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 06-Jul-2021 08:48:10 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/2_msa/Q8N7U6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/2_msa/Q8N7U6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 650 taxa and 341 sites

WARNING: Sequences tr_B4QQ02_B4QQ02_DROSI_7240 and sp_P48593_E631_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QQ02_B4QQ02_DROSI_7240 and tr_B4HTW1_B4HTW1_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4QQ02_B4QQ02_DROSI_7240 and tr_A0A1W4VQ76_A0A1W4VQ76_DROFC_30025 are exactly identical!
WARNING: Sequences tr_H2QM61_H2QM61_PANTR_9598 and tr_A0A2R8ZVE6_A0A2R8ZVE6_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q06850_CDPK1_ARATH_3702 and tr_D7LY67_D7LY67_ARALL_81972 are exactly identical!
WARNING: Sequences tr_A0A0E0GBF1_A0A0E0GBF1_ORYNI_4536 and tr_A2X8E5_A2X8E5_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0GBF1_A0A0E0GBF1_ORYNI_4536 and tr_I1P373_I1P373_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GBF1_A0A0E0GBF1_ORYNI_4536 and tr_A0A0E0CPW5_A0A0E0CPW5_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0GBF1_A0A0E0GBF1_ORYNI_4536 and tr_A0A0E0NJC7_A0A0E0NJC7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GBF1_A0A0E0GBF1_ORYNI_4536 and tr_A0A0D9YWK4_A0A0D9YWK4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0GBF1_A0A0E0GBF1_ORYNI_4536 and sp_Q0DYK7_CDPK5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and tr_A2XMQ5_A2XMQ5_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and tr_I1QER5_I1QER5_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and tr_A0A0E0P2A3_A0A0E0P2A3_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and tr_A0A0D3FPZ4_A0A0D3FPZ4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP0_A0A0E0GUP0_ORYNI_4536 and sp_Q6F3A6_CDPKA_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and tr_B8ALC3_B8ALC3_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and tr_I1PG77_I1PG77_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and tr_A0A0E0D7Y8_A0A0E0D7Y8_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and tr_A0A0E0P2A9_A0A0E0P2A9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and tr_A0A0D3FPZ7_A0A0D3FPZ7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and tr_A0A0D9ZE64_A0A0D9ZE64_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0GUP4_A0A0E0GUP4_ORYNI_4536 and sp_Q852N6_CDPKB_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0H559_A0A0E0H559_ORYNI_4536 and tr_B8ATC8_B8ATC8_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0H559_A0A0E0H559_ORYNI_4536 and tr_A0A0E0PD86_A0A0E0PD86_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0H559_A0A0E0H559_ORYNI_4536 and tr_A0A0D3FZF4_A0A0D3FZF4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0H559_A0A0E0H559_ORYNI_4536 and sp_Q9FXQ3_CDPKD_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0HWX4_A0A0E0HWX4_ORYNI_4536 and tr_I1Q884_I1Q884_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HWX4_A0A0E0HWX4_ORYNI_4536 and tr_A0A0E0E7P4_A0A0E0E7P4_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0HWX4_A0A0E0HWX4_ORYNI_4536 and tr_A0A0E0Q4C2_A0A0E0Q4C2_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HWX4_A0A0E0HWX4_ORYNI_4536 and tr_A0A0D3GMK1_A0A0D3GMK1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0HWX4_A0A0E0HWX4_ORYNI_4536 and tr_A0A0E0AG12_A0A0E0AG12_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_F6ZB01_F6ZB01_MACMU_9544 and tr_A0A2K6BXK8_A0A2K6BXK8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A2YIE4_A2YIE4_ORYSI_39946 and sp_Q7XIM0_CDPKH_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1R6F0_I1R6F0_ORYGL_4538 and tr_A0A0E0RHE1_A0A0E0RHE1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1R6F0_I1R6F0_ORYGL_4538 and sp_Q2QQR2_CDPKR_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0DHP3_A0A0E0DHP3_9ORYZ_40149 and tr_A0A0D9ZPT3_A0A0D9ZPT3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_B3SDH5_B3SDH5_TRIAD_10228 and tr_A0A369RWC0_A0A369RWC0_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A0D2YC47_A0A0D2YC47_FUSO4_426428 and tr_X0CUR5_X0CUR5_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2YC47_A0A0D2YC47_FUSO4_426428 and tr_A0A2H3GE91_A0A2H3GE91_FUSOX_327505 are exactly identical!
WARNING: Sequences sp_A5A7I7_CDPK4_SOLTU_4113 and tr_M1BEF5_M1BEF5_SOLTU_4113 are exactly identical!
WARNING: Sequences tr_M4C7C7_M4C7C7_BRARP_51351 and tr_A0A0D3B5S1_A0A0D3B5S1_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4D548_M4D548_BRARP_51351 and tr_A0A0D3A1S9_A0A0D3A1S9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4EM39_M4EM39_BRARP_51351 and tr_A0A078F6B7_A0A078F6B7_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M8AQD2_M8AQD2_TRIUA_4572 and tr_A0A3B6KN92_A0A3B6KN92_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_M8AQD2_M8AQD2_TRIUA_4572 and tr_A0A3B6LUH5_A0A3B6LUH5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_M8AQD2_M8AQD2_TRIUA_4572 and tr_A0A3B6MZ15_A0A3B6MZ15_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_S0EGE2_S0EGE2_GIBF5_1279085 and tr_A0A365NGT0_A0A365NGT0_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_A0A1D5UK41_A0A1D5UK41_WHEAT_4565 and tr_A0A3B6CCT4_A0A3B6CCT4_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B6NSY3_A0A3B6NSY3_WHEAT_4565 and tr_A0A3B6PM61_A0A3B6PM61_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B6NSY3_A0A3B6NSY3_WHEAT_4565 and tr_A0A3B6QJG2_A0A3B6QJG2_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A067EBX2_A0A067EBX2_CITSI_2711 and tr_V4U4L9_V4U4L9_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067EBX2_A0A067EBX2_CITSI_2711 and tr_A0A2H5PVS7_A0A2H5PVS7_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A067FQG3_A0A067FQG3_CITSI_2711 and tr_V4RMX8_V4RMX8_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067FTI8_A0A067FTI8_CITSI_2711 and tr_V4S716_V4S716_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067FTI8_A0A067FTI8_CITSI_2711 and tr_A0A2H5MXZ8_A0A2H5MXZ8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A078F7M3_A0A078F7M3_BRANA_3708 and tr_A0A078FNE3_A0A078FNE3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A0A0K2W9_A0A0A0K2W9_CUCSA_3659 and tr_A0A1S3BQY7_A0A1S3BQY7_CUCME_3656 are exactly identical!
WARNING: Sequences tr_V4T184_V4T184_9ROSI_85681 and tr_A0A2H5MZR1_A0A2H5MZR1_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2PM25_A0A0D2PM25_GOSRA_29730 and tr_A0A1U8LNS6_A0A1U8LNS6_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_I1RKF4_I1RKF4_GIBZE_229533 and tr_A0A2T4GSN2_A0A2T4GSN2_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1S3XWQ8_A0A1S3XWQ8_TOBAC_4097 and tr_A0A1U7X7I7_A0A1U7X7I7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4ASR5_A0A1S4ASR5_TOBAC_4097 and tr_A0A1U7X617_A0A1U7X617_NICSY_4096 are exactly identical!
WARNING: Sequences tr_Q93YF3_Q93YF3_TOBAC_4097 and tr_A0A1U7UTS3_A0A1U7UTS3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_Q93YF4_Q93YF4_TOBAC_4097 and tr_A0A1U7VH25_A0A1U7VH25_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1U8JU96_A0A1U8JU96_GOSHI_3635 and tr_A0A1U8NT38_A0A1U8NT38_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A1U8DYI8_A0A1U8DYI8_CAPAN_4072 and tr_A0A2G3BWH1_A0A2G3BWH1_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2G2ZGG8_A0A2G2ZGG8_CAPAN_4072 and tr_A0A2G3CE77_A0A2G3CE77_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2P5EAL0_A0A2P5EAL0_TREOI_63057 and tr_A0A2P5E2R8_A0A2P5E2R8_PARAD_3476 are exactly identical!
WARNING: Duplicate sequences found: 69

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/Q8N7U6/3_mltree/Q8N7U6.raxml.reduced.phy

Alignment comprises 1 partitions and 341 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 341 / 341
Gaps: 9.51 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6.raxml.rba

Parallelization scheme autoconfig: 5 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 650 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 341 / 27280
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -306380.359617] Initial branch length optimization
[00:00:04 -230122.993988] Model parameter optimization (eps = 10.000000)
[00:01:59 -229016.118409] AUTODETECT spr round 1 (radius: 5)
[00:03:57 -162961.119454] AUTODETECT spr round 2 (radius: 10)
[00:06:17 -117870.261812] AUTODETECT spr round 3 (radius: 15)
[00:09:12 -98542.655347] AUTODETECT spr round 4 (radius: 20)
[00:12:47 -91576.954830] AUTODETECT spr round 5 (radius: 25)
[00:16:41 -90133.903788] SPR radius for FAST iterations: 25 (autodetect)
[00:16:41 -90133.903788] Model parameter optimization (eps = 3.000000)
[00:17:23 -89452.575818] FAST spr round 1 (radius: 25)
[00:19:46 -75776.873151] FAST spr round 2 (radius: 25)
[00:21:37 -75164.321429] FAST spr round 3 (radius: 25)
[00:23:15 -75101.943005] FAST spr round 4 (radius: 25)
[00:24:39 -75097.096335] FAST spr round 5 (radius: 25)
[00:25:59 -75095.295335] FAST spr round 6 (radius: 25)
[00:27:15 -75095.294846] Model parameter optimization (eps = 1.000000)
[00:27:32 -75083.306388] SLOW spr round 1 (radius: 5)
[00:29:44 -75061.613943] SLOW spr round 2 (radius: 5)
[00:31:42 -75059.474304] SLOW spr round 3 (radius: 5)
[00:33:37 -75059.474001] SLOW spr round 4 (radius: 10)
[00:35:33 -75059.473997] SLOW spr round 5 (radius: 15)
[00:38:58 -75059.473996] SLOW spr round 6 (radius: 20)
[00:43:29 -75059.473996] SLOW spr round 7 (radius: 25)
[00:49:21 -75059.473996] Model parameter optimization (eps = 0.100000)

[00:49:32] [worker #0] ML tree search #1, logLikelihood: -75059.329291

[00:49:32 -307656.336999] Initial branch length optimization
[00:49:36 -230289.959813] Model parameter optimization (eps = 10.000000)
[00:50:51 -229152.900566] AUTODETECT spr round 1 (radius: 5)
[00:51:09] [worker #3] ML tree search #4, logLikelihood: -75054.888356
[00:52:49 -161630.260885] AUTODETECT spr round 2 (radius: 10)
[00:55:05 -117343.558522] AUTODETECT spr round 3 (radius: 15)
[00:57:44 -98240.322977] AUTODETECT spr round 4 (radius: 20)
[01:01:11 -91808.940574] AUTODETECT spr round 5 (radius: 25)
[01:05:26 -90191.653222] SPR radius for FAST iterations: 25 (autodetect)
[01:05:26 -90191.653222] Model parameter optimization (eps = 3.000000)
[01:05:38] [worker #4] ML tree search #5, logLikelihood: -75040.248108
[01:06:11 -89201.985238] FAST spr round 1 (radius: 25)
[01:08:31 -76939.129128] FAST spr round 2 (radius: 25)
[01:08:52] [worker #2] ML tree search #3, logLikelihood: -75067.427292
[01:10:26 -75658.331651] FAST spr round 3 (radius: 25)
[01:12:09 -75402.281935] FAST spr round 4 (radius: 25)
[01:13:38 -75143.832843] FAST spr round 5 (radius: 25)
[01:15:04 -75100.050350] FAST spr round 6 (radius: 25)
[01:16:22 -75100.049218] Model parameter optimization (eps = 1.000000)
[01:16:40 -75091.922007] SLOW spr round 1 (radius: 5)
[01:18:46 -75059.047516] SLOW spr round 2 (radius: 5)
[01:20:46 -75057.912162] SLOW spr round 3 (radius: 5)
[01:22:42 -75057.911152] SLOW spr round 4 (radius: 10)
[01:24:39 -75056.397809] SLOW spr round 5 (radius: 5)
[01:25:59] [worker #1] ML tree search #2, logLikelihood: -75046.214031
[01:27:20 -75054.134468] SLOW spr round 6 (radius: 5)
[01:29:36 -75054.134408] SLOW spr round 7 (radius: 10)
[01:31:37 -75054.134388] SLOW spr round 8 (radius: 15)
[01:34:59 -75054.134373] SLOW spr round 9 (radius: 20)
[01:39:27 -75054.134361] SLOW spr round 10 (radius: 25)
[01:45:34 -75054.134352] Model parameter optimization (eps = 0.100000)

[01:45:46] [worker #0] ML tree search #6, logLikelihood: -75053.675721

[01:45:46 -304367.973833] Initial branch length optimization
[01:45:50 -227395.812081] Model parameter optimization (eps = 10.000000)
[01:47:40 -226198.298369] AUTODETECT spr round 1 (radius: 5)
[01:49:40 -166337.130602] AUTODETECT spr round 2 (radius: 10)
[01:51:57 -118264.196031] AUTODETECT spr round 3 (radius: 15)
[01:54:48 -99535.458031] AUTODETECT spr round 4 (radius: 20)
[01:58:26 -92053.590868] AUTODETECT spr round 5 (radius: 25)
[02:02:42 -89551.791887] SPR radius for FAST iterations: 25 (autodetect)
[02:02:42 -89551.791887] Model parameter optimization (eps = 3.000000)
[02:03:26 -88700.392099] FAST spr round 1 (radius: 25)
[02:05:46 -75511.039316] FAST spr round 2 (radius: 25)
[02:07:27 -75143.776419] FAST spr round 3 (radius: 25)
[02:08:32] [worker #4] ML tree search #10, logLikelihood: -75034.324961
[02:09:00 -75123.791851] FAST spr round 4 (radius: 25)
[02:10:18 -75123.791749] Model parameter optimization (eps = 1.000000)
[02:10:35 -75117.744858] SLOW spr round 1 (radius: 5)
[02:12:44 -75107.331512] SLOW spr round 2 (radius: 5)
[02:14:42 -75107.113782] SLOW spr round 3 (radius: 5)
[02:16:40 -75107.112967] SLOW spr round 4 (radius: 10)
[02:18:36 -75106.574845] SLOW spr round 5 (radius: 5)
[02:18:42] [worker #2] ML tree search #8, logLikelihood: -75036.346152
[02:21:14 -75106.574843] SLOW spr round 6 (radius: 10)
[02:23:28 -75106.065081] SLOW spr round 7 (radius: 5)
[02:26:06 -75100.940308] SLOW spr round 8 (radius: 5)
[02:28:21 -75100.940112] SLOW spr round 9 (radius: 10)
[02:30:22 -75100.940103] SLOW spr round 10 (radius: 15)
[02:33:40 -75100.940101] SLOW spr round 11 (radius: 20)
[02:38:26 -75099.508512] SLOW spr round 12 (radius: 5)
[02:41:16 -75099.497594] SLOW spr round 13 (radius: 10)
[02:43:42 -75099.494547] SLOW spr round 14 (radius: 15)
[02:46:44 -75099.493642] SLOW spr round 15 (radius: 20)
[02:49:42] [worker #3] ML tree search #9, logLikelihood: -75032.366926
[02:51:33 -75099.493370] SLOW spr round 16 (radius: 25)
[02:51:57] [worker #1] ML tree search #7, logLikelihood: -75040.217868
[02:57:40 -75099.493288] Model parameter optimization (eps = 0.100000)

[02:57:46] [worker #0] ML tree search #11, logLikelihood: -75099.447713

[02:57:46 -306198.498263] Initial branch length optimization
[02:57:50 -229220.720361] Model parameter optimization (eps = 10.000000)
[03:00:15 -228062.923491] AUTODETECT spr round 1 (radius: 5)
[03:02:12 -159035.848609] AUTODETECT spr round 2 (radius: 10)
[03:04:26 -116017.430214] AUTODETECT spr round 3 (radius: 15)
[03:07:22 -94527.379812] AUTODETECT spr round 4 (radius: 20)
[03:10:59 -86015.295458] AUTODETECT spr round 5 (radius: 25)
[03:15:05 -84835.208992] SPR radius for FAST iterations: 25 (autodetect)
[03:15:05 -84835.208992] Model parameter optimization (eps = 3.000000)
[03:15:36] [worker #2] ML tree search #13, logLikelihood: -75031.034505
[03:15:45 -84124.560976] FAST spr round 1 (radius: 25)
[03:17:56 -75516.856047] FAST spr round 2 (radius: 25)
[03:19:36 -75107.216043] FAST spr round 3 (radius: 25)
[03:21:05 -75079.426098] FAST spr round 4 (radius: 25)
[03:22:27 -75065.827731] FAST spr round 5 (radius: 25)
[03:23:43 -75065.825758] Model parameter optimization (eps = 1.000000)
[03:24:01 -75046.898302] SLOW spr round 1 (radius: 5)
[03:26:06 -75033.164001] SLOW spr round 2 (radius: 5)
[03:28:09 -75032.475770] SLOW spr round 3 (radius: 5)
[03:29:40] [worker #4] ML tree search #15, logLikelihood: -75041.798549
[03:30:08 -75032.475396] SLOW spr round 4 (radius: 10)
[03:32:02 -75032.300817] SLOW spr round 5 (radius: 5)
[03:34:41 -75032.300348] SLOW spr round 6 (radius: 10)
[03:36:56 -75032.300221] SLOW spr round 7 (radius: 15)
[03:40:06 -75032.300131] SLOW spr round 8 (radius: 20)
[03:45:17 -75032.300046] SLOW spr round 9 (radius: 25)
[03:45:33] [worker #3] ML tree search #14, logLikelihood: -75036.429648
[03:51:51 -75032.119107] SLOW spr round 10 (radius: 5)
[03:54:42 -75032.118705] SLOW spr round 11 (radius: 10)
[03:57:11 -75031.925788] SLOW spr round 12 (radius: 5)
[03:59:47 -75031.441868] SLOW spr round 13 (radius: 5)
[04:02:01 -75031.441675] SLOW spr round 14 (radius: 10)
[04:03:59 -75031.441588] SLOW spr round 15 (radius: 15)
[04:07:18 -75031.441501] SLOW spr round 16 (radius: 20)
[04:12:02 -75029.678901] SLOW spr round 17 (radius: 5)
[04:14:51 -75029.452639] SLOW spr round 18 (radius: 5)
[04:17:12 -75029.451389] SLOW spr round 19 (radius: 10)
[04:18:29] [worker #2] ML tree search #18, logLikelihood: -75061.318253
[04:19:16 -75028.280702] SLOW spr round 20 (radius: 5)
[04:21:53 -75026.724707] SLOW spr round 21 (radius: 5)
[04:24:06 -75026.701761] SLOW spr round 22 (radius: 10)
[04:25:12] [worker #1] ML tree search #12, logLikelihood: -75029.823228
[04:25:27] [worker #4] ML tree search #20, logLikelihood: -75045.776169
[04:26:03 -75026.700892] SLOW spr round 23 (radius: 15)
[04:29:22 -75026.700702] SLOW spr round 24 (radius: 20)
[04:33:46 -75026.700593] SLOW spr round 25 (radius: 25)
[04:39:57 -75026.700499] Model parameter optimization (eps = 0.100000)

[04:40:02] [worker #0] ML tree search #16, logLikelihood: -75026.668532

[04:41:41] [worker #3] ML tree search #19, logLikelihood: -75037.603368
[05:20:36] [worker #1] ML tree search #17, logLikelihood: -75035.199100

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.225160,0.684447) (0.134503,0.707674) (0.469978,0.906927) (0.170359,1.904626) 
   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: -75026.668532

AIC score: 152659.337064 / AICc score: 3550883.337064 / BIC score: 157652.279932
Free parameters (model + branch lengths): 1303

WARNING: Number of free parameters (K=1303) is larger than alignment size (n=341).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 70 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N7U6/3_mltree/Q8N7U6.raxml.log

Analysis started: 06-Jul-2021 08:48:10 / finished: 06-Jul-2021 14:08:47

Elapsed time: 19237.096 seconds

Consumed energy: 1580.851 Wh (= 8 km in an electric car, or 40 km with an e-scooter!)