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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 02-Jul-2021 00:51:53 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/2_msa/Q9NRK6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/3_mltree/Q9NRK6 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/2_msa/Q9NRK6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 505 sites

WARNING: Sequences tr_B4R3Y6_B4R3Y6_DROSI_7240 and tr_B4IGH2_B4IGH2_DROSE_7238 are exactly identical!
WARNING: Sequences tr_J3KLC8_J3KLC8_COCIM_246410 and tr_A0A0J6YQI9_A0A0J6YQI9_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2VU78_B2VU78_PYRTR_426418 and tr_A0A2W1HLL7_A0A2W1HLL7_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_D8RMN8_D8RMN8_SELML_88036 and tr_D8SLR9_D8SLR9_SELML_88036 are exactly identical!
WARNING: Sequences tr_G3S798_G3S798_GORGO_9595 and sp_Q9NRK6_ABCBA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_B8N0R2_B8N0R2_ASPFN_332952 and tr_Q2UJG0_Q2UJG0_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8N0R2_B8N0R2_ASPFN_332952 and tr_A0A1S9DL73_A0A1S9DL73_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UTM4_A0A179UTM4_BLAGS_559298 and tr_C5GNT7_C5GNT7_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2Q1B1_H2Q1B1_PANTR_9598 and tr_A0A2R8ZDC2_A0A2R8ZDC2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R3F4_H2R3F4_PANTR_9598 and tr_A0A2R9AK50_A0A2R9AK50_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_A0A0D2XJY1_A0A0D2XJY1_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_N4TUX9_N4TUX9_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_X0CAT2_X0CAT2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_A0A2H3SXP6_A0A2H3SXP6_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9F932_F9F932_FUSOF_660025 and tr_A0A2H3HI99_A0A2H3HI99_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_E9EUH8_E9EUH8_METRA_655844 and tr_A0A0D9NNX5_A0A0D9NNX5_METAN_1291518 are exactly identical!
WARNING: Sequences tr_J5JD71_J5JD71_BEAB2_655819 and tr_A0A2N6NL46_A0A2N6NL46_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A0E0GTY4_A0A0E0GTY4_ORYNI_4536 and tr_A0A0E0D6Z1_A0A0E0D6Z1_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_G7XXM7_G7XXM7_ASPKW_1033177 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_G3Y9P6_G3Y9P6_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_A0A100IBI3_A0A100IBI3_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_A0A146FJZ8_A0A146FJZ8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_A0A1L9MVB1_A0A1L9MVB1_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_A0A317VC94_A0A317VC94_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A2QJH1_A2QJH1_ASPNC_425011 and tr_A0A319AHX1_A0A319AHX1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F6W6T0_F6W6T0_MACMU_9544 and tr_G7P213_G7P213_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6W6T0_F6W6T0_MACMU_9544 and tr_A0A2K6DYQ7_A0A2K6DYQ7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_B8AK86_B8AK86_ORYSI_39946 and sp_Q9FNU2_AB25B_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4NXN7_F4NXN7_BATDJ_684364 and tr_A0A177WK60_A0A177WK60_BATDE_403673 are exactly identical!
WARNING: Sequences tr_F9X7H6_F9X7H6_ZYMTI_336722 and tr_A0A1X7RPR1_A0A1X7RPR1_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YK02_G2YK02_BOTF4_999810 and tr_M7UN73_M7UN73_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_E3LJ95_E3LJ95_CAERE_31234 and tr_A0A261CJE8_A0A261CJE8_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8WJQ6_A8WJQ6_CAEBR_6238 and tr_A0A2G5TQK1_A0A2G5TQK1_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_F2SVA7_F2SVA7_TRIRC_559305 and tr_D4AJ67_D4AJ67_ARTBC_663331 are exactly identical!
WARNING: Sequences tr_F2SVA7_F2SVA7_TRIRC_559305 and tr_A0A178F6E0_A0A178F6E0_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3S545_B3S545_TRIAD_10228 and tr_A0A369SHY0_A0A369SHY0_9METZ_287889 are exactly identical!
WARNING: Sequences tr_W7M6F2_W7M6F2_GIBM7_334819 and tr_A0A2K0WRA2_A0A2K0WRA2_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_G7NXL3_G7NXL3_MACFA_9541 and tr_A0A2K5NF55_A0A2K5NF55_CERAT_9531 are exactly identical!
WARNING: Sequences tr_L2FYT0_L2FYT0_COLFN_1213859 and tr_T0M9A7_T0M9A7_COLGC_1237896 are exactly identical!
WARNING: Sequences tr_S0EGW9_S0EGW9_GIBF5_1279085 and tr_A0A365MZ72_A0A365MZ72_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_W2Q091_W2Q091_PHYPN_761204 and tr_W2KW73_W2KW73_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A078HJ41_A0A078HJ41_BRANA_3708 and tr_A0A0D3BZR8_A0A0D3BZR8_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094DJJ4_A0A094DJJ4_9PEZI_1420910 and tr_A0A1B8EAC8_A0A1B8EAC8_9PEZI_1524831 are exactly identical!
WARNING: Sequences tr_A0A094FA18_A0A094FA18_9PEZI_1420912 and tr_A0A1B8GU98_A0A1B8GU98_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F8XGI3_A0A0F8XGI3_9EURO_308745 and tr_A0A2T5M6S0_A0A2T5M6S0_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A101MM18_A0A101MM18_9EURO_48697 and tr_A0A1V6NNV0_A0A1V6NNV0_9EURO_60169 are exactly identical!
WARNING: Sequences tr_I1RE13_I1RE13_GIBZE_229533 and tr_A0A2T4H774_A0A2T4H774_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A164NL51_A0A164NL51_9HOMO_1314777 and tr_A0A166GRT7_A0A166GRT7_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S3XHV7_A0A1S3XHV7_TOBAC_4097 and tr_A0A1U7VZ33_A0A1U7VZ33_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1I7T079_A0A1I7T079_9PELO_1561998 and tr_A0A1I7T080_A0A1I7T080_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1V8TWX1_A0A1V8TWX1_9PEZI_1974281 and tr_A0A1V8SDX9_A0A1V8SDX9_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A2D0QP95_A0A2D0QP95_ICTPU_7998 and tr_A0A2D0QRL8_A0A2D0QRL8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QR44_A0A2D0QR44_ICTPU_7998 and tr_A0A2D0QRE8_A0A2D0QRE8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A319C4R1_A0A319C4R1_9EURO_1448315 and tr_A0A2V5HMU3_A0A2V5HMU3_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A319C4R1_A0A319C4R1_9EURO_1448315 and tr_A0A2V5H0W2_A0A2V5H0W2_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 55

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/3_mltree/Q9NRK6.raxml.reduced.phy

Alignment comprises 1 partitions and 505 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 505 / 505
Gaps: 0.71 %
Invariant sites: 0.59 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/3_mltree/Q9NRK6.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 253 / 20240
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -809554.740510] Initial branch length optimization
[00:00:08 -672254.590424] Model parameter optimization (eps = 10.000000)
[00:01:15 -671137.961438] AUTODETECT spr round 1 (radius: 5)
[00:04:31 -488049.772674] AUTODETECT spr round 2 (radius: 10)
[00:08:04 -374789.618059] AUTODETECT spr round 3 (radius: 15)
[00:11:57 -304993.295622] AUTODETECT spr round 4 (radius: 20)
[00:16:51 -252556.516355] AUTODETECT spr round 5 (radius: 25)
[00:21:51 -249396.971050] SPR radius for FAST iterations: 25 (autodetect)
[00:21:51 -249396.971050] Model parameter optimization (eps = 3.000000)
[00:22:15 -249102.546963] FAST spr round 1 (radius: 25)
[00:26:01 -219260.019144] FAST spr round 2 (radius: 25)
[00:28:45 -218038.774028] FAST spr round 3 (radius: 25)
[00:31:04 -217996.840263] FAST spr round 4 (radius: 25)
[00:33:07 -217987.876773] FAST spr round 5 (radius: 25)
[00:35:02 -217987.876734] Model parameter optimization (eps = 1.000000)
[00:35:19 -217978.242994] SLOW spr round 1 (radius: 5)
[00:38:26 -217893.684201] SLOW spr round 2 (radius: 5)
[00:41:21 -217884.242529] SLOW spr round 3 (radius: 5)
[00:44:04 -217884.242501] SLOW spr round 4 (radius: 10)
[00:46:47 -217883.506399] SLOW spr round 5 (radius: 5)
[00:50:24 -217882.917198] SLOW spr round 6 (radius: 5)
[00:53:29 -217882.916486] SLOW spr round 7 (radius: 10)
[00:56:16 -217882.916484] SLOW spr round 8 (radius: 15)
[01:00:56 -217882.916484] SLOW spr round 9 (radius: 20)
[01:08:00 -217882.916484] SLOW spr round 10 (radius: 25)
[01:11:30] [worker #2] ML tree search #3, logLikelihood: -217865.982360
[01:17:32 -217882.916484] Model parameter optimization (eps = 0.100000)

[01:17:42] [worker #0] ML tree search #1, logLikelihood: -217882.699173

[01:17:42 -805069.118746] Initial branch length optimization
[01:17:48 -668095.340888] Model parameter optimization (eps = 10.000000)
[01:18:38 -667139.102085] AUTODETECT spr round 1 (radius: 5)
[01:21:58 -477884.690778] AUTODETECT spr round 2 (radius: 10)
[01:25:38 -360428.167392] AUTODETECT spr round 3 (radius: 15)
[01:26:21] [worker #1] ML tree search #2, logLikelihood: -217853.703275
[01:29:50 -285592.786480] AUTODETECT spr round 4 (radius: 20)
[01:34:14 -265069.561714] AUTODETECT spr round 5 (radius: 25)
[01:38:50 -260616.273019] SPR radius for FAST iterations: 25 (autodetect)
[01:38:50 -260616.273019] Model parameter optimization (eps = 3.000000)
[01:39:22 -260292.136927] FAST spr round 1 (radius: 25)
[01:43:11 -220353.553661] FAST spr round 2 (radius: 25)
[01:45:57 -218144.573006] FAST spr round 3 (radius: 25)
[01:48:19 -217992.702727] FAST spr round 4 (radius: 25)
[01:50:19 -217990.304451] FAST spr round 5 (radius: 25)
[01:52:16 -217986.726075] FAST spr round 6 (radius: 25)
[01:54:10 -217986.725918] Model parameter optimization (eps = 1.000000)
[01:54:29 -217966.430249] SLOW spr round 1 (radius: 5)
[01:57:36 -217896.493286] SLOW spr round 2 (radius: 5)
[02:00:35 -217876.201242] SLOW spr round 3 (radius: 5)
[02:03:22 -217876.201166] SLOW spr round 4 (radius: 10)
[02:06:04 -217875.919503] SLOW spr round 5 (radius: 5)
[02:09:41 -217869.453704] SLOW spr round 6 (radius: 5)
[02:12:47 -217868.826276] SLOW spr round 7 (radius: 5)
[02:15:38 -217868.826250] SLOW spr round 8 (radius: 10)
[02:18:19 -217868.826250] SLOW spr round 9 (radius: 15)
[02:23:03 -217868.826250] SLOW spr round 10 (radius: 20)
[02:25:17] [worker #2] ML tree search #6, logLikelihood: -217867.635969
[02:29:48 -217868.826250] SLOW spr round 11 (radius: 25)
[02:38:40 -217868.826250] Model parameter optimization (eps = 0.100000)

[02:38:52] [worker #0] ML tree search #4, logLikelihood: -217868.492644

[02:38:52 -806690.944991] Initial branch length optimization
[02:38:58 -668199.418014] Model parameter optimization (eps = 10.000000)
[02:39:48 -667142.844284] AUTODETECT spr round 1 (radius: 5)
[02:43:02 -483529.799197] AUTODETECT spr round 2 (radius: 10)
[02:46:38 -377743.957942] AUTODETECT spr round 3 (radius: 15)
[02:49:23] [worker #1] ML tree search #5, logLikelihood: -217857.998391
[02:50:23 -301947.740570] AUTODETECT spr round 4 (radius: 20)
[02:55:15 -266178.280536] AUTODETECT spr round 5 (radius: 25)
[03:00:10 -254229.745946] SPR radius for FAST iterations: 25 (autodetect)
[03:00:10 -254229.745946] Model parameter optimization (eps = 3.000000)
[03:00:37 -253830.391817] FAST spr round 1 (radius: 25)
[03:04:23 -219222.288891] FAST spr round 2 (radius: 25)
[03:07:07 -218040.321006] FAST spr round 3 (radius: 25)
[03:09:18 -217987.886137] FAST spr round 4 (radius: 25)
[03:11:17 -217982.768838] FAST spr round 5 (radius: 25)
[03:13:12 -217980.930293] FAST spr round 6 (radius: 25)
[03:15:03 -217980.930201] Model parameter optimization (eps = 1.000000)
[03:15:07 -217980.894499] SLOW spr round 1 (radius: 5)
[03:18:06 -217903.095371] SLOW spr round 2 (radius: 5)
[03:21:03 -217881.780552] SLOW spr round 3 (radius: 5)
[03:23:53 -217877.058385] SLOW spr round 4 (radius: 5)
[03:26:35 -217876.401828] SLOW spr round 5 (radius: 5)
[03:29:15 -217876.401794] SLOW spr round 6 (radius: 10)
[03:31:55 -217876.401790] SLOW spr round 7 (radius: 15)
[03:36:52 -217876.401790] SLOW spr round 8 (radius: 20)
[03:43:46 -217876.401790] SLOW spr round 9 (radius: 25)
[03:48:10] [worker #2] ML tree search #9, logLikelihood: -217871.313726
[03:52:53 -217876.401790] Model parameter optimization (eps = 0.100000)

[03:53:34] [worker #0] ML tree search #7, logLikelihood: -217874.132518

[03:53:34 -808424.396198] Initial branch length optimization
[03:53:40 -670814.862066] Model parameter optimization (eps = 10.000000)
[03:54:37 -669697.464160] AUTODETECT spr round 1 (radius: 5)
[03:56:46] [worker #1] ML tree search #8, logLikelihood: -217865.374161
[03:57:47 -487285.472095] AUTODETECT spr round 2 (radius: 10)
[04:01:20 -365451.481895] AUTODETECT spr round 3 (radius: 15)
[04:05:27 -290003.368719] AUTODETECT spr round 4 (radius: 20)
[04:09:48 -266670.097583] AUTODETECT spr round 5 (radius: 25)
[04:15:49 -254561.484180] SPR radius for FAST iterations: 25 (autodetect)
[04:15:49 -254561.484180] Model parameter optimization (eps = 3.000000)
[04:16:11 -254173.423823] FAST spr round 1 (radius: 25)
[04:20:02 -219407.789407] FAST spr round 2 (radius: 25)
[04:22:49 -218052.044489] FAST spr round 3 (radius: 25)
[04:25:16 -217975.659961] FAST spr round 4 (radius: 25)
[04:27:20 -217955.545568] FAST spr round 5 (radius: 25)
[04:29:23 -217931.059584] FAST spr round 6 (radius: 25)
[04:31:16 -217929.615272] FAST spr round 7 (radius: 25)
[04:33:08 -217929.615257] Model parameter optimization (eps = 1.000000)
[04:33:26 -217917.982727] SLOW spr round 1 (radius: 5)
[04:36:31 -217865.858063] SLOW spr round 2 (radius: 5)
[04:39:21 -217861.985970] SLOW spr round 3 (radius: 5)
[04:42:07 -217861.945056] SLOW spr round 4 (radius: 10)
[04:44:52 -217856.846986] SLOW spr round 5 (radius: 5)
[04:48:38 -217855.296129] SLOW spr round 6 (radius: 5)
[04:51:44 -217851.203167] SLOW spr round 7 (radius: 5)
[04:54:35 -217851.203167] SLOW spr round 8 (radius: 10)
[04:56:37] [worker #2] ML tree search #12, logLikelihood: -217860.427291
[04:57:17 -217851.203167] SLOW spr round 9 (radius: 15)
[05:02:02 -217851.203167] SLOW spr round 10 (radius: 20)
[05:08:52 -217851.203167] SLOW spr round 11 (radius: 25)
[05:11:16] [worker #1] ML tree search #11, logLikelihood: -217876.847853
[05:17:55 -217851.203167] Model parameter optimization (eps = 0.100000)

[05:18:04] [worker #0] ML tree search #10, logLikelihood: -217851.090854

[05:18:04 -803111.548140] Initial branch length optimization
[05:18:10 -667670.794320] Model parameter optimization (eps = 10.000000)
[05:18:55 -666745.090572] AUTODETECT spr round 1 (radius: 5)
[05:22:15 -479906.040646] AUTODETECT spr round 2 (radius: 10)
[05:25:57 -364343.653838] AUTODETECT spr round 3 (radius: 15)
[05:30:17 -297735.965493] AUTODETECT spr round 4 (radius: 20)
[05:35:03 -256583.085540] AUTODETECT spr round 5 (radius: 25)
[05:39:41 -254059.490876] SPR radius for FAST iterations: 25 (autodetect)
[05:39:41 -254059.490876] Model parameter optimization (eps = 3.000000)
[05:40:12 -253723.918880] FAST spr round 1 (radius: 25)
[05:44:04 -219250.134999] FAST spr round 2 (radius: 25)
[05:46:40 -218087.503061] FAST spr round 3 (radius: 25)
[05:48:55 -218025.802210] FAST spr round 4 (radius: 25)
[05:51:03 -217949.536228] FAST spr round 5 (radius: 25)
[05:52:58 -217948.180535] FAST spr round 6 (radius: 25)
[05:54:50 -217948.180448] Model parameter optimization (eps = 1.000000)
[05:55:13 -217940.995405] SLOW spr round 1 (radius: 5)
[05:58:14 -217868.686936] SLOW spr round 2 (radius: 5)
[06:01:10 -217859.098430] SLOW spr round 3 (radius: 5)
[06:03:57 -217851.925616] SLOW spr round 4 (radius: 5)
[06:06:38 -217851.925528] SLOW spr round 5 (radius: 10)
[06:08:10] [worker #2] ML tree search #15, logLikelihood: -217868.152542
[06:09:19 -217851.925528] SLOW spr round 6 (radius: 15)
[06:14:18 -217851.925528] SLOW spr round 7 (radius: 20)
[06:21:11 -217851.925527] SLOW spr round 8 (radius: 25)
[06:30:28 -217851.925527] Model parameter optimization (eps = 0.100000)

[06:30:44] [worker #0] ML tree search #13, logLikelihood: -217851.499265

[06:30:45 -799620.514421] Initial branch length optimization
[06:30:52 -664510.271485] Model parameter optimization (eps = 10.000000)
[06:31:42 -663538.154929] AUTODETECT spr round 1 (radius: 5)
[06:32:11] [worker #1] ML tree search #14, logLikelihood: -217870.726243
[06:34:57 -469904.418082] AUTODETECT spr round 2 (radius: 10)
[06:38:41 -349873.958768] AUTODETECT spr round 3 (radius: 15)
[06:42:49 -289653.443603] AUTODETECT spr round 4 (radius: 20)
[06:47:10 -259197.687089] AUTODETECT spr round 5 (radius: 25)
[06:52:14 -253109.790458] SPR radius for FAST iterations: 25 (autodetect)
[06:52:14 -253109.790458] Model parameter optimization (eps = 3.000000)
[06:52:34 -252802.557094] FAST spr round 1 (radius: 25)
[06:56:22 -219118.558059] FAST spr round 2 (radius: 25)
[06:59:03 -218006.694784] FAST spr round 3 (radius: 25)
[07:01:24 -217961.379853] FAST spr round 4 (radius: 25)
[07:03:26 -217948.127271] FAST spr round 5 (radius: 25)
[07:05:22 -217946.148432] FAST spr round 6 (radius: 25)
[07:07:15 -217946.148323] Model parameter optimization (eps = 1.000000)
[07:07:35 -217928.146711] SLOW spr round 1 (radius: 5)
[07:10:43 -217867.397149] SLOW spr round 2 (radius: 5)
[07:13:37 -217861.711883] SLOW spr round 3 (radius: 5)
[07:16:21 -217861.711151] SLOW spr round 4 (radius: 10)
[07:19:02 -217861.711135] SLOW spr round 5 (radius: 15)
[07:19:34] [worker #2] ML tree search #18, logLikelihood: -217864.024743
[07:23:55 -217861.711134] SLOW spr round 6 (radius: 20)
[07:30:47 -217861.711134] SLOW spr round 7 (radius: 25)
[07:40:05 -217861.711134] Model parameter optimization (eps = 0.100000)

[07:40:22] [worker #0] ML tree search #16, logLikelihood: -217859.771032

[07:40:22 -803476.611625] Initial branch length optimization
[07:40:29 -667818.088119] Model parameter optimization (eps = 10.000000)
[07:41:19 -667027.951162] AUTODETECT spr round 1 (radius: 5)
[07:44:35 -482438.144032] AUTODETECT spr round 2 (radius: 10)
[07:48:16 -375111.238881] AUTODETECT spr round 3 (radius: 15)
[07:52:26 -312454.103749] AUTODETECT spr round 4 (radius: 20)
[07:53:34] [worker #1] ML tree search #17, logLikelihood: -217903.658071
[07:56:58 -287380.777806] AUTODETECT spr round 5 (radius: 25)
[08:02:15 -269025.936019] SPR radius for FAST iterations: 25 (autodetect)
[08:02:15 -269025.936019] Model parameter optimization (eps = 3.000000)
[08:02:53 -268643.362894] FAST spr round 1 (radius: 25)
[08:06:58 -220201.044252] FAST spr round 2 (radius: 25)
[08:09:58 -218031.294532] FAST spr round 3 (radius: 25)
[08:12:30 -217950.630550] FAST spr round 4 (radius: 25)
[08:14:31 -217947.606101] FAST spr round 5 (radius: 25)
[08:16:27 -217947.606061] Model parameter optimization (eps = 1.000000)
[08:16:44 -217942.636204] SLOW spr round 1 (radius: 5)
[08:19:58 -217886.773388] SLOW spr round 2 (radius: 5)
[08:22:57 -217877.411203] SLOW spr round 3 (radius: 5)
[08:25:46 -217876.431213] SLOW spr round 4 (radius: 5)
[08:28:31 -217876.431020] SLOW spr round 5 (radius: 10)
[08:31:15 -217875.894031] SLOW spr round 6 (radius: 5)
[08:34:54 -217873.435580] SLOW spr round 7 (radius: 5)
[08:38:02 -217873.431749] SLOW spr round 8 (radius: 10)
[08:40:49 -217873.431646] SLOW spr round 9 (radius: 15)
[08:45:31 -217873.431640] SLOW spr round 10 (radius: 20)
[08:52:27 -217873.431640] SLOW spr round 11 (radius: 25)
[09:01:32 -217873.431640] Model parameter optimization (eps = 0.100000)

[09:01:44] [worker #0] ML tree search #19, logLikelihood: -217873.033768

[09:13:22] [worker #1] ML tree search #20, logLikelihood: -217877.014957

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.213274,0.288334) (0.378597,0.464093) (0.277702,1.327521) (0.130427,3.021967) 
   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: -217851.090854

AIC score: 439712.181708 / AICc score: 8483772.181708 / BIC score: 448182.421358
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=505).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/3_mltree/Q9NRK6.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/3_mltree/Q9NRK6.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/3_mltree/Q9NRK6.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRK6/3_mltree/Q9NRK6.raxml.log

Analysis started: 02-Jul-2021 00:51:53 / finished: 02-Jul-2021 10:05:16

Elapsed time: 33202.612 seconds

Consumed energy: 2976.915 Wh (= 15 km in an electric car, or 74 km with an e-scooter!)