_A0A158NL73_ATTCE_12957 and tr_A0A151WHD2_A0A151WHD2_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A158NL73_A0A158NL73_ATTCE_12957 and tr_A0A151JT12_A0A151JT12_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158NL73_A0A158NL73_ATTCE_12957 and tr_A0A195F1T0_A0A195F1T0_9HYME_34720 are exactly identical!
WARNING: Sequences tr_I3KTG4_I3KTG4_ORENI_8128 and tr_A0A2U9CSD3_A0A2U9CSD3_SCOMX_52904 are exactly identical!
WARNING: Sequences tr_G5E730_G5E730_LOXAF_9785 and tr_A0A2Y9DEJ7_A0A2Y9DEJ7_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_H0YYA8_H0YYA8_TAEGU_59729 and tr_U3JQY4_U3JQY4_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0YYA8_H0YYA8_TAEGU_59729 and tr_A0A091F6B3_A0A091F6B3_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0YYA8_H0YYA8_TAEGU_59729 and tr_A0A218UQP0_A0A218UQP0_9PASE_299123 are exactly identical!
WARNING: Sequences tr_F6V0C0_F6V0C0_XENTR_8364 and tr_A0A1L8EQR0_A0A1L8EQR0_XENLA_8355 are exactly identical!
WARNING: Sequences tr_G1LNL9_G1LNL9_AILME_9646 and tr_A0A2I2UT83_A0A2I2UT83_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1LNL9_G1LNL9_AILME_9646 and tr_A0A2U3W4Z6_A0A2U3W4Z6_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1LNL9_G1LNL9_AILME_9646 and tr_A0A2Y9KFQ4_A0A2Y9KFQ4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1LNL9_G1LNL9_AILME_9646 and tr_A0A384CLH7_A0A384CLH7_URSMA_29073 are exactly identical!
WARNING: Sequences tr_B3RW98_B3RW98_TRIAD_10228 and tr_A0A369RVA3_A0A369RVA3_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A151N6N4_A0A151N6N4_ALLMI_8496 and tr_A0A3Q0GKG4_A0A3Q0GKG4_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0V1NAC6_A0A0V1NAC6_9BILA_268474 and tr_A0A0V1I8V2_A0A0V1I8V2_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1S3R5R3_A0A1S3R5R3_SALSA_8030 and tr_A0A060WI03_A0A060WI03_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2U4BM13_A0A2U4BM13_TURTR_9739 and tr_A0A2Y9PXC4_A0A2Y9PXC4_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4BM13_A0A2U4BM13_TURTR_9739 and tr_A0A2Y9EER9_A0A2Y9EER9_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4BM13_A0A2U4BM13_TURTR_9739 and tr_A0A384A346_A0A384A346_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 60

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/Q96RY5/3_mltree/Q96RY5.raxml.reduced.phy

Alignment comprises 1 partitions and 162 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 162 / 162
Gaps: 5.09 %
Invariant sites: 2.47 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/3_mltree/Q96RY5.raxml.rba

Parallelization scheme autoconfig: 3 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 186 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 162 / 12960
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -34498.313990] Initial branch length optimization
[00:00:00 -24235.627101] Model parameter optimization (eps = 10.000000)
[00:00:08 -24057.155574] AUTODETECT spr round 1 (radius: 5)
[00:00:15 -19698.201233] AUTODETECT spr round 2 (radius: 10)
[00:00:26 -15123.891719] AUTODETECT spr round 3 (radius: 15)
[00:00:42 -13104.465878] AUTODETECT spr round 4 (radius: 20)
[00:00:55 -13066.757085] AUTODETECT spr round 5 (radius: 25)
[00:01:06 -13056.215017] SPR radius for FAST iterations: 25 (autodetect)
[00:01:06 -13056.215017] Model parameter optimization (eps = 3.000000)
[00:01:11 -13022.502668] FAST spr round 1 (radius: 25)
[00:01:19 -12414.053910] FAST spr round 2 (radius: 25)
[00:01:26 -12360.670909] FAST spr round 3 (radius: 25)
[00:01:34 -12352.083435] FAST spr round 4 (radius: 25)
[00:01:40 -12352.081419] Model parameter optimization (eps = 1.000000)
[00:01:42 -12351.714377] SLOW spr round 1 (radius: 5)
[00:01:52 -12347.817546] SLOW spr round 2 (radius: 5)
[00:02:03 -12347.815209] SLOW spr round 3 (radius: 10)
[00:02:14 -12347.646483] SLOW spr round 4 (radius: 5)
[00:02:29 -12347.646047] SLOW spr round 5 (radius: 10)
[00:02:43 -12347.645884] SLOW spr round 6 (radius: 15)
[00:03:01 -12347.645812] SLOW spr round 7 (radius: 20)
[00:03:20 -12347.645770] SLOW spr round 8 (radius: 25)
[00:03:29] [worker #1] ML tree search #2, logLikelihood: -12317.656971
[00:03:41 -12347.645741] Model parameter optimization (eps = 0.100000)

[00:03:42] [worker #0] ML tree search #1, logLikelihood: -12347.587290

[00:03:42 -34228.744475] Initial branch length optimization
[00:03:42 -24313.025884] Model parameter optimization (eps = 10.000000)
[00:03:51 -24122.777280] AUTODETECT spr round 1 (radius: 5)
[00:03:58 -19901.759797] AUTODETECT spr round 2 (radius: 10)
[00:04:08 -16063.306114] AUTODETECT spr round 3 (radius: 15)
[00:04:12] [worker #2] ML tree search #3, logLikelihood: -12319.182885
[00:04:19 -14259.190937] AUTODETECT spr round 4 (radius: 20)
[00:04:33 -13426.358648] AUTODETECT spr round 5 (radius: 25)
[00:04:46 -13405.449722] SPR radius for FAST iterations: 25 (autodetect)
[00:04:46 -13405.449722] Model parameter optimization (eps = 3.000000)
[00:04:54 -13350.935244] FAST spr round 1 (radius: 25)
[00:05:02 -12366.540753] FAST spr round 2 (radius: 25)
[00:05:10 -12332.603743] FAST spr round 3 (radius: 25)
[00:05:17 -12329.986397] FAST spr round 4 (radius: 25)
[00:05:23 -12328.986936] FAST spr round 5 (radius: 25)
[00:05:29 -12328.986203] Model parameter optimization (eps = 1.000000)
[00:05:34 -12323.957246] SLOW spr round 1 (radius: 5)
[00:05:45 -12320.411852] SLOW spr round 2 (radius: 5)
[00:05:57 -12320.078387] SLOW spr round 3 (radius: 5)
[00:06:07 -12320.074180] SLOW spr round 4 (radius: 10)
[00:06:18 -12319.971150] SLOW spr round 5 (radius: 5)
[00:06:33 -12319.970869] SLOW spr round 6 (radius: 10)
[00:06:47 -12319.970798] SLOW spr round 7 (radius: 15)
[00:07:05 -12319.273484] SLOW spr round 8 (radius: 5)
[00:07:21 -12319.273321] SLOW spr round 9 (radius: 10)
[00:07:35 -12319.122482] SLOW spr round 10 (radius: 5)
[00:07:39] [worker #1] ML tree search #5, logLikelihood: -12319.082732
[00:07:49 -12319.122476] SLOW spr round 11 (radius: 10)
[00:08:03 -12319.122475] SLOW spr round 12 (radius: 15)
[00:08:21 -12319.122474] SLOW spr round 13 (radius: 20)
[00:08:43 -12316.426685] SLOW spr round 14 (radius: 5)
[00:08:59 -12316.426582] SLOW spr round 15 (radius: 10)
[00:09:00] [worker #2] ML tree search #6, logLikelihood: -12318.573947
[00:09:13 -12316.426570] SLOW spr round 16 (radius: 15)
[00:09:31 -12316.426566] SLOW spr round 17 (radius: 20)
[00:09:51 -12316.426564] SLOW spr round 18 (radius: 25)
[00:10:10 -12316.426564] Model parameter optimization (eps = 0.100000)

[00:10:13] [worker #0] ML tree search #4, logLikelihood: -12315.998923

[00:10:13 -34180.631909] Initial branch length optimization
[00:10:14 -24170.828425] Model parameter optimization (eps = 10.000000)
[00:10:22 -23988.754749] AUTODETECT spr round 1 (radius: 5)
[00:10:29 -19182.364003] AUTODETECT spr round 2 (radius: 10)
[00:10:40 -15227.522433] AUTODETECT spr round 3 (radius: 15)
[00:10:52 -14062.889526] AUTODETECT spr round 4 (radius: 20)
[00:11:05 -13832.494097] AUTODETECT spr round 5 (radius: 25)
[00:11:10] [worker #1] ML tree search #8, logLikelihood: -12310.517331
[00:11:16 -13495.547796] SPR radius for FAST iterations: 25 (autodetect)
[00:11:16 -13495.547796] Model parameter optimization (eps = 3.000000)
[00:11:25 -13417.255455] FAST spr round 1 (radius: 25)
[00:11:35 -12358.896307] FAST spr round 2 (radius: 25)
[00:11:43 -12333.782715] FAST spr round 3 (radius: 25)
[00:11:50 -12333.154832] FAST spr round 4 (radius: 25)
[00:11:56 -12333.154767] Model parameter optimization (eps = 1.000000)
[00:11:58 -12332.611183] SLOW spr round 1 (radius: 5)
[00:12:09 -12324.528698] SLOW spr round 2 (radius: 5)
[00:12:21 -12320.088383] SLOW spr round 3 (radius: 5)
[00:12:32 -12320.086880] SLOW spr round 4 (radius: 10)
[00:12:38] [worker #2] ML tree search #9, logLikelihood: -12317.943890
[00:12:44 -12319.178777] SLOW spr round 5 (radius: 5)
[00:13:01 -12318.655971] SLOW spr round 6 (radius: 5)
[00:13:14 -12318.655081] SLOW spr round 7 (radius: 10)
[00:13:28 -12318.655064] SLOW spr round 8 (radius: 15)
[00:13:52 -12318.384022] SLOW spr round 9 (radius: 5)
[00:14:08 -12318.383532] SLOW spr round 10 (radius: 10)
[00:14:25 -12318.383513] SLOW spr round 11 (radius: 15)
[00:14:48 -12318.383509] SLOW spr round 12 (radius: 20)
[00:15:08] [worker #1] ML tree search #11, logLikelihood: -12319.192196
[00:15:11 -12318.383507] SLOW spr round 13 (radius: 25)
[00:15:27 -12318.383506] Model parameter optimization (eps = 0.100000)

[00:15:30] [worker #0] ML tree search #7, logLikelihood: -12317.584156

[00:15:30 -33788.096059] Initial branch length optimization
[00:15:31 -24224.614607] Model parameter optimization (eps = 10.000000)
[00:15:39 -24053.239314] AUTODETECT spr round 1 (radius: 5)
[00:15:46 -19714.276776] AUTODETECT spr round 2 (radius: 10)
[00:15:56 -17066.798843] AUTODETECT spr round 3 (radius: 15)
[00:16:08 -15468.006431] AUTODETECT spr round 4 (radius: 20)
[00:16:21 -14484.536441] AUTODETECT spr round 5 (radius: 25)
[00:16:34 -14441.572656] SPR radius for FAST iterations: 25 (autodetect)
[00:16:34 -14441.572656] Model parameter optimization (eps = 3.000000)
[00:16:36] [worker #2] ML tree search #12, logLikelihood: -12345.416681
[00:16:43 -14359.023564] FAST spr round 1 (radius: 25)
[00:16:55 -12382.536447] FAST spr round 2 (radius: 25)
[00:17:03 -12330.615603] FAST spr round 3 (radius: 25)
[00:17:09 -12330.615433] Model parameter optimization (eps = 1.000000)
[00:17:15 -12320.402489] SLOW spr round 1 (radius: 5)
[00:17:27 -12315.957917] SLOW spr round 2 (radius: 5)
[00:17:37 -12315.956474] SLOW spr round 3 (radius: 10)
[00:17:49 -12314.536221] SLOW spr round 4 (radius: 5)
[00:18:04 -12314.495212] SLOW spr round 5 (radius: 10)
[00:18:19 -12314.495190] SLOW spr round 6 (radius: 15)
[00:18:40 -12314.435353] SLOW spr round 7 (radius: 20)
[00:19:02 -12314.119278] SLOW spr round 8 (radius: 5)
[00:19:18 -12314.111895] SLOW spr round 9 (radius: 10)
[00:19:33 -12314.110095] SLOW spr round 10 (radius: 15)
[00:19:53 -12314.109376] SLOW spr round 11 (radius: 20)
[00:20:16 -12314.109083] SLOW spr round 12 (radius: 25)
[00:20:33] [worker #1] ML tree search #14, logLikelihood: -12317.331588
[00:20:36 -12314.108958] Model parameter optimization (eps = 0.100000)

[00:20:38] [worker #0] ML tree search #10, logLikelihood: -12314.020506

[00:20:38 -34213.888337] Initial branch length optimization
[00:20:38 -24294.104392] Model parameter optimization (eps = 10.000000)
[00:20:46 -24112.229657] AUTODETECT spr round 1 (radius: 5)
[00:20:53 -19719.268771] AUTODETECT spr round 2 (radius: 10)
[00:21:03] [worker #2] ML tree search #15, logLikelihood: -12315.168528
[00:21:03 -15103.415441] AUTODETECT spr round 3 (radius: 15)
[00:21:15 -13674.696303] AUTODETECT spr round 4 (radius: 20)
[00:21:27 -13400.852538] AUTODETECT spr round 5 (radius: 25)
[00:21:40 -13289.942443] SPR radius for FAST iterations: 25 (autodetect)
[00:21:40 -13289.942443] Model parameter optimization (eps = 3.000000)
[00:21:44 -13258.181728] FAST spr round 1 (radius: 25)
[00:21:53 -12406.572041] FAST spr round 2 (radius: 25)
[00:22:01 -12358.867254] FAST spr round 3 (radius: 25)
[00:22:09 -12351.569423] FAST spr round 4 (radius: 25)
[00:22:15 -12351.569213] Model parameter optimization (eps = 1.000000)
[00:22:17 -12350.855847] SLOW spr round 1 (radius: 5)
[00:22:28 -12348.962874] SLOW spr round 2 (radius: 5)
[00:22:38 -12348.942868] SLOW spr round 3 (radius: 10)
[00:22:51 -12348.941956] SLOW spr round 4 (radius: 15)
[00:23:14 -12348.715497] SLOW spr round 5 (radius: 5)
[00:23:30 -12348.714552] SLOW spr round 6 (radius: 10)
[00:23:46 -12348.714496] SLOW spr round 7 (radius: 15)
[00:24:09 -12348.714469] SLOW spr round 8 (radius: 20)
[00:24:30 -12348.714456] SLOW spr round 9 (radius: 25)
[00:24:36] [worker #1] ML tree search #17, logLikelihood: -12318.423529
[00:24:48 -12348.714450] Model parameter optimization (eps = 0.100000)

[00:24:49] [worker #0] ML tree search #13, logLikelihood: -12348.677031

[00:24:49 -33977.159297] Initial branch length optimization
[00:24:50 -24378.357601] Model parameter optimization (eps = 10.000000)
[00:24:53] [worker #2] ML tree search #18, logLikelihood: -12317.638145
[00:25:01 -24196.002136] AUTODETECT spr round 1 (radius: 5)
[00:25:07 -19406.909239] AUTODETECT spr round 2 (radius: 10)
[00:25:17 -16054.594695] AUTODETECT spr round 3 (radius: 15)
[00:25:29 -14931.268417] AUTODETECT spr round 4 (radius: 20)
[00:25:41 -14310.058212] AUTODETECT spr round 5 (radius: 25)
[00:25:54 -14178.267577] SPR radius for FAST iterations: 25 (autodetect)
[00:25:54 -14178.267577] Model parameter optimization (eps = 3.000000)
[00:26:02 -14106.551890] FAST spr round 1 (radius: 25)
[00:26:14 -12369.744714] FAST spr round 2 (radius: 25)
[00:26:24 -12328.503551] FAST spr round 3 (radius: 25)
[00:26:30 -12327.224467] FAST spr round 4 (radius: 25)
[00:26:36 -12324.673457] FAST spr round 5 (radius: 25)
[00:26:42 -12324.673135] Model parameter optimization (eps = 1.000000)
[00:26:46 -12323.214055] SLOW spr round 1 (radius: 5)
[00:26:57 -12318.363031] SLOW spr round 2 (radius: 5)
[00:27:08 -12317.427155] SLOW spr round 3 (radius: 5)
[00:27:19 -12317.299444] SLOW spr round 4 (radius: 5)
[00:27:29 -12317.298276] SLOW spr round 5 (radius: 10)
[00:27:41 -12317.297999] SLOW spr round 6 (radius: 15)
[00:28:04 -12317.297861] SLOW spr round 7 (radius: 20)
[00:28:25 -12317.297798] SLOW spr round 8 (radius: 25)
[00:28:43 -12317.297767] Model parameter optimization (eps = 0.100000)

[00:28:47] [worker #0] ML tree search #16, logLikelihood: -12316.486533

[00:28:47 -33895.768872] Initial branch length optimization
[00:28:47 -24106.290374] Model parameter optimization (eps = 10.000000)
[00:28:56 -23938.984051] AUTODETECT spr round 1 (radius: 5)
[00:29:03 -19491.309659] AUTODETECT spr round 2 (radius: 10)
[00:29:13 -16547.871454] AUTODETECT spr round 3 (radius: 15)
[00:29:24 -13492.097555] AUTODETECT spr round 4 (radius: 20)
[00:29:26] [worker #1] ML tree search #20, logLikelihood: -12318.422805
[00:29:38 -13221.368427] AUTODETECT spr round 5 (radius: 25)
[00:29:50 -13221.145373] SPR radius for FAST iterations: 25 (autodetect)
[00:29:50 -13221.145373] Model parameter optimization (eps = 3.000000)
[00:29:59 -13156.397087] FAST spr round 1 (radius: 25)
[00:30:10 -12363.893445] FAST spr round 2 (radius: 25)
[00:30:18 -12321.704384] FAST spr round 3 (radius: 25)
[00:30:25 -12318.551651] FAST spr round 4 (radius: 25)
[00:30:31 -12318.551423] Model parameter optimization (eps = 1.000000)
[00:30:35 -12316.772955] SLOW spr round 1 (radius: 5)
[00:30:45 -12315.150747] SLOW spr round 2 (radius: 5)
[00:30:57 -12315.138953] SLOW spr round 3 (radius: 10)
[00:31:09 -12315.138367] SLOW spr round 4 (radius: 15)
[00:31:28 -12314.949127] SLOW spr round 5 (radius: 5)
[00:31:44 -12314.948207] SLOW spr round 6 (radius: 10)
[00:31:59 -12314.948097] SLOW spr round 7 (radius: 15)
[00:32:16 -12314.948041] SLOW spr round 8 (radius: 20)
[00:32:37 -12314.948022] SLOW spr round 9 (radius: 25)
[00:32:53 -12314.948013] Model parameter optimization (eps = 0.100000)

[00:32:55] [worker #0] ML tree search #19, logLikelihood: -12314.938149


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.261214,0.563760) (0.280276,0.901511) (0.296816,1.625528) (0.161694,0.727195) 
   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: -12310.517331

AIC score: 25371.034661 / AICc score: 307371.034661 / BIC score: 26528.883287
Free parameters (model + branch lengths): 375

WARNING: Number of free parameters (K=375) is larger than alignment size (n=162).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 79 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/3_mltree/Q96RY5.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/3_mltree/Q96RY5.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/3_mltree/Q96RY5.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/3_mltree/Q96RY5.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96RY5/3_mltree/Q96RY5.raxml.log

Analysis started: 08-Jul-2021 18:31:12 / finished: 08-Jul-2021 19:04:08

Elapsed time: 1975.576 seconds