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 07-Jul-2021 20:56:04 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX1/2_msa/Q9UHX1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX1/3_mltree/Q9UHX1 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX1/2_msa/Q9UHX1_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 622 sites

WARNING: Sequences tr_A0A1D5NV31_A0A1D5NV31_CHICK_9031 and tr_A0A151MVS1_A0A151MVS1_ALLMI_8496 are exactly identical!
WARNING: Sequences sp_Q3UEB3_PUF60_MOUSE_10090 and sp_Q9WV25_PUF60_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3YSJ7_M3YSJ7_MUSPF_9669 and tr_A0A2I2UUL7_A0A2I2UUL7_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3YSJ7_M3YSJ7_MUSPF_9669 and tr_A0A2Y9ITF7_A0A2Y9ITF7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_A0A2I2ZC99_A0A2I2ZC99_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_A0A2I3S0E4_A0A2I3S0E4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and sp_Q9UHX1_PUF60_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_A0A1D5QV23_A0A1D5QV23_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_F7ILP0_F7ILP0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_A0A3Q0E057_A0A3Q0E057_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_A0A2K5MFC0_A0A2K5MFC0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_A0A2K6BRI7_A0A2K6BRI7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3HMJ8_A0A2I3HMJ8_NOMLE_61853 and tr_A0A2R9AA46_A0A2R9AA46_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q1DXH0_PABP_COCIM_246410 and tr_E9DFJ0_E9DFJ0_COCPS_443226 are exactly identical!
WARNING: Sequences tr_B6QBT2_B6QBT2_TALMQ_441960 and tr_A0A093VB82_A0A093VB82_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3QN25_G3QN25_GORGO_9595 and tr_H2N7W0_H2N7W0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QN25_G3QN25_GORGO_9595 and tr_H2QZS4_H2QZS4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QN25_G3QN25_GORGO_9595 and tr_A0A2R9CJF4_A0A2R9CJF4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q29FG8_Q29FG8_DROPS_46245 and tr_B4H1B8_B4H1B8_DROPE_7234 are exactly identical!
WARNING: Sequences tr_J9P4I7_J9P4I7_CANLF_9615 and tr_A0A2I3RGU7_A0A2I3RGU7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_J9P4I7_J9P4I7_CANLF_9615 and tr_F6SJL8_F6SJL8_HORSE_9796 are exactly identical!
WARNING: Sequences tr_J4ULE3_J4ULE3_BEAB2_655819 and tr_A0A0A2VVW9_A0A0A2VVW9_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4ULE3_J4ULE3_BEAB2_655819 and tr_A0A2N6NIM9_A0A2N6NIM9_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A158NVT8_A0A158NVT8_ATTCE_12957 and tr_A0A195BB57_A0A195BB57_9HYME_520822 are exactly identical!
WARNING: Sequences sp_Q2UK72_PABP_ASPOR_510516 and tr_A0A1S9DLW3_A0A1S9DLW3_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A1P6C8K5_A0A1P6C8K5_BRUMA_6279 and tr_A0A0N4TQR9_A0A0N4TQR9_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_F6QKE0_F6QKE0_MACMU_9544 and tr_A0A096NDE7_A0A096NDE7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6QKE0_F6QKE0_MACMU_9544 and tr_A0A0D9S7P0_A0A0D9S7P0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6QKE0_F6QKE0_MACMU_9544 and tr_A0A2K5NNJ0_A0A2K5NNJ0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6QKE0_F6QKE0_MACMU_9544 and tr_A0A2K5ZZ67_A0A2K5ZZ67_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3SL64_G3SL64_LOXAF_9785 and tr_A0A2Y9N8D9_A0A2Y9N8D9_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A0E0QP07_A0A0E0QP07_ORYRU_4529 and tr_Q6H443_Q6H443_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F9X645_F9X645_ZYMTI_336722 and tr_A0A0F4GQ56_A0A0F4GQ56_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9X645_F9X645_ZYMTI_336722 and tr_A0A1X7RME8_A0A1X7RME8_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YIW5_G2YIW5_BOTF4_999810 and tr_M7UAI6_M7UAI6_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SQN1_F2SQN1_TRIRC_559305 and tr_A0A178EWR5_A0A178EWR5_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G3XRJ6_G3XRJ6_ASPNA_380704 and tr_A0A318ZWN0_A0A318ZWN0_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A0D2XH20_A0A0D2XH20_FUSO4_426428 and tr_X0DXG8_X0DXG8_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2XH20_A0A0D2XH20_FUSO4_426428 and tr_A0A2H3TDJ3_A0A2H3TDJ3_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0D2XH20_A0A0D2XH20_FUSO4_426428 and tr_A0A2H3GZ10_A0A2H3GZ10_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_R0KTS6_R0KTS6_ANAPL_8839 and tr_A0A091ULT5_A0A091ULT5_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_R0KTS6_R0KTS6_ANAPL_8839 and tr_A0A087QTA8_A0A087QTA8_APTFO_9233 are exactly identical!
WARNING: Sequences tr_R0KTS6_R0KTS6_ANAPL_8839 and tr_A0A093HJF3_A0A093HJF3_STRCA_441894 are exactly identical!
WARNING: Sequences tr_R0KTS6_R0KTS6_ANAPL_8839 and tr_A0A099ZNI2_A0A099ZNI2_TINGU_94827 are exactly identical!
WARNING: Sequences tr_R0KTS6_R0KTS6_ANAPL_8839 and tr_A0A0A0A4I0_A0A0A0A4I0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_R0KTS6_R0KTS6_ANAPL_8839 and tr_A0A091HSR3_A0A091HSR3_CALAN_9244 are exactly identical!
WARNING: Sequences tr_W2RI05_W2RI05_PHYPN_761204 and tr_A0A0W8C9W7_A0A0W8C9W7_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2RI05_W2RI05_PHYPN_761204 and tr_W2JUE6_W2JUE6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015LJ51_A0A015LJ51_9GLOM_1432141 and tr_A0A2I1FYG3_A0A2I1FYG3_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A044TDF5_A0A044TDF5_ONCVO_6282 and tr_A0A182E4Y4_A0A182E4Y4_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A044TYU6_A0A044TYU6_ONCVO_6282 and tr_A0A182E1U6_A0A182E1U6_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A094F7W0_A0A094F7W0_9PEZI_1420912 and tr_A0A1B8GDJ8_A0A1B8GDJ8_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A094F7W0_A0A094F7W0_9PEZI_1420912 and tr_A0A1B8EL08_A0A1B8EL08_9PEZI_1622149 are exactly identical!
WARNING: Sequences tr_A0A0D9R949_A0A0D9R949_CHLSB_60711 and tr_A0A2K5ZV27_A0A2K5ZV27_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D9R949_A0A0D9R949_CHLSB_60711 and tr_A0A2U3YP13_A0A2U3YP13_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A0F8TY37_A0A0F8TY37_9EURO_308745 and tr_A0A2T5LWD9_A0A2T5LWD9_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0K0F035_A0A0K0F035_STRVS_75913 and tr_A0A0N5BGK6_A0A0N5BGK6_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A0M8P4X7_A0A0M8P4X7_9EURO_229535 and tr_A0A117NPK5_A0A117NPK5_9EURO_48697 are exactly identical!
WARNING: Sequences tr_A0A0M8P4X7_A0A0M8P4X7_9EURO_229535 and tr_A0A1V6NJS6_A0A1V6NJS6_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A0M8P4X7_A0A0M8P4X7_9EURO_229535 and tr_A0A1V6RLL9_A0A1V6RLL9_9EURO_60172 are exactly identical!
WARNING: Sequences tr_A0A0V0SJH9_A0A0V0SJH9_9BILA_6336 and tr_A0A0V0V8S9_A0A0V0V8S9_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0W9C0_A0A0V0W9C0_9BILA_92179 and tr_A0A0V1L6P3_A0A0V1L6P3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0WVK1_A0A0V0WVK1_9BILA_92179 and tr_A0A0V1LSJ7_A0A0V1LSJ7_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1AFQ2_A0A0V1AFQ2_9BILA_990121 and tr_A0A0V1P923_A0A0V1P923_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A100I2A4_A0A100I2A4_ASPNG_5061 and tr_A0A1L9NCY5_A0A1L9NCY5_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A100I2A4_A0A100I2A4_ASPNG_5061 and tr_A0A317WGG0_A0A317WGG0_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A0A151WQ56_A0A151WQ56_9HYME_64791 and tr_A0A151IYR9_A0A151IYR9_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A151WQ56_A0A151WQ56_9HYME_64791 and tr_A0A195C5G5_A0A195C5G5_9HYME_456900 are exactly identical!
WARNING: Sequences tr_A0A1S4B6E2_A0A1S4B6E2_TOBAC_4097 and tr_A0A1J6IL06_A0A1J6IL06_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S4B6E2_A0A1S4B6E2_TOBAC_4097 and tr_A0A1U7YCY9_A0A1U7YCY9_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4C155_A0A1S4C155_TOBAC_4097 and tr_A0A1U7YBD3_A0A1U7YBD3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1V8TZW8_A0A1V8TZW8_9PEZI_1974281 and tr_A0A1V8UJ98_A0A1V8UJ98_9PEZI_1974281 are exactly identical!
WARNING: Sequences tr_A0A2S7P2K0_A0A2S7P2K0_9HELO_2070414 and tr_A0A2S7QSK6_A0A2S7QSK6_9HELO_2070412 are exactly identical!
WARNING: Duplicate sequences found: 73

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/Q9UHX1/3_mltree/Q9UHX1.raxml.reduced.phy

Alignment comprises 1 partitions and 622 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 622 / 622
Gaps: 30.54 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX1/3_mltree/Q9UHX1.raxml.rba

Parallelization scheme autoconfig: 4 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 / 311 / 24880
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -814673.075854] Initial branch length optimization
[00:00:23 -651549.400827] Model parameter optimization (eps = 10.000000)
[00:04:29 -649270.715365] AUTODETECT spr round 1 (radius: 5)
[00:11:04 -436723.241940] AUTODETECT spr round 2 (radius: 10)
[00:17:51 -320127.899894] AUTODETECT spr round 3 (radius: 15)
[00:25:31 -249256.128870] AUTODETECT spr round 4 (radius: 20)
[00:33:52 -232395.756273] AUTODETECT spr round 5 (radius: 25)
[00:44:42 -220369.356307] SPR radius for FAST iterations: 25 (autodetect)
[00:44:42 -220369.356307] Model parameter optimization (eps = 3.000000)
[00:46:05 -219834.636026] FAST spr round 1 (radius: 25)
[00:54:21 -190352.116679] FAST spr round 2 (radius: 25)
[01:00:25 -188101.137222] FAST spr round 3 (radius: 25)
[01:05:39 -187996.358638] FAST spr round 4 (radius: 25)
[01:10:20 -187986.082020] FAST spr round 5 (radius: 25)
[01:14:17 -187986.080821] Model parameter optimization (eps = 1.000000)
[01:15:00 -187962.843043] SLOW spr round 1 (radius: 5)
[01:20:49 -187916.395277] SLOW spr round 2 (radius: 5)
[01:26:29 -187911.884818] SLOW spr round 3 (radius: 5)
[01:31:50 -187911.883412] SLOW spr round 4 (radius: 10)
[01:37:31 -187911.882412] SLOW spr round 5 (radius: 15)
[01:46:44 -187911.882412] SLOW spr round 6 (radius: 20)
[02:01:43 -187911.882412] SLOW spr round 7 (radius: 25)
[02:19:50 -187911.882412] Model parameter optimization (eps = 0.100000)

[02:20:17] [worker #0] ML tree search #1, logLikelihood: -187911.505866

[02:20:17 -813171.527665] Initial branch length optimization
[02:20:30 -651210.267375] Model parameter optimization (eps = 10.000000)
[02:24:03 -648813.502145] AUTODETECT spr round 1 (radius: 5)
[02:26:36] [worker #2] ML tree search #3, logLikelihood: -187923.233101
[02:30:30 -443977.148107] AUTODETECT spr round 2 (radius: 10)
[02:36:26] [worker #3] ML tree search #4, logLikelihood: -187937.085914
[02:37:18 -326798.826396] AUTODETECT spr round 3 (radius: 15)
[02:44:37 -256215.603148] AUTODETECT spr round 4 (radius: 20)
[02:49:00] [worker #1] ML tree search #2, logLikelihood: -187924.059101
[02:53:46 -240398.927234] AUTODETECT spr round 5 (radius: 25)
[03:04:56 -226643.123975] SPR radius for FAST iterations: 25 (autodetect)
[03:04:56 -226643.123975] Model parameter optimization (eps = 3.000000)
[03:05:44 -226232.767522] FAST spr round 1 (radius: 25)
[03:14:05 -189992.343657] FAST spr round 2 (radius: 25)
[03:20:05 -188178.916258] FAST spr round 3 (radius: 25)
[03:25:08 -188067.008335] FAST spr round 4 (radius: 25)
[03:29:23 -188064.285777] FAST spr round 5 (radius: 25)
[03:33:24 -188064.284863] Model parameter optimization (eps = 1.000000)
[03:34:15 -188026.802689] SLOW spr round 1 (radius: 5)
[03:40:10 -187973.042285] SLOW spr round 2 (radius: 5)
[03:45:46 -187971.966208] SLOW spr round 3 (radius: 5)
[03:51:08 -187971.965519] SLOW spr round 4 (radius: 10)
[03:56:48 -187971.965435] SLOW spr round 5 (radius: 15)
[04:06:29 -187971.965381] SLOW spr round 6 (radius: 20)
[04:21:27 -187971.656764] SLOW spr round 7 (radius: 5)
[04:29:17 -187971.644238] SLOW spr round 8 (radius: 10)
[04:36:13 -187971.644227] SLOW spr round 9 (radius: 15)
[04:45:33 -187971.493640] SLOW spr round 10 (radius: 5)
[04:53:19 -187971.491914] SLOW spr round 11 (radius: 10)
[05:00:02 -187971.491909] SLOW spr round 12 (radius: 15)
[05:09:11 -187971.491907] SLOW spr round 13 (radius: 20)
[05:24:32 -187971.491905] SLOW spr round 14 (radius: 25)
[05:32:30] [worker #2] ML tree search #7, logLikelihood: -187913.990668
[05:43:17 -187971.491904] Model parameter optimization (eps = 0.100000)

[05:44:20] [worker #0] ML tree search #5, logLikelihood: -187936.970462

[05:44:21 -813323.457598] Initial branch length optimization
[05:44:34 -651979.960649] Model parameter optimization (eps = 10.000000)
[05:49:34] [worker #1] ML tree search #6, logLikelihood: -187941.733919
[05:49:48 -649861.918612] AUTODETECT spr round 1 (radius: 5)
[05:56:22 -440840.007376] AUTODETECT spr round 2 (radius: 10)
[06:03:14 -325638.257194] AUTODETECT spr round 3 (radius: 15)
[06:11:01 -273398.583717] AUTODETECT spr round 4 (radius: 20)
[06:21:36 -228341.934512] AUTODETECT spr round 5 (radius: 25)
[06:31:29 -218954.326026] SPR radius for FAST iterations: 25 (autodetect)
[06:31:29 -218954.326026] Model parameter optimization (eps = 3.000000)
[06:31:57 -218890.876952] FAST spr round 1 (radius: 25)
[06:40:37 -191297.967584] FAST spr round 2 (radius: 25)
[06:46:47 -188742.781725] FAST spr round 3 (radius: 25)
[06:51:56 -188528.493699] FAST spr round 4 (radius: 25)
[06:52:56] [worker #3] ML tree search #8, logLikelihood: -188584.481000
[06:56:29 -188511.655541] FAST spr round 5 (radius: 25)
[07:00:48 -188503.345941] FAST spr round 6 (radius: 25)
[07:04:44 -188503.345320] Model parameter optimization (eps = 1.000000)
[07:05:40 -188080.288974] SLOW spr round 1 (radius: 5)
[07:11:30 -188007.734889] SLOW spr round 2 (radius: 5)
[07:17:03 -187996.098194] SLOW spr round 3 (radius: 5)
[07:22:40 -187994.123999] SLOW spr round 4 (radius: 5)
[07:27:58 -187994.123732] SLOW spr round 5 (radius: 10)
[07:33:38 -187994.123712] SLOW spr round 6 (radius: 15)
[07:43:18 -187994.123707] SLOW spr round 7 (radius: 20)
[07:58:50 -187994.123704] SLOW spr round 8 (radius: 25)
[08:08:31] [worker #2] ML tree search #11, logLikelihood: -187922.107876
[08:18:11 -187994.123700] Model parameter optimization (eps = 0.100000)

[08:19:05] [worker #0] ML tree search #9, logLikelihood: -187959.200797

[08:19:05 -815217.630246] Initial branch length optimization
[08:19:21 -657394.084592] Model parameter optimization (eps = 10.000000)
[08:22:55 -655083.324990] AUTODETECT spr round 1 (radius: 5)
[08:29:29 -442735.171654] AUTODETECT spr round 2 (radius: 10)
[08:36:18 -314404.887093] AUTODETECT spr round 3 (radius: 15)
[08:43:39 -267237.727779] AUTODETECT spr round 4 (radius: 20)
[08:53:22 -232415.995777] AUTODETECT spr round 5 (radius: 25)
[09:03:35 -226879.266941] SPR radius for FAST iterations: 25 (autodetect)
[09:03:35 -226879.266941] Model parameter optimization (eps = 3.000000)
[09:04:40 -226371.812299] FAST spr round 1 (radius: 25)
[09:12:34 -189960.941424] FAST spr round 2 (radius: 25)
[09:18:44 -188376.560186] FAST spr round 3 (radius: 25)
[09:23:32 -188188.222208] FAST spr round 4 (radius: 25)
[09:27:57 -188169.412900] FAST spr round 5 (radius: 25)
[09:31:59 -188169.411553] Model parameter optimization (eps = 1.000000)
[09:32:44 -188143.266558] SLOW spr round 1 (radius: 5)
[09:38:21 -188081.307443] SLOW spr round 2 (radius: 5)
[09:43:59 -188075.273873] SLOW spr round 3 (radius: 5)
[09:49:23 -188075.046680] SLOW spr round 4 (radius: 5)
[09:50:29] [worker #3] ML tree search #12, logLikelihood: -187929.429081
[09:54:43 -188075.046158] SLOW spr round 5 (radius: 10)
[10:00:24 -188075.045950] SLOW spr round 6 (radius: 15)
[10:10:00 -188075.045852] SLOW spr round 7 (radius: 20)
[10:25:20 -188075.045754] SLOW spr round 8 (radius: 25)
[10:44:12 -188075.045655] Model parameter optimization (eps = 0.100000)
[10:44:34] [worker #1] ML tree search #10, logLikelihood: -187966.560188

[10:44:42] [worker #0] ML tree search #13, logLikelihood: -188074.181767

[10:44:42 -814633.934702] Initial branch length optimization
[10:44:55 -651426.644232] Model parameter optimization (eps = 10.000000)
[10:48:48 -649160.208338] AUTODETECT spr round 1 (radius: 5)
[10:55:17 -434881.959942] AUTODETECT spr round 2 (radius: 10)
[11:02:12 -311165.516074] AUTODETECT spr round 3 (radius: 15)
[11:09:46 -248008.861113] AUTODETECT spr round 4 (radius: 20)
[11:12:30] [worker #2] ML tree search #15, logLikelihood: -187930.380854
[11:18:26 -221689.528982] AUTODETECT spr round 5 (radius: 25)
[11:30:56 -217761.540321] SPR radius for FAST iterations: 25 (autodetect)
[11:30:56 -217761.540321] Model parameter optimization (eps = 3.000000)
[11:32:29 -217296.999536] FAST spr round 1 (radius: 25)
[11:40:54 -188988.321009] FAST spr round 2 (radius: 25)
[11:46:57 -188124.474737] FAST spr round 3 (radius: 25)
[11:52:09 -188031.502896] FAST spr round 4 (radius: 25)
[11:56:34 -188010.067864] FAST spr round 5 (radius: 25)
[12:00:40 -188002.590614] FAST spr round 6 (radius: 25)
[12:04:31 -188002.590051] Model parameter optimization (eps = 1.000000)
[12:05:13 -187983.498569] SLOW spr round 1 (radius: 5)
[12:11:05 -187915.263233] SLOW spr round 2 (radius: 5)
[12:16:34 -187912.443939] SLOW spr round 3 (radius: 5)
[12:21:54 -187909.894956] SLOW spr round 4 (radius: 5)
[12:27:18 -187908.926276] SLOW spr round 5 (radius: 5)
[12:32:33 -187908.925874] SLOW spr round 6 (radius: 10)
[12:38:09 -187908.925756] SLOW spr round 7 (radius: 15)
[12:47:42 -187908.925755] SLOW spr round 8 (radius: 20)
[13:02:34 -187908.925754] SLOW spr round 9 (radius: 25)
[13:06:59] [worker #3] ML tree search #16, logLikelihood: -187906.103392
[13:20:51 -187908.925753] Model parameter optimization (eps = 0.100000)

[13:21:24] [worker #0] ML tree search #17, logLikelihood: -187907.276661

[13:33:14] [worker #1] ML tree search #14, logLikelihood: -187925.012631
[13:46:07] [worker #2] ML tree search #19, logLikelihood: -187926.057953
[15:59:17] [worker #3] ML tree search #20, logLikelihood: -187949.595936
[16:18:29] [worker #1] ML tree search #18, logLikelihood: -187937.715821

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.185853,0.585092) (0.123950,1.286229) (0.327438,0.654698) (0.362759,1.426451) 
   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: -187906.103392

AIC score: 379822.206784 / AICc score: 8423882.206784 / BIC score: 388710.251669
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=622).
         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/Q9UHX1/3_mltree/Q9UHX1.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX1/3_mltree/Q9UHX1.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX1/3_mltree/Q9UHX1.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX1/3_mltree/Q9UHX1.raxml.log

Analysis started: 07-Jul-2021 20:56:04 / finished: 08-Jul-2021 13:14:34

Elapsed time: 58710.253 seconds

Consumed energy: 3584.175 Wh (= 18 km in an electric car, or 90 km with an e-scooter!)