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 19-Jul-2021 14:18:37 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/2_msa/Q587I9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/3_mltree/Q587I9 --seed 2 --threads 3 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/2_msa/Q587I9_trimmed_msa.fasta
[00:00:00] Loaded alignment with 566 taxa and 155 sites

WARNING: Sequences tr_B4Q5N4_B4Q5N4_DROSI_7240 and tr_B4ICT0_B4ICT0_DROSE_7238 are exactly identical!
WARNING: Sequences tr_J3K150_J3K150_COCIM_246410 and tr_E9D3E5_E9D3E5_COCPS_443226 are exactly identical!
WARNING: Sequences tr_B6Q6V9_B6Q6V9_TALMQ_441960 and tr_A0A093VLK7_A0A093VLK7_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_A0A2I2YWZ0_A0A2I2YWZ0_GORGO_9595 and tr_H2R6K7_H2R6K7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YWZ0_A0A2I2YWZ0_GORGO_9595 and sp_Q587I9_SFT2C_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_C0NJJ3_C0NJJ3_AJECG_447093 and tr_F0UBM0_F0UBM0_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_Q7SGC6_Q7SGC6_NEUCR_367110 and tr_G4U9V2_G4U9V2_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B5DI31_B5DI31_DROPS_46245 and tr_B4G8F4_B4G8F4_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A179USM8_A0A179USM8_BLAGS_559298 and tr_C5GKG7_C5GKG7_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_Q4WTD5_Q4WTD5_ASPFU_330879 and tr_A1D3A7_A1D3A7_NEOFI_331117 are exactly identical!
WARNING: Sequences tr_J5JI07_J5JI07_BEAB2_655819 and tr_A0A0A2V9K5_A0A0A2V9K5_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_A0A088AVN6_A0A088AVN6_APIME_7460 and tr_A0A2A3EK70_A0A2A3EK70_APICC_94128 are exactly identical!
WARNING: Sequences tr_A2QQ64_A2QQ64_ASPNC_425011 and tr_G3YFS9_G3YFS9_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_G7XKI3_G7XKI3_ASPKW_1033177 and tr_A0A317V3J3_A0A317V3J3_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_F9WYL6_F9WYL6_ZYMTI_336722 and tr_A0A0F4GG29_A0A0F4GG29_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9WYL6_F9WYL6_ZYMTI_336722 and tr_A0A1X7RHW8_A0A1X7RHW8_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YC16_G2YC16_BOTF4_999810 and tr_M7UBH3_M7UBH3_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_W7LHW0_W7LHW0_GIBM7_334819 and tr_A0A0D2X873_A0A0D2X873_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_W7LHW0_W7LHW0_GIBM7_334819 and tr_S0DKV0_S0DKV0_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_W7LHW0_W7LHW0_GIBM7_334819 and tr_N4TBL0_N4TBL0_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_W7LHW0_W7LHW0_GIBM7_334819 and tr_A0A2H3SUG3_A0A2H3SUG3_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_W7LHW0_W7LHW0_GIBM7_334819 and tr_A0A2H3HS94_A0A2H3HS94_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_W7LHW0_W7LHW0_GIBM7_334819 and tr_A0A365MSS5_A0A365MSS5_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_W2PSN9_W2PSN9_PHYPN_761204 and tr_W2KP68_W2KP68_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A017S687_A0A017S687_9EURO_1388766 and tr_A0A1L9VHH5_A0A1L9VHH5_ASPGL_1160497 are exactly identical!
WARNING: Sequences tr_A0A015MZG1_A0A015MZG1_9GLOM_1432141 and tr_A0A2I1GH21_A0A2I1GH21_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A0E9NML7_A0A0E9NML7_SAICN_698492 and tr_A0A0E9NMQ9_A0A0E9NMQ9_SAICN_698492 are exactly identical!
WARNING: Sequences tr_A0A0F0IF56_A0A0F0IF56_ASPPU_1403190 and tr_A0A2G7FY37_A0A2G7FY37_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0F8V0I4_A0A0F8V0I4_9EURO_308745 and tr_A0A2T5M1R8_A0A2T5M1R8_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0L1IJX5_A0A0L1IJX5_ASPNO_1509407 and tr_A0A1F7ZJE6_A0A1F7ZJE6_9EURO_109264 are exactly identical!
WARNING: Sequences tr_A0A0G4P0A8_A0A0G4P0A8_PENCA_1429867 and tr_A0A101MCZ9_A0A101MCZ9_9EURO_48697 are exactly identical!
WARNING: Sequences tr_A0A0G4P0A8_A0A0G4P0A8_PENCA_1429867 and tr_A0A1V6NEB4_A0A1V6NEB4_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A100IHS8_A0A100IHS8_ASPNG_5061 and tr_A0A1L9NN55_A0A1L9NN55_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A100IHS8_A0A100IHS8_ASPNG_5061 and tr_A0A1L9UQP1_A0A1L9UQP1_9EURO_767769 are exactly identical!
WARNING: Sequences tr_I1RCI9_I1RCI9_GIBZE_229533 and tr_A0A2T4H7E5_A0A2T4H7E5_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1L9WW42_A0A1L9WW42_ASPAC_690307 and tr_A0A319CCB5_A0A319CCB5_9EURO_1448315 are exactly identical!
WARNING: Sequences tr_A0A1L9WW42_A0A1L9WW42_ASPAC_690307 and tr_A0A2V5J9T1_A0A2V5J9T1_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A1L9WW42_A0A1L9WW42_ASPAC_690307 and tr_A0A395HUA8_A0A395HUA8_9EURO_1450537 are exactly identical!
WARNING: Sequences tr_A0A1L9WW42_A0A1L9WW42_ASPAC_690307 and tr_A0A2V5H4S7_A0A2V5H4S7_9EURO_1450538 are exactly identical!
WARNING: Sequences tr_A0A1V8UNC0_A0A1V8UNC0_9PEZI_1974281 and tr_A0A1V8T0W3_A0A1V8T0W3_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A2G5ID68_A0A2G5ID68_CERBT_122368 and tr_A0A2S6C9B6_A0A2S6C9B6_9PEZI_357750 are exactly identical!
WARNING: Duplicate sequences found: 41

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/Q587I9/3_mltree/Q587I9.raxml.reduced.phy

Alignment comprises 1 partitions and 155 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 155 / 155
Gaps: 4.06 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/3_mltree/Q587I9.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 566 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 155 / 12400
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -148632.178284] Initial branch length optimization
[00:00:02 -120730.820662] Model parameter optimization (eps = 10.000000)
[00:00:43 -119515.280214] AUTODETECT spr round 1 (radius: 5)
[00:01:38 -90097.375583] AUTODETECT spr round 2 (radius: 10)
[00:02:44 -66519.204297] AUTODETECT spr round 3 (radius: 15)
[00:03:55 -60363.218138] AUTODETECT spr round 4 (radius: 20)
[00:05:31 -57111.524419] AUTODETECT spr round 5 (radius: 25)
[00:07:01 -55184.389922] SPR radius for FAST iterations: 25 (autodetect)
[00:07:01 -55184.389922] Model parameter optimization (eps = 3.000000)
[00:07:24 -55072.381573] FAST spr round 1 (radius: 25)
[00:08:30 -47094.982161] FAST spr round 2 (radius: 25)
[00:09:23 -46633.801698] FAST spr round 3 (radius: 25)
[00:10:10 -46609.357551] FAST spr round 4 (radius: 25)
[00:10:52 -46600.099813] FAST spr round 5 (radius: 25)
[00:11:33 -46594.413659] FAST spr round 6 (radius: 25)
[00:12:11 -46594.413618] Model parameter optimization (eps = 1.000000)
[00:12:20 -46591.017926] SLOW spr round 1 (radius: 5)
[00:13:22 -46577.366062] SLOW spr round 2 (radius: 5)
[00:14:21 -46572.299534] SLOW spr round 3 (radius: 5)
[00:15:17 -46570.910792] SLOW spr round 4 (radius: 5)
[00:16:12 -46570.910675] SLOW spr round 5 (radius: 10)
[00:17:10 -46569.104700] SLOW spr round 6 (radius: 5)
[00:18:28 -46566.599357] SLOW spr round 7 (radius: 5)
[00:19:33 -46566.599281] SLOW spr round 8 (radius: 10)
[00:20:33 -46566.073164] SLOW spr round 9 (radius: 5)
[00:21:47 -46566.073158] SLOW spr round 10 (radius: 10)
[00:22:51 -46566.073158] SLOW spr round 11 (radius: 15)
[00:24:33 -46566.073158] SLOW spr round 12 (radius: 20)
[00:25:11] [worker #1] ML tree search #2, logLikelihood: -46568.988136
[00:27:19 -46566.073158] SLOW spr round 13 (radius: 25)
[00:30:10 -46566.073158] Model parameter optimization (eps = 0.100000)

[00:30:15] [worker #0] ML tree search #1, logLikelihood: -46566.046317

[00:30:15 -148471.830308] Initial branch length optimization
[00:30:17 -119966.249724] Model parameter optimization (eps = 10.000000)
[00:30:43 -118959.468837] AUTODETECT spr round 1 (radius: 5)
[00:31:40 -88356.335494] AUTODETECT spr round 2 (radius: 10)
[00:32:51 -64296.098809] AUTODETECT spr round 3 (radius: 15)
[00:33:10] [worker #2] ML tree search #3, logLikelihood: -46568.654123
[00:34:06 -53433.140648] AUTODETECT spr round 4 (radius: 20)
[00:35:32 -52353.559363] AUTODETECT spr round 5 (radius: 25)
[00:37:17 -51943.619272] SPR radius for FAST iterations: 25 (autodetect)
[00:37:17 -51943.619272] Model parameter optimization (eps = 3.000000)
[00:37:44 -51811.584993] FAST spr round 1 (radius: 25)
[00:38:47 -46837.785924] FAST spr round 2 (radius: 25)
[00:39:41 -46613.072924] FAST spr round 3 (radius: 25)
[00:40:28 -46589.615080] FAST spr round 4 (radius: 25)
[00:41:07 -46587.490237] FAST spr round 5 (radius: 25)
[00:41:46 -46587.176974] FAST spr round 6 (radius: 25)
[00:42:24 -46587.174925] Model parameter optimization (eps = 1.000000)
[00:42:34 -46585.391609] SLOW spr round 1 (radius: 5)
[00:43:38 -46572.915614] SLOW spr round 2 (radius: 5)
[00:44:39 -46565.932916] SLOW spr round 3 (radius: 5)
[00:45:36 -46565.816517] SLOW spr round 4 (radius: 5)
[00:46:32 -46565.815563] SLOW spr round 5 (radius: 10)
[00:47:29 -46565.133352] SLOW spr round 6 (radius: 5)
[00:48:47 -46564.232761] SLOW spr round 7 (radius: 5)
[00:49:55 -46562.790577] SLOW spr round 8 (radius: 5)
[00:50:55 -46562.790449] SLOW spr round 9 (radius: 10)
[00:51:53 -46562.790447] SLOW spr round 10 (radius: 15)
[00:53:39 -46562.790447] SLOW spr round 11 (radius: 20)
[00:56:12 -46562.790447] SLOW spr round 12 (radius: 25)
[00:56:21] [worker #2] ML tree search #6, logLikelihood: -46568.906239
[00:57:46] [worker #1] ML tree search #5, logLikelihood: -46565.350768
[00:59:08 -46562.790447] Model parameter optimization (eps = 0.100000)

[00:59:15] [worker #0] ML tree search #4, logLikelihood: -46562.570810

[00:59:15 -145784.281937] Initial branch length optimization
[00:59:17 -119584.943145] Model parameter optimization (eps = 10.000000)
[00:59:58 -118343.337448] AUTODETECT spr round 1 (radius: 5)
[01:00:54 -88837.446374] AUTODETECT spr round 2 (radius: 10)
[01:01:58 -67027.002862] AUTODETECT spr round 3 (radius: 15)
[01:03:11 -59080.103819] AUTODETECT spr round 4 (radius: 20)
[01:04:43 -56235.957730] AUTODETECT spr round 5 (radius: 25)
[01:06:19 -55289.335676] SPR radius for FAST iterations: 25 (autodetect)
[01:06:19 -55289.335676] Model parameter optimization (eps = 3.000000)
[01:06:35 -55206.429526] FAST spr round 1 (radius: 25)
[01:07:36 -47099.859788] FAST spr round 2 (radius: 25)
[01:08:27 -46648.117001] FAST spr round 3 (radius: 25)
[01:09:13 -46610.338844] FAST spr round 4 (radius: 25)
[01:09:55 -46603.078709] FAST spr round 5 (radius: 25)
[01:10:35 -46598.009977] FAST spr round 6 (radius: 25)
[01:11:14 -46598.009875] Model parameter optimization (eps = 1.000000)
[01:11:22 -46597.864731] SLOW spr round 1 (radius: 5)
[01:12:25 -46582.233803] SLOW spr round 2 (radius: 5)
[01:13:22 -46581.838725] SLOW spr round 3 (radius: 5)
[01:14:18 -46581.837600] SLOW spr round 4 (radius: 10)
[01:15:15 -46581.837573] SLOW spr round 5 (radius: 15)
[01:17:05 -46581.837572] SLOW spr round 6 (radius: 20)
[01:19:25 -46579.039395] SLOW spr round 7 (radius: 5)
[01:20:43] [worker #1] ML tree search #8, logLikelihood: -46556.444425
[01:20:50 -46576.773839] SLOW spr round 8 (radius: 5)
[01:21:58 -46576.745872] SLOW spr round 9 (radius: 10)
[01:22:58 -46576.745505] SLOW spr round 10 (radius: 15)
[01:24:42 -46573.840253] SLOW spr round 11 (radius: 5)
[01:26:03 -46570.857529] SLOW spr round 12 (radius: 5)
[01:27:09 -46570.761504] SLOW spr round 13 (radius: 10)
[01:28:09 -46570.761217] SLOW spr round 14 (radius: 15)
[01:29:55 -46570.761214] SLOW spr round 15 (radius: 20)
[01:32:17] [worker #2] ML tree search #9, logLikelihood: -46575.415341
[01:32:20 -46570.761214] SLOW spr round 16 (radius: 25)
[01:34:58 -46570.761214] Model parameter optimization (eps = 0.100000)

[01:35:05] [worker #0] ML tree search #7, logLikelihood: -46570.650078

[01:35:05 -147408.786305] Initial branch length optimization
[01:35:07 -120818.775822] Model parameter optimization (eps = 10.000000)
[01:35:44 -119665.718654] AUTODETECT spr round 1 (radius: 5)
[01:36:40 -88986.157020] AUTODETECT spr round 2 (radius: 10)
[01:37:45 -64995.428036] AUTODETECT spr round 3 (radius: 15)
[01:39:01 -56739.994289] AUTODETECT spr round 4 (radius: 20)
[01:40:32 -55171.645537] AUTODETECT spr round 5 (radius: 25)
[01:42:19 -53477.903049] SPR radius for FAST iterations: 25 (autodetect)
[01:42:19 -53477.903049] Model parameter optimization (eps = 3.000000)
[01:42:41 -53335.204979] FAST spr round 1 (radius: 25)
[01:43:45 -47004.554518] FAST spr round 2 (radius: 25)
[01:44:38 -46651.734523] FAST spr round 3 (radius: 25)
[01:44:50] [worker #1] ML tree search #11, logLikelihood: -46572.459832
[01:45:28 -46633.008557] FAST spr round 4 (radius: 25)
[01:46:12 -46624.494218] FAST spr round 5 (radius: 25)
[01:46:52 -46621.377501] FAST spr round 6 (radius: 25)
[01:47:31 -46621.002220] FAST spr round 7 (radius: 25)
[01:48:10 -46621.002215] Model parameter optimization (eps = 1.000000)
[01:48:23 -46617.157372] SLOW spr round 1 (radius: 5)
[01:49:28 -46589.506300] SLOW spr round 2 (radius: 5)
[01:50:28 -46574.512070] SLOW spr round 3 (radius: 5)
[01:51:26 -46573.647079] SLOW spr round 4 (radius: 5)
[01:52:25 -46568.732584] SLOW spr round 5 (radius: 5)
[01:53:20 -46568.595448] SLOW spr round 6 (radius: 5)
[01:54:15 -46568.595068] SLOW spr round 7 (radius: 10)
[01:55:14 -46567.642039] SLOW spr round 8 (radius: 5)
[01:56:30 -46565.348601] SLOW spr round 9 (radius: 5)
[01:57:35 -46565.347700] SLOW spr round 10 (radius: 10)
[01:58:36 -46560.825701] SLOW spr round 11 (radius: 5)
[01:59:55 -46551.952023] SLOW spr round 12 (radius: 5)
[02:01:00 -46551.500679] SLOW spr round 13 (radius: 5)
[02:01:59 -46551.500653] SLOW spr round 14 (radius: 10)
[02:02:57 -46551.500649] SLOW spr round 15 (radius: 15)
[02:03:21] [worker #2] ML tree search #12, logLikelihood: -46575.586432
[02:04:41 -46551.500645] SLOW spr round 16 (radius: 20)
[02:07:20 -46551.500640] SLOW spr round 17 (radius: 25)
[02:10:22 -46551.500636] Model parameter optimization (eps = 0.100000)

[02:10:32] [worker #0] ML tree search #10, logLikelihood: -46551.279534

[02:10:32 -147946.872707] Initial branch length optimization
[02:10:34 -120989.022674] Model parameter optimization (eps = 10.000000)
[02:11:03 -119745.184072] AUTODETECT spr round 1 (radius: 5)
[02:11:58 -89817.579536] AUTODETECT spr round 2 (radius: 10)
[02:13:02 -69866.118712] AUTODETECT spr round 3 (radius: 15)
[02:14:20 -57087.135698] AUTODETECT spr round 4 (radius: 20)
[02:15:49 -54421.450570] AUTODETECT spr round 5 (radius: 25)
[02:17:40 -54371.543272] SPR radius for FAST iterations: 25 (autodetect)
[02:17:40 -54371.543272] Model parameter optimization (eps = 3.000000)
[02:18:01 -54293.771971] FAST spr round 1 (radius: 25)
[02:19:02 -47113.371766] FAST spr round 2 (radius: 25)
[02:19:50 -46655.919737] FAST spr round 3 (radius: 25)
[02:20:36 -46619.999997] FAST spr round 4 (radius: 25)
[02:21:17 -46606.130060] FAST spr round 5 (radius: 25)
[02:21:53] [worker #1] ML tree search #14, logLikelihood: -46562.751686
[02:21:56 -46604.390573] FAST spr round 6 (radius: 25)
[02:22:35 -46601.116237] FAST spr round 7 (radius: 25)
[02:23:13 -46598.130781] FAST spr round 8 (radius: 25)
[02:23:51 -46598.130724] Model parameter optimization (eps = 1.000000)
[02:24:02 -46593.541927] SLOW spr round 1 (radius: 5)
[02:25:03 -46572.871288] SLOW spr round 2 (radius: 5)
[02:26:01 -46572.871028] SLOW spr round 3 (radius: 10)
[02:26:58 -46572.871022] SLOW spr round 4 (radius: 15)
[02:28:46 -46572.871022] SLOW spr round 5 (radius: 20)
[02:31:16 -46572.871022] SLOW spr round 6 (radius: 25)
[02:34:06 -46572.871022] Model parameter optimization (eps = 0.100000)

[02:34:10] [worker #0] ML tree search #13, logLikelihood: -46572.779683

[02:34:10 -147460.332730] Initial branch length optimization
[02:34:12 -119741.801547] Model parameter optimization (eps = 10.000000)
[02:34:43 -118580.856255] AUTODETECT spr round 1 (radius: 5)
[02:35:38 -88660.592320] AUTODETECT spr round 2 (radius: 10)
[02:36:40 -66298.855268] AUTODETECT spr round 3 (radius: 15)
[02:37:32] [worker #2] ML tree search #15, logLikelihood: -46557.919358
[02:38:01 -58182.880660] AUTODETECT spr round 4 (radius: 20)
[02:39:21 -54703.766866] AUTODETECT spr round 5 (radius: 25)
[02:40:56 -54123.344706] SPR radius for FAST iterations: 25 (autodetect)
[02:40:56 -54123.344706] Model parameter optimization (eps = 3.000000)
[02:41:12 -54011.306194] FAST spr round 1 (radius: 25)
[02:42:19 -47034.078274] FAST spr round 2 (radius: 25)
[02:43:15 -46616.495072] FAST spr round 3 (radius: 25)
[02:44:00 -46598.050273] FAST spr round 4 (radius: 25)
[02:44:43 -46585.295226] FAST spr round 5 (radius: 25)
[02:45:21 -46584.479891] FAST spr round 6 (radius: 25)
[02:45:59 -46584.479884] Model parameter optimization (eps = 1.000000)
[02:46:09 -46582.356676] SLOW spr round 1 (radius: 5)
[02:47:14 -46570.245244] SLOW spr round 2 (radius: 5)
[02:48:10 -46570.244866] SLOW spr round 3 (radius: 10)
[02:49:07 -46570.244864] SLOW spr round 4 (radius: 15)
[02:50:54 -46570.244864] SLOW spr round 5 (radius: 20)
[02:51:43] [worker #1] ML tree search #17, logLikelihood: -46582.213082
[02:53:16 -46570.244864] SLOW spr round 6 (radius: 25)
[02:55:38 -46570.244864] Model parameter optimization (eps = 0.100000)

[02:55:42] [worker #0] ML tree search #16, logLikelihood: -46570.238034

[02:55:42 -147741.300292] Initial branch length optimization
[02:55:44 -120373.390646] Model parameter optimization (eps = 10.000000)
[02:56:23 -119167.856064] AUTODETECT spr round 1 (radius: 5)
[02:57:18 -88103.430721] AUTODETECT spr round 2 (radius: 10)
[02:58:21 -66955.651232] AUTODETECT spr round 3 (radius: 15)
[02:59:35 -59611.802329] AUTODETECT spr round 4 (radius: 20)
[03:01:01 -55640.082566] AUTODETECT spr round 5 (radius: 25)
[03:02:32 -54788.848316] SPR radius for FAST iterations: 25 (autodetect)
[03:02:32 -54788.848316] Model parameter optimization (eps = 3.000000)
[03:02:56 -54731.767602] FAST spr round 1 (radius: 25)
[03:03:59 -47116.740145] FAST spr round 2 (radius: 25)
[03:04:49 -46674.636577] FAST spr round 3 (radius: 25)
[03:05:34 -46628.664257] FAST spr round 4 (radius: 25)
[03:06:15 -46617.453619] FAST spr round 5 (radius: 25)
[03:06:54 -46614.512823] FAST spr round 6 (radius: 25)
[03:07:32 -46613.738968] FAST spr round 7 (radius: 25)
[03:08:10 -46613.738875] Model parameter optimization (eps = 1.000000)
[03:08:22 -46604.408461] SLOW spr round 1 (radius: 5)
[03:09:24 -46589.083745] SLOW spr round 2 (radius: 5)
[03:10:21 -46588.217580] SLOW spr round 3 (radius: 5)
[03:11:17 -46588.217564] SLOW spr round 4 (radius: 10)
[03:12:15 -46586.105067] SLOW spr round 5 (radius: 5)
[03:13:33 -46584.472190] SLOW spr round 6 (radius: 5)
[03:14:39 -46575.462728] SLOW spr round 7 (radius: 5)
[03:15:39 -46575.462712] SLOW spr round 8 (radius: 10)
[03:16:33] [worker #1] ML tree search #20, logLikelihood: -46559.592966
[03:16:36 -46575.462712] SLOW spr round 9 (radius: 15)
[03:18:19 -46574.287552] SLOW spr round 10 (radius: 5)
[03:19:39 -46574.287499] SLOW spr round 11 (radius: 10)
[03:20:46 -46574.287498] SLOW spr round 12 (radius: 15)
[03:22:20 -46574.287498] SLOW spr round 13 (radius: 20)
[03:24:50 -46574.287498] SLOW spr round 14 (radius: 25)
[03:25:33] [worker #2] ML tree search #18, logLikelihood: -46567.736712
[03:27:36 -46574.287498] Model parameter optimization (eps = 0.100000)

[03:27:46] [worker #0] ML tree search #19, logLikelihood: -46573.836597


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.243465,0.651396) (0.371741,1.171242) (0.320696,0.957509) (0.064098,1.543580) 
   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: -46551.279534

AIC score: 95372.559068 / AICc score: 2674092.559068 / BIC score: 98826.846576
Free parameters (model + branch lengths): 1135

WARNING: Number of free parameters (K=1135) is larger than alignment size (n=155).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 44 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/3_mltree/Q587I9.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/3_mltree/Q587I9.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/3_mltree/Q587I9.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/3_mltree/Q587I9.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q587I9/3_mltree/Q587I9.raxml.log

Analysis started: 19-Jul-2021 14:18:37 / finished: 19-Jul-2021 17:46:24

Elapsed time: 12466.871 seconds