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 13-Jul-2021 16:49:42 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZS30/2_msa/Q6ZS30_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZS30/3_mltree/Q6ZS30 --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/Q6ZS30/2_msa/Q6ZS30_trimmed_msa.fasta
[00:00:00] Loaded alignment with 980 taxa and 503 sites

WARNING: Sequences tr_F1P3D1_F1P3D1_CHICK_9031 and tr_A0A226P315_A0A226P315_COLVI_9014 are exactly identical!
WARNING: Sequences tr_M3XS11_M3XS11_MUSPF_9669 and tr_E2QWB6_E2QWB6_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3XS11_M3XS11_MUSPF_9669 and tr_A0A337S5P0_A0A337S5P0_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3XS11_M3XS11_MUSPF_9669 and tr_A0A2Y9L499_A0A2Y9L499_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XS11_M3XS11_MUSPF_9669 and tr_A0A384C7K2_A0A384C7K2_URSMA_29073 are exactly identical!
WARNING: Sequences tr_M3YG96_M3YG96_MUSPF_9669 and tr_D2GX72_D2GX72_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YG96_M3YG96_MUSPF_9669 and tr_M3VZG1_M3VZG1_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3YG96_M3YG96_MUSPF_9669 and tr_A0A2Y9KMF9_A0A2Y9KMF9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YG96_M3YG96_MUSPF_9669 and tr_A0A384C9Q3_A0A384C9Q3_URSMA_29073 are exactly identical!
WARNING: Sequences sp_Q9W4E2_NBEA_DROME_7227 and tr_A0A0P8XK79_A0A0P8XK79_DROAN_7217 are exactly identical!
WARNING: Sequences sp_Q9W4E2_NBEA_DROME_7227 and tr_A0A1W4VIU2_A0A1W4VIU2_DROFC_30025 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_H2NJL4_H2NJL4_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2I3S7H5_A0A2I3S7H5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and sp_Q8NFP9_NBEA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_F6YF98_F6YF98_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_G7PW03_G7PW03_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2I3LQH6_A0A2I3LQH6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A0D9RZ68_A0A0D9RZ68_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2K5LHX6_A0A2K5LHX6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2K6BCF5_A0A2K6BCF5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2R8Z7K0_A0A2R8Z7K0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_D8SFW0_D8SFW0_SELML_88036 and tr_D8TCV2_D8TCV2_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A2I2YSL1_A0A2I2YSL1_GORGO_9595 and tr_H2PEH7_H2PEH7_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2YSL1_A0A2I2YSL1_GORGO_9595 and tr_H2R444_H2R444_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YSL1_A0A2I2YSL1_GORGO_9595 and sp_P50851_LRBA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YSL1_A0A2I2YSL1_GORGO_9595 and tr_A0A2R9CGM9_A0A2R9CGM9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0R3P7E8_A0A0R3P7E8_DROPS_46245 and tr_B4H7W9_B4H7W9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2QPU0_H2QPU0_PANTR_9598 and sp_Q8IZQ1_WDFY3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QPU0_H2QPU0_PANTR_9598 and tr_A0A2R9CBV9_A0A2R9CBV9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R007_H2R007_PANTR_9598 and sp_Q6ZNJ1_NBEL2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R007_H2R007_PANTR_9598 and tr_A0A2R9CMK4_A0A2R9CMK4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6YF36_F6YF36_HORSE_9796 and tr_F6SQL1_F6SQL1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_W5NZW5_W5NZW5_SHEEP_9940 and tr_E1BPS3_E1BPS3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5NZW5_W5NZW5_SHEEP_9940 and tr_A0A2U3VAX7_A0A2U3VAX7_ODORO_9708 are exactly identical!
WARNING: Sequences tr_W5PLT8_W5PLT8_SHEEP_9940 and tr_F1MF64_F1MF64_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A158N9E3_A0A158N9E3_ATTCE_12957 and tr_A0A195BGQ2_A0A195BGQ2_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NCD1_A0A158NCD1_ATTCE_12957 and tr_A0A195BY71_A0A195BY71_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0GD48_A0A0E0GD48_ORYNI_4536 and tr_A0A0E0Q1N0_A0A0E0Q1N0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GD48_A0A0E0GD48_ORYNI_4536 and tr_A0A0D3GJW8_A0A0D3GJW8_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0H426_A0A0E0H426_ORYNI_4536 and tr_A0A0D3FYS0_A0A0D3FYS0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0K0J9K6_A0A0K0J9K6_BRUMA_6279 and tr_A0A0N4TPB7_A0A0N4TPB7_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_G7P517_G7P517_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A096MWM6_A0A096MWM6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A2K5L9D9_A0A2K5L9D9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A2K6CVR0_A0A2K6CVR0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A2K5YXQ4_A0A2K5YXQ4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6W7V2_F6W7V2_MACMU_9544 and tr_A0A2K5MPI5_A0A2K5MPI5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6W7V2_F6W7V2_MACMU_9544 and tr_A0A2K6B0W8_A0A2K6B0W8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6W7V2_F6W7V2_MACMU_9544 and tr_A0A2K5Y3U6_A0A2K5Y3U6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7BMD6_F7BMD6_MACMU_9544 and tr_A0A2K6DQE3_A0A2K6DQE3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HUD8_F7HUD8_MACMU_9544 and tr_G7PL84_G7PL84_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HUD8_F7HUD8_MACMU_9544 and tr_A0A2K6E3C3_A0A2K6E3C3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F4NWR1_F4NWR1_BATDJ_684364 and tr_A0A177WH97_A0A177WH97_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1NXI6_I1NXI6_ORYGL_4538 and tr_A0A0E0CG13_A0A0E0CG13_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A287BJF5_A0A287BJF5_PIG_9823 and tr_A0A2Y9ESM2_A0A2Y9ESM2_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_Q16FK4_Q16FK4_AEDAE_7159 and tr_Q17F08_Q17F08_AEDAE_7159 are exactly identical!
WARNING: Sequences tr_B3RWH0_B3RWH0_TRIAD_10228 and tr_A0A369RW15_A0A369RW15_9METZ_287889 are exactly identical!
WARNING: Sequences tr_U3JS34_U3JS34_FICAL_59894 and tr_A0A091FUH1_A0A091FUH1_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3K113_U3K113_FICAL_59894 and tr_A0A218V7K1_A0A218V7K1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_U3IR82_U3IR82_ANAPL_8839 and tr_A0A091INM1_A0A091INM1_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_U3IR82_U3IR82_ANAPL_8839 and tr_A0A091VV99_A0A091VV99_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_W2RCN7_W2RCN7_PHYPN_761204 and tr_W2LF55_W2LF55_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015LBY6_A0A015LBY6_9GLOM_1432141 and tr_A0A2H5SRG4_A0A2H5SRG4_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LMU6_A0A015LMU6_9GLOM_1432141 and tr_A0A2H5RZT9_A0A2H5RZT9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A044USC1_A0A044USC1_ONCVO_6282 and tr_A0A182EJ11_A0A182EJ11_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0D9RUC5_A0A0D9RUC5_CHLSB_60711 and tr_A0A2K5LH77_A0A2K5LH77_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9RUC5_A0A0D9RUC5_CHLSB_60711 and tr_A0A2K6A124_A0A2K6A124_MANLE_9568 are exactly identical!
WARNING: Sequences tr_U4UI48_U4UI48_DENPD_77166 and tr_U4UTW7_U4UTW7_DENPD_77166 are exactly identical!
WARNING: Sequences tr_A0A091J7P0_A0A091J7P0_EGRGA_188379 and tr_A0A091UPV5_A0A091UPV5_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091J7P0_A0A091J7P0_EGRGA_188379 and tr_A0A087R3Z2_A0A087R3Z2_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091J7P0_A0A091J7P0_EGRGA_188379 and tr_A0A0A0AXP7_A0A0A0AXP7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091JTD1_A0A091JTD1_EGRGA_188379 and tr_A0A087QGX7_A0A087QGX7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A0L9TX07_A0A0L9TX07_PHAAN_3914 and tr_A0A1S3V4K2_A0A1S3V4K2_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A0V1CDN0_A0A0V1CDN0_TRIBR_45882 and tr_A0A0V1NKL8_A0A0V1NKL8_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CDN0_A0A0V1CDN0_TRIBR_45882 and tr_A0A0V0TC87_A0A0V0TC87_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1CG95_A0A0V1CG95_TRIBR_45882 and tr_A0A0V0WCE8_A0A0V0WCE8_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1CG95_A0A0V1CG95_TRIBR_45882 and tr_A0A0V0VEV7_A0A0V0VEV7_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CG95_A0A0V1CG95_TRIBR_45882 and tr_A0A0V1KYD0_A0A0V1KYD0_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CG95_A0A0V1CG95_TRIBR_45882 and tr_A0A0V1NVE9_A0A0V1NVE9_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CG95_A0A0V1CG95_TRIBR_45882 and tr_A0A0V0UDH9_A0A0V0UDH9_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0WSW7_A0A0V0WSW7_9BILA_92179 and tr_A0A0V1KYP3_A0A0V1KYP3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A1S3Z8K6_A0A1S3Z8K6_TOBAC_4097 and tr_A0A1U7WK33_A0A1U7WK33_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3T8S9_A0A1S3T8S9_VIGRR_3916 and tr_A0A1S3U4S6_A0A1S3U4S6_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1I7T2D8_A0A1I7T2D8_9PELO_1561998 and tr_A0A1I7T2D9_A0A1I7T2D9_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1I7TDJ0_A0A1I7TDJ0_9PELO_1561998 and tr_A0A1I7TDJ1_A0A1I7TDJ1_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1U8F8M9_A0A1U8F8M9_CAPAN_4072 and tr_A0A2G3CP95_A0A2G3CP95_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2U4AMN7_A0A2U4AMN7_TURTR_9739 and tr_A0A2Y9M8G0_A0A2Y9M8G0_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4AMN7_A0A2U4AMN7_TURTR_9739 and tr_A0A384AXN8_A0A384AXN8_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 88

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/Q6ZS30/3_mltree/Q6ZS30.raxml.reduced.phy

Alignment comprises 1 partitions and 503 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 503 / 503
Gaps: 3.79 %
Invariant sites: 0.80 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZS30/3_mltree/Q6ZS30.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 980 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 252 / 20160
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -756724.224517] Initial branch length optimization
[00:00:12 -638581.750666] Model parameter optimization (eps = 10.000000)
[00:01:22 -637394.122501] AUTODETECT spr round 1 (radius: 5)
[00:04:58 -370759.655762] AUTODETECT spr round 2 (radius: 10)
[00:08:39 -275345.617594] AUTODETECT spr round 3 (radius: 15)
[00:12:29 -211844.085436] AUTODETECT spr round 4 (radius: 20)
[00:16:34 -193678.560979] AUTODETECT spr round 5 (radius: 25)
[00:21:38 -178958.594744] SPR radius for FAST iterations: 25 (autodetect)
[00:21:38 -178958.594744] Model parameter optimization (eps = 3.000000)
[00:22:02 -178719.789711] FAST spr round 1 (radius: 25)
[00:25:41 -148647.446057] FAST spr round 2 (radius: 25)
[00:28:28 -147495.967499] FAST spr round 3 (radius: 25)
[00:30:52 -147451.876540] FAST spr round 4 (radius: 25)
[00:33:00 -147449.981827] FAST spr round 5 (radius: 25)
[00:35:03 -147449.981582] Model parameter optimization (eps = 1.000000)
[00:35:20 -147446.922134] SLOW spr round 1 (radius: 5)
[00:38:13 -147421.205600] SLOW spr round 2 (radius: 5)
[00:40:58 -147419.332289] SLOW spr round 3 (radius: 5)
[00:43:40 -147419.330989] SLOW spr round 4 (radius: 10)
[00:46:30 -147409.231268] SLOW spr round 5 (radius: 5)
[00:50:03 -147393.932930] SLOW spr round 6 (radius: 5)
[00:53:06 -147393.932869] SLOW spr round 7 (radius: 10)
[00:55:59 -147393.932867] SLOW spr round 8 (radius: 15)
[00:59:54 -147393.932867] SLOW spr round 9 (radius: 20)
[01:03:35] [worker #2] ML tree search #3, logLikelihood: -147380.944590
[01:05:33 -147393.932867] SLOW spr round 10 (radius: 25)
[01:11:04] [worker #1] ML tree search #2, logLikelihood: -147412.514431
[01:12:36 -147393.932867] Model parameter optimization (eps = 0.100000)

[01:12:49] [worker #0] ML tree search #1, logLikelihood: -147393.720296

[01:12:49 -758692.058994] Initial branch length optimization
[01:13:00 -638709.817126] Model parameter optimization (eps = 10.000000)
[01:14:00 -637453.290750] AUTODETECT spr round 1 (radius: 5)
[01:17:33 -367349.448949] AUTODETECT spr round 2 (radius: 10)
[01:21:17 -259586.444960] AUTODETECT spr round 3 (radius: 15)
[01:24:59 -201212.109867] AUTODETECT spr round 4 (radius: 20)
[01:29:05 -183946.867850] AUTODETECT spr round 5 (radius: 25)
[01:33:24 -176373.344227] SPR radius for FAST iterations: 25 (autodetect)
[01:33:24 -176373.344227] Model parameter optimization (eps = 3.000000)
[01:33:53 -176100.599805] FAST spr round 1 (radius: 25)
[01:37:41 -149011.164541] FAST spr round 2 (radius: 25)
[01:40:34 -147532.737552] FAST spr round 3 (radius: 25)
[01:43:08 -147448.133133] FAST spr round 4 (radius: 25)
[01:45:18 -147439.581005] FAST spr round 5 (radius: 25)
[01:47:20 -147439.580930] Model parameter optimization (eps = 1.000000)
[01:47:33 -147437.041409] SLOW spr round 1 (radius: 5)
[01:50:27 -147397.859475] SLOW spr round 2 (radius: 5)
[01:53:14 -147389.378430] SLOW spr round 3 (radius: 5)
[01:55:56 -147389.378386] SLOW spr round 4 (radius: 10)
[01:58:41 -147389.378375] SLOW spr round 5 (radius: 15)
[02:02:45 -147389.378217] SLOW spr round 6 (radius: 20)
[02:07:46] [worker #2] ML tree search #6, logLikelihood: -147379.822982
[02:08:20 -147388.640615] SLOW spr round 7 (radius: 5)
[02:12:08 -147385.997690] SLOW spr round 8 (radius: 5)
[02:15:26 -147385.240393] SLOW spr round 9 (radius: 5)
[02:18:21 -147385.240386] SLOW spr round 10 (radius: 10)
[02:21:11 -147385.240380] SLOW spr round 11 (radius: 15)
[02:25:10 -147385.240373] SLOW spr round 12 (radius: 20)
[02:30:45 -147385.240367] SLOW spr round 13 (radius: 25)
[02:37:51 -147385.240360] Model parameter optimization (eps = 0.100000)

[02:38:04] [worker #0] ML tree search #4, logLikelihood: -147384.844414

[02:38:05 -749877.986690] Initial branch length optimization
[02:38:11 -632537.427240] Model parameter optimization (eps = 10.000000)
[02:39:05 -631215.364915] AUTODETECT spr round 1 (radius: 5)
[02:42:30] [worker #1] ML tree search #5, logLikelihood: -147416.685836
[02:42:31 -373731.463759] AUTODETECT spr round 2 (radius: 10)
[02:46:13 -256971.488527] AUTODETECT spr round 3 (radius: 15)
[02:49:58 -203515.646431] AUTODETECT spr round 4 (radius: 20)
[02:53:53 -179988.260761] AUTODETECT spr round 5 (radius: 25)
[02:58:13 -176178.512230] SPR radius for FAST iterations: 25 (autodetect)
[02:58:13 -176178.512230] Model parameter optimization (eps = 3.000000)
[02:58:40 -175968.869996] FAST spr round 1 (radius: 25)
[03:02:25 -148681.769272] FAST spr round 2 (radius: 25)
[03:05:25 -147530.131686] FAST spr round 3 (radius: 25)
[03:08:00 -147436.304466] FAST spr round 4 (radius: 25)
[03:10:08 -147432.862750] FAST spr round 5 (radius: 25)
[03:12:10 -147432.862535] Model parameter optimization (eps = 1.000000)
[03:12:28 -147430.702824] SLOW spr round 1 (radius: 5)
[03:15:27 -147401.147582] SLOW spr round 2 (radius: 5)
[03:18:19 -147397.368628] SLOW spr round 3 (radius: 5)
[03:21:02 -147397.367178] SLOW spr round 4 (radius: 10)
[03:23:49 -147397.365795] SLOW spr round 5 (radius: 15)
[03:25:29] [worker #2] ML tree search #9, logLikelihood: -147389.835213
[03:27:49 -147397.364833] SLOW spr round 6 (radius: 20)
[03:33:34 -147397.364825] SLOW spr round 7 (radius: 25)
[03:40:46 -147397.364816] Model parameter optimization (eps = 0.100000)

[03:40:53] [worker #0] ML tree search #7, logLikelihood: -147397.269311

[03:40:53 -759685.646071] Initial branch length optimization
[03:41:03 -640243.100021] Model parameter optimization (eps = 10.000000)
[03:41:58 -638982.395439] AUTODETECT spr round 1 (radius: 5)
[03:45:28 -361528.467635] AUTODETECT spr round 2 (radius: 10)
[03:46:36] [worker #1] ML tree search #8, logLikelihood: -147379.978896
[03:49:00 -265310.273277] AUTODETECT spr round 3 (radius: 15)
[03:52:46 -212846.322915] AUTODETECT spr round 4 (radius: 20)
[03:56:56 -191030.749586] AUTODETECT spr round 5 (radius: 25)
[04:02:06 -178929.308434] SPR radius for FAST iterations: 25 (autodetect)
[04:02:06 -178929.308434] Model parameter optimization (eps = 3.000000)
[04:02:29 -178727.751793] FAST spr round 1 (radius: 25)
[04:05:59 -148847.799836] FAST spr round 2 (radius: 25)
[04:08:35 -147586.903140] FAST spr round 3 (radius: 25)
[04:11:01 -147494.070589] FAST spr round 4 (radius: 25)
[04:13:17 -147474.482021] FAST spr round 5 (radius: 25)
[04:15:22 -147473.015589] FAST spr round 6 (radius: 25)
[04:17:26 -147472.524046] FAST spr round 7 (radius: 25)
[04:19:26 -147472.523938] Model parameter optimization (eps = 1.000000)
[04:19:38 -147471.606548] SLOW spr round 1 (radius: 5)
[04:22:28 -147419.208547] SLOW spr round 2 (radius: 5)
[04:25:17 -147407.028090] SLOW spr round 3 (radius: 5)
[04:27:59 -147407.025293] SLOW spr round 4 (radius: 10)
[04:30:48 -147407.025050] SLOW spr round 5 (radius: 15)
[04:31:27] [worker #2] ML tree search #12, logLikelihood: -147373.313360
[04:34:56 -147407.025026] SLOW spr round 6 (radius: 20)
[04:40:49 -147407.025018] SLOW spr round 7 (radius: 25)
[04:48:02 -147407.025012] Model parameter optimization (eps = 0.100000)

[04:48:15] [worker #0] ML tree search #10, logLikelihood: -147406.861096

[04:48:15 -759702.302447] Initial branch length optimization
[04:48:24 -645243.666343] Model parameter optimization (eps = 10.000000)
[04:49:17 -643828.921260] AUTODETECT spr round 1 (radius: 5)
[04:52:50 -368945.678380] AUTODETECT spr round 2 (radius: 10)
[04:56:27 -260556.649936] AUTODETECT spr round 3 (radius: 15)
[05:00:06 -208350.373556] AUTODETECT spr round 4 (radius: 20)
[05:04:20 -184386.127933] AUTODETECT spr round 5 (radius: 25)
[05:06:04] [worker #1] ML tree search #11, logLikelihood: -147395.083394
[05:09:04 -178433.791142] SPR radius for FAST iterations: 25 (autodetect)
[05:09:04 -178433.791142] Model parameter optimization (eps = 3.000000)
[05:09:27 -178245.699743] FAST spr round 1 (radius: 25)
[05:13:19 -148804.865177] FAST spr round 2 (radius: 25)
[05:16:06 -147520.875286] FAST spr round 3 (radius: 25)
[05:18:30 -147470.458508] FAST spr round 4 (radius: 25)
[05:20:37 -147470.411364] Model parameter optimization (eps = 1.000000)
[05:20:55 -147466.128091] SLOW spr round 1 (radius: 5)
[05:24:00 -147421.190458] SLOW spr round 2 (radius: 5)
[05:26:57 -147405.272577] SLOW spr round 3 (radius: 5)
[05:29:49 -147398.867394] SLOW spr round 4 (radius: 5)
[05:32:32 -147398.304786] SLOW spr round 5 (radius: 5)
[05:35:14 -147398.304242] SLOW spr round 6 (radius: 10)
[05:38:03 -147395.261790] SLOW spr round 7 (radius: 5)
[05:41:32 -147395.261292] SLOW spr round 8 (radius: 10)
[05:44:39 -147395.260808] SLOW spr round 9 (radius: 15)
[05:48:28 -147395.260324] SLOW spr round 10 (radius: 20)
[05:52:12] [worker #2] ML tree search #15, logLikelihood: -147379.031595
[05:54:11 -147395.259841] SLOW spr round 11 (radius: 25)
[06:01:08 -147395.259359] Model parameter optimization (eps = 0.100000)

[06:01:20] [worker #0] ML tree search #13, logLikelihood: -147395.018992

[06:01:20 -754828.944279] Initial branch length optimization
[06:01:34 -638586.315814] Model parameter optimization (eps = 10.000000)
[06:02:28 -637245.933319] AUTODETECT spr round 1 (radius: 5)
[06:05:58 -360161.454947] AUTODETECT spr round 2 (radius: 10)
[06:09:37 -269400.168451] AUTODETECT spr round 3 (radius: 15)
[06:13:15 -224292.837026] AUTODETECT spr round 4 (radius: 20)
[06:16:59] [worker #1] ML tree search #14, logLikelihood: -147399.484144
[06:17:40 -190219.487002] AUTODETECT spr round 5 (radius: 25)
[06:22:24 -179219.998863] SPR radius for FAST iterations: 25 (autodetect)
[06:22:24 -179219.998863] Model parameter optimization (eps = 3.000000)
[06:22:54 -178984.009744] FAST spr round 1 (radius: 25)
[06:26:45 -148838.085384] FAST spr round 2 (radius: 25)
[06:29:34 -147496.105548] FAST spr round 3 (radius: 25)
[06:32:02 -147441.521999] FAST spr round 4 (radius: 25)
[06:34:20 -147428.917541] FAST spr round 5 (radius: 25)
[06:36:22 -147428.917426] Model parameter optimization (eps = 1.000000)
[06:36:40 -147424.384386] SLOW spr round 1 (radius: 5)
[06:39:42 -147397.438638] SLOW spr round 2 (radius: 5)
[06:42:29 -147395.598842] SLOW spr round 3 (radius: 5)
[06:45:12 -147395.598466] SLOW spr round 4 (radius: 10)
[06:48:00 -147395.569110] SLOW spr round 5 (radius: 15)
[06:52:06 -147395.569096] SLOW spr round 6 (radius: 20)
[06:57:51 -147395.569081] SLOW spr round 7 (radius: 25)
[07:05:05 -147395.569066] Model parameter optimization (eps = 0.100000)

[07:05:12] [worker #0] ML tree search #16, logLikelihood: -147395.543200

[07:05:12 -752578.582387] Initial branch length optimization
[07:05:19 -634378.218828] Model parameter optimization (eps = 10.000000)
[07:06:17 -633010.055932] AUTODETECT spr round 1 (radius: 5)
[07:09:51 -373054.401169] AUTODETECT spr round 2 (radius: 10)
[07:13:30 -273131.618615] AUTODETECT spr round 3 (radius: 15)
[07:17:16 -216027.977057] AUTODETECT spr round 4 (radius: 20)
[07:21:34 -180737.803178] AUTODETECT spr round 5 (radius: 25)
[07:26:38 -176621.579855] SPR radius for FAST iterations: 25 (autodetect)
[07:26:38 -176621.579855] Model parameter optimization (eps = 3.000000)
[07:27:03 -176320.961022] FAST spr round 1 (radius: 25)
[07:28:59] [worker #2] ML tree search #18, logLikelihood: -147396.202808
[07:30:48 -148425.343708] FAST spr round 2 (radius: 25)
[07:33:35 -147520.057890] FAST spr round 3 (radius: 25)
[07:36:00 -147460.287853] FAST spr round 4 (radius: 25)
[07:38:08 -147459.551026] FAST spr round 5 (radius: 25)
[07:40:11 -147457.493959] FAST spr round 6 (radius: 25)
[07:41:21] [worker #1] ML tree search #17, logLikelihood: -147417.421033
[07:42:12 -147457.493464] Model parameter optimization (eps = 1.000000)
[07:42:32 -147450.133187] SLOW spr round 1 (radius: 5)
[07:45:27 -147411.022945] SLOW spr round 2 (radius: 5)
[07:48:11 -147406.002904] SLOW spr round 3 (radius: 5)
[07:50:50 -147406.001948] SLOW spr round 4 (radius: 10)
[07:53:36 -147405.526125] SLOW spr round 5 (radius: 5)
[07:57:04 -147405.525292] SLOW spr round 6 (radius: 10)
[08:00:08 -147405.524464] SLOW spr round 7 (radius: 15)
[08:04:02 -147405.523637] SLOW spr round 8 (radius: 20)
[08:09:49 -147405.522811] SLOW spr round 9 (radius: 25)
[08:17:03 -147405.521987] Model parameter optimization (eps = 0.100000)

[08:17:20] [worker #0] ML tree search #19, logLikelihood: -147403.289959

[08:58:04] [worker #1] ML tree search #20, logLikelihood: -147413.596455

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.234475,0.448488) (0.298141,0.726203) (0.336916,1.134819) (0.130469,2.268677) 
   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: -147373.313360

AIC score: 298672.626720 / AICc score: 8009336.626720 / BIC score: 306957.645224
Free parameters (model + branch lengths): 1963

WARNING: Number of free parameters (K=1963) is larger than alignment size (n=503).
         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/Q6ZS30/3_mltree/Q6ZS30.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZS30/3_mltree/Q6ZS30.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZS30/3_mltree/Q6ZS30.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6ZS30/3_mltree/Q6ZS30.raxml.log

Analysis started: 13-Jul-2021 16:49:42 / finished: 14-Jul-2021 01:47:47

Elapsed time: 32285.008 seconds