RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 11-Jul-2021 09:56:14 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/2_msa/Q96CM4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4 --seed 2 --threads 3 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/2_msa/Q96CM4_trimmed_msa.fasta
[00:00:00] Loaded alignment with 462 taxa and 147 sites

WARNING: Sequences tr_A0A1L1RYW6_A0A1L1RYW6_CHICK_9031 and tr_U3HZ60_U3HZ60_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_A0A2I3STE4_A0A2I3STE4_PANTR_9598 and tr_A0A2R9C0H1_A0A2R9C0H1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R1V8_H2R1V8_PANTR_9598 and sp_Q96CM4_NXNL1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R1V8_H2R1V8_PANTR_9598 and tr_A0A2R8ZYM7_A0A2R8ZYM7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_B8AAX8_B8AAX8_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_I1NSC6_I1NSC6_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_A0A0E0N3J1_A0A0E0N3J1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_A0A0D3EUZ5_A0A0D3EUZ5_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and sp_Q0JIL1_NRX2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_B8ATV8_B8ATV8_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_I1PPJ9_I1PPJ9_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_A0A0E0PDV1_A0A0E0PDV1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_A0A0D3FZZ1_A0A0D3FZZ1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_A0A0D9ZQF3_A0A0D9ZQF3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and sp_Q7XPE8_NRX3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0K0K0J2_A0A0K0K0J2_BRUMA_6279 and tr_A0A0N4TBR2_A0A0N4TBR2_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A0K0K0J2_A0A0K0K0J2_BRUMA_6279 and tr_A0A0R3R431_A0A0R3R431_9BILA_42155 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0SM09_A0A0V0SM09_9BILA_6336 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1DG63_A0A0V1DG63_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0WQT2_A0A0V0WQT2_9BILA_92179 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0VF13_A0A0V0VF13_9BILA_181606 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1LQ31_A0A0V1LQ31_9BILA_6335 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1A2V4_A0A0V1A2V4_9BILA_990121 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0YIH6_A0A0V0YIH6_TRIPS_6337 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1NA69_A0A0V1NA69_9BILA_268474 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1PP89_A0A0V1PP89_9BILA_92180 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1I9F4_A0A0V1I9F4_9BILA_268475 are exactly identical!
WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0UCD0_A0A0V0UCD0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_I1PC51_I1PC51_ORYGL_4538 and tr_A0A0D3FJM5_A0A0D3FJM5_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A8WTV6_A8WTV6_CAEBR_6238 and tr_A0A2G5V3V4_A0A2G5V3V4_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_A0A044VHD1_A0A044VHD1_ONCVO_6282 and tr_A0A182EJ26_A0A182EJ26_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A044VHD7_A0A044VHD7_ONCVO_6282 and tr_A0A182EI61_A0A182EI61_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0D9Z8P5_A0A0D9Z8P5_9ORYZ_40148 and sp_Q7Y0E8_NRX11_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A067FVD5_A0A067FVD5_CITSI_2711 and tr_V4TS08_V4TS08_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A0A0MW69_A0A0A0MW69_PAPAN_9555 and tr_A0A2K6CIL0_A0A2K6CIL0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0D9R4R0_A0A0D9R4R0_CHLSB_60711 and tr_A0A2K5N2K4_A0A2K5N2K4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9R4R0_A0A0D9R4R0_CHLSB_60711 and tr_A0A2K6AVK7_A0A2K6AVK7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0D2NXV3_A0A0D2NXV3_GOSRA_29730 and tr_A0A1U8NN36_A0A1U8NN36_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V0WJ51_A0A0V0WJ51_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V0VDC8_A0A0V0VDC8_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V1L3U2_A0A0V1L3U2_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V0TXP9_A0A0V0TXP9_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0VCE7_A0A0V0VCE7_9BILA_181606 and tr_A0A0V0ZZB5_A0A0V0ZZB5_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0VCE7_A0A0V0VCE7_9BILA_181606 and tr_A0A0V1P7A4_A0A0V1P7A4_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0VCE7_A0A0V0VCE7_9BILA_181606 and tr_A0A0V0TXU1_A0A0V0TXU1_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S4BT60_A0A1S4BT60_TOBAC_4097 and tr_A0A1U7Y411_A0A1U7Y411_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4CQA3_A0A1S4CQA3_TOBAC_4097 and tr_A0A1U7V7K4_A0A1U7V7K4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1I7VQM2_A0A1I7VQM2_LOALO_7209 and tr_A0A1I7VWJ0_A0A1I7VWJ0_LOALO_7209 are exactly identical!
WARNING: Sequences tr_A0A2D0Q3D2_A0A2D0Q3D2_ICTPU_7998 and tr_A0A2D0Q4K5_A0A2D0Q4K5_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 49

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4.raxml.reduced.phy

Alignment comprises 1 partitions and 147 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 147 / 147
Gaps: 11.31 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4.raxml.rba

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

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

[00:00:00] Generating 20 random starting tree(s) with 462 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 147 / 11760
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -122442.491653] Initial branch length optimization
[00:00:01 -104019.817175] Model parameter optimization (eps = 10.000000)
[00:00:16 -103767.099345] AUTODETECT spr round 1 (radius: 5)
[00:00:52 -74945.989555] AUTODETECT spr round 2 (radius: 10)
[00:01:34 -57351.916471] AUTODETECT spr round 3 (radius: 15)
[00:02:24 -51079.722061] AUTODETECT spr round 4 (radius: 20)
[00:03:19 -48019.067147] AUTODETECT spr round 5 (radius: 25)
[00:04:28 -47424.676755] SPR radius for FAST iterations: 25 (autodetect)
[00:04:28 -47424.676755] Model parameter optimization (eps = 3.000000)
[00:04:39 -47347.432341] FAST spr round 1 (radius: 25)
[00:05:30 -40076.916734] FAST spr round 2 (radius: 25)
[00:06:05 -39808.973841] FAST spr round 3 (radius: 25)
[00:06:39 -39781.554801] FAST spr round 4 (radius: 25)
[00:07:07 -39780.209230] FAST spr round 5 (radius: 25)
[00:07:35 -39780.209106] Model parameter optimization (eps = 1.000000)
[00:07:40 -39779.047808] SLOW spr round 1 (radius: 5)
[00:08:25 -39768.091698] SLOW spr round 2 (radius: 5)
[00:09:07 -39768.089871] SLOW spr round 3 (radius: 10)
[00:09:50 -39766.360239] SLOW spr round 4 (radius: 5)
[00:10:45 -39765.803695] SLOW spr round 5 (radius: 5)
[00:11:33 -39765.802453] SLOW spr round 6 (radius: 10)
[00:12:16 -39765.802390] SLOW spr round 7 (radius: 15)
[00:13:38 -39765.802387] SLOW spr round 8 (radius: 20)
[00:15:34 -39765.802386] SLOW spr round 9 (radius: 25)
[00:17:30 -39765.802386] Model parameter optimization (eps = 0.100000)

[00:17:33] [worker #0] ML tree search #1, logLikelihood: -39765.782855

[00:17:33 -121627.475838] Initial branch length optimization
[00:17:35 -103782.080924] Model parameter optimization (eps = 10.000000)
[00:17:58 -103446.877045] AUTODETECT spr round 1 (radius: 5)
[00:18:34 -76284.488262] AUTODETECT spr round 2 (radius: 10)
[00:19:14] [worker #1] ML tree search #2, logLikelihood: -39757.732159
[00:19:15 -58784.209250] AUTODETECT spr round 3 (radius: 15)
[00:20:07 -47210.904331] AUTODETECT spr round 4 (radius: 20)
[00:21:05 -44808.736974] AUTODETECT spr round 5 (radius: 25)
[00:21:23] [worker #2] ML tree search #3, logLikelihood: -39751.334225
[00:22:04 -44705.706179] SPR radius for FAST iterations: 25 (autodetect)
[00:22:04 -44705.706179] Model parameter optimization (eps = 3.000000)
[00:22:11 -44701.521096] FAST spr round 1 (radius: 25)
[00:22:58 -39968.115313] FAST spr round 2 (radius: 25)
[00:23:36 -39808.593838] FAST spr round 3 (radius: 25)
[00:24:09 -39776.408332] FAST spr round 4 (radius: 25)
[00:24:39 -39767.658670] FAST spr round 5 (radius: 25)
[00:25:08 -39767.658258] Model parameter optimization (eps = 1.000000)
[00:25:14 -39763.388555] SLOW spr round 1 (radius: 5)
[00:25:59 -39756.357820] SLOW spr round 2 (radius: 5)
[00:26:44 -39751.154332] SLOW spr round 3 (radius: 5)
[00:27:25 -39751.153299] SLOW spr round 4 (radius: 10)
[00:28:08 -39751.153081] SLOW spr round 5 (radius: 15)
[00:29:33 -39751.152898] SLOW spr round 6 (radius: 20)
[00:31:28 -39751.152714] SLOW spr round 7 (radius: 25)
[00:33:26 -39751.152530] Model parameter optimization (eps = 0.100000)

[00:33:28] [worker #0] ML tree search #4, logLikelihood: -39751.138966

[00:33:28 -121761.359898] Initial branch length optimization
[00:33:30 -104109.244353] Model parameter optimization (eps = 10.000000)
[00:33:47 -103841.674911] AUTODETECT spr round 1 (radius: 5)
[00:34:23 -73323.080678] AUTODETECT spr round 2 (radius: 10)
[00:35:08 -54187.104622] AUTODETECT spr round 3 (radius: 15)
[00:36:02 -46473.727313] AUTODETECT spr round 4 (radius: 20)
[00:37:14 -45229.063610] AUTODETECT spr round 5 (radius: 25)
[00:37:47] [worker #1] ML tree search #5, logLikelihood: -39754.600178
[00:38:20 -44333.870089] SPR radius for FAST iterations: 25 (autodetect)
[00:38:20 -44333.870089] Model parameter optimization (eps = 3.000000)
[00:38:29 -44321.416184] FAST spr round 1 (radius: 25)
[00:39:14 -40123.315337] FAST spr round 2 (radius: 25)
[00:39:50 -39817.378673] FAST spr round 3 (radius: 25)
[00:39:52] [worker #2] ML tree search #6, logLikelihood: -39775.599836
[00:40:24 -39781.401376] FAST spr round 4 (radius: 25)
[00:40:54 -39776.973570] FAST spr round 5 (radius: 25)
[00:41:23 -39774.686745] FAST spr round 6 (radius: 25)
[00:41:51 -39774.685387] Model parameter optimization (eps = 1.000000)
[00:41:56 -39773.590608] SLOW spr round 1 (radius: 5)
[00:42:42 -39764.044884] SLOW spr round 2 (radius: 5)
[00:43:25 -39759.595238] SLOW spr round 3 (radius: 5)
[00:44:07 -39759.595078] SLOW spr round 4 (radius: 10)
[00:44:50 -39759.479411] SLOW spr round 5 (radius: 5)
[00:45:47 -39758.422813] SLOW spr round 6 (radius: 5)
[00:46:35 -39758.422543] SLOW spr round 7 (radius: 10)
[00:47:19 -39758.422387] SLOW spr round 8 (radius: 15)
[00:48:43 -39758.422240] SLOW spr round 9 (radius: 20)
[00:50:39 -39758.422094] SLOW spr round 10 (radius: 25)
[00:52:38 -39758.421947] Model parameter optimization (eps = 0.100000)

[00:52:41] [worker #0] ML tree search #7, logLikelihood: -39758.409778

[00:52:41 -122100.081067] Initial branch length optimization
[00:52:43 -104491.058401] Model parameter optimization (eps = 10.000000)
[00:52:59 -104214.929534] AUTODETECT spr round 1 (radius: 5)
[00:53:35 -74285.847085] AUTODETECT spr round 2 (radius: 10)
[00:54:17 -55829.672230] AUTODETECT spr round 3 (radius: 15)
[00:55:07 -47972.869508] AUTODETECT spr round 4 (radius: 20)
[00:56:08 -45156.414290] AUTODETECT spr round 5 (radius: 25)
[00:56:31] [worker #1] ML tree search #8, logLikelihood: -39760.115128
[00:57:27 -45047.703562] SPR radius for FAST iterations: 25 (autodetect)
[00:57:27 -45047.703562] Model parameter optimization (eps = 3.000000)
[00:57:36 -45042.997776] FAST spr round 1 (radius: 25)
[00:58:24 -39967.444121] FAST spr round 2 (radius: 25)
[00:59:02 -39791.315867] FAST spr round 3 (radius: 25)
[00:59:05] [worker #2] ML tree search #9, logLikelihood: -39759.548131
[00:59:37 -39777.470579] FAST spr round 4 (radius: 25)
[01:00:07 -39772.828938] FAST spr round 5 (radius: 25)
[01:00:35 -39772.054867] FAST spr round 6 (radius: 25)
[01:01:03 -39772.054156] Model parameter optimization (eps = 1.000000)
[01:01:07 -39771.623190] SLOW spr round 1 (radius: 5)
[01:01:52 -39761.471969] SLOW spr round 2 (radius: 5)
[01:02:36 -39758.864089] SLOW spr round 3 (radius: 5)
[01:03:18 -39758.330797] SLOW spr round 4 (radius: 5)
[01:04:00 -39758.330535] SLOW spr round 5 (radius: 10)
[01:04:40 -39758.330480] SLOW spr round 6 (radius: 15)
[01:06:05 -39758.330459] SLOW spr round 7 (radius: 20)
[01:07:58 -39758.330451] SLOW spr round 8 (radius: 25)
[01:10:02 -39758.330447] Model parameter optimization (eps = 0.100000)

[01:10:08] [worker #0] ML tree search #10, logLikelihood: -39758.223733

[01:10:08 -122622.079526] Initial branch length optimization
[01:10:10 -104943.008196] Model parameter optimization (eps = 10.000000)
[01:10:26 -104614.279986] AUTODETECT spr round 1 (radius: 5)
[01:11:02 -74115.350440] AUTODETECT spr round 2 (radius: 10)
[01:11:46 -54566.795350] AUTODETECT spr round 3 (radius: 15)
[01:12:26] [worker #1] ML tree search #11, logLikelihood: -39756.310302
[01:12:33 -50176.126862] AUTODETECT spr round 4 (radius: 20)
[01:13:25 -47561.733520] AUTODETECT spr round 5 (radius: 25)
[01:14:27 -46076.391820] SPR radius for FAST iterations: 25 (autodetect)
[01:14:27 -46076.391820] Model parameter optimization (eps = 3.000000)
[01:14:36 -46072.364611] FAST spr round 1 (radius: 25)
[01:15:20 -40187.533456] FAST spr round 2 (radius: 25)
[01:15:57 -39835.535546] FAST spr round 3 (radius: 25)
[01:16:30 -39779.699515] FAST spr round 4 (radius: 25)
[01:17:00 -39776.671548] FAST spr round 5 (radius: 25)
[01:17:28 -39775.078344] FAST spr round 6 (radius: 25)
[01:17:57 -39774.729361] FAST spr round 7 (radius: 25)
[01:18:25 -39774.728325] Model parameter optimization (eps = 1.000000)
[01:18:31 -39772.700987] SLOW spr round 1 (radius: 5)
[01:18:31] [worker #2] ML tree search #12, logLikelihood: -39757.242106
[01:19:17 -39760.390250] SLOW spr round 2 (radius: 5)
[01:20:00 -39760.063513] SLOW spr round 3 (radius: 5)
[01:20:42 -39760.062858] SLOW spr round 4 (radius: 10)
[01:21:27 -39756.257651] SLOW spr round 5 (radius: 5)
[01:22:23 -39755.332501] SLOW spr round 6 (radius: 5)
[01:23:11 -39755.331670] SLOW spr round 7 (radius: 10)
[01:23:57 -39755.331634] SLOW spr round 8 (radius: 15)
[01:25:23 -39755.331631] SLOW spr round 9 (radius: 20)
[01:27:22 -39755.331626] SLOW spr round 10 (radius: 25)
[01:29:31 -39755.331625] Model parameter optimization (eps = 0.100000)

[01:29:38] [worker #0] ML tree search #13, logLikelihood: -39755.068300

[01:29:38 -121870.089732] Initial branch length optimization
[01:29:40 -104262.507283] Model parameter optimization (eps = 10.000000)
[01:29:55 -104050.263700] AUTODETECT spr round 1 (radius: 5)
[01:30:30 -73277.429074] AUTODETECT spr round 2 (radius: 10)
[01:30:36] [worker #1] ML tree search #14, logLikelihood: -39760.158482
[01:31:13 -53456.906754] AUTODETECT spr round 3 (radius: 15)
[01:32:05 -48105.737156] AUTODETECT spr round 4 (radius: 20)
[01:33:13 -45466.630180] AUTODETECT spr round 5 (radius: 25)
[01:34:23 -45313.114893] SPR radius for FAST iterations: 25 (autodetect)
[01:34:23 -45313.114893] Model parameter optimization (eps = 3.000000)
[01:34:35 -45304.837124] FAST spr round 1 (radius: 25)
[01:35:21 -39979.832453] FAST spr round 2 (radius: 25)
[01:35:31] [worker #2] ML tree search #15, logLikelihood: -39758.971384
[01:35:59 -39824.189143] FAST spr round 3 (radius: 25)
[01:36:31 -39808.721777] FAST spr round 4 (radius: 25)
[01:37:01 -39806.442494] FAST spr round 5 (radius: 25)
[01:37:29 -39806.441531] Model parameter optimization (eps = 1.000000)
[01:37:36 -39803.326178] SLOW spr round 1 (radius: 5)
[01:38:25 -39785.077949] SLOW spr round 2 (radius: 5)
[01:39:08 -39781.883662] SLOW spr round 3 (radius: 5)
[01:39:49 -39781.883192] SLOW spr round 4 (radius: 10)
[01:40:31 -39779.837615] SLOW spr round 5 (radius: 5)
[01:41:26 -39779.836823] SLOW spr round 6 (radius: 10)
[01:42:15 -39779.836795] SLOW spr round 7 (radius: 15)
[01:43:30 -39779.445178] SLOW spr round 8 (radius: 5)
[01:44:29 -39773.519667] SLOW spr round 9 (radius: 5)
[01:45:20 -39770.887785] SLOW spr round 10 (radius: 5)
[01:46:05 -39770.088576] SLOW spr round 11 (radius: 5)
[01:46:48 -39770.083567] SLOW spr round 12 (radius: 10)
[01:47:28 -39770.083565] SLOW spr round 13 (radius: 15)
[01:48:49 -39769.906552] SLOW spr round 14 (radius: 5)
[01:49:48 -39768.440531] SLOW spr round 15 (radius: 5)
[01:50:36 -39768.321689] SLOW spr round 16 (radius: 5)
[01:51:20 -39768.321565] SLOW spr round 17 (radius: 10)
[01:51:37] [worker #1] ML tree search #17, logLikelihood: -39761.798864
[01:52:03 -39766.800943] SLOW spr round 18 (radius: 5)
[01:52:14] [worker #2] ML tree search #18, logLikelihood: -39756.451147
[01:52:57 -39766.800038] SLOW spr round 19 (radius: 10)
[01:53:45 -39766.799991] SLOW spr round 20 (radius: 15)
[01:55:07 -39766.799987] SLOW spr round 21 (radius: 20)
[01:57:09 -39766.799987] SLOW spr round 22 (radius: 25)
[01:59:20 -39766.799987] Model parameter optimization (eps = 0.100000)

[01:59:23] [worker #0] ML tree search #16, logLikelihood: -39766.753040

[01:59:23 -121487.316263] Initial branch length optimization
[01:59:24 -103605.615732] Model parameter optimization (eps = 10.000000)
[01:59:40 -103372.816697] AUTODETECT spr round 1 (radius: 5)
[02:00:16 -73312.103392] AUTODETECT spr round 2 (radius: 10)
[02:00:56 -53089.342511] AUTODETECT spr round 3 (radius: 15)
[02:01:49 -48023.811544] AUTODETECT spr round 4 (radius: 20)
[02:02:45 -45151.318694] AUTODETECT spr round 5 (radius: 25)
[02:03:45 -44909.519184] SPR radius for FAST iterations: 25 (autodetect)
[02:03:45 -44909.519184] Model parameter optimization (eps = 3.000000)
[02:03:56 -44899.015261] FAST spr round 1 (radius: 25)
[02:04:38 -40065.386157] FAST spr round 2 (radius: 25)
[02:05:13 -39855.904305] FAST spr round 3 (radius: 25)
[02:05:46 -39797.634629] FAST spr round 4 (radius: 25)
[02:06:16 -39788.478249] FAST spr round 5 (radius: 25)
[02:06:45 -39785.818931] FAST spr round 6 (radius: 25)
[02:07:13 -39785.357728] FAST spr round 7 (radius: 25)
[02:07:41 -39785.356658] Model parameter optimization (eps = 1.000000)
[02:07:48 -39784.296299] SLOW spr round 1 (radius: 5)
[02:08:32 -39780.209838] SLOW spr round 2 (radius: 5)
[02:09:14 -39775.225134] SLOW spr round 3 (radius: 5)
[02:09:56 -39775.224955] SLOW spr round 4 (radius: 10)
[02:10:38 -39774.345688] SLOW spr round 5 (radius: 5)
[02:11:23] [worker #1] ML tree search #20, logLikelihood: -39763.636538
[02:11:38 -39759.464726] SLOW spr round 6 (radius: 5)
[02:12:27 -39757.980345] SLOW spr round 7 (radius: 5)
[02:13:12 -39757.180177] SLOW spr round 8 (radius: 5)
[02:13:55 -39755.243207] SLOW spr round 9 (radius: 5)
[02:14:37 -39755.242739] SLOW spr round 10 (radius: 10)
[02:15:17 -39755.242707] SLOW spr round 11 (radius: 15)
[02:16:42 -39755.242705] SLOW spr round 12 (radius: 20)
[02:18:42 -39755.242705] SLOW spr round 13 (radius: 25)
[02:20:58 -39755.242705] Model parameter optimization (eps = 0.100000)

[02:21:01] [worker #0] ML tree search #19, logLikelihood: -39755.227956


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.135320,0.291705) (0.150272,0.379617) (0.328951,0.830786) (0.385457,1.634924) 
   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: -39751.138966

AIC score: 81356.277933 / AICc score: 1801868.277933 / BIC score: 84128.408941
Free parameters (model + branch lengths): 927

WARNING: Number of free parameters (K=927) is larger than alignment size (n=147).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4.raxml.log

Analysis started: 11-Jul-2021 09:56:14 / finished: 11-Jul-2021 12:17:15

Elapsed time: 8461.646 seconds