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 03-Jul-2021 18:42:04 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q99996/2_msa/Q99996_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q99996/3_mltree/Q99996 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q99996/2_msa/Q99996_trimmed_msa.fasta
[00:00:00] Loaded alignment with 189 taxa and 77 sites

WARNING: Sequences tr_A0A1D5PNE9_A0A1D5PNE9_CHICK_9031 and tr_G1N8Y3_G1N8Y3_MELGA_9103 are exactly identical!
WARNING: Sequences tr_A0A1D5PNE9_A0A1D5PNE9_CHICK_9031 and tr_H0YT78_H0YT78_TAEGU_59729 are exactly identical!
WARNING: Sequences tr_A0A1D5PNE9_A0A1D5PNE9_CHICK_9031 and tr_U3IGB9_U3IGB9_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_A0A1D5PNE9_A0A1D5PNE9_CHICK_9031 and tr_A0A091IQ20_A0A091IQ20_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_M3XQI3_M3XQI3_MUSPF_9669 and tr_A0A2Y9KDQ8_A0A2Y9KDQ8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YAW0_M3YAW0_MUSPF_9669 and tr_A0A2Y9JES9_A0A2Y9JES9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_G3QWV6_G3QWV6_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_H2PMY1_H2PMY1_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_H2R568_H2R568_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_H0WIG7_H0WIG7_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and sp_Q99996_AKAP9_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_G3TUL2_G3TUL2_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_G7P1U2_G7P1U2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_A0A2I3N765_A0A2I3N765_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_A0A0D9RJC5_A0A0D9RJC5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_A0A2K5LCL0_A0A2K5LCL0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_A0A2K6DY61_A0A2K6DY61_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_A0A2K5ZIX3_A0A2K5ZIX3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RZ19_G1RZ19_NOMLE_61853 and tr_A0A2R9B968_A0A2R9B968_PANPA_9597 are exactly identical!
WARNING: Sequences tr_J9P4D9_J9P4D9_CANLF_9615 and tr_G1LGT9_G1LGT9_AILME_9646 are exactly identical!
WARNING: Sequences tr_J9P4D9_J9P4D9_CANLF_9615 and tr_A0A2U3XML9_A0A2U3XML9_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_W5Q6D6_W5Q6D6_SHEEP_9940 and tr_F1MXF5_F1MXF5_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M4ALC2_M4ALC2_XIPMA_8083 and tr_A0A087XMJ9_A0A087XMJ9_POEFO_48698 are exactly identical!
WARNING: Sequences tr_G5C7V2_G5C7V2_HETGA_10181 and tr_A0A091DC45_A0A091DC45_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_H0ZLU3_H0ZLU3_TAEGU_59729 and tr_A0A093PP92_A0A093PP92_9PASS_328815 are exactly identical!
WARNING: Sequences tr_F4WTX8_F4WTX8_ACREC_103372 and tr_A0A151J1L7_A0A151J1L7_9HYME_471704 are exactly identical!
WARNING: Sequences tr_F4WTX8_F4WTX8_ACREC_103372 and tr_A0A195AUM6_A0A195AUM6_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F4WTX8_F4WTX8_ACREC_103372 and tr_A0A151JUP6_A0A151JUP6_9HYME_34720 are exactly identical!
WARNING: Sequences tr_F4WTX8_F4WTX8_ACREC_103372 and tr_A0A151IPA4_A0A151IPA4_9HYME_456900 are exactly identical!
WARNING: Sequences tr_L5KMG8_L5KMG8_PTEAL_9402 and tr_A0A2Y9T6W3_A0A2Y9T6W3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_L5KMG8_L5KMG8_PTEAL_9402 and tr_A0A384B8J5_A0A384B8J5_BALAS_310752 are exactly identical!
WARNING: Sequences tr_U3K7E4_U3K7E4_FICAL_59894 and tr_A0A2I0MQE6_A0A2I0MQE6_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A015KCC2_A0A015KCC2_9GLOM_1432141 and tr_A0A2H5SM06_A0A2H5SM06_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A151MQ31_A0A151MQ31_ALLMI_8496 and tr_A0A1U8DHR9_A0A1U8DHR9_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091V618_A0A091V618_NIPNI_128390 and tr_A0A087R9H4_A0A087R9H4_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091V618_A0A091V618_NIPNI_128390 and tr_A0A0A0AWS4_A0A0A0AWS4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091V618_A0A091V618_NIPNI_128390 and tr_A0A091HKT3_A0A091HKT3_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A226MF54_A0A226MF54_CALSU_9009 and tr_A0A226PYE0_A0A226PYE0_COLVI_9014 are exactly identical!
WARNING: Duplicate sequences found: 38

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/Q99996/3_mltree/Q99996.raxml.reduced.phy

Alignment comprises 1 partitions and 77 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 77 / 77
Gaps: 9.04 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q99996/3_mltree/Q99996.raxml.rba

Parallelization scheme autoconfig: 2 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 189 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 77 / 6160
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -15028.579696] Initial branch length optimization
[00:00:00 -11595.310449] Model parameter optimization (eps = 10.000000)
[00:00:03 -11388.255527] AUTODETECT spr round 1 (radius: 5)
[00:00:06 -8361.288667] AUTODETECT spr round 2 (radius: 10)
[00:00:11 -6906.667269] AUTODETECT spr round 3 (radius: 15)
[00:00:16 -5695.027757] AUTODETECT spr round 4 (radius: 20)
[00:00:21 -5572.404544] AUTODETECT spr round 5 (radius: 25)
[00:00:27 -5564.265768] SPR radius for FAST iterations: 25 (autodetect)
[00:00:27 -5564.265768] Model parameter optimization (eps = 3.000000)
[00:00:29 -5556.100362] FAST spr round 1 (radius: 25)
[00:00:35 -5137.042541] FAST spr round 2 (radius: 25)
[00:00:40 -5080.711582] FAST spr round 3 (radius: 25)
[00:00:44 -5075.438501] FAST spr round 4 (radius: 25)
[00:00:47 -5073.002792] FAST spr round 5 (radius: 25)
[00:00:50 -5073.000948] Model parameter optimization (eps = 1.000000)
[00:00:53 -5071.205265] SLOW spr round 1 (radius: 5)
[00:00:58 -5070.852749] SLOW spr round 2 (radius: 5)
[00:01:04 -5070.604859] SLOW spr round 3 (radius: 5)
[00:01:09 -5070.604496] SLOW spr round 4 (radius: 10)
[00:01:14 -5067.222041] SLOW spr round 5 (radius: 5)
[00:01:22 -5067.221856] SLOW spr round 6 (radius: 10)
[00:01:28 -5067.221833] SLOW spr round 7 (radius: 15)
[00:01:36 -5066.393135] SLOW spr round 8 (radius: 5)
[00:01:44 -5066.381770] SLOW spr round 9 (radius: 10)
[00:01:50 -5066.381545] SLOW spr round 10 (radius: 15)
[00:01:59 -5066.381539] SLOW spr round 11 (radius: 20)
[00:02:09 -5066.381532] SLOW spr round 12 (radius: 25)
[00:02:17 -5066.381526] Model parameter optimization (eps = 0.100000)

[00:02:19] [worker #0] ML tree search #1, logLikelihood: -5065.643034

[00:02:19 -14759.507897] Initial branch length optimization
[00:02:19 -11369.030686] Model parameter optimization (eps = 10.000000)
[00:02:24 -11188.150949] AUTODETECT spr round 1 (radius: 5)
[00:02:27 -8461.251875] AUTODETECT spr round 2 (radius: 10)
[00:02:32 -6763.610509] AUTODETECT spr round 3 (radius: 15)
[00:02:37 -5799.182958] AUTODETECT spr round 4 (radius: 20)
[00:02:43 -5574.730138] AUTODETECT spr round 5 (radius: 25)
[00:02:49 -5563.767653] SPR radius for FAST iterations: 25 (autodetect)
[00:02:49 -5563.767653] Model parameter optimization (eps = 3.000000)
[00:02:51 -5556.664729] FAST spr round 1 (radius: 25)
[00:02:55] [worker #1] ML tree search #2, logLikelihood: -5063.285979
[00:02:56 -5128.499230] FAST spr round 2 (radius: 25)
[00:03:00 -5083.898159] FAST spr round 3 (radius: 25)
[00:03:04 -5083.896072] Model parameter optimization (eps = 1.000000)
[00:03:06 -5082.752418] SLOW spr round 1 (radius: 5)
[00:03:11 -5080.609923] SLOW spr round 2 (radius: 5)
[00:03:16 -5080.485022] SLOW spr round 3 (radius: 5)
[00:03:21 -5080.484799] SLOW spr round 4 (radius: 10)
[00:03:27 -5070.409292] SLOW spr round 5 (radius: 5)
[00:03:34 -5070.266386] SLOW spr round 6 (radius: 5)
[00:03:40 -5070.266357] SLOW spr round 7 (radius: 10)
[00:03:46 -5070.266314] SLOW spr round 8 (radius: 15)
[00:03:54 -5069.313721] SLOW spr round 9 (radius: 5)
[00:04:02 -5069.302140] SLOW spr round 10 (radius: 10)
[00:04:09 -5069.290664] SLOW spr round 11 (radius: 15)
[00:04:17 -5069.289559] SLOW spr round 12 (radius: 20)
[00:04:26 -5069.288452] SLOW spr round 13 (radius: 25)
[00:04:35 -5069.287343] Model parameter optimization (eps = 0.100000)

[00:04:37] [worker #0] ML tree search #3, logLikelihood: -5068.761037

[00:04:37 -14787.600308] Initial branch length optimization
[00:04:37 -11448.772611] Model parameter optimization (eps = 10.000000)
[00:04:40 -11257.025437] AUTODETECT spr round 1 (radius: 5)
[00:04:44 -8645.687223] AUTODETECT spr round 2 (radius: 10)
[00:04:49 -6880.807341] AUTODETECT spr round 3 (radius: 15)
[00:04:54 -6000.276390] AUTODETECT spr round 4 (radius: 20)
[00:05:00 -5790.719444] AUTODETECT spr round 5 (radius: 25)
[00:05:06 -5785.217719] SPR radius for FAST iterations: 25 (autodetect)
[00:05:06 -5785.217719] Model parameter optimization (eps = 3.000000)
[00:05:09 -5774.216226] FAST spr round 1 (radius: 25)
[00:05:13 -5123.200427] FAST spr round 2 (radius: 25)
[00:05:17 -5101.206999] FAST spr round 3 (radius: 25)
[00:05:20 -5100.587961] FAST spr round 4 (radius: 25)
[00:05:21] [worker #1] ML tree search #4, logLikelihood: -5062.145001
[00:05:24 -5100.587712] Model parameter optimization (eps = 1.000000)
[00:05:26 -5098.259532] SLOW spr round 1 (radius: 5)
[00:05:31 -5094.122081] SLOW spr round 2 (radius: 5)
[00:05:36 -5094.121993] SLOW spr round 3 (radius: 10)
[00:05:41 -5090.916256] SLOW spr round 4 (radius: 5)
[00:05:49 -5086.687323] SLOW spr round 5 (radius: 5)
[00:05:55 -5086.687300] SLOW spr round 6 (radius: 10)
[00:06:01 -5086.420388] SLOW spr round 7 (radius: 5)
[00:06:08 -5086.420328] SLOW spr round 8 (radius: 10)
[00:06:14 -5086.420203] SLOW spr round 9 (radius: 15)
[00:06:23 -5085.829291] SLOW spr round 10 (radius: 5)
[00:06:30 -5085.825401] SLOW spr round 11 (radius: 10)
[00:06:37 -5085.825323] SLOW spr round 12 (radius: 15)
[00:06:45 -5085.825313] SLOW spr round 13 (radius: 20)
[00:06:54 -5068.326571] SLOW spr round 14 (radius: 5)
[00:07:03 -5066.814971] SLOW spr round 15 (radius: 5)
[00:07:10 -5066.636399] SLOW spr round 16 (radius: 5)
[00:07:16 -5066.635810] SLOW spr round 17 (radius: 10)
[00:07:21 -5066.635773] SLOW spr round 18 (radius: 15)
[00:07:30 -5066.635764] SLOW spr round 19 (radius: 20)
[00:07:39 -5066.394859] SLOW spr round 20 (radius: 5)
[00:07:47 -5066.344052] SLOW spr round 21 (radius: 10)
[00:07:54 -5066.343637] SLOW spr round 22 (radius: 15)
[00:08:02 -5066.343587] SLOW spr round 23 (radius: 20)
[00:08:06] [worker #1] ML tree search #6, logLikelihood: -5063.679313
[00:08:11 -5066.343566] SLOW spr round 24 (radius: 25)
[00:08:20 -5066.343555] Model parameter optimization (eps = 0.100000)

[00:08:21] [worker #0] ML tree search #5, logLikelihood: -5065.930609

[00:08:22 -14941.673441] Initial branch length optimization
[00:08:22 -11534.962039] Model parameter optimization (eps = 10.000000)
[00:08:25 -11359.542024] AUTODETECT spr round 1 (radius: 5)
[00:08:28 -8568.657580] AUTODETECT spr round 2 (radius: 10)
[00:08:33 -6699.697687] AUTODETECT spr round 3 (radius: 15)
[00:08:39 -5717.104765] AUTODETECT spr round 4 (radius: 20)
[00:08:45 -5550.081953] AUTODETECT spr round 5 (radius: 25)
[00:08:52 -5544.881882] SPR radius for FAST iterations: 25 (autodetect)
[00:08:52 -5544.881882] Model parameter optimization (eps = 3.000000)
[00:08:55 -5535.883591] FAST spr round 1 (radius: 25)
[00:09:00 -5091.994062] FAST spr round 2 (radius: 25)
[00:09:04 -5086.473065] FAST spr round 3 (radius: 25)
[00:09:08 -5080.750865] FAST spr round 4 (radius: 25)
[00:09:11 -5077.672039] FAST spr round 5 (radius: 25)
[00:09:14 -5077.671818] Model parameter optimization (eps = 1.000000)
[00:09:16 -5076.817061] SLOW spr round 1 (radius: 5)
[00:09:21 -5074.899097] SLOW spr round 2 (radius: 5)
[00:09:27 -5074.670739] SLOW spr round 3 (radius: 5)
[00:09:32 -5074.669961] SLOW spr round 4 (radius: 10)
[00:09:37 -5074.669853] SLOW spr round 5 (radius: 15)
[00:09:47 -5068.256191] SLOW spr round 6 (radius: 5)
[00:09:51] [worker #1] ML tree search #8, logLikelihood: -5070.768577
[00:09:55 -5068.234439] SLOW spr round 7 (radius: 10)
[00:10:02 -5066.839192] SLOW spr round 8 (radius: 5)
[00:10:10 -5065.649596] SLOW spr round 9 (radius: 5)
[00:10:16 -5065.649326] SLOW spr round 10 (radius: 10)
[00:10:21 -5065.564212] SLOW spr round 11 (radius: 15)
[00:10:31 -5065.532308] SLOW spr round 12 (radius: 20)
[00:10:40 -5065.532305] SLOW spr round 13 (radius: 25)
[00:10:48 -5065.532305] Model parameter optimization (eps = 0.100000)

[00:10:50] [worker #0] ML tree search #7, logLikelihood: -5064.854030

[00:10:50 -14819.430413] Initial branch length optimization
[00:10:50 -11473.515783] Model parameter optimization (eps = 10.000000)
[00:10:54 -11278.357807] AUTODETECT spr round 1 (radius: 5)
[00:10:57 -8685.248865] AUTODETECT spr round 2 (radius: 10)
[00:11:02 -6880.229803] AUTODETECT spr round 3 (radius: 15)
[00:11:08 -5648.411177] AUTODETECT spr round 4 (radius: 20)
[00:11:14 -5607.553018] AUTODETECT spr round 5 (radius: 25)
[00:11:21 -5596.151530] SPR radius for FAST iterations: 25 (autodetect)
[00:11:21 -5596.151530] Model parameter optimization (eps = 3.000000)
[00:11:24 -5585.181352] FAST spr round 1 (radius: 25)
[00:11:29 -5274.495305] FAST spr round 2 (radius: 25)
[00:11:34 -5097.611547] FAST spr round 3 (radius: 25)
[00:11:38 -5089.433504] FAST spr round 4 (radius: 25)
[00:11:41 -5089.432899] Model parameter optimization (eps = 1.000000)
[00:11:43 -5087.833667] SLOW spr round 1 (radius: 5)
[00:11:48 -5087.779918] SLOW spr round 2 (radius: 10)
[00:11:53 -5082.428756] SLOW spr round 3 (radius: 5)
[00:12:01 -5078.832153] SLOW spr round 4 (radius: 5)
[00:12:08 -5078.737189] SLOW spr round 5 (radius: 10)
[00:12:14 -5077.392172] SLOW spr round 6 (radius: 5)
[00:12:21 -5077.392166] SLOW spr round 7 (radius: 10)
[00:12:27 -5077.392165] SLOW spr round 8 (radius: 15)
[00:12:35 -5077.254887] SLOW spr round 9 (radius: 5)
[00:12:43 -5077.254291] SLOW spr round 10 (radius: 10)
[00:12:49 -5076.372617] SLOW spr round 11 (radius: 5)
[00:12:57 -5076.372348] SLOW spr round 12 (radius: 10)
[00:13:03 -5076.372325] SLOW spr round 13 (radius: 15)
[00:13:11 -5076.257941] SLOW spr round 14 (radius: 5)
[00:13:18] [worker #1] ML tree search #10, logLikelihood: -5065.780859
[00:13:19 -5076.257917] SLOW spr round 15 (radius: 10)
[00:13:25 -5076.257911] SLOW spr round 16 (radius: 15)
[00:13:33 -5076.257907] SLOW spr round 17 (radius: 20)
[00:13:42 -5075.639119] SLOW spr round 18 (radius: 5)
[00:13:50 -5075.629637] SLOW spr round 19 (radius: 10)
[00:13:57 -5073.204052] SLOW spr round 20 (radius: 5)
[00:14:05 -5073.203847] SLOW spr round 21 (radius: 10)
[00:14:11 -5073.203847] SLOW spr round 22 (radius: 15)
[00:14:20 -5073.203843] SLOW spr round 23 (radius: 20)
[00:14:30 -5073.203843] SLOW spr round 24 (radius: 25)
[00:14:38 -5071.682019] SLOW spr round 25 (radius: 5)
[00:14:47 -5071.682014] SLOW spr round 26 (radius: 10)
[00:14:54 -5071.682013] SLOW spr round 27 (radius: 15)
[00:15:03 -5071.682013] SLOW spr round 28 (radius: 20)
[00:15:14 -5071.682013] SLOW spr round 29 (radius: 25)
[00:15:22 -5071.682013] Model parameter optimization (eps = 0.100000)

[00:15:24] [worker #0] ML tree search #9, logLikelihood: -5071.267388

[00:15:24 -14789.282111] Initial branch length optimization
[00:15:24 -11456.413269] Model parameter optimization (eps = 10.000000)
[00:15:28 -11283.296537] AUTODETECT spr round 1 (radius: 5)
[00:15:31 -8590.561431] AUTODETECT spr round 2 (radius: 10)
[00:15:36 -6400.692537] AUTODETECT spr round 3 (radius: 15)
[00:15:41 -5951.215384] AUTODETECT spr round 4 (radius: 20)
[00:15:47 -5604.763115] AUTODETECT spr round 5 (radius: 25)
[00:15:53 -5563.967009] SPR radius for FAST iterations: 25 (autodetect)
[00:15:53 -5563.967009] Model parameter optimization (eps = 3.000000)
[00:15:56 -5557.477269] FAST spr round 1 (radius: 25)
[00:16:01 -5117.030585] FAST spr round 2 (radius: 25)
[00:16:02] [worker #1] ML tree search #12, logLikelihood: -5064.893326
[00:16:05 -5076.268822] FAST spr round 3 (radius: 25)
[00:16:09 -5071.590909] FAST spr round 4 (radius: 25)
[00:16:12 -5070.773821] FAST spr round 5 (radius: 25)
[00:16:15 -5070.773799] Model parameter optimization (eps = 1.000000)
[00:16:18 -5067.628662] SLOW spr round 1 (radius: 5)
[00:16:23 -5065.134910] SLOW spr round 2 (radius: 5)
[00:16:28 -5065.134695] SLOW spr round 3 (radius: 10)
[00:16:33 -5064.835638] SLOW spr round 4 (radius: 5)
[00:16:41 -5064.834349] SLOW spr round 5 (radius: 10)
[00:16:47 -5062.543997] SLOW spr round 6 (radius: 5)
[00:16:54 -5062.528875] SLOW spr round 7 (radius: 10)
[00:17:01 -5062.528363] SLOW spr round 8 (radius: 15)
[00:17:08 -5062.424026] SLOW spr round 9 (radius: 5)
[00:17:16 -5062.423996] SLOW spr round 10 (radius: 10)
[00:17:23 -5062.423996] SLOW spr round 11 (radius: 15)
[00:17:30 -5062.423996] SLOW spr round 12 (radius: 20)
[00:17:39 -5062.423996] SLOW spr round 13 (radius: 25)
[00:17:48 -5062.366708] Model parameter optimization (eps = 0.100000)

[00:17:50] [worker #0] ML tree search #11, logLikelihood: -5061.451014

[00:17:50 -14935.645842] Initial branch length optimization
[00:17:50 -11604.698678] Model parameter optimization (eps = 10.000000)
[00:17:54 -11402.868479] AUTODETECT spr round 1 (radius: 5)
[00:17:57 -8808.851323] AUTODETECT spr round 2 (radius: 10)
[00:18:02 -6985.911139] AUTODETECT spr round 3 (radius: 15)
[00:18:07 -5876.517609] AUTODETECT spr round 4 (radius: 20)
[00:18:13 -5853.431546] AUTODETECT spr round 5 (radius: 25)
[00:18:19 -5853.381311] SPR radius for FAST iterations: 20 (autodetect)
[00:18:19 -5853.381311] Model parameter optimization (eps = 3.000000)
[00:18:21] [worker #1] ML tree search #14, logLikelihood: -5081.240572
[00:18:22 -5840.017689] FAST spr round 1 (radius: 20)
[00:18:27 -5135.099673] FAST spr round 2 (radius: 20)
[00:18:32 -5079.322461] FAST spr round 3 (radius: 20)
[00:18:36 -5073.617068] FAST spr round 4 (radius: 20)
[00:18:39 -5072.941399] FAST spr round 5 (radius: 20)
[00:18:42 -5072.940078] Model parameter optimization (eps = 1.000000)
[00:18:44 -5071.604663] SLOW spr round 1 (radius: 5)
[00:18:49 -5068.641465] SLOW spr round 2 (radius: 5)
[00:18:54 -5068.639660] SLOW spr round 3 (radius: 10)
[00:19:00 -5068.639393] SLOW spr round 4 (radius: 15)
[00:19:09 -5066.327092] SLOW spr round 5 (radius: 5)
[00:19:17 -5063.122919] SLOW spr round 6 (radius: 5)
[00:19:23 -5063.122908] SLOW spr round 7 (radius: 10)
[00:19:29 -5063.122902] SLOW spr round 8 (radius: 15)
[00:19:37 -5063.122897] SLOW spr round 9 (radius: 20)
[00:19:47 -5063.122892] SLOW spr round 10 (radius: 25)
[00:19:55 -5062.656821] SLOW spr round 11 (radius: 5)
[00:20:03 -5062.602511] SLOW spr round 12 (radius: 10)
[00:20:10 -5062.602328] SLOW spr round 13 (radius: 15)
[00:20:18 -5062.602321] SLOW spr round 14 (radius: 20)
[00:20:27 -5062.602316] SLOW spr round 15 (radius: 25)
[00:20:36 -5062.602311] Model parameter optimization (eps = 0.100000)

[00:20:38] [worker #0] ML tree search #13, logLikelihood: -5062.094148

[00:20:38 -14867.587200] Initial branch length optimization
[00:20:38 -11429.120153] Model parameter optimization (eps = 10.000000)
[00:20:41 -11251.382147] AUTODETECT spr round 1 (radius: 5)
[00:20:45 -8572.306327] AUTODETECT spr round 2 (radius: 10)
[00:20:49 -6848.278752] AUTODETECT spr round 3 (radius: 15)
[00:20:53] [worker #1] ML tree search #16, logLikelihood: -5061.831186
[00:20:56 -5753.918713] AUTODETECT spr round 4 (radius: 20)
[00:21:03 -5588.802407] AUTODETECT spr round 5 (radius: 25)
[00:21:08 -5584.331531] SPR radius for FAST iterations: 25 (autodetect)
[00:21:08 -5584.331531] Model parameter optimization (eps = 3.000000)
[00:21:12 -5574.257032] FAST spr round 1 (radius: 25)
[00:21:17 -5130.971592] FAST spr round 2 (radius: 25)
[00:21:21 -5088.781378] FAST spr round 3 (radius: 25)
[00:21:25 -5084.844316] FAST spr round 4 (radius: 25)
[00:21:28 -5083.576541] FAST spr round 5 (radius: 25)
[00:21:31 -5083.574159] Model parameter optimization (eps = 1.000000)
[00:21:34 -5081.588463] SLOW spr round 1 (radius: 5)
[00:21:39 -5077.140329] SLOW spr round 2 (radius: 5)
[00:21:44 -5077.132912] SLOW spr round 3 (radius: 10)
[00:21:50 -5076.670140] SLOW spr round 4 (radius: 5)
[00:21:57 -5076.642631] SLOW spr round 5 (radius: 10)
[00:22:04 -5072.208961] SLOW spr round 6 (radius: 5)
[00:22:12 -5069.436368] SLOW spr round 7 (radius: 5)
[00:22:18 -5068.770216] SLOW spr round 8 (radius: 5)
[00:22:24 -5066.430174] SLOW spr round 9 (radius: 5)
[00:22:29 -5066.429498] SLOW spr round 10 (radius: 10)
[00:22:35 -5066.429011] SLOW spr round 11 (radius: 15)
[00:22:44 -5066.352667] SLOW spr round 12 (radius: 20)
[00:22:47] [worker #1] ML tree search #18, logLikelihood: -5062.942813
[00:22:54 -5066.322458] SLOW spr round 13 (radius: 25)
[00:23:02 -5066.315707] Model parameter optimization (eps = 0.100000)

[00:23:04] [worker #0] ML tree search #15, logLikelihood: -5066.057962

[00:23:04 -14602.982357] Initial branch length optimization
[00:23:04 -11459.403283] Model parameter optimization (eps = 10.000000)
[00:23:07 -11282.178342] AUTODETECT spr round 1 (radius: 5)
[00:23:10 -8308.392425] AUTODETECT spr round 2 (radius: 10)
[00:23:15 -6782.847172] AUTODETECT spr round 3 (radius: 15)
[00:23:20 -5950.795719] AUTODETECT spr round 4 (radius: 20)
[00:23:26 -5756.208970] AUTODETECT spr round 5 (radius: 25)
[00:23:31 -5746.183597] SPR radius for FAST iterations: 25 (autodetect)
[00:23:31 -5746.183597] Model parameter optimization (eps = 3.000000)
[00:23:34 -5737.008658] FAST spr round 1 (radius: 25)
[00:23:39 -5122.051903] FAST spr round 2 (radius: 25)
[00:23:43 -5079.967929] FAST spr round 3 (radius: 25)
[00:23:47 -5076.155274] FAST spr round 4 (radius: 25)
[00:23:51 -5074.939587] FAST spr round 5 (radius: 25)
[00:23:54 -5074.939522] Model parameter optimization (eps = 1.000000)
[00:23:57 -5072.532701] SLOW spr round 1 (radius: 5)
[00:24:02 -5070.322367] SLOW spr round 2 (radius: 5)
[00:24:07 -5070.314129] SLOW spr round 3 (radius: 10)
[00:24:12 -5069.552291] SLOW spr round 4 (radius: 5)
[00:24:20 -5069.551225] SLOW spr round 5 (radius: 10)
[00:24:26 -5069.550155] SLOW spr round 6 (radius: 15)
[00:24:35 -5067.055562] SLOW spr round 7 (radius: 5)
[00:24:42 -5067.054346] SLOW spr round 8 (radius: 10)
[00:24:49 -5067.053179] SLOW spr round 9 (radius: 15)
[00:24:57 -5067.052009] SLOW spr round 10 (radius: 20)
[00:25:07 -5067.051669] SLOW spr round 11 (radius: 25)
[00:25:16 -5067.051667] Model parameter optimization (eps = 0.100000)

[00:25:17] [worker #0] ML tree search #17, logLikelihood: -5066.965256

[00:25:17 -14716.717618] Initial branch length optimization
[00:25:17 -11163.023248] Model parameter optimization (eps = 10.000000)
[00:25:20 -10973.930777] AUTODETECT spr round 1 (radius: 5)
[00:25:23 -8869.604927] AUTODETECT spr round 2 (radius: 10)
[00:25:28 -6776.563546] AUTODETECT spr round 3 (radius: 15)
[00:25:34 -5729.142441] AUTODETECT spr round 4 (radius: 20)
[00:25:41 -5712.960937] AUTODETECT spr round 5 (radius: 25)
[00:25:47 -5589.573257] SPR radius for FAST iterations: 25 (autodetect)
[00:25:47 -5589.573257] Model parameter optimization (eps = 3.000000)
[00:25:49] [worker #1] ML tree search #20, logLikelihood: -5061.282682
[00:25:50 -5582.115857] FAST spr round 1 (radius: 25)
[00:25:54 -5110.281742] FAST spr round 2 (radius: 25)
[00:25:59 -5088.646788] FAST spr round 3 (radius: 25)
[00:26:02 -5084.266130] FAST spr round 4 (radius: 25)
[00:26:05 -5084.266063] Model parameter optimization (eps = 1.000000)
[00:26:08 -5080.009522] SLOW spr round 1 (radius: 5)
[00:26:13 -5079.089750] SLOW spr round 2 (radius: 5)
[00:26:18 -5079.087853] SLOW spr round 3 (radius: 10)
[00:26:24 -5078.114839] SLOW spr round 4 (radius: 5)
[00:26:32 -5070.429166] SLOW spr round 5 (radius: 5)
[00:26:38 -5067.038926] SLOW spr round 6 (radius: 5)
[00:26:44 -5067.022332] SLOW spr round 7 (radius: 10)
[00:26:49 -5066.916674] SLOW spr round 8 (radius: 5)
[00:26:56 -5066.915416] SLOW spr round 9 (radius: 10)
[00:27:02 -5066.914453] SLOW spr round 10 (radius: 15)
[00:27:10 -5066.914429] SLOW spr round 11 (radius: 20)
[00:27:18 -5066.914414] SLOW spr round 12 (radius: 25)
[00:27:27 -5065.372897] SLOW spr round 13 (radius: 5)
[00:27:35 -5065.372874] SLOW spr round 14 (radius: 10)
[00:27:42 -5065.372865] SLOW spr round 15 (radius: 15)
[00:27:49 -5065.372858] SLOW spr round 16 (radius: 20)
[00:27:58 -5065.372852] SLOW spr round 17 (radius: 25)
[00:28:06 -5065.372846] Model parameter optimization (eps = 0.100000)

[00:28:09] [worker #0] ML tree search #19, logLikelihood: -5064.623842


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.342902,0.693385) (0.243202,0.897861) (0.348575,0.821203) (0.065321,3.943963) 
   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: -5061.282682

AIC score: 10884.565364 / AICc score: 301968.565364 / BIC score: 11777.555230
Free parameters (model + branch lengths): 381

WARNING: Number of free parameters (K=381) is larger than alignment size (n=77).
         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/Q99996/3_mltree/Q99996.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q99996/3_mltree/Q99996.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q99996/3_mltree/Q99996.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q99996/3_mltree/Q99996.raxml.log

Analysis started: 03-Jul-2021 18:42:04 / finished: 03-Jul-2021 19:10:13

Elapsed time: 1689.292 seconds

Consumed energy: 126.357 Wh