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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 30-Jun-2021 17:58:59 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/2_msa/P53804_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/3_mltree/P53804 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/2_msa/P53804_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 414 sites

WARNING: Sequences tr_M3Y1N6_M3Y1N6_MUSPF_9669 and tr_D2HL56_D2HL56_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3Y1N6_M3Y1N6_MUSPF_9669 and tr_A0A2U3VZE3_A0A2U3VZE3_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y1N6_M3Y1N6_MUSPF_9669 and tr_A0A2Y9LDR3_A0A2Y9LDR3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Y5H0_M3Y5H0_MUSPF_9669 and tr_A0A2U3VKI9_A0A2U3VKI9_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y5H0_M3Y5H0_MUSPF_9669 and tr_A0A2Y9L7K9_A0A2Y9L7K9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YGR5_M3YGR5_MUSPF_9669 and tr_A0A2Y9JV48_A0A2Y9JV48_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_B6Q8X2_B6Q8X2_TALMQ_441960 and tr_A0A093XQK2_A0A093XQK2_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and tr_H2QD10_H2QD10_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and sp_Q99615_DNJC7_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and tr_F7FQQ0_F7FQQ0_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and tr_F6SA44_F6SA44_CALJA_9483 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and tr_G7PUT8_G7PUT8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and tr_A0A2I3NGL6_A0A2I3NGL6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and tr_A0A2K6C0K4_A0A2K6C0K4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2NU16_H2NU16_PONAB_9601 and tr_A0A2K5XFV7_A0A2K5XFV7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2NZB3_H2NZB3_PONAB_9601 and tr_F6XI05_F6XI05_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NZB3_H2NZB3_PONAB_9601 and tr_G7PXY4_G7PXY4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2NZB3_H2NZB3_PONAB_9601 and tr_A0A0D9S291_A0A0D9S291_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_C0NB99_C0NB99_AJECG_447093 and tr_F0UKC0_F0UKC0_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_C0NB99_C0NB99_AJECG_447093 and tr_A6R4B3_A6R4B3_AJECN_339724 are exactly identical!
WARNING: Sequences tr_A0A2I3RQR2_A0A2I3RQR2_PANTR_9598 and tr_A0A2R9BPI8_A0A2R9BPI8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158NIE7_A0A158NIE7_ATTCE_12957 and tr_A0A151HZC0_A0A151HZC0_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158P267_A0A158P267_ATTCE_12957 and tr_A0A195AW63_A0A195AW63_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A286XD25_A0A286XD25_CAVPO_10141 and tr_G5AUZ1_G5AUZ1_HETGA_10181 are exactly identical!
WARNING: Sequences tr_A0A0E0GI94_A0A0E0GI94_ORYNI_4536 and tr_A2ZN45_A2ZN45_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0H3M2_A0A0E0H3M2_ORYNI_4536 and tr_A0A0E0PC32_A0A0E0PC32_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_G7XW48_G7XW48_ASPKW_1033177 and tr_A0A100ISQ6_A0A100ISQ6_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XW48_G7XW48_ASPKW_1033177 and tr_A0A146EZE8_A0A146EZE8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XW48_G7XW48_ASPKW_1033177 and tr_A0A1L9NHC8_A0A1L9NHC8_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_I1R7M7_I1R7M7_ORYGL_4538 and tr_Q2QML3_Q2QML3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1R871_I1R871_ORYGL_4538 and tr_A0A0E0RKG7_A0A0E0RKG7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1R871_I1R871_ORYGL_4538 and tr_A0A0D3HX53_A0A0D3HX53_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1R871_I1R871_ORYGL_4538 and tr_Q2QLM7_Q2QLM7_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2Y1R0_G2Y1R0_BOTF4_999810 and tr_M7UTM8_M7UTM8_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_U3HZC6_U3HZC6_ANAPL_8839 and tr_A0A226NP57_A0A226NP57_COLVI_9014 are exactly identical!
WARNING: Sequences tr_W2Q9H4_W2Q9H4_PHYPN_761204 and tr_A0A0W8D0C7_A0A0W8D0C7_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A015JP87_A0A015JP87_9GLOM_1432141 and tr_A0A2H5TVJ2_A0A2H5TVJ2_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0D3FMF1_A0A0D3FMF1_9ORYZ_65489 and tr_A0A0D9ZBL7_A0A0D9ZBL7_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A2I3MUS9_A0A2I3MUS9_PAPAN_9555 and tr_A0A2K6AII1_A0A2K6AII1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091E5Y9_A0A091E5Y9_CORBR_85066 and tr_A0A093SE08_A0A093SE08_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A087R350_A0A087R350_APTFO_9233 and tr_A0A0A0ABZ4_A0A0A0ABZ4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091W7Q3_A0A091W7Q3_OPIHO_30419 and tr_A0A0A0A0N7_A0A0A0A0N7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091W7Q3_A0A091W7Q3_OPIHO_30419 and tr_A0A091HNQ6_A0A091HNQ6_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A0G4PKX9_A0A0G4PKX9_PENCA_1429867 and tr_A0A1V6NCZ7_A0A1V6NCZ7_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A0V1CP32_A0A0V1CP32_TRIBR_45882 and tr_A0A0V0VIR7_A0A0V0VIR7_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CP32_A0A0V1CP32_TRIBR_45882 and tr_A0A0V0TL13_A0A0V0TL13_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S4BU78_A0A1S4BU78_TOBAC_4097 and tr_A0A1U7WHW4_A0A1U7WHW4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4D2M9_A0A1S4D2M9_TOBAC_4097 and tr_G5ELZ4_G5ELZ4_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A226N8V5_A0A226N8V5_CALSU_9009 and tr_A0A226NTN9_A0A226NTN9_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2G2XX96_A0A2G2XX96_CAPAN_4072 and tr_A0A2G3CSW8_A0A2G3CSW8_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A383ZRL3_A0A383ZRL3_BALAS_310752 and tr_A0A383ZRX4_A0A383ZRX4_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 51

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/P53804/3_mltree/P53804.raxml.reduced.phy

Alignment comprises 1 partitions and 414 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 414 / 414
Gaps: 24.22 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/3_mltree/P53804.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 207 / 16560
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -747832.307321] Initial branch length optimization
[00:00:09 -632879.659131] Model parameter optimization (eps = 10.000000)
[00:01:09 -629394.402209] AUTODETECT spr round 1 (radius: 5)
[00:05:02 -428451.997069] AUTODETECT spr round 2 (radius: 10)
[00:09:02 -321928.619650] AUTODETECT spr round 3 (radius: 15)
[00:13:26 -262612.355955] AUTODETECT spr round 4 (radius: 20)
[00:18:24 -232711.937945] AUTODETECT spr round 5 (radius: 25)
[00:24:04 -225505.107236] SPR radius for FAST iterations: 25 (autodetect)
[00:24:04 -225505.107236] Model parameter optimization (eps = 3.000000)
[00:24:39 -225271.922036] FAST spr round 1 (radius: 25)
[00:29:56 -197641.544705] FAST spr round 2 (radius: 25)
[00:33:58 -196602.057492] FAST spr round 3 (radius: 25)
[00:37:16 -196532.275997] FAST spr round 4 (radius: 25)
[00:40:08 -196520.815178] FAST spr round 5 (radius: 25)
[00:42:47 -196519.846426] FAST spr round 6 (radius: 25)
[00:45:20 -196518.612070] FAST spr round 7 (radius: 25)
[00:47:47 -196518.611373] Model parameter optimization (eps = 1.000000)
[00:48:06 -196513.366838] SLOW spr round 1 (radius: 5)
[00:51:39 -196465.786103] SLOW spr round 2 (radius: 5)
[00:55:00 -196461.900545] SLOW spr round 3 (radius: 5)
[00:58:11 -196461.899641] SLOW spr round 4 (radius: 10)
[01:01:38 -196453.413662] SLOW spr round 5 (radius: 5)
[01:05:40 -196452.223899] SLOW spr round 6 (radius: 5)
[01:09:12 -196452.054650] SLOW spr round 7 (radius: 5)
[01:12:30 -196452.053052] SLOW spr round 8 (radius: 10)
[01:15:52 -196452.052827] SLOW spr round 9 (radius: 15)
[01:22:08 -196450.118314] SLOW spr round 10 (radius: 5)
[01:26:17 -196449.996541] SLOW spr round 11 (radius: 5)
[01:29:53 -196448.947603] SLOW spr round 12 (radius: 5)
[01:32:12] [worker #1] ML tree search #2, logLikelihood: -196439.540892
[01:33:15 -196448.946259] SLOW spr round 13 (radius: 10)
[01:36:40 -196448.946007] SLOW spr round 14 (radius: 15)
[01:42:56 -196448.945902] SLOW spr round 15 (radius: 20)
[01:52:22 -196448.945837] SLOW spr round 16 (radius: 25)
[02:04:24 -196448.945790] Model parameter optimization (eps = 0.100000)

[02:04:34] [worker #0] ML tree search #1, logLikelihood: -196448.912899

[02:04:35 -752527.835890] Initial branch length optimization
[02:04:41 -638776.252278] Model parameter optimization (eps = 10.000000)
[02:05:55 -635178.238533] AUTODETECT spr round 1 (radius: 5)
[02:09:36 -442517.079625] AUTODETECT spr round 2 (radius: 10)
[02:13:26 -328419.979261] AUTODETECT spr round 3 (radius: 15)
[02:16:39] [worker #2] ML tree search #3, logLikelihood: -196430.675073
[02:17:37 -274718.249982] AUTODETECT spr round 4 (radius: 20)
[02:22:39 -239668.786643] AUTODETECT spr round 5 (radius: 25)
[02:28:04 -230814.914754] SPR radius for FAST iterations: 25 (autodetect)
[02:28:04 -230814.914754] Model parameter optimization (eps = 3.000000)
[02:28:50 -230567.278841] FAST spr round 1 (radius: 25)
[02:34:04 -197984.841955] FAST spr round 2 (radius: 25)
[02:37:45 -196629.259450] FAST spr round 3 (radius: 25)
[02:40:52 -196560.074342] FAST spr round 4 (radius: 25)
[02:43:44 -196545.623917] FAST spr round 5 (radius: 25)
[02:46:21 -196539.796456] FAST spr round 6 (radius: 25)
[02:48:55 -196537.590137] FAST spr round 7 (radius: 25)
[02:51:26 -196531.292392] FAST spr round 8 (radius: 25)
[02:53:58 -196520.088647] FAST spr round 9 (radius: 25)
[02:56:32 -196510.688936] FAST spr round 10 (radius: 25)
[02:58:59 -196510.687865] Model parameter optimization (eps = 1.000000)
[02:59:18 -196506.081849] SLOW spr round 1 (radius: 5)
[03:02:51 -196451.385674] SLOW spr round 2 (radius: 5)
[03:06:11 -196444.209803] SLOW spr round 3 (radius: 5)
[03:09:24 -196444.145136] SLOW spr round 4 (radius: 10)
[03:12:49 -196441.446187] SLOW spr round 5 (radius: 5)
[03:16:13] [worker #1] ML tree search #5, logLikelihood: -196453.971784
[03:16:51 -196439.537964] SLOW spr round 6 (radius: 5)
[03:20:25 -196439.288349] SLOW spr round 7 (radius: 5)
[03:23:47 -196439.288225] SLOW spr round 8 (radius: 10)
[03:27:14 -196439.288169] SLOW spr round 9 (radius: 15)
[03:33:45 -196438.976934] SLOW spr round 10 (radius: 5)
[03:38:00 -196436.966039] SLOW spr round 11 (radius: 5)
[03:41:44 -196436.443844] SLOW spr round 12 (radius: 5)
[03:45:09 -196436.442716] SLOW spr round 13 (radius: 10)
[03:48:34 -196436.442528] SLOW spr round 14 (radius: 15)
[03:55:00 -196436.442452] SLOW spr round 15 (radius: 20)
[04:05:04 -196436.442405] SLOW spr round 16 (radius: 25)
[04:17:49 -196436.442367] Model parameter optimization (eps = 0.100000)

[04:18:01] [worker #0] ML tree search #4, logLikelihood: -196436.338394

[04:18:02 -750109.824848] Initial branch length optimization
[04:18:09 -635783.275276] Model parameter optimization (eps = 10.000000)
[04:19:20 -632187.946272] AUTODETECT spr round 1 (radius: 5)
[04:23:02 -443136.545307] AUTODETECT spr round 2 (radius: 10)
[04:26:51 -309970.811983] AUTODETECT spr round 3 (radius: 15)
[04:30:53] [worker #2] ML tree search #6, logLikelihood: -196422.617111
[04:31:07 -252652.097826] AUTODETECT spr round 4 (radius: 20)
[04:35:56 -226226.039216] AUTODETECT spr round 5 (radius: 25)
[04:41:34 -221649.602153] SPR radius for FAST iterations: 25 (autodetect)
[04:41:34 -221649.602153] Model parameter optimization (eps = 3.000000)
[04:42:11 -221424.254051] FAST spr round 1 (radius: 25)
[04:47:07 -197502.260894] FAST spr round 2 (radius: 25)
[04:50:52 -196571.037344] FAST spr round 3 (radius: 25)
[04:54:06 -196514.587261] FAST spr round 4 (radius: 25)
[04:56:48 -196507.769938] FAST spr round 5 (radius: 25)
[04:57:27] [worker #1] ML tree search #8, logLikelihood: -196421.475366
[04:59:21 -196506.353411] FAST spr round 6 (radius: 25)
[05:01:50 -196504.628033] FAST spr round 7 (radius: 25)
[05:04:17 -196504.627951] Model parameter optimization (eps = 1.000000)
[05:04:38 -196497.676451] SLOW spr round 1 (radius: 5)
[05:08:06 -196458.256153] SLOW spr round 2 (radius: 5)
[05:11:28 -196455.597687] SLOW spr round 3 (radius: 5)
[05:14:41 -196453.898697] SLOW spr round 4 (radius: 5)
[05:17:51 -196453.897795] SLOW spr round 5 (radius: 10)
[05:21:17 -196444.840036] SLOW spr round 6 (radius: 5)
[05:25:13 -196444.646651] SLOW spr round 7 (radius: 5)
[05:28:42 -196444.645351] SLOW spr round 8 (radius: 10)
[05:32:14 -196444.645231] SLOW spr round 9 (radius: 15)
[05:38:28 -196444.645191] SLOW spr round 10 (radius: 20)
[05:48:21 -196444.645152] SLOW spr round 11 (radius: 25)
[06:00:29 -196444.645115] Model parameter optimization (eps = 0.100000)

[06:00:49] [worker #0] ML tree search #7, logLikelihood: -196444.515833

[06:00:49 -748862.543571] Initial branch length optimization
[06:00:58 -633311.500693] Model parameter optimization (eps = 10.000000)
[06:01:53 -629614.542445] AUTODETECT spr round 1 (radius: 5)
[06:05:27 -444922.678408] AUTODETECT spr round 2 (radius: 10)
[06:09:10 -326941.568602] AUTODETECT spr round 3 (radius: 15)
[06:13:07 -269104.307879] AUTODETECT spr round 4 (radius: 20)
[06:17:57 -236899.457780] AUTODETECT spr round 5 (radius: 25)
[06:22:31] [worker #2] ML tree search #9, logLikelihood: -196430.290819
[06:23:41 -230651.366895] SPR radius for FAST iterations: 25 (autodetect)
[06:23:41 -230651.366895] Model parameter optimization (eps = 3.000000)
[06:24:21 -230441.333517] FAST spr round 1 (radius: 25)
[06:29:26 -198317.135168] FAST spr round 2 (radius: 25)
[06:33:10 -196638.933288] FAST spr round 3 (radius: 25)
[06:36:12 -196542.347678] FAST spr round 4 (radius: 25)
[06:38:55 -196526.562311] FAST spr round 5 (radius: 25)
[06:41:24 -196526.542977] Model parameter optimization (eps = 1.000000)
[06:41:45 -196520.842844] SLOW spr round 1 (radius: 5)
[06:45:05 -196461.340462] SLOW spr round 2 (radius: 5)
[06:48:15 -196459.307719] SLOW spr round 3 (radius: 5)
[06:51:19 -196459.307519] SLOW spr round 4 (radius: 10)
[06:54:37 -196454.024798] SLOW spr round 5 (radius: 5)
[06:58:30 -196450.374100] SLOW spr round 6 (radius: 5)
[07:00:16] [worker #1] ML tree search #11, logLikelihood: -196439.544707
[07:01:57 -196447.959681] SLOW spr round 7 (radius: 5)
[07:05:16 -196447.056466] SLOW spr round 8 (radius: 5)
[07:08:25 -196446.356334] SLOW spr round 9 (radius: 5)
[07:11:38 -196444.493982] SLOW spr round 10 (radius: 5)
[07:14:43 -196443.360074] SLOW spr round 11 (radius: 5)
[07:17:46 -196443.359259] SLOW spr round 12 (radius: 10)
[07:21:02 -196440.198715] SLOW spr round 13 (radius: 5)
[07:25:02 -196433.699615] SLOW spr round 14 (radius: 5)
[07:28:31 -196430.608495] SLOW spr round 15 (radius: 5)
[07:31:44 -196430.607524] SLOW spr round 16 (radius: 10)
[07:35:03 -196430.607265] SLOW spr round 17 (radius: 15)
[07:41:30 -196430.607180] SLOW spr round 18 (radius: 20)
[07:51:42 -196430.607137] SLOW spr round 19 (radius: 25)
[08:04:27 -196430.607104] Model parameter optimization (eps = 0.100000)

[08:04:47] [worker #0] ML tree search #10, logLikelihood: -196429.476482

[08:04:47 -744545.366390] Initial branch length optimization
[08:04:53 -631148.118652] Model parameter optimization (eps = 10.000000)
[08:05:51 -627727.842612] AUTODETECT spr round 1 (radius: 5)
[08:07:04] [worker #2] ML tree search #12, logLikelihood: -196435.929350
[08:09:22 -435911.119350] AUTODETECT spr round 2 (radius: 10)
[08:12:58 -324780.131512] AUTODETECT spr round 3 (radius: 15)
[08:17:13 -260283.520886] AUTODETECT spr round 4 (radius: 20)
[08:21:42 -229712.560088] AUTODETECT spr round 5 (radius: 25)
[08:26:33 -225259.112897] SPR radius for FAST iterations: 25 (autodetect)
[08:26:33 -225259.112897] Model parameter optimization (eps = 3.000000)
[08:27:09 -225002.227513] FAST spr round 1 (radius: 25)
[08:32:04 -197684.967122] FAST spr round 2 (radius: 25)
[08:35:44 -196633.588288] FAST spr round 3 (radius: 25)
[08:38:50 -196539.048663] FAST spr round 4 (radius: 25)
[08:41:26 -196529.435154] FAST spr round 5 (radius: 25)
[08:43:53 -196527.938961] FAST spr round 6 (radius: 25)
[08:46:16 -196527.937838] Model parameter optimization (eps = 1.000000)
[08:46:34 -196524.264975] SLOW spr round 1 (radius: 5)
[08:49:52 -196475.543287] SLOW spr round 2 (radius: 5)
[08:53:08 -196460.992729] SLOW spr round 3 (radius: 5)
[08:56:19 -196454.465429] SLOW spr round 4 (radius: 5)
[08:59:22 -196454.464877] SLOW spr round 5 (radius: 10)
[09:02:38 -196453.123738] SLOW spr round 6 (radius: 5)
[09:06:25 -196453.103059] SLOW spr round 7 (radius: 10)
[09:10:06 -196452.261423] SLOW spr round 8 (radius: 5)
[09:13:53 -196451.478874] SLOW spr round 9 (radius: 5)
[09:15:14] [worker #1] ML tree search #14, logLikelihood: -196439.230850
[09:17:13 -196451.478324] SLOW spr round 10 (radius: 10)
[09:20:38 -196447.304840] SLOW spr round 11 (radius: 5)
[09:24:27 -196442.695817] SLOW spr round 12 (radius: 5)
[09:27:51 -196442.695503] SLOW spr round 13 (radius: 10)
[09:31:15 -196442.695262] SLOW spr round 14 (radius: 15)
[09:37:13 -196440.815746] SLOW spr round 15 (radius: 5)
[09:41:26 -196434.199934] SLOW spr round 16 (radius: 5)
[09:44:59 -196431.013333] SLOW spr round 17 (radius: 5)
[09:48:13 -196431.012885] SLOW spr round 18 (radius: 10)
[09:51:32 -196431.012804] SLOW spr round 19 (radius: 15)
[09:57:33 -196431.012753] SLOW spr round 20 (radius: 20)
[10:06:56 -196431.012709] SLOW spr round 21 (radius: 25)
[10:13:10] [worker #2] ML tree search #15, logLikelihood: -196417.444106
[10:18:57 -196431.012665] Model parameter optimization (eps = 0.100000)

[10:19:06] [worker #0] ML tree search #13, logLikelihood: -196430.923391

[10:19:06 -748094.003425] Initial branch length optimization
[10:19:13 -635007.542233] Model parameter optimization (eps = 10.000000)
[10:20:08 -631368.302538] AUTODETECT spr round 1 (radius: 5)
[10:23:39 -423118.203977] AUTODETECT spr round 2 (radius: 10)
[10:29:27 -319048.574499] AUTODETECT spr round 3 (radius: 15)
[10:38:08 -258276.660101] AUTODETECT spr round 4 (radius: 20)
[10:47:22 -230097.243714] AUTODETECT spr round 5 (radius: 25)
[10:59:39 -225567.141557] SPR radius for FAST iterations: 25 (autodetect)
[10:59:39 -225567.141557] Model parameter optimization (eps = 3.000000)
[11:00:50 -225262.158845] FAST spr round 1 (radius: 25)
[11:11:05 -197653.217142] FAST spr round 2 (radius: 25)
[11:18:33 -196668.488212] FAST spr round 3 (radius: 25)
[11:24:36 -196573.452609] FAST spr round 4 (radius: 25)
[11:29:55 -196566.292856] FAST spr round 5 (radius: 25)
[11:34:50 -196566.292239] Model parameter optimization (eps = 1.000000)
[11:35:19 -196561.113865] SLOW spr round 1 (radius: 5)
[11:40:45] [worker #1] ML tree search #17, logLikelihood: -196444.755057
[11:42:20 -196477.538570] SLOW spr round 2 (radius: 5)
[11:49:30 -196468.696565] SLOW spr round 3 (radius: 5)
[11:55:37 -196468.695248] SLOW spr round 4 (radius: 10)
[11:58:53 -196453.701218] SLOW spr round 5 (radius: 5)
[12:02:47 -196443.503494] SLOW spr round 6 (radius: 5)
[12:06:16 -196441.959476] SLOW spr round 7 (radius: 5)
[12:09:26 -196441.958907] SLOW spr round 8 (radius: 10)
[12:11:17] [worker #2] ML tree search #18, logLikelihood: -196436.767633
[12:12:43 -196439.560993] SLOW spr round 9 (radius: 5)
[12:16:30 -196439.521930] SLOW spr round 10 (radius: 10)
[12:20:06 -196439.521365] SLOW spr round 11 (radius: 15)
[12:25:42 -196439.521344] SLOW spr round 12 (radius: 20)
[12:34:54 -196439.521342] SLOW spr round 13 (radius: 25)
[12:47:58 -196439.521342] Model parameter optimization (eps = 0.100000)

[12:48:20] [worker #0] ML tree search #16, logLikelihood: -196438.814928

[12:48:20 -750700.100652] Initial branch length optimization
[12:48:31 -635062.373694] Model parameter optimization (eps = 10.000000)
[12:49:56 -631504.979678] AUTODETECT spr round 1 (radius: 5)
[12:55:05 -445088.799327] AUTODETECT spr round 2 (radius: 10)
[13:00:39 -323215.492088] AUTODETECT spr round 3 (radius: 15)
[13:06:32 -263463.278259] AUTODETECT spr round 4 (radius: 20)
[13:11:17 -232007.469121] AUTODETECT spr round 5 (radius: 25)
[13:17:29 -227977.548674] SPR radius for FAST iterations: 25 (autodetect)
[13:17:29 -227977.548674] Model parameter optimization (eps = 3.000000)
[13:18:02 -227581.915396] FAST spr round 1 (radius: 25)
[13:23:01 -197995.839314] FAST spr round 2 (radius: 25)
[13:26:41 -196637.399592] FAST spr round 3 (radius: 25)
[13:29:47 -196573.864930] FAST spr round 4 (radius: 25)
[13:33:24 -196553.831717] FAST spr round 5 (radius: 25)
[13:37:02 -196545.493972] FAST spr round 6 (radius: 25)
[13:40:32 -196544.719985] FAST spr round 7 (radius: 25)
[13:43:58 -196544.719191] Model parameter optimization (eps = 1.000000)
[13:44:27 -196539.815727] SLOW spr round 1 (radius: 5)
[13:49:33 -196476.010657] SLOW spr round 2 (radius: 5)
[13:54:21 -196465.346726] SLOW spr round 3 (radius: 5)
[13:58:59 -196464.140830] SLOW spr round 4 (radius: 5)
[14:03:31 -196464.138990] SLOW spr round 5 (radius: 10)
[14:08:23 -196460.051240] SLOW spr round 6 (radius: 5)
[14:12:33] [worker #1] ML tree search #20, logLikelihood: -196452.214148
[14:14:02 -196459.516249] SLOW spr round 7 (radius: 5)
[14:19:06 -196458.586908] SLOW spr round 8 (radius: 5)
[14:23:48 -196458.586857] SLOW spr round 9 (radius: 10)
[14:28:40 -196458.586826] SLOW spr round 10 (radius: 15)
[14:37:45 -196458.275254] SLOW spr round 11 (radius: 5)
[14:43:46 -196458.274685] SLOW spr round 12 (radius: 10)
[14:49:16 -196458.274582] SLOW spr round 13 (radius: 15)
[14:54:52 -196458.274534] SLOW spr round 14 (radius: 20)
[15:04:26 -196458.274499] SLOW spr round 15 (radius: 25)
[15:16:26 -196458.274468] Model parameter optimization (eps = 0.100000)

[15:16:37] [worker #0] ML tree search #19, logLikelihood: -196458.076969


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.086334,0.498391) (0.082596,0.533438) (0.445246,0.786266) (0.385825,1.458773) 
   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: -196417.444106

AIC score: 396844.888213 / AICc score: 8440904.888213 / BIC score: 404916.749491
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=414).
         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/P53804/3_mltree/P53804.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/3_mltree/P53804.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/3_mltree/P53804.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53804/3_mltree/P53804.raxml.log

Analysis started: 30-Jun-2021 17:58:59 / finished: 01-Jul-2021 09:15:37

Elapsed time: 54998.044 seconds

Consumed energy: 3849.374 Wh (= 19 km in an electric car, or 96 km with an e-scooter!)