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 14:44:44 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/B2RC85/2_msa/B2RC85_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/B2RC85/3_mltree/B2RC85 --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/B2RC85/2_msa/B2RC85_trimmed_msa.fasta
[00:00:00] Loaded alignment with 999 taxa and 227 sites

WARNING: Sequences tr_A0BBI2_A0BBI2_PARTE_5888 and tr_Q6BG34_Q6BG34_PARTE_5888 are exactly identical!
WARNING: Sequences tr_D8QYN7_D8QYN7_SELML_88036 and tr_D8R900_D8R900_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A0F7VBC6_A0A0F7VBC6_TOXGV_432359 and tr_A0A074STU9_A0A074STU9_HAMHA_99158 are exactly identical!
WARNING: Sequences tr_K4D6C2_K4D6C2_SOLLC_4081 and tr_M1CU05_M1CU05_SOLTU_4113 are exactly identical!
WARNING: Sequences sp_B2RC85_R10B2_HUMAN_9606 and sp_P0C881_R10B1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_A0A0E0GSI1_A0A0E0GSI1_ORYNI_4536 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_B8AQB0_B8AQB0_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_I1PEU2_I1PEU2_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_A0A0E0D5D7_A0A0E0D5D7_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_A0A0E0P070_A0A0E0P070_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_A0A0D3FN04_A0A0D3FN04_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_A0A0D9ZC73_A0A0D9ZC73_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_A0A0E0KI02_A0A0E0KI02_ORYPU_4537 are exactly identical!
WARNING: Sequences tr_J3LS02_J3LS02_ORYBR_4533 and tr_Q8LN60_Q8LN60_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0GSF6_A0A0E0GSF6_ORYNI_4536 and tr_A0A0E0P037_A0A0E0P037_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GSF6_A0A0E0GSF6_ORYNI_4536 and tr_A0A0D3FMX5_A0A0D3FMX5_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0IWL6_A0A0E0IWL6_ORYNI_4536 and tr_A0A0E0MAV5_A0A0E0MAV5_ORYPU_4537 are exactly identical!
WARNING: Sequences tr_B8AQD4_B8AQD4_ORYSI_39946 and sp_Q6EX42_PI5K1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1R3Y3_I1R3Y3_ORYGL_4538 and tr_Q2QXW3_Q2QXW3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_B3S2M3_B3S2M3_TRIAD_10228 and tr_A0A369SMW2_A0A369SMW2_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A287N2K8_A0A287N2K8_HORVV_112509 and tr_A0A3B6HZW5_A0A3B6HZW5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_F2CSZ0_F2CSZ0_HORVV_112509 and tr_A0A3B6U9L9_A0A3B6U9L9_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_M4CU62_M4CU62_BRARP_51351 and tr_A0A078FEV5_A0A078FEV5_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4CVS4_M4CVS4_BRARP_51351 and tr_A0A078I5Z8_A0A078I5Z8_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4CVS4_M4CVS4_BRARP_51351 and tr_A0A0D3ARA0_A0A0D3ARA0_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4CVT4_M4CVT4_BRARP_51351 and tr_A0A078FP56_A0A078FP56_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4CVT4_M4CVT4_BRARP_51351 and tr_A0A078JF58_A0A078JF58_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4CVT4_M4CVT4_BRARP_51351 and tr_A0A0D3ARB5_A0A0D3ARB5_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4EEA9_M4EEA9_BRARP_51351 and tr_A0A078FEQ6_A0A078FEQ6_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M7ZNL0_M7ZNL0_TRIUA_4572 and tr_A0A3B6I0X0_A0A3B6I0X0_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_W2REG2_W2REG2_PHYPN_761204 and tr_A0A0W8BN13_A0A0W8BN13_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A3B6INX1_A0A3B6INX1_WHEAT_4565 and tr_A0A3B6JGX4_A0A3B6JGX4_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A067DM44_A0A067DM44_CITSI_2711 and tr_V4S2Y0_V4S2Y0_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067DM44_A0A067DM44_CITSI_2711 and tr_A0A2H5QKB0_A0A2H5QKB0_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A067GZN7_A0A067GZN7_CITSI_2711 and tr_V4TCJ0_V4TCJ0_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067GZN7_A0A067GZN7_CITSI_2711 and tr_A0A2H5NNG8_A0A2H5NNG8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0A0LB60_A0A0A0LB60_CUCSA_3659 and tr_A0A1S3B5X1_A0A1S3B5X1_CUCME_3656 are exactly identical!
WARNING: Sequences tr_V4S233_V4S233_9ROSI_85681 and tr_A0A2H5Q1T8_A0A2H5Q1T8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4T1A9_V4T1A9_9ROSI_85681 and tr_A0A2H5QQG8_A0A2H5QQG8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2SGG8_A0A0D2SGG8_GOSRA_29730 and tr_A0A1U8L6S1_A0A1U8L6S1_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2UVZ3_A0A0D2UVZ3_GOSRA_29730 and tr_A0A1U8J8X7_A0A1U8J8X7_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2W1B9_A0A0D2W1B9_GOSRA_29730 and tr_A0A1U8MA36_A0A1U8MA36_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0L9TC86_A0A0L9TC86_PHAAN_3914 and tr_A0A1S3UFU3_A0A1S3UFU3_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A0L9V369_A0A0L9V369_PHAAN_3914 and tr_A0A1S3VX98_A0A1S3VX98_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3X5R0_A0A1S3X5R0_TOBAC_4097 and tr_A0A1U7WB42_A0A1U7WB42_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3YFY6_A0A1S3YFY6_TOBAC_4097 and tr_A0A1U7WUD7_A0A1U7WUD7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3YS04_A0A1S3YS04_TOBAC_4097 and tr_J7K3W0_J7K3W0_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3Z237_A0A1S3Z237_TOBAC_4097 and tr_A0A1U7YW74_A0A1U7YW74_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4A7F0_A0A1S4A7F0_TOBAC_4097 and tr_A0A1U7YFT1_A0A1U7YFT1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BSC9_A0A1S4BSC9_TOBAC_4097 and tr_A0A1S4CTK7_A0A1S4CTK7_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S4BZ99_A0A1S4BZ99_TOBAC_4097 and tr_A0A314KR35_A0A314KR35_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S4BZ99_A0A1S4BZ99_TOBAC_4097 and tr_A0A1U7WWE4_A0A1U7WWE4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4DNX7_A0A1S4DNX7_TOBAC_4097 and tr_A0A1U7XMT0_A0A1U7XMT0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3TG26_A0A1S3TG26_VIGRR_3916 and tr_A0A3Q0ES22_A0A3Q0ES22_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3U3Z0_A0A1S3U3Z0_VIGRR_3916 and tr_A0A3Q0EYW8_A0A3Q0EYW8_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3VKU4_A0A1S3VKU4_VIGRR_3916 and tr_A0A3Q0FFS6_A0A3Q0FFS6_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3VKU4_A0A1S3VKU4_VIGRR_3916 and tr_A0A3Q0FIW2_A0A3Q0FIW2_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A314KRG1_A0A314KRG1_NICAT_49451 and tr_A0A1U7Y131_A0A1U7Y131_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1U8N2I2_A0A1U8N2I2_GOSHI_3635 and tr_A0A1U8PTD3_A0A1U8PTD3_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A2U1N1L7_A0A2U1N1L7_ARTAN_35608 and tr_A0A2U1QH66_A0A2U1QH66_ARTAN_35608 are exactly identical!
WARNING: Duplicate sequences found: 60

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/B2RC85/3_mltree/B2RC85.raxml.reduced.phy

Alignment comprises 1 partitions and 227 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 227 / 227
Gaps: 8.37 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/B2RC85/3_mltree/B2RC85.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 999 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 227 / 18160
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -426192.129118] Initial branch length optimization
[00:00:05 -361547.468335] Model parameter optimization (eps = 10.000000)
[00:01:26 -360194.682346] AUTODETECT spr round 1 (radius: 5)
[00:05:16 -273953.978804] AUTODETECT spr round 2 (radius: 10)
[00:09:19 -216948.380162] AUTODETECT spr round 3 (radius: 15)
[00:13:55 -190311.182700] AUTODETECT spr round 4 (radius: 20)
[00:19:35 -178828.686275] AUTODETECT spr round 5 (radius: 25)
[00:25:34 -176463.875986] SPR radius for FAST iterations: 25 (autodetect)
[00:25:34 -176463.875986] Model parameter optimization (eps = 3.000000)
[00:25:48 -176454.083164] FAST spr round 1 (radius: 25)
[00:31:50 -156798.383073] FAST spr round 2 (radius: 25)
[00:36:18 -156317.005812] FAST spr round 3 (radius: 25)
[00:39:56 -156232.830130] FAST spr round 4 (radius: 25)
[00:43:11 -156222.720839] FAST spr round 5 (radius: 25)
[00:46:08 -156216.262507] FAST spr round 6 (radius: 25)
[00:49:01 -156212.314666] FAST spr round 7 (radius: 25)
[00:51:49 -156207.783107] FAST spr round 8 (radius: 25)
[00:54:29 -156207.781982] Model parameter optimization (eps = 1.000000)
[00:54:54 -156029.274862] SLOW spr round 1 (radius: 5)
[00:58:42 -155972.677918] SLOW spr round 2 (radius: 5)
[01:02:22 -155957.560843] SLOW spr round 3 (radius: 5)
[01:05:58 -155955.870986] SLOW spr round 4 (radius: 5)
[01:09:24 -155955.579892] SLOW spr round 5 (radius: 5)
[01:12:49 -155955.577683] SLOW spr round 6 (radius: 10)
[01:16:38 -155951.010492] SLOW spr round 7 (radius: 5)
[01:20:48 -155949.211933] SLOW spr round 8 (radius: 5)
[01:24:31 -155949.211683] SLOW spr round 9 (radius: 10)
[01:28:29 -155948.487493] SLOW spr round 10 (radius: 5)
[01:32:32 -155948.487152] SLOW spr round 11 (radius: 10)
[01:36:50 -155948.381498] SLOW spr round 12 (radius: 5)
[01:40:51 -155948.381098] SLOW spr round 13 (radius: 10)
[01:44:40 -155948.306509] SLOW spr round 14 (radius: 15)
[01:50:31 -155941.670050] SLOW spr round 15 (radius: 5)
[01:54:44 -155929.656730] SLOW spr round 16 (radius: 5)
[01:58:23 -155927.499799] SLOW spr round 17 (radius: 5)
[02:01:56 -155924.404052] SLOW spr round 18 (radius: 5)
[02:05:14 -155924.403951] SLOW spr round 19 (radius: 10)
[02:08:54 -155923.486236] SLOW spr round 20 (radius: 5)
[02:12:46 -155922.971684] SLOW spr round 21 (radius: 5)
[02:15:17] [worker #4] ML tree search #5, logLikelihood: -155922.148093
[02:16:16 -155922.753102] SLOW spr round 22 (radius: 5)
[02:19:14] [worker #1] ML tree search #2, logLikelihood: -155943.194406
[02:19:36 -155922.752590] SLOW spr round 23 (radius: 10)
[02:23:16 -155922.272820] SLOW spr round 24 (radius: 5)
[02:27:08 -155922.088956] SLOW spr round 25 (radius: 5)
[02:30:37 -155922.088906] SLOW spr round 26 (radius: 10)
[02:33:22] [worker #2] ML tree search #3, logLikelihood: -156084.305449
[02:34:23 -155922.063997] SLOW spr round 27 (radius: 15)
[02:39:59 -155920.420608] SLOW spr round 28 (radius: 5)
[02:40:09] [worker #3] ML tree search #4, logLikelihood: -156124.907398
[02:43:33 -155919.312540] SLOW spr round 29 (radius: 5)
[02:46:43 -155918.161868] SLOW spr round 30 (radius: 5)
[02:49:40 -155918.160551] SLOW spr round 31 (radius: 10)
[02:52:56 -155915.736865] SLOW spr round 32 (radius: 5)
[02:56:18 -155915.736268] SLOW spr round 33 (radius: 10)
[02:59:53 -155915.736259] SLOW spr round 34 (radius: 15)
[03:04:46 -155915.022387] SLOW spr round 35 (radius: 5)
[03:08:23 -155911.329784] SLOW spr round 36 (radius: 5)
[03:11:31 -155911.328630] SLOW spr round 37 (radius: 10)
[03:14:54 -155910.907198] SLOW spr round 38 (radius: 5)
[03:18:15 -155910.640608] SLOW spr round 39 (radius: 5)
[03:21:19 -155909.818837] SLOW spr round 40 (radius: 5)
[03:24:15 -155909.432582] SLOW spr round 41 (radius: 5)
[03:27:07 -155909.020548] SLOW spr round 42 (radius: 5)
[03:29:56 -155909.020343] SLOW spr round 43 (radius: 10)
[03:33:06 -155909.020340] SLOW spr round 44 (radius: 15)
[03:38:21 -155909.020339] SLOW spr round 45 (radius: 20)
[03:45:10 -155909.020339] SLOW spr round 46 (radius: 25)
[03:53:56 -155909.020339] Model parameter optimization (eps = 0.100000)

[03:54:06] [worker #0] ML tree search #1, logLikelihood: -155908.181268

[03:54:06 -423329.848269] Initial branch length optimization
[03:54:10 -360078.944935] Model parameter optimization (eps = 10.000000)
[03:54:56 -358885.787096] AUTODETECT spr round 1 (radius: 5)
[03:58:01 -272818.772023] AUTODETECT spr round 2 (radius: 10)
[04:01:18 -219925.177775] AUTODETECT spr round 3 (radius: 15)
[04:04:10] [worker #1] ML tree search #7, logLikelihood: -155932.079556
[04:04:58 -195163.712041] AUTODETECT spr round 4 (radius: 20)
[04:09:07 -181861.268390] AUTODETECT spr round 5 (radius: 25)
[04:14:29 -179290.317538] SPR radius for FAST iterations: 25 (autodetect)
[04:14:29 -179290.317538] Model parameter optimization (eps = 3.000000)
[04:14:42 -179286.361028] FAST spr round 1 (radius: 25)
[04:20:35 -157020.635384] FAST spr round 2 (radius: 25)
[04:24:54 -156409.268726] FAST spr round 3 (radius: 25)
[04:28:30 -156299.701813] FAST spr round 4 (radius: 25)
[04:31:28 -156277.528263] FAST spr round 5 (radius: 25)
[04:34:09 -156273.433028] FAST spr round 6 (radius: 25)
[04:36:41 -156272.542518] FAST spr round 7 (radius: 25)
[04:39:08 -156272.542416] Model parameter optimization (eps = 1.000000)
[04:39:29 -156120.237199] SLOW spr round 1 (radius: 5)
[04:42:59 -156065.744232] SLOW spr round 2 (radius: 5)
[04:46:20 -156061.807482] SLOW spr round 3 (radius: 5)
[04:48:30] [worker #2] ML tree search #8, logLikelihood: -155968.339303
[04:49:33 -156061.805599] SLOW spr round 4 (radius: 10)
[04:51:44] [worker #3] ML tree search #9, logLikelihood: -156148.792630
[04:52:58 -156056.032885] SLOW spr round 5 (radius: 5)
[04:56:46 -156053.112952] SLOW spr round 6 (radius: 5)
[05:00:13 -156052.435811] SLOW spr round 7 (radius: 5)
[05:03:28 -156052.435534] SLOW spr round 8 (radius: 10)
[05:06:55 -156050.334281] SLOW spr round 9 (radius: 5)
[05:10:44 -156049.440841] SLOW spr round 10 (radius: 5)
[05:14:17 -156045.730962] SLOW spr round 11 (radius: 5)
[05:17:33 -156045.169719] SLOW spr round 12 (radius: 5)
[05:20:42 -156045.169536] SLOW spr round 13 (radius: 10)
[05:23:35] [worker #4] ML tree search #10, logLikelihood: -155896.097006
[05:24:08 -156045.169522] SLOW spr round 14 (radius: 15)
[05:30:28 -156041.420397] SLOW spr round 15 (radius: 5)
[05:34:24 -156041.321950] SLOW spr round 16 (radius: 10)
[05:38:20 -156041.321714] SLOW spr round 17 (radius: 15)
[05:43:27 -156041.321709] SLOW spr round 18 (radius: 20)
[05:51:04 -156040.434498] SLOW spr round 19 (radius: 5)
[05:54:42 -156040.008616] SLOW spr round 20 (radius: 5)
[05:55:21] [worker #1] ML tree search #12, logLikelihood: -155942.718944
[05:57:51 -156040.008248] SLOW spr round 21 (radius: 10)
[06:01:15 -156039.872291] SLOW spr round 22 (radius: 5)
[06:04:31 -156035.603515] SLOW spr round 23 (radius: 5)
[06:07:29 -156035.603457] SLOW spr round 24 (radius: 10)
[06:10:59 -156035.603457] SLOW spr round 25 (radius: 15)
[06:16:44 -156035.603457] SLOW spr round 26 (radius: 20)
[06:25:12 -156035.603457] SLOW spr round 27 (radius: 25)
[06:35:34 -156035.603457] Model parameter optimization (eps = 0.100000)

[06:35:53] [worker #0] ML tree search #6, logLikelihood: -156033.698625

[06:35:53 -427159.063034] Initial branch length optimization
[06:35:57 -361290.889248] Model parameter optimization (eps = 10.000000)
[06:36:45 -359958.141165] AUTODETECT spr round 1 (radius: 5)
[06:39:52 -277231.963053] AUTODETECT spr round 2 (radius: 10)
[06:43:13 -222495.817444] AUTODETECT spr round 3 (radius: 15)
[06:46:43 -197706.646681] AUTODETECT spr round 4 (radius: 20)
[06:50:48 -189802.803564] AUTODETECT spr round 5 (radius: 25)
[06:56:10 -181596.143462] SPR radius for FAST iterations: 25 (autodetect)
[06:56:10 -181596.143462] Model parameter optimization (eps = 3.000000)
[06:56:43 -181365.778460] FAST spr round 1 (radius: 25)
[07:02:29 -156988.884136] FAST spr round 2 (radius: 25)
[07:06:29 -156100.351645] FAST spr round 3 (radius: 25)
[07:09:50 -156046.169959] FAST spr round 4 (radius: 25)
[07:12:40 -156035.891617] FAST spr round 5 (radius: 25)
[07:15:20 -156024.486718] FAST spr round 6 (radius: 25)
[07:17:55 -156020.857656] FAST spr round 7 (radius: 25)
[07:20:25 -156020.561683] FAST spr round 8 (radius: 25)
[07:22:52 -156020.561480] Model parameter optimization (eps = 1.000000)
[07:23:11 -156019.352351] SLOW spr round 1 (radius: 5)
[07:23:23] [worker #2] ML tree search #13, logLikelihood: -155897.114682
[07:26:37 -155989.816958] SLOW spr round 2 (radius: 5)
[07:29:56 -155984.940731] SLOW spr round 3 (radius: 5)
[07:30:32] [worker #4] ML tree search #15, logLikelihood: -155947.998251
[07:33:09 -155984.583236] SLOW spr round 4 (radius: 5)
[07:36:18 -155984.583055] SLOW spr round 5 (radius: 10)
[07:39:43 -155981.375277] SLOW spr round 6 (radius: 5)
[07:43:25 -155981.374501] SLOW spr round 7 (radius: 10)
[07:47:17 -155980.952131] SLOW spr round 8 (radius: 5)
[07:51:01 -155974.659634] SLOW spr round 9 (radius: 5)
[07:54:23 -155973.399704] SLOW spr round 10 (radius: 5)
[07:57:38 -155968.403763] SLOW spr round 11 (radius: 5)
[08:00:49 -155964.885683] SLOW spr round 12 (radius: 5)
[08:03:58 -155961.532728] SLOW spr round 13 (radius: 5)
[08:07:07 -155960.663896] SLOW spr round 14 (radius: 5)
[08:10:14 -155960.663674] SLOW spr round 15 (radius: 10)
[08:13:38 -155960.379754] SLOW spr round 16 (radius: 5)
[08:17:28 -155955.912902] SLOW spr round 17 (radius: 5)
[08:20:51 -155955.912505] SLOW spr round 18 (radius: 10)
[08:24:28 -155954.554098] SLOW spr round 19 (radius: 5)
[08:28:12 -155952.416216] SLOW spr round 20 (radius: 5)
[08:31:33 -155952.415403] SLOW spr round 21 (radius: 10)
[08:35:05 -155952.415373] SLOW spr round 22 (radius: 15)
[08:40:00] [worker #1] ML tree search #17, logLikelihood: -155917.248342
[08:40:33 -155952.415370] SLOW spr round 23 (radius: 20)
[08:43:13] [worker #3] ML tree search #14, logLikelihood: -156096.751447
[08:47:31 -155952.415368] SLOW spr round 24 (radius: 25)
[08:56:34 -155952.415368] Model parameter optimization (eps = 0.100000)

[08:56:42] [worker #0] ML tree search #11, logLikelihood: -155952.404122

[08:56:42 -425911.762779] Initial branch length optimization
[08:56:47 -360741.048106] Model parameter optimization (eps = 10.000000)
[08:57:45 -359502.839338] AUTODETECT spr round 1 (radius: 5)
[09:01:17 -273116.981518] AUTODETECT spr round 2 (radius: 10)
[09:05:05 -213071.457471] AUTODETECT spr round 3 (radius: 15)
[09:09:02 -186858.803624] AUTODETECT spr round 4 (radius: 20)
[09:13:28 -174825.563500] AUTODETECT spr round 5 (radius: 25)
[09:18:50 -173778.942019] SPR radius for FAST iterations: 25 (autodetect)
[09:18:50 -173778.942019] Model parameter optimization (eps = 3.000000)
[09:19:47 -173569.057581] FAST spr round 1 (radius: 25)
[09:25:01 -156652.798864] FAST spr round 2 (radius: 25)
[09:28:49 -156114.017960] FAST spr round 3 (radius: 25)
[09:31:58 -156031.848531] FAST spr round 4 (radius: 25)
[09:34:45 -156019.671349] FAST spr round 5 (radius: 25)
[09:37:18 -156019.670140] Model parameter optimization (eps = 1.000000)
[09:37:34 -156016.933015] SLOW spr round 1 (radius: 5)
[09:41:12 -155979.936957] SLOW spr round 2 (radius: 5)
[09:44:37 -155970.706222] SLOW spr round 3 (radius: 5)
[09:47:56 -155967.385784] SLOW spr round 4 (radius: 5)
[09:51:04 -155967.385449] SLOW spr round 5 (radius: 10)
[09:54:27 -155961.925474] SLOW spr round 6 (radius: 5)
[09:58:13 -155960.600525] SLOW spr round 7 (radius: 5)
[10:01:35 -155960.598336] SLOW spr round 8 (radius: 10)
[10:05:07 -155960.209587] SLOW spr round 9 (radius: 5)
[10:07:45] [worker #2] ML tree search #18, logLikelihood: -155923.252162
[10:08:51 -155957.585497] SLOW spr round 10 (radius: 5)
[10:12:12 -155957.584841] SLOW spr round 11 (radius: 10)
[10:15:43 -155954.556135] SLOW spr round 12 (radius: 5)
[10:19:23 -155954.556054] SLOW spr round 13 (radius: 10)
[10:23:10 -155954.556052] SLOW spr round 14 (radius: 15)
[10:25:57] [worker #4] ML tree search #20, logLikelihood: -155954.929607
[10:28:24 -155954.556051] SLOW spr round 15 (radius: 20)
[10:35:53 -155954.556051] SLOW spr round 16 (radius: 25)
[10:45:24 -155950.281564] SLOW spr round 17 (radius: 5)
[10:49:30 -155944.160137] SLOW spr round 18 (radius: 5)
[10:53:01 -155944.026080] SLOW spr round 19 (radius: 5)
[10:56:16 -155944.025823] SLOW spr round 20 (radius: 10)
[10:59:46 -155935.713745] SLOW spr round 21 (radius: 5)
[11:03:33 -155935.212001] SLOW spr round 22 (radius: 5)
[11:06:39] [worker #3] ML tree search #19, logLikelihood: -155951.739560
[11:06:54 -155935.211857] SLOW spr round 23 (radius: 10)
[11:10:22 -155935.211854] SLOW spr round 24 (radius: 15)
[11:15:37 -155935.211853] SLOW spr round 25 (radius: 20)
[11:22:48 -155935.211852] SLOW spr round 26 (radius: 25)
[11:32:01 -155935.211852] Model parameter optimization (eps = 0.100000)

[11:32:16] [worker #0] ML tree search #16, logLikelihood: -155934.933237


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.049420,0.250809) (0.180360,0.702178) (0.390352,0.703020) (0.379867,1.544051) 
   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: -155896.097006

AIC score: 315794.194012 / AICc score: 8327798.194012 / BIC score: 322647.518997
Free parameters (model + branch lengths): 2001

WARNING: Number of free parameters (K=2001) is larger than alignment size (n=227).
         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/B2RC85/3_mltree/B2RC85.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/B2RC85/3_mltree/B2RC85.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/B2RC85/3_mltree/B2RC85.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/B2RC85/3_mltree/B2RC85.raxml.log

Analysis started: 06-Jul-2021 14:44:44 / finished: 07-Jul-2021 02:17:00

Elapsed time: 41536.657 seconds

Consumed energy: 3837.018 Wh (= 19 km in an electric car, or 96 km with an e-scooter!)