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 07-Jul-2021 03:05:52 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/2_msa/Q8N4F7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/3_mltree/Q8N4F7 --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/Q8N4F7/2_msa/Q8N4F7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 653 taxa and 123 sites

WARNING: Sequences sp_Q8R1Z9_RN121_MOUSE_10090 and tr_J9NV19_J9NV19_CANLF_9615 are exactly identical!
WARNING: Sequences sp_Q8R1Z9_RN121_MOUSE_10090 and tr_D3ZN19_D3ZN19_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q8R1Z9_RN121_MOUSE_10090 and tr_G5AVT0_G5AVT0_HETGA_10181 are exactly identical!
WARNING: Sequences sp_Q8R1Z9_RN121_MOUSE_10090 and tr_A0A1S3F1I9_A0A1S3F1I9_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2I3HRX1_A0A2I3HRX1_NOMLE_61853 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_G3SB30_G3SB30_GORGO_9595 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_H2NEJ4_H2NEJ4_PONAB_9601 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_H2R3C0_H2R3C0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_F6QT59_F6QT59_HORSE_9796 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_H0WHK7_H0WHK7_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and sp_Q9H920_RN121_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_F7EE81_F7EE81_MACMU_9544 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_G7PR07_G7PR07_MACFA_9541 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_F1MM46_F1MM46_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_M3W3V2_M3W3V2_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A096MMB2_A0A096MMB2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A0D9QW22_A0A0D9QW22_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A1S3A0T3_A0A1S3A0T3_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2K6AS20_A0A2K6AS20_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2K6AEM6_A0A2K6AEM6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2R9AR76_A0A2R9AR76_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2U4BPE8_A0A2U4BPE8_TURTR_9739 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2U3VBB6_A0A2U3VBB6_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2Y9KV66_A0A2Y9KV66_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2Y9MH57_A0A2Y9MH57_DELLE_9749 are exactly identical!
WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2Y9S7R6_A0A2Y9S7R6_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_Q9VX13_Q9VX13_DROME_7227 and tr_B4I6K3_B4I6K3_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_K7DCB3_K7DCB3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and sp_Q9BV68_RN126_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_F7F3B5_F7F3B5_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_A0A0A0MV20_A0A0A0MV20_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_A0A2K5P2K7_A0A2K5P2K7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_A0A2K6D4A5_A0A2K6D4A5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A096MS08_A0A096MS08_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A0D9RGK1_A0A0D9RGK1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A2K6A6Z9_A0A2K6A6Z9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A2R9BEY4_A0A2R9BEY4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2PEJ5_H2PEJ5_PONAB_9601 and tr_H2QQA9_H2QQA9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2PEJ5_H2PEJ5_PONAB_9601 and sp_Q8N4F7_RN175_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H9H1Y1_H9H1Y1_MELGA_9103 and tr_H0ZTP0_H0ZTP0_TAEGU_59729 are exactly identical!
WARNING: Sequences tr_H9H1Y1_H9H1Y1_MELGA_9103 and tr_A0A091EM14_A0A091EM14_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H9H1Y1_H9H1Y1_MELGA_9103 and tr_A0A093QNJ0_A0A093QNJ0_9PASS_328815 are exactly identical!
WARNING: Sequences tr_H9H1Y1_H9H1Y1_MELGA_9103 and tr_A0A091V0P6_A0A091V0P6_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_H9H1Y1_H9H1Y1_MELGA_9103 and tr_A0A093HNR2_A0A093HNR2_STRCA_441894 are exactly identical!
WARNING: Sequences tr_H9H1Y1_H9H1Y1_MELGA_9103 and tr_A0A093GPV2_A0A093GPV2_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_H9H1Y1_H9H1Y1_MELGA_9103 and tr_A0A218UK99_A0A218UK99_9PASE_299123 are exactly identical!
WARNING: Sequences tr_W5P3L5_W5P3L5_SHEEP_9940 and sp_Q0VD51_RNF13_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5RBK3_A0A3B5RBK3_XIPMA_8083 and tr_A0A096M9B3_A0A096M9B3_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A088AC30_A0A088AC30_APIME_7460 and tr_A0A2A3EHU1_A0A2A3EHU1_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NXK0_A0A158NXK0_ATTCE_12957 and tr_A0A151WKZ3_A0A151WKZ3_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A158NXK0_A0A158NXK0_ATTCE_12957 and tr_A0A195FF66_A0A195FF66_9HYME_34720 are exactly identical!
WARNING: Sequences tr_F7C8F7_F7C8F7_MACMU_9544 and tr_G8F2Z8_G8F2Z8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7C8F7_F7C8F7_MACMU_9544 and tr_A0A2K5MTF3_A0A2K5MTF3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7C8F7_F7C8F7_MACMU_9544 and tr_A0A2K6AFD2_A0A2K6AFD2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_I1NNT6_I1NNT6_ORYGL_4538 and tr_A0A0D3EPV4_A0A0D3EPV4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_H0YQT9_H0YQT9_TAEGU_59729 and tr_A0A218UFN0_A0A218UFN0_9PASE_299123 are exactly identical!
WARNING: Sequences tr_F4WQ12_F4WQ12_ACREC_103372 and tr_A0A195ECT3_A0A195ECT3_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A0E0MXK7_A0A0E0MXK7_ORYRU_4529 and tr_A0A0D9YA43_A0A0D9YA43_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A8XXA9_A8XXA9_CAEBR_6238 and tr_A0A2G5UJK0_A0A2G5UJK0_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_D2HM63_D2HM63_AILME_9646 and tr_M3WD03_M3WD03_FELCA_9685 are exactly identical!
WARNING: Sequences tr_D2HM63_D2HM63_AILME_9646 and tr_A0A2Y9JN45_A0A2Y9JN45_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_D2HM63_D2HM63_AILME_9646 and tr_A0A384DEL1_A0A384DEL1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I2UIC9_A0A2I2UIC9_FELCA_9685 and tr_A0A2U3VKQ6_A0A2U3VKQ6_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M4EQB1_M4EQB1_BRARP_51351 and tr_A0A078JPG3_A0A078JPG3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A067FGN6_A0A067FGN6_CITSI_2711 and tr_V4UEM0_V4UEM0_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067FGN6_A0A067FGN6_CITSI_2711 and tr_A0A2H5PG43_A0A2H5PG43_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A087XDT8_A0A087XDT8_POEFO_48698 and tr_A0A096LVW1_A0A096LVW1_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A0D2QDA2_A0A0D2QDA2_GOSRA_29730 and tr_A0A1U8NP03_A0A1U8NP03_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0K0F7N0_A0A0K0F7N0_STRVS_75913 and tr_A0A0N5B8P5_A0A0N5B8P5_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A0A1NDR7_A0A0A1NDR7_9FUNG_58291 and tr_A0A2G4SYF1_A0A2G4SYF1_9FUNG_1340429 are exactly identical!
WARNING: Sequences tr_A0A151PK01_A0A151PK01_ALLMI_8496 and tr_A0A1U7SHT3_A0A1U7SHT3_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0Q3PWS1_A0A0Q3PWS1_AMAAE_12930 and tr_A0A091W2B7_A0A091W2B7_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091WIS7_A0A091WIS7_NIPNI_128390 and tr_A0A093HR27_A0A093HR27_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091WIS7_A0A091WIS7_NIPNI_128390 and tr_A0A0A0B2I3_A0A0A0B2I3_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V1CPR5_A0A0V1CPR5_TRIBR_45882 and tr_A0A0V0WK23_A0A0V0WK23_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1CPR5_A0A0V1CPR5_TRIBR_45882 and tr_A0A0V0V1R3_A0A0V0V1R3_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CPR5_A0A0V1CPR5_TRIBR_45882 and tr_A0A0V1L595_A0A0V1L595_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CPR5_A0A0V1CPR5_TRIBR_45882 and tr_A0A0V1NRV4_A0A0V1NRV4_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CPR5_A0A0V1CPR5_TRIBR_45882 and tr_A0A0V0TJR3_A0A0V0TJR3_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A164T7A7_A0A164T7A7_9HOMO_1314777 and tr_A0A166A4Z9_A0A166A4Z9_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S4CLR6_A0A1S4CLR6_TOBAC_4097 and tr_A0A1U7X5L3_A0A1U7X5L3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3LQE8_A0A1S3LQE8_SALSA_8030 and tr_A0A060YFR7_A0A060YFR7_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3M042_A0A1S3M042_SALSA_8030 and tr_A0A060XBD4_A0A060XBD4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3QCD9_A0A1S3QCD9_SALSA_8030 and tr_A0A1S3RZE9_A0A1S3RZE9_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3R346_A0A1S3R346_SALSA_8030 and tr_A0A060VRE3_A0A060VRE3_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1U7TGH6_A0A1U7TGH6_TARSY_1868482 and tr_A0A2U4B9L0_A0A2U4B9L0_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A1U7TGH6_A0A1U7TGH6_TARSY_1868482 and tr_A0A2Y9NTW9_A0A2Y9NTW9_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A1U7TGH6_A0A1U7TGH6_TARSY_1868482 and tr_A0A2Y9TBE7_A0A2Y9TBE7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A1U7TGH6_A0A1U7TGH6_TARSY_1868482 and tr_A0A384ALH4_A0A384ALH4_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A226N4D0_A0A226N4D0_CALSU_9009 and tr_A0A226PEP7_A0A226PEP7_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0Q5Y0_A0A2D0Q5Y0_ICTPU_7998 and tr_A0A2D0Q7L3_A0A2D0Q7L3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2Y9MW08_A0A2Y9MW08_DELLE_9749 and tr_A0A2Y9THN9_A0A2Y9THN9_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 92

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/Q8N4F7/3_mltree/Q8N4F7.raxml.reduced.phy

Alignment comprises 1 partitions and 123 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 123 / 123
Gaps: 13.62 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/3_mltree/Q8N4F7.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 653 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 123 / 9840
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -133981.898578] Initial branch length optimization
[00:00:01 -103270.595196] Model parameter optimization (eps = 10.000000)
[00:00:18 -103076.370892] AUTODETECT spr round 1 (radius: 5)
[00:01:07 -75689.022041] AUTODETECT spr round 2 (radius: 10)
[00:02:02 -60234.217064] AUTODETECT spr round 3 (radius: 15)
[00:03:02 -53131.132587] AUTODETECT spr round 4 (radius: 20)
[00:04:14 -49726.534543] AUTODETECT spr round 5 (radius: 25)
[00:05:36 -48611.679259] SPR radius for FAST iterations: 25 (autodetect)
[00:05:36 -48611.679259] Model parameter optimization (eps = 3.000000)
[00:05:46 -48592.668127] FAST spr round 1 (radius: 25)
[00:07:01 -41536.012246] FAST spr round 2 (radius: 25)
[00:07:56 -41235.999932] FAST spr round 3 (radius: 25)
[00:08:44 -41164.799269] FAST spr round 4 (radius: 25)
[00:09:28 -41153.747475] FAST spr round 5 (radius: 25)
[00:10:08 -41151.983952] FAST spr round 6 (radius: 25)
[00:10:46 -41150.436182] FAST spr round 7 (radius: 25)
[00:11:24 -41150.435042] Model parameter optimization (eps = 1.000000)
[00:11:35 -41132.305795] SLOW spr round 1 (radius: 5)
[00:12:26 -41126.308094] SLOW spr round 2 (radius: 5)
[00:13:17 -41123.421942] SLOW spr round 3 (radius: 5)
[00:14:07 -41122.492038] SLOW spr round 4 (radius: 5)
[00:14:56 -41122.490948] SLOW spr round 5 (radius: 10)
[00:15:49 -41122.490022] SLOW spr round 6 (radius: 15)
[00:17:04 -41122.261535] SLOW spr round 7 (radius: 5)
[00:18:08 -41122.260537] SLOW spr round 8 (radius: 10)
[00:19:10 -41121.991392] SLOW spr round 9 (radius: 5)
[00:20:12 -41113.622164] SLOW spr round 10 (radius: 5)
[00:21:08 -41112.959974] SLOW spr round 11 (radius: 5)
[00:21:59 -41109.776843] SLOW spr round 12 (radius: 5)
[00:22:48 -41109.251115] SLOW spr round 13 (radius: 5)
[00:23:37 -41109.250318] SLOW spr round 14 (radius: 10)
[00:24:29 -41103.125171] SLOW spr round 15 (radius: 5)
[00:25:30 -41101.814704] SLOW spr round 16 (radius: 5)
[00:26:24 -41101.813204] SLOW spr round 17 (radius: 10)
[00:27:20 -41087.879727] SLOW spr round 18 (radius: 5)
[00:28:23 -41079.031864] SLOW spr round 19 (radius: 5)
[00:29:18 -41078.907006] SLOW spr round 20 (radius: 5)
[00:30:09 -41078.905816] SLOW spr round 21 (radius: 10)
[00:31:03 -41066.902502] SLOW spr round 22 (radius: 5)
[00:32:06 -41061.286601] SLOW spr round 23 (radius: 5)
[00:32:49] [worker #1] ML tree search #2, logLikelihood: -39917.022546
[00:33:02 -41059.992165] SLOW spr round 24 (radius: 5)
[00:33:53 -41059.990661] SLOW spr round 25 (radius: 10)
[00:34:45 -41059.990318] SLOW spr round 26 (radius: 15)
[00:36:13 -41058.396769] SLOW spr round 27 (radius: 5)
[00:37:18 -41057.332600] SLOW spr round 28 (radius: 5)
[00:38:16 -41056.126483] SLOW spr round 29 (radius: 5)
[00:39:08 -41056.126329] SLOW spr round 30 (radius: 10)
[00:40:00 -41056.126276] SLOW spr round 31 (radius: 15)
[00:41:29 -41056.126252] SLOW spr round 32 (radius: 20)
[00:43:43 -40509.213782] SLOW spr round 33 (radius: 5)
[00:44:49 -40268.886046] SLOW spr round 34 (radius: 5)
[00:45:48 -40236.430464] SLOW spr round 35 (radius: 5)
[00:46:42 -40234.212474] SLOW spr round 36 (radius: 5)
[00:47:35 -40129.503137] SLOW spr round 37 (radius: 5)
[00:48:26 -39948.430034] SLOW spr round 38 (radius: 5)
[00:49:15 -39947.072283] SLOW spr round 39 (radius: 5)
[00:50:03 -39947.071605] SLOW spr round 40 (radius: 10)
[00:50:53 -39947.071540] SLOW spr round 41 (radius: 15)
[00:52:21 -39933.380039] SLOW spr round 42 (radius: 5)
[00:53:26 -39927.640305] SLOW spr round 43 (radius: 5)
[00:54:23 -39925.831014] SLOW spr round 44 (radius: 5)
[00:55:15 -39925.657575] SLOW spr round 45 (radius: 5)
[00:56:03 -39925.657030] SLOW spr round 46 (radius: 10)
[00:56:54 -39925.657007] SLOW spr round 47 (radius: 15)
[00:58:17 -39924.664082] SLOW spr round 48 (radius: 5)
[00:59:23 -39923.160007] SLOW spr round 49 (radius: 5)
[01:00:19 -39923.153993] SLOW spr round 50 (radius: 10)
[01:01:13 -39922.219293] SLOW spr round 51 (radius: 5)
[01:02:12 -39922.216569] SLOW spr round 52 (radius: 10)
[01:03:09 -39922.216219] SLOW spr round 53 (radius: 15)
[01:04:27 -39922.216168] SLOW spr round 54 (radius: 20)
[01:06:27 -39922.216153] SLOW spr round 55 (radius: 25)
[01:08:48 -39917.230708] SLOW spr round 56 (radius: 5)
[01:09:54 -39916.707488] SLOW spr round 57 (radius: 5)
[01:10:35] [worker #1] ML tree search #4, logLikelihood: -39919.580003
[01:10:51 -39916.706763] SLOW spr round 58 (radius: 10)
[01:11:46 -39916.706681] SLOW spr round 59 (radius: 15)
[01:13:06 -39916.706662] SLOW spr round 60 (radius: 20)
[01:15:07 -39916.706657] SLOW spr round 61 (radius: 25)
[01:17:30 -39916.706654] Model parameter optimization (eps = 0.100000)

[01:17:38] [worker #0] ML tree search #1, logLikelihood: -39915.519544

[01:17:38 -135774.667452] Initial branch length optimization
[01:17:40 -104403.034666] Model parameter optimization (eps = 10.000000)
[01:17:57 -104202.881367] AUTODETECT spr round 1 (radius: 5)
[01:18:46 -76752.440047] AUTODETECT spr round 2 (radius: 10)
[01:19:41 -60792.385302] AUTODETECT spr round 3 (radius: 15)
[01:20:46 -50234.756243] AUTODETECT spr round 4 (radius: 20)
[01:22:06 -46428.407650] AUTODETECT spr round 5 (radius: 25)
[01:23:22 -45112.034760] SPR radius for FAST iterations: 25 (autodetect)
[01:23:22 -45112.034760] Model parameter optimization (eps = 3.000000)
[01:23:32 -45080.269684] FAST spr round 1 (radius: 25)
[01:24:35 -40878.030525] FAST spr round 2 (radius: 25)
[01:25:27 -40247.186424] FAST spr round 3 (radius: 25)
[01:26:13 -40007.782094] FAST spr round 4 (radius: 25)
[01:26:56 -39967.894177] FAST spr round 5 (radius: 25)
[01:27:35 -39960.225893] FAST spr round 6 (radius: 25)
[01:28:13 -39957.901051] FAST spr round 7 (radius: 25)
[01:28:51 -39956.575626] FAST spr round 8 (radius: 25)
[01:29:28 -39955.501875] FAST spr round 9 (radius: 25)
[01:30:04 -39955.498770] Model parameter optimization (eps = 1.000000)
[01:30:13 -39947.905785] SLOW spr round 1 (radius: 5)
[01:31:04 -39938.742230] SLOW spr round 2 (radius: 5)
[01:31:53 -39932.567388] SLOW spr round 3 (radius: 5)
[01:32:41 -39932.503921] SLOW spr round 4 (radius: 10)
[01:33:32 -39931.354732] SLOW spr round 5 (radius: 5)
[01:34:33 -39931.353734] SLOW spr round 6 (radius: 10)
[01:35:30 -39931.353625] SLOW spr round 7 (radius: 15)
[01:36:51 -39930.301692] SLOW spr round 8 (radius: 5)
[01:37:56 -39927.649176] SLOW spr round 9 (radius: 5)
[01:38:52 -39927.649003] SLOW spr round 10 (radius: 10)
[01:39:45 -39927.649000] SLOW spr round 11 (radius: 15)
[01:41:07 -39927.648999] SLOW spr round 12 (radius: 20)
[01:43:09 -39927.558457] SLOW spr round 13 (radius: 25)
[01:44:04] [worker #1] ML tree search #6, logLikelihood: -39937.812789
[01:45:22 -39926.742653] SLOW spr round 14 (radius: 5)
[01:46:24 -39925.920286] SLOW spr round 15 (radius: 5)
[01:47:18 -39925.544209] SLOW spr round 16 (radius: 5)
[01:48:07 -39925.543556] SLOW spr round 17 (radius: 10)
[01:49:00 -39922.412959] SLOW spr round 18 (radius: 5)
[01:50:02 -39922.412793] SLOW spr round 19 (radius: 10)
[01:51:00 -39922.412775] SLOW spr round 20 (radius: 15)
[01:52:22 -39922.412772] SLOW spr round 21 (radius: 20)
[01:54:29 -39922.412772] SLOW spr round 22 (radius: 25)
[01:56:51 -39922.412771] Model parameter optimization (eps = 0.100000)

[01:56:55] [worker #0] ML tree search #3, logLikelihood: -39922.356773

[01:56:55 -133918.273462] Initial branch length optimization
[01:56:57 -103135.602934] Model parameter optimization (eps = 10.000000)
[01:57:14 -102943.166285] AUTODETECT spr round 1 (radius: 5)
[01:58:04 -75836.157918] AUTODETECT spr round 2 (radius: 10)
[01:58:58 -61339.911530] AUTODETECT spr round 3 (radius: 15)
[02:00:01 -53172.628155] AUTODETECT spr round 4 (radius: 20)
[02:01:19 -47818.560738] AUTODETECT spr round 5 (radius: 25)
[02:02:53 -46436.036158] SPR radius for FAST iterations: 25 (autodetect)
[02:02:53 -46436.036158] Model parameter optimization (eps = 3.000000)
[02:03:05 -46391.469239] FAST spr round 1 (radius: 25)
[02:04:22 -40370.699198] FAST spr round 2 (radius: 25)
[02:05:18 -40031.807386] FAST spr round 3 (radius: 25)
[02:06:07 -39987.228523] FAST spr round 4 (radius: 25)
[02:06:51 -39970.528660] FAST spr round 5 (radius: 25)
[02:07:31 -39969.433039] FAST spr round 6 (radius: 25)
[02:08:09 -39969.213733] FAST spr round 7 (radius: 25)
[02:08:47 -39969.212159] Model parameter optimization (eps = 1.000000)
[02:08:57 -39965.358961] SLOW spr round 1 (radius: 5)
[02:09:50 -39953.842392] SLOW spr round 2 (radius: 5)
[02:10:42 -39948.485951] SLOW spr round 3 (radius: 5)
[02:11:33 -39948.101865] SLOW spr round 4 (radius: 5)
[02:12:22 -39948.101142] SLOW spr round 5 (radius: 10)
[02:13:13 -39948.100540] SLOW spr round 6 (radius: 15)
[02:14:36 -39947.357307] SLOW spr round 7 (radius: 5)
[02:15:40 -39947.075776] SLOW spr round 8 (radius: 5)
[02:16:36 -39947.075772] SLOW spr round 9 (radius: 10)
[02:17:31 -39947.075770] SLOW spr round 10 (radius: 15)
[02:18:49 -39947.075769] SLOW spr round 11 (radius: 20)
[02:18:54] [worker #1] ML tree search #8, logLikelihood: -39913.167368
[02:20:45 -39946.350539] SLOW spr round 12 (radius: 5)
[02:21:51 -39946.346657] SLOW spr round 13 (radius: 10)
[02:22:54 -39946.346438] SLOW spr round 14 (radius: 15)
[02:24:10 -39946.346424] SLOW spr round 15 (radius: 20)
[02:26:07 -39946.346422] SLOW spr round 16 (radius: 25)
[02:28:24 -39946.346422] Model parameter optimization (eps = 0.100000)

[02:28:28] [worker #0] ML tree search #5, logLikelihood: -39946.320722

[02:28:28 -134398.857999] Initial branch length optimization
[02:28:29 -103333.875239] Model parameter optimization (eps = 10.000000)
[02:28:46 -103169.285892] AUTODETECT spr round 1 (radius: 5)
[02:29:35 -75390.380546] AUTODETECT spr round 2 (radius: 10)
[02:30:32 -58812.247629] AUTODETECT spr round 3 (radius: 15)
[02:31:34 -51647.860892] AUTODETECT spr round 4 (radius: 20)
[02:32:53 -46044.727371] AUTODETECT spr round 5 (radius: 25)
[02:34:18 -44688.266341] SPR radius for FAST iterations: 25 (autodetect)
[02:34:18 -44688.266341] Model parameter optimization (eps = 3.000000)
[02:34:30 -44649.468862] FAST spr round 1 (radius: 25)
[02:35:44 -40329.258288] FAST spr round 2 (radius: 25)
[02:36:40 -39976.239353] FAST spr round 3 (radius: 25)
[02:37:29 -39954.811883] FAST spr round 4 (radius: 25)
[02:38:10 -39951.119278] FAST spr round 5 (radius: 25)
[02:38:48 -39951.117680] Model parameter optimization (eps = 1.000000)
[02:38:56 -39947.556999] SLOW spr round 1 (radius: 5)
[02:39:47 -39933.135154] SLOW spr round 2 (radius: 5)
[02:40:38 -39932.555149] SLOW spr round 3 (radius: 5)
[02:41:27 -39931.949221] SLOW spr round 4 (radius: 5)
[02:42:18 -39927.180732] SLOW spr round 5 (radius: 5)
[02:43:06 -39926.781170] SLOW spr round 6 (radius: 5)
[02:43:54 -39926.780089] SLOW spr round 7 (radius: 10)
[02:44:46 -39922.268358] SLOW spr round 8 (radius: 5)
[02:45:48 -39919.265031] SLOW spr round 9 (radius: 5)
[02:46:42 -39919.264918] SLOW spr round 10 (radius: 10)
[02:47:36 -39919.264863] SLOW spr round 11 (radius: 15)
[02:48:55 -39919.264806] SLOW spr round 12 (radius: 20)
[02:50:52 -39919.264755] SLOW spr round 13 (radius: 25)
[02:50:59] [worker #1] ML tree search #10, logLikelihood: -39920.251741
[02:53:12 -39919.092109] SLOW spr round 14 (radius: 5)
[02:54:19 -39917.845343] SLOW spr round 15 (radius: 5)
[02:55:19 -39917.034058] SLOW spr round 16 (radius: 5)
[02:56:11 -39917.032805] SLOW spr round 17 (radius: 10)
[02:57:04 -39917.032700] SLOW spr round 18 (radius: 15)
[02:58:25 -39917.032645] SLOW spr round 19 (radius: 20)
[03:00:23 -39911.978618] SLOW spr round 20 (radius: 5)
[03:01:29 -39910.935491] SLOW spr round 21 (radius: 5)
[03:02:27 -39910.934803] SLOW spr round 22 (radius: 10)
[03:03:22 -39909.658597] SLOW spr round 23 (radius: 5)
[03:04:23 -39909.656897] SLOW spr round 24 (radius: 10)
[03:05:21 -39909.656663] SLOW spr round 25 (radius: 15)
[03:06:39 -39909.656584] SLOW spr round 26 (radius: 20)
[03:08:37 -39909.656524] SLOW spr round 27 (radius: 25)
[03:10:59 -39909.656466] Model parameter optimization (eps = 0.100000)

[03:11:05] [worker #0] ML tree search #7, logLikelihood: -39909.378725

[03:11:05 -136211.486508] Initial branch length optimization
[03:11:07 -104644.243345] Model parameter optimization (eps = 10.000000)
[03:11:24 -104471.655390] AUTODETECT spr round 1 (radius: 5)
[03:12:14 -75804.398624] AUTODETECT spr round 2 (radius: 10)
[03:13:08 -60256.178080] AUTODETECT spr round 3 (radius: 15)
[03:14:10 -53131.000877] AUTODETECT spr round 4 (radius: 20)
[03:15:33 -47233.706106] AUTODETECT spr round 5 (radius: 25)
[03:16:50 -46537.508963] SPR radius for FAST iterations: 25 (autodetect)
[03:16:50 -46537.508963] Model parameter optimization (eps = 3.000000)
[03:17:02 -46518.812875] FAST spr round 1 (radius: 25)
[03:18:19 -40646.973627] FAST spr round 2 (radius: 25)
[03:19:18 -40208.321283] FAST spr round 3 (radius: 25)
[03:20:08 -40060.742813] FAST spr round 4 (radius: 25)
[03:20:53 -39962.953604] FAST spr round 5 (radius: 25)
[03:21:32 -39958.095575] FAST spr round 6 (radius: 25)
[03:22:10 -39958.094573] Model parameter optimization (eps = 1.000000)
[03:22:19 -39950.300370] SLOW spr round 1 (radius: 5)
[03:23:09 -39945.070367] SLOW spr round 2 (radius: 5)
[03:24:00 -39944.607806] SLOW spr round 3 (radius: 5)
[03:24:50 -39944.605675] SLOW spr round 4 (radius: 10)
[03:25:42 -39943.442688] SLOW spr round 5 (radius: 5)
[03:26:44 -39943.407151] SLOW spr round 6 (radius: 10)
[03:27:42 -39943.406374] SLOW spr round 7 (radius: 15)
[03:29:06 -39941.655039] SLOW spr round 8 (radius: 5)
[03:30:11 -39941.645372] SLOW spr round 9 (radius: 10)
[03:31:11 -39941.644040] SLOW spr round 10 (radius: 15)
[03:32:34 -39941.643842] SLOW spr round 11 (radius: 20)
[03:34:41 -39939.811332] SLOW spr round 12 (radius: 5)
[03:35:09] [worker #1] ML tree search #12, logLikelihood: -39922.464546
[03:35:47 -39939.804258] SLOW spr round 13 (radius: 10)
[03:36:51 -39934.634290] SLOW spr round 14 (radius: 5)
[03:37:55 -39927.983852] SLOW spr round 15 (radius: 5)
[03:38:50 -39924.902032] SLOW spr round 16 (radius: 5)
[03:39:41 -39923.091939] SLOW spr round 17 (radius: 5)
[03:40:29 -39923.091472] SLOW spr round 18 (radius: 10)
[03:41:20 -39923.091407] SLOW spr round 19 (radius: 15)
[03:42:46 -39923.091359] SLOW spr round 20 (radius: 20)
[03:44:45 -39923.091305] SLOW spr round 21 (radius: 25)
[03:47:04 -39922.925151] SLOW spr round 22 (radius: 5)
[03:48:11 -39922.923290] SLOW spr round 23 (radius: 10)
[03:49:14 -39922.923062] SLOW spr round 24 (radius: 15)
[03:50:33 -39922.922989] SLOW spr round 25 (radius: 20)
[03:52:31 -39922.922935] SLOW spr round 26 (radius: 25)
[03:54:49 -39922.922881] Model parameter optimization (eps = 0.100000)

[03:54:55] [worker #0] ML tree search #9, logLikelihood: -39922.704659

[03:54:56 -135291.612722] Initial branch length optimization
[03:54:57 -103716.646567] Model parameter optimization (eps = 10.000000)
[03:55:15 -103528.458132] AUTODETECT spr round 1 (radius: 5)
[03:56:06 -77370.856772] AUTODETECT spr round 2 (radius: 10)
[03:57:03 -60208.399724] AUTODETECT spr round 3 (radius: 15)
[03:58:09 -52248.361267] AUTODETECT spr round 4 (radius: 20)
[03:59:43 -47931.278168] AUTODETECT spr round 5 (radius: 25)
[04:01:10 -46252.765365] SPR radius for FAST iterations: 25 (autodetect)
[04:01:10 -46252.765365] Model parameter optimization (eps = 3.000000)
[04:01:21 -46200.468506] FAST spr round 1 (radius: 25)
[04:02:43 -40567.192463] FAST spr round 2 (radius: 25)
[04:03:41 -40001.327856] FAST spr round 3 (radius: 25)
[04:04:29 -39963.388562] FAST spr round 4 (radius: 25)
[04:05:12 -39956.295297] FAST spr round 5 (radius: 25)
[04:05:51 -39955.583153] FAST spr round 6 (radius: 25)
[04:06:29 -39955.509571] Model parameter optimization (eps = 1.000000)
[04:06:37 -39953.567292] SLOW spr round 1 (radius: 5)
[04:07:29 -39948.845849] SLOW spr round 2 (radius: 5)
[04:08:20 -39946.531038] SLOW spr round 3 (radius: 5)
[04:09:12 -39943.701003] SLOW spr round 4 (radius: 5)
[04:10:03 -39943.641269] SLOW spr round 5 (radius: 10)
[04:10:56 -39941.473702] SLOW spr round 6 (radius: 5)
[04:12:00 -39941.351628] SLOW spr round 7 (radius: 5)
[04:12:55 -39941.351407] SLOW spr round 8 (radius: 10)
[04:13:48 -39939.958678] SLOW spr round 9 (radius: 5)
[04:14:51 -39938.507274] SLOW spr round 10 (radius: 5)
[04:15:45 -39938.506646] SLOW spr round 11 (radius: 10)
[04:16:39 -39938.506484] SLOW spr round 12 (radius: 15)
[04:18:03 -39938.506379] SLOW spr round 13 (radius: 20)
[04:20:00 -39938.506280] SLOW spr round 14 (radius: 25)
[04:22:19 -39936.909860] SLOW spr round 15 (radius: 5)
[04:23:28 -39935.750778] SLOW spr round 16 (radius: 5)
[04:24:28 -39934.690505] SLOW spr round 17 (radius: 5)
[04:25:21 -39934.689742] SLOW spr round 18 (radius: 10)
[04:26:14 -39934.689707] SLOW spr round 19 (radius: 15)
[04:27:39 -39934.689700] SLOW spr round 20 (radius: 20)
[04:29:37 -39929.080108] SLOW spr round 21 (radius: 5)
[04:30:45 -39929.078923] SLOW spr round 22 (radius: 10)
[04:31:48 -39929.078886] SLOW spr round 23 (radius: 15)
[04:33:07 -39929.078882] SLOW spr round 24 (radius: 20)
[04:33:12] [worker #1] ML tree search #14, logLikelihood: -39918.077288
[04:35:06 -39929.078881] SLOW spr round 25 (radius: 25)
[04:37:24 -39929.078880] Model parameter optimization (eps = 0.100000)

[04:37:29] [worker #0] ML tree search #11, logLikelihood: -39929.001802

[04:37:29 -134754.315882] Initial branch length optimization
[04:37:30 -103626.166852] Model parameter optimization (eps = 10.000000)
[04:37:56 -103461.794192] AUTODETECT spr round 1 (radius: 5)
[04:38:46 -75940.210822] AUTODETECT spr round 2 (radius: 10)
[04:39:41 -59687.713011] AUTODETECT spr round 3 (radius: 15)
[04:40:45 -52870.025482] AUTODETECT spr round 4 (radius: 20)
[04:42:01 -47738.466440] AUTODETECT spr round 5 (radius: 25)
[04:43:40 -46284.173239] SPR radius for FAST iterations: 25 (autodetect)
[04:43:40 -46284.173239] Model parameter optimization (eps = 3.000000)
[04:43:54 -46265.365068] FAST spr round 1 (radius: 25)
[04:45:03 -40591.671750] FAST spr round 2 (radius: 25)
[04:45:57 -40111.048904] FAST spr round 3 (radius: 25)
[04:46:46 -40007.145422] FAST spr round 4 (radius: 25)
[04:47:27 -40001.427394] FAST spr round 5 (radius: 25)
[04:48:07 -39995.647727] FAST spr round 6 (radius: 25)
[04:48:45 -39994.649799] FAST spr round 7 (radius: 25)
[04:49:23 -39992.122222] FAST spr round 8 (radius: 25)
[04:50:00 -39992.121982] Model parameter optimization (eps = 1.000000)
[04:50:11 -39977.018049] SLOW spr round 1 (radius: 5)
[04:51:01 -39966.796304] SLOW spr round 2 (radius: 5)
[04:51:52 -39958.708735] SLOW spr round 3 (radius: 5)
[04:52:43 -39958.705748] SLOW spr round 4 (radius: 10)
[04:53:36 -39958.367376] SLOW spr round 5 (radius: 5)
[04:54:39 -39957.027245] SLOW spr round 6 (radius: 5)
[04:55:34 -39957.027146] SLOW spr round 7 (radius: 10)
[04:56:29 -39957.027055] SLOW spr round 8 (radius: 15)
[04:57:59 -39957.026964] SLOW spr round 9 (radius: 20)
[05:00:10 -39956.793900] SLOW spr round 10 (radius: 5)
[05:01:16 -39956.793803] SLOW spr round 11 (radius: 10)
[05:02:22 -39956.793707] SLOW spr round 12 (radius: 15)
[05:03:47 -39956.793609] SLOW spr round 13 (radius: 20)
[05:05:59 -39956.793504] SLOW spr round 14 (radius: 25)
[05:08:28 -39956.793403] Model parameter optimization (eps = 0.100000)

[05:08:31] [worker #0] ML tree search #13, logLikelihood: -39956.769325

[05:08:31 -134978.741181] Initial branch length optimization
[05:08:32 -102306.086022] Model parameter optimization (eps = 10.000000)
[05:08:52 -102172.965132] AUTODETECT spr round 1 (radius: 5)
[05:09:42 -75606.280484] AUTODETECT spr round 2 (radius: 10)
[05:10:37 -60651.648018] AUTODETECT spr round 3 (radius: 15)
[05:11:20] [worker #1] ML tree search #16, logLikelihood: -39923.542549
[05:11:41 -49853.261640] AUTODETECT spr round 4 (radius: 20)
[05:13:03 -46803.849612] AUTODETECT spr round 5 (radius: 25)
[05:14:44 -46042.739624] SPR radius for FAST iterations: 25 (autodetect)
[05:14:44 -46042.739624] Model parameter optimization (eps = 3.000000)
[05:14:56 -46018.772847] FAST spr round 1 (radius: 25)
[05:16:10 -40334.232746] FAST spr round 2 (radius: 25)
[05:17:04 -40021.684110] FAST spr round 3 (radius: 25)
[05:17:51 -39981.240587] FAST spr round 4 (radius: 25)
[05:18:36 -39960.217910] FAST spr round 5 (radius: 25)
[05:19:17 -39949.157599] FAST spr round 6 (radius: 25)
[05:19:56 -39946.257536] FAST spr round 7 (radius: 25)
[05:20:33 -39946.257122] Model parameter optimization (eps = 1.000000)
[05:20:43 -39941.967112] SLOW spr round 1 (radius: 5)
[05:21:34 -39934.771415] SLOW spr round 2 (radius: 5)
[05:22:24 -39932.834607] SLOW spr round 3 (radius: 5)
[05:23:15 -39932.825065] SLOW spr round 4 (radius: 10)
[05:24:08 -39931.815180] SLOW spr round 5 (radius: 5)
[05:25:12 -39930.149245] SLOW spr round 6 (radius: 5)
[05:26:08 -39930.130152] SLOW spr round 7 (radius: 10)
[05:27:02 -39930.129995] SLOW spr round 8 (radius: 15)
[05:28:26 -39927.564972] SLOW spr round 9 (radius: 5)
[05:29:33 -39922.986825] SLOW spr round 10 (radius: 5)
[05:30:30 -39922.984902] SLOW spr round 11 (radius: 10)
[05:31:26 -39922.984282] SLOW spr round 12 (radius: 15)
[05:32:48 -39922.983998] SLOW spr round 13 (radius: 20)
[05:34:41 -39920.520485] SLOW spr round 14 (radius: 5)
[05:35:50 -39918.092244] SLOW spr round 15 (radius: 5)
[05:36:49 -39916.740831] SLOW spr round 16 (radius: 5)
[05:37:42 -39916.738757] SLOW spr round 17 (radius: 10)
[05:38:35 -39916.738555] SLOW spr round 18 (radius: 15)
[05:39:54 -39916.738497] SLOW spr round 19 (radius: 20)
[05:41:34 -39916.738444] SLOW spr round 20 (radius: 25)
[05:43:26 -39916.430333] SLOW spr round 21 (radius: 5)
[05:44:33 -39916.429769] SLOW spr round 22 (radius: 10)
[05:45:38 -39916.429696] SLOW spr round 23 (radius: 15)
[05:46:53 -39916.429648] SLOW spr round 24 (radius: 20)
[05:48:35 -39916.429602] SLOW spr round 25 (radius: 25)
[05:50:11] [worker #1] ML tree search #18, logLikelihood: -40096.876560
[05:50:26 -39916.429555] Model parameter optimization (eps = 0.100000)

[05:50:32] [worker #0] ML tree search #15, logLikelihood: -39916.245217

[05:50:32 -134965.228954] Initial branch length optimization
[05:50:33 -103920.426751] Model parameter optimization (eps = 10.000000)
[05:50:57 -103742.944878] AUTODETECT spr round 1 (radius: 5)
[05:51:47 -76677.950164] AUTODETECT spr round 2 (radius: 10)
[05:52:43 -61515.899670] AUTODETECT spr round 3 (radius: 15)
[05:53:46 -52777.548323] AUTODETECT spr round 4 (radius: 20)
[05:55:08 -49468.815873] AUTODETECT spr round 5 (radius: 25)
[05:56:30 -47797.599083] SPR radius for FAST iterations: 25 (autodetect)
[05:56:30 -47797.599083] Model parameter optimization (eps = 3.000000)
[05:56:41 -47779.633670] FAST spr round 1 (radius: 25)
[05:57:58 -40751.580312] FAST spr round 2 (radius: 25)
[05:58:54 -40074.406788] FAST spr round 3 (radius: 25)
[05:59:46 -40001.128533] FAST spr round 4 (radius: 25)
[06:00:29 -39990.073405] FAST spr round 5 (radius: 25)
[06:01:11 -39983.727281] FAST spr round 6 (radius: 25)
[06:01:51 -39980.557232] FAST spr round 7 (radius: 25)
[06:02:29 -39980.554759] Model parameter optimization (eps = 1.000000)
[06:02:37 -39970.013583] SLOW spr round 1 (radius: 5)
[06:03:29 -39950.820137] SLOW spr round 2 (radius: 5)
[06:04:20 -39949.144130] SLOW spr round 3 (radius: 5)
[06:05:10 -39949.143656] SLOW spr round 4 (radius: 10)
[06:06:03 -39949.143537] SLOW spr round 5 (radius: 15)
[06:07:38 -39942.446862] SLOW spr round 6 (radius: 5)
[06:08:44 -39934.156451] SLOW spr round 7 (radius: 5)
[06:09:44 -39931.634070] SLOW spr round 8 (radius: 5)
[06:10:38 -39930.567052] SLOW spr round 9 (radius: 5)
[06:11:30 -39929.407705] SLOW spr round 10 (radius: 5)
[06:12:21 -39929.020115] SLOW spr round 11 (radius: 5)
[06:13:11 -39927.742339] SLOW spr round 12 (radius: 5)
[06:13:59 -39927.740737] SLOW spr round 13 (radius: 10)
[06:14:52 -39927.177214] SLOW spr round 14 (radius: 5)
[06:15:55 -39927.174735] SLOW spr round 15 (radius: 10)
[06:16:55 -39927.174458] SLOW spr round 16 (radius: 15)
[06:18:18 -39924.273187] SLOW spr round 17 (radius: 5)
[06:19:24 -39924.255282] SLOW spr round 18 (radius: 10)
[06:20:29 -39924.255062] SLOW spr round 19 (radius: 15)
[06:21:52 -39924.255048] SLOW spr round 20 (radius: 20)
[06:23:53 -39923.057055] SLOW spr round 21 (radius: 5)
[06:25:00 -39923.045544] SLOW spr round 22 (radius: 10)
[06:26:07 -39923.044815] SLOW spr round 23 (radius: 15)
[06:27:30 -39922.635307] SLOW spr round 24 (radius: 5)
[06:28:37 -39922.390924] SLOW spr round 25 (radius: 5)
[06:29:34 -39922.390578] SLOW spr round 26 (radius: 10)
[06:30:30 -39922.390575] SLOW spr round 27 (radius: 15)
[06:31:57 -39922.390575] SLOW spr round 28 (radius: 20)
[06:34:01 -39922.222096] SLOW spr round 29 (radius: 5)
[06:35:02] [worker #1] ML tree search #20, logLikelihood: -39907.561322
[06:35:08 -39922.220682] SLOW spr round 30 (radius: 10)
[06:36:14 -39922.220630] SLOW spr round 31 (radius: 15)
[06:37:38 -39922.220623] SLOW spr round 32 (radius: 20)
[06:39:42 -39922.083125] SLOW spr round 33 (radius: 5)
[06:40:49 -39921.335214] SLOW spr round 34 (radius: 5)
[06:41:47 -39921.177697] SLOW spr round 35 (radius: 5)
[06:42:40 -39921.137850] SLOW spr round 36 (radius: 10)
[06:43:32 -39921.137802] SLOW spr round 37 (radius: 15)
[06:45:02 -39918.921337] SLOW spr round 38 (radius: 5)
[06:46:07 -39918.920741] SLOW spr round 39 (radius: 10)
[06:47:09 -39918.920734] SLOW spr round 40 (radius: 15)
[06:48:33 -39918.920733] SLOW spr round 41 (radius: 20)
[06:50:36 -39918.920733] SLOW spr round 42 (radius: 25)
[06:52:56 -39918.405263] SLOW spr round 43 (radius: 5)
[06:54:03 -39918.402785] SLOW spr round 44 (radius: 10)
[06:55:09 -39918.402668] SLOW spr round 45 (radius: 15)
[06:56:32 -39918.402658] SLOW spr round 46 (radius: 20)
[06:58:34 -39918.402657] SLOW spr round 47 (radius: 25)
[07:00:53 -39918.402657] Model parameter optimization (eps = 0.100000)

[07:01:01] [worker #0] ML tree search #17, logLikelihood: -39917.400558

[07:01:01 -136406.350861] Initial branch length optimization
[07:01:02 -104566.556473] Model parameter optimization (eps = 10.000000)
[07:01:28 -104372.322464] AUTODETECT spr round 1 (radius: 5)
[07:02:18 -77876.524187] AUTODETECT spr round 2 (radius: 10)
[07:03:12 -61485.838086] AUTODETECT spr round 3 (radius: 15)
[07:04:19 -52252.037374] AUTODETECT spr round 4 (radius: 20)
[07:05:39 -47959.349775] AUTODETECT spr round 5 (radius: 25)
[07:07:04 -45622.665726] SPR radius for FAST iterations: 25 (autodetect)
[07:07:04 -45622.665726] Model parameter optimization (eps = 3.000000)
[07:07:15 -45568.386746] FAST spr round 1 (radius: 25)
[07:08:28 -41073.949421] FAST spr round 2 (radius: 25)
[07:09:25 -40068.798972] FAST spr round 3 (radius: 25)
[07:10:13 -40004.452164] FAST spr round 4 (radius: 25)
[07:10:56 -39992.063670] FAST spr round 5 (radius: 25)
[07:11:35 -39987.764551] FAST spr round 6 (radius: 25)
[07:12:12 -39987.581269] FAST spr round 7 (radius: 25)
[07:12:49 -39987.578841] Model parameter optimization (eps = 1.000000)
[07:12:58 -39985.995057] SLOW spr round 1 (radius: 5)
[07:13:47 -39970.548313] SLOW spr round 2 (radius: 5)
[07:14:38 -39963.637246] SLOW spr round 3 (radius: 5)
[07:15:29 -39959.676305] SLOW spr round 4 (radius: 5)
[07:16:19 -39958.163611] SLOW spr round 5 (radius: 5)
[07:17:07 -39958.163045] SLOW spr round 6 (radius: 10)
[07:18:00 -39954.536627] SLOW spr round 7 (radius: 5)
[07:19:02 -39951.873126] SLOW spr round 8 (radius: 5)
[07:19:56 -39951.872968] SLOW spr round 9 (radius: 10)
[07:20:47 -39951.872936] SLOW spr round 10 (radius: 15)
[07:22:08 -39943.014135] SLOW spr round 11 (radius: 5)
[07:23:11 -39940.687108] SLOW spr round 12 (radius: 5)
[07:24:07 -39939.335093] SLOW spr round 13 (radius: 5)
[07:24:56 -39939.334580] SLOW spr round 14 (radius: 10)
[07:25:45 -39939.334566] SLOW spr round 15 (radius: 15)
[07:27:06 -39939.334558] SLOW spr round 16 (radius: 20)
[07:29:02 -39937.935336] SLOW spr round 17 (radius: 5)
[07:30:04 -39937.934966] SLOW spr round 18 (radius: 10)
[07:31:06 -39937.934917] SLOW spr round 19 (radius: 15)
[07:32:22 -39937.934902] SLOW spr round 20 (radius: 20)
[07:34:20 -39937.934889] SLOW spr round 21 (radius: 25)
[07:36:37 -39935.733097] SLOW spr round 22 (radius: 5)
[07:37:42 -39934.494837] SLOW spr round 23 (radius: 5)
[07:38:38 -39934.493186] SLOW spr round 24 (radius: 10)
[07:39:32 -39928.876392] SLOW spr round 25 (radius: 5)
[07:40:31 -39928.345262] SLOW spr round 26 (radius: 5)
[07:41:22 -39928.344844] SLOW spr round 27 (radius: 10)
[07:42:13 -39928.344717] SLOW spr round 28 (radius: 15)
[07:43:33 -39928.141819] SLOW spr round 29 (radius: 5)
[07:44:34 -39927.379760] SLOW spr round 30 (radius: 5)
[07:45:28 -39927.379670] SLOW spr round 31 (radius: 10)
[07:46:20 -39927.379660] SLOW spr round 32 (radius: 15)
[07:47:39 -39927.379657] SLOW spr round 33 (radius: 20)
[07:49:41 -39927.379655] SLOW spr round 34 (radius: 25)
[07:52:00 -39927.379654] Model parameter optimization (eps = 0.100000)

[07:52:06] [worker #0] ML tree search #19, logLikelihood: -39927.204418


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.097093,0.189702) (0.090123,0.434308) (0.605017,0.998845) (0.207767,1.627407) 
   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: -39907.561322

AIC score: 82433.122645 / AICc score: 3512013.122645 / BIC score: 86114.271966
Free parameters (model + branch lengths): 1309

WARNING: Number of free parameters (K=1309) is larger than alignment size (n=123).
         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/Q8N4F7/3_mltree/Q8N4F7.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/3_mltree/Q8N4F7.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/3_mltree/Q8N4F7.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/3_mltree/Q8N4F7.raxml.log

Analysis started: 07-Jul-2021 03:05:52 / finished: 07-Jul-2021 10:57:59

Elapsed time: 28326.506 seconds

Consumed energy: 1765.799 Wh (= 9 km in an electric car, or 44 km with an e-scooter!)