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 02-Jul-2021 00:32:17 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXA9/2_msa/Q9BXA9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXA9/3_mltree/Q9BXA9 --seed 2 --threads 5 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXA9/2_msa/Q9BXA9_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 322 sites

WARNING: Sequences tr_B4QAD9_B4QAD9_DROSI_7240 and tr_B4HX43_B4HX43_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4QAE0_B4QAE0_DROSI_7240 and sp_P39770_SALM_DROME_7227 are exactly identical!
WARNING: Sequences tr_A0A1D5NTG3_A0A1D5NTG3_CHICK_9031 and tr_G1MZP8_G1MZP8_MELGA_9103 are exactly identical!
WARNING: Sequences tr_A0A1D5NTG3_A0A1D5NTG3_CHICK_9031 and tr_A0A226MR22_A0A226MR22_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A1D5NTG3_A0A1D5NTG3_CHICK_9031 and tr_A0A226PV31_A0A226PV31_COLVI_9014 are exactly identical!
WARNING: Sequences sp_Q9QX96_SALL2_MOUSE_10090 and tr_D4ADE6_D4ADE6_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3Y0I6_M3Y0I6_MUSPF_9669 and tr_J9NXD5_J9NXD5_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3Y0I6_M3Y0I6_MUSPF_9669 and tr_A0A2U3ZE74_A0A2U3ZE74_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y0I6_M3Y0I6_MUSPF_9669 and tr_A0A384DSE2_A0A384DSE2_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I3HYS1_A0A2I3HYS1_NOMLE_61853 and tr_G3QSA3_G3QSA3_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3HYS1_A0A2I3HYS1_NOMLE_61853 and tr_H2NXN2_H2NXN2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3HYS1_A0A2I3HYS1_NOMLE_61853 and tr_H2QFF2_H2QFF2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3HYS1_A0A2I3HYS1_NOMLE_61853 and tr_A0A2R8ZEJ9_A0A2R8ZEJ9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1R5S9_G1R5S9_NOMLE_61853 and tr_H2P2B5_H2P2B5_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RWY0_G1RWY0_NOMLE_61853 and tr_G3S5L2_G3S5L2_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1RWY0_G1RWY0_NOMLE_61853 and tr_H2Q7Y6_H2Q7Y6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1RWY0_G1RWY0_NOMLE_61853 and sp_Q9Y467_SALL2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1RWY0_G1RWY0_NOMLE_61853 and tr_A0A096NNR9_A0A096NNR9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RWY0_G1RWY0_NOMLE_61853 and tr_A0A2K5P805_A0A2K5P805_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RWY0_G1RWY0_NOMLE_61853 and tr_A0A2K5Z9T2_A0A2K5Z9T2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RWY0_G1RWY0_NOMLE_61853 and tr_A0A2R9BLH7_A0A2R9BLH7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QEF7_G3QEF7_GORGO_9595 and sp_Q9NSC2_SALL1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QEF7_G3QEF7_GORGO_9595 and tr_F7HGM0_F7HGM0_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3QEF7_G3QEF7_GORGO_9595 and tr_F7DWF8_F7DWF8_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3QEF7_G3QEF7_GORGO_9595 and tr_A0A096NI89_A0A096NI89_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3QEF7_G3QEF7_GORGO_9595 and tr_A0A2K5KK07_A0A2K5KK07_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3QEF7_G3QEF7_GORGO_9595 and tr_A0A2K6CET8_A0A2K6CET8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3QEF7_G3QEF7_GORGO_9595 and tr_A0A2K5Z9J1_A0A2K5Z9J1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3R6A1_G3R6A1_GORGO_9595 and sp_Q8N972_ZN709_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RZI8_G3RZI8_GORGO_9595 and tr_A0A2I3SGB5_A0A2I3SGB5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RZI8_G3RZI8_GORGO_9595 and sp_Q9UJQ4_SALL4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RZI8_G3RZI8_GORGO_9595 and tr_A0A2R9BKC1_A0A2R9BKC1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2NY74_H2NY74_PONAB_9601 and sp_Q5R9F0_ZNF14_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3RIT7_A0A2I3RIT7_PANTR_9598 and tr_A0A091E592_A0A091E592_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_A0A2I3RIT7_A0A2I3RIT7_PANTR_9598 and tr_A0A2R9B9T1_A0A2R9B9T1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3RJ81_A0A2I3RJ81_PANTR_9598 and tr_F7HHH5_F7HHH5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_H2R4V8_H2R4V8_PANTR_9598 and sp_Q96BV0_ZN775_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F7B753_F7B753_HORSE_9796 and tr_G1LJT2_G1LJT2_AILME_9646 are exactly identical!
WARNING: Sequences tr_W5PSR5_W5PSR5_SHEEP_9940 and tr_A0A2U4C0M9_A0A2U4C0M9_TURTR_9739 are exactly identical!
WARNING: Sequences tr_W5PT26_W5PT26_SHEEP_9940 and tr_F1MEJ1_F1MEJ1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M4APA1_M4APA1_XIPMA_8083 and tr_A0A087YCU5_A0A087YCU5_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A158P3J3_A0A158P3J3_ATTCE_12957 and tr_A0A151IZB5_A0A151IZB5_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158P3J3_A0A158P3J3_ATTCE_12957 and tr_A0A195BX25_A0A195BX25_9HYME_520822 are exactly identical!
WARNING: Sequences tr_H0XMN9_H0XMN9_OTOGA_30611 and tr_G5C253_G5C253_HETGA_10181 are exactly identical!
WARNING: Sequences sp_Q9BXA9_SALL3_HUMAN_9606 and tr_A0A2I3MNU3_A0A2I3MNU3_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_Q9BXA9_SALL3_HUMAN_9606 and tr_A0A0D9S071_A0A0D9S071_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q9BXA9_SALL3_HUMAN_9606 and tr_A0A2K5LDB6_A0A2K5LDB6_CERAT_9531 are exactly identical!
WARNING: Sequences sp_Q9BXA9_SALL3_HUMAN_9606 and tr_A0A2K6BI03_A0A2K6BI03_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6XKK1_F6XKK1_MACMU_9544 and tr_A0A2I3N067_A0A2I3N067_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7CT89_F7CT89_MACMU_9544 and tr_G7PZG7_G7PZG7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7CT89_F7CT89_MACMU_9544 and tr_A0A2I3LKX2_A0A2I3LKX2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7CT89_F7CT89_MACMU_9544 and tr_A0A2K6CV10_A0A2K6CV10_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7CT89_F7CT89_MACMU_9544 and tr_A0A2K6A5E0_A0A2K6A5E0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7FE79_F7FE79_MACMU_9544 and tr_A0A2K6A9M2_A0A2K6A9M2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7H7Z8_F7H7Z8_MACMU_9544 and tr_A0A096NNM8_A0A096NNM8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7H7Z8_F7H7Z8_MACMU_9544 and tr_A0A0D9RRX1_A0A0D9RRX1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7H7Z8_F7H7Z8_MACMU_9544 and tr_A0A2K5LJU0_A0A2K5LJU0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7H7Z8_F7H7Z8_MACMU_9544 and tr_A0A2K6CMT3_A0A2K6CMT3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7H7Z8_F7H7Z8_MACMU_9544 and tr_A0A2K5YAJ1_A0A2K5YAJ1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A091F3L5_A0A091F3L5_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A091J1U6_A0A091J1U6_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A093PWA0_A0A093PWA0_9PASS_328815 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A091UYI3_A0A091UYI3_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A087QX52_A0A087QX52_APTFO_9233 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A091VNF1_A0A091VNF1_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A091FZZ7_A0A091FZZ7_9AVES_55661 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A0A0AIK6_A0A0A0AIK6_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A093GSM8_A0A093GSM8_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A1V4K1V8_A0A1V4K1V8_PATFA_372326 are exactly identical!
WARNING: Sequences tr_H0ZAX5_H0ZAX5_TAEGU_59729 and tr_A0A218UZ25_A0A218UZ25_9PASE_299123 are exactly identical!
WARNING: Sequences tr_G7P9P4_G7P9P4_MACFA_9541 and tr_A0A2K6BLE7_A0A2K6BLE7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7Q2M0_G7Q2M0_MACFA_9541 and tr_A0A2K5LV43_A0A2K5LV43_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NE47_A0A096NE47_PAPAN_9555 and tr_A0A0D9SDT4_A0A0D9SDT4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NE47_A0A096NE47_PAPAN_9555 and tr_A0A2K5KNP5_A0A2K5KNP5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0K0G3C7_A0A0K0G3C7_STRVS_75913 and tr_A0A0N5C4B8_A0A0N5C4B8_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A0Q3P0C9_A0A0Q3P0C9_AMAAE_12930 and tr_A0A091J2C6_A0A091J2C6_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A0Q3P0C9_A0A0Q3P0C9_AMAAE_12930 and tr_A0A091W2Y2_A0A091W2Y2_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A0Q3P0C9_A0A0Q3P0C9_AMAAE_12930 and tr_A0A087QXY5_A0A087QXY5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A0Q3P0C9_A0A0Q3P0C9_AMAAE_12930 and tr_A0A091WJZ5_A0A091WJZ5_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A0Q3P0C9_A0A0Q3P0C9_AMAAE_12930 and tr_A0A0A0A6V9_A0A0A0A6V9_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0M5Y2_A0A2I0M5Y2_COLLI_8932 and tr_A0A1V4KE00_A0A1V4KE00_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1CGZ6_A0A0V1CGZ6_TRIBR_45882 and tr_A0A0V1PCD2_A0A0V1PCD2_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A151XDM8_A0A151XDM8_9HYME_64791 and tr_A0A195F083_A0A195F083_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A151XDM8_A0A151XDM8_9HYME_64791 and tr_A0A151IEV9_A0A151IEV9_9HYME_456900 are exactly identical!
WARNING: Sequences tr_A0A226N3E9_A0A226N3E9_CALSU_9009 and tr_A0A226PH28_A0A226PH28_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226N7C4_A0A226N7C4_CALSU_9009 and tr_A0A226NXV7_A0A226NXV7_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0Q8P0_A0A2D0Q8P0_ICTPU_7998 and tr_W5UI42_W5UI42_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RCG2_A0A2D0RCG2_ICTPU_7998 and tr_A0A2D0RD63_A0A2D0RD63_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4AZF2_A0A2U4AZF2_TURTR_9739 and tr_A0A2Y9LYM5_A0A2Y9LYM5_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4AZF2_A0A2U4AZF2_TURTR_9739 and tr_A0A383ZAU0_A0A383ZAU0_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2U3ZP32_A0A2U3ZP32_ODORO_9708 and tr_A0A2U3YRN3_A0A2U3YRN3_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9NU36_A0A2Y9NU36_DELLE_9749 and tr_A0A2Y9EUY2_A0A2Y9EUY2_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/Q9BXA9/3_mltree/Q9BXA9.raxml.reduced.phy

Alignment comprises 1 partitions and 322 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 322 / 322
Gaps: 14.81 %
Invariant sites: 0.31 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXA9/3_mltree/Q9BXA9.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 322 / 25760
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -486154.583696] Initial branch length optimization
[00:00:06 -395171.594699] Model parameter optimization (eps = 10.000000)
[00:01:05 -394599.562995] AUTODETECT spr round 1 (radius: 5)
[00:04:55 -302324.149763] AUTODETECT spr round 2 (radius: 10)
[00:09:06 -235096.313997] AUTODETECT spr round 3 (radius: 15)
[00:13:53 -197328.033450] AUTODETECT spr round 4 (radius: 20)
[00:19:36 -179962.627864] AUTODETECT spr round 5 (radius: 25)
[00:25:15 -173332.350880] SPR radius for FAST iterations: 25 (autodetect)
[00:25:15 -173332.350880] Model parameter optimization (eps = 3.000000)
[00:25:50 -172815.927537] FAST spr round 1 (radius: 25)
[00:31:34 -154319.376939] FAST spr round 2 (radius: 25)
[00:35:50 -153649.272267] FAST spr round 3 (radius: 25)
[00:39:32 -153474.987592] FAST spr round 4 (radius: 25)
[00:42:48 -153451.163175] FAST spr round 5 (radius: 25)
[00:45:45 -153445.026197] FAST spr round 6 (radius: 25)
[00:48:26 -153445.025253] Model parameter optimization (eps = 1.000000)
[00:48:48 -153440.278980] SLOW spr round 1 (radius: 5)
[00:52:31 -153413.523881] SLOW spr round 2 (radius: 5)
[00:56:05 -153405.802830] SLOW spr round 3 (radius: 5)
[00:59:36 -153402.429923] SLOW spr round 4 (radius: 5)
[01:02:56 -153402.113691] SLOW spr round 5 (radius: 5)
[01:06:16 -153402.113612] SLOW spr round 6 (radius: 10)
[01:09:45 -153395.661782] SLOW spr round 7 (radius: 5)
[01:13:52 -153395.661459] SLOW spr round 8 (radius: 10)
[01:17:54 -153395.661452] SLOW spr round 9 (radius: 15)
[01:23:53 -153394.646133] SLOW spr round 10 (radius: 5)
[01:28:09 -153393.485490] SLOW spr round 11 (radius: 5)
[01:31:55 -153393.485383] SLOW spr round 12 (radius: 10)
[01:35:38 -153393.485374] SLOW spr round 13 (radius: 15)
[01:41:49 -153393.485367] SLOW spr round 14 (radius: 20)
[01:50:48 -153390.932516] SLOW spr round 15 (radius: 5)
[01:55:08 -153390.764468] SLOW spr round 16 (radius: 5)
[01:58:57 -153390.764060] SLOW spr round 17 (radius: 10)
[02:02:40 -153390.764042] SLOW spr round 18 (radius: 15)
[02:08:45 -153390.764035] SLOW spr round 19 (radius: 20)
[02:17:34 -153390.764028] SLOW spr round 20 (radius: 25)
[02:29:21 -153382.426220] SLOW spr round 21 (radius: 5)
[02:33:49 -153373.224426] SLOW spr round 22 (radius: 5)
[02:36:58] [worker #3] ML tree search #4, logLikelihood: -153328.371370
[02:37:42 -153371.983963] SLOW spr round 23 (radius: 5)
[02:41:20 -153368.080146] SLOW spr round 24 (radius: 5)
[02:44:44 -153368.079426] SLOW spr round 25 (radius: 10)
[02:48:12 -153367.254653] SLOW spr round 26 (radius: 5)
[02:52:16 -153367.254066] SLOW spr round 27 (radius: 10)
[02:56:15 -153367.254007] SLOW spr round 28 (radius: 15)
[03:02:10 -153367.253986] SLOW spr round 29 (radius: 20)
[03:11:03 -153367.253975] SLOW spr round 30 (radius: 25)
[03:22:49 -153365.127859] SLOW spr round 31 (radius: 5)
[03:27:21 -153351.681012] SLOW spr round 32 (radius: 5)
[03:31:22 -153349.654363] SLOW spr round 33 (radius: 5)
[03:34:56 -153349.654000] SLOW spr round 34 (radius: 10)
[03:38:26 -153349.653983] SLOW spr round 35 (radius: 15)
[03:44:43 -153349.653974] SLOW spr round 36 (radius: 20)
[03:46:11] [worker #2] ML tree search #3, logLikelihood: -153368.070628
[03:53:29 -153349.653967] SLOW spr round 37 (radius: 25)
[04:05:14 -153349.280224] SLOW spr round 38 (radius: 5)
[04:09:20] [worker #4] ML tree search #5, logLikelihood: -153267.306009
[04:09:35 -153349.279636] SLOW spr round 39 (radius: 10)
[04:14:08 -153346.292535] SLOW spr round 40 (radius: 5)
[04:18:06 -153346.292481] SLOW spr round 41 (radius: 10)
[04:22:00 -153346.292473] SLOW spr round 42 (radius: 15)
[04:28:01 -153346.292466] SLOW spr round 43 (radius: 20)
[04:36:52 -153346.292459] SLOW spr round 44 (radius: 25)
[04:37:06] [worker #1] ML tree search #2, logLikelihood: -153267.663260
[04:48:40 -153346.292452] Model parameter optimization (eps = 0.100000)

[04:48:51] [worker #0] ML tree search #1, logLikelihood: -153346.139851

[04:48:51 -485305.893891] Initial branch length optimization
[04:48:58 -394647.937386] Model parameter optimization (eps = 10.000000)
[04:50:00 -394071.865488] AUTODETECT spr round 1 (radius: 5)
[04:53:51 -301257.021349] AUTODETECT spr round 2 (radius: 10)
[04:58:05 -232601.318148] AUTODETECT spr round 3 (radius: 15)
[05:02:37 -194977.216697] AUTODETECT spr round 4 (radius: 20)
[05:07:45 -182889.211183] AUTODETECT spr round 5 (radius: 25)
[05:14:19 -175702.896268] SPR radius for FAST iterations: 25 (autodetect)
[05:14:19 -175702.896268] Model parameter optimization (eps = 3.000000)
[05:14:53 -175267.656894] FAST spr round 1 (radius: 25)
[05:21:03 -154286.691866] FAST spr round 2 (radius: 25)
[05:25:13 -153526.972008] FAST spr round 3 (radius: 25)
[05:28:46 -153423.807693] FAST spr round 4 (radius: 25)
[05:31:56 -153400.481573] FAST spr round 5 (radius: 25)
[05:34:44 -153399.742668] FAST spr round 6 (radius: 25)
[05:37:23 -153399.742222] Model parameter optimization (eps = 1.000000)
[05:37:51 -153394.506056] SLOW spr round 1 (radius: 5)
[05:41:32 -153341.011051] SLOW spr round 2 (radius: 5)
[05:45:10 -153330.130045] SLOW spr round 3 (radius: 5)
[05:48:36 -153328.921608] SLOW spr round 4 (radius: 5)
[05:51:59 -153328.921526] SLOW spr round 5 (radius: 10)
[05:55:31 -153324.869631] SLOW spr round 6 (radius: 5)
[05:59:42 -153324.115855] SLOW spr round 7 (radius: 5)
[06:03:26 -153324.115760] SLOW spr round 8 (radius: 10)
[06:07:08 -153324.115683] SLOW spr round 9 (radius: 15)
[06:13:22 -153320.744449] SLOW spr round 10 (radius: 5)
[06:17:44 -153319.984353] SLOW spr round 11 (radius: 5)
[06:21:34 -153319.983544] SLOW spr round 12 (radius: 10)
[06:25:19 -153319.983497] SLOW spr round 13 (radius: 15)
[06:25:29] [worker #2] ML tree search #8, logLikelihood: -153314.773795
[06:31:30 -153319.983486] SLOW spr round 14 (radius: 20)
[06:39:57 -153319.094315] SLOW spr round 15 (radius: 5)
[06:44:18 -153319.094063] SLOW spr round 16 (radius: 10)
[06:48:38 -153319.094053] SLOW spr round 17 (radius: 15)
[06:54:34 -153319.094044] SLOW spr round 18 (radius: 20)
[07:03:06 -153319.094035] SLOW spr round 19 (radius: 25)
[07:13:28 -153313.369255] SLOW spr round 20 (radius: 5)
[07:17:55 -153309.002992] SLOW spr round 21 (radius: 5)
[07:21:52 -153307.935820] SLOW spr round 22 (radius: 5)
[07:25:30 -153307.935792] SLOW spr round 23 (radius: 10)
[07:29:06 -153307.799539] SLOW spr round 24 (radius: 5)
[07:33:16 -153307.798783] SLOW spr round 25 (radius: 10)
[07:37:18 -153307.798773] SLOW spr round 26 (radius: 15)
[07:43:18 -153307.798763] SLOW spr round 27 (radius: 20)
[07:45:54] [worker #3] ML tree search #9, logLikelihood: -153280.915640
[07:51:53] [worker #4] ML tree search #10, logLikelihood: -153279.569697
[07:51:54 -153307.645837] SLOW spr round 28 (radius: 5)
[07:56:14 -153307.645574] SLOW spr round 29 (radius: 10)
[08:00:34 -153307.645559] SLOW spr round 30 (radius: 15)
[08:06:30 -153307.645550] SLOW spr round 31 (radius: 20)
[08:15:04 -153307.645540] SLOW spr round 32 (radius: 25)
[08:25:27 -153307.307295] SLOW spr round 33 (radius: 5)
[08:30:00 -153299.226648] SLOW spr round 34 (radius: 5)
[08:33:57 -153298.982348] SLOW spr round 35 (radius: 5)
[08:37:36 -153298.981518] SLOW spr round 36 (radius: 10)
[08:41:15 -153298.981471] SLOW spr round 37 (radius: 15)
[08:42:45] [worker #1] ML tree search #7, logLikelihood: -153388.034802
[08:47:35 -153298.981460] SLOW spr round 38 (radius: 20)
[08:56:07 -153298.929364] SLOW spr round 39 (radius: 25)
[09:06:48 -153298.929089] Model parameter optimization (eps = 0.100000)

[09:06:57] [worker #0] ML tree search #6, logLikelihood: -153298.898094

[09:06:57 -487474.107652] Initial branch length optimization
[09:07:04 -395020.945898] Model parameter optimization (eps = 10.000000)
[09:08:05 -394386.937731] AUTODETECT spr round 1 (radius: 5)
[09:11:57 -302748.700364] AUTODETECT spr round 2 (radius: 10)
[09:16:09 -234414.494892] AUTODETECT spr round 3 (radius: 15)
[09:21:13 -198506.622067] AUTODETECT spr round 4 (radius: 20)
[09:26:45 -173790.839910] AUTODETECT spr round 5 (radius: 25)
[09:32:58 -171455.509685] SPR radius for FAST iterations: 25 (autodetect)
[09:32:58 -171455.509685] Model parameter optimization (eps = 3.000000)
[09:33:59 -171034.783323] FAST spr round 1 (radius: 25)
[09:39:40 -154995.955931] FAST spr round 2 (radius: 25)
[09:44:03 -153533.615425] FAST spr round 3 (radius: 25)
[09:47:45 -153453.539026] FAST spr round 4 (radius: 25)
[09:51:06 -153401.329430] FAST spr round 5 (radius: 25)
[09:54:00 -153390.572202] FAST spr round 6 (radius: 25)
[09:55:42] [worker #2] ML tree search #13, logLikelihood: -153293.208622
[09:56:41 -153389.204882] FAST spr round 7 (radius: 25)
[09:59:18 -153389.204157] Model parameter optimization (eps = 1.000000)
[09:59:46 -153382.139664] SLOW spr round 1 (radius: 5)
[10:03:28 -153351.791108] SLOW spr round 2 (radius: 5)
[10:07:03 -153322.334076] SLOW spr round 3 (radius: 5)
[10:10:36 -153311.955119] SLOW spr round 4 (radius: 5)
[10:13:59 -153311.953945] SLOW spr round 5 (radius: 10)
[10:17:38 -153303.859606] SLOW spr round 6 (radius: 5)
[10:21:50 -153301.843398] SLOW spr round 7 (radius: 5)
[10:22:49] [worker #3] ML tree search #14, logLikelihood: -153283.215312
[10:25:32 -153301.842004] SLOW spr round 8 (radius: 10)
[10:29:12 -153301.841893] SLOW spr round 9 (radius: 15)
[10:35:46 -153301.841861] SLOW spr round 10 (radius: 20)
[10:41:38] [worker #4] ML tree search #15, logLikelihood: -153266.000132
[10:45:13 -153300.899581] SLOW spr round 11 (radius: 5)
[10:49:33 -153300.898590] SLOW spr round 12 (radius: 10)
[10:53:58 -153300.898532] SLOW spr round 13 (radius: 15)
[11:00:12 -153300.898515] SLOW spr round 14 (radius: 20)
[11:09:46 -153300.898500] SLOW spr round 15 (radius: 25)
[11:21:25 -153300.001346] SLOW spr round 16 (radius: 5)
[11:25:48 -153300.001091] SLOW spr round 17 (radius: 10)
[11:30:19 -153300.001078] SLOW spr round 18 (radius: 15)
[11:36:32 -153300.001066] SLOW spr round 19 (radius: 20)
[11:46:04 -153300.001054] SLOW spr round 20 (radius: 25)
[11:57:54 -153300.001042] Model parameter optimization (eps = 0.100000)

[11:58:14] [worker #0] ML tree search #11, logLikelihood: -153299.629801

[11:58:14 -486100.561446] Initial branch length optimization
[11:58:20 -394301.362504] Model parameter optimization (eps = 10.000000)
[11:59:16 -393699.354847] AUTODETECT spr round 1 (radius: 5)
[12:03:15 -301757.095751] AUTODETECT spr round 2 (radius: 10)
[12:07:34 -236169.013605] AUTODETECT spr round 3 (radius: 15)
[12:12:39 -184186.629659] AUTODETECT spr round 4 (radius: 20)
[12:18:34 -172360.497335] AUTODETECT spr round 5 (radius: 25)
[12:24:52 -170826.299541] SPR radius for FAST iterations: 25 (autodetect)
[12:24:52 -170826.299541] Model parameter optimization (eps = 3.000000)
[12:25:31 -170437.739248] FAST spr round 1 (radius: 25)
[12:31:00 -154155.038548] FAST spr round 2 (radius: 25)
[12:35:11 -153475.283993] FAST spr round 3 (radius: 25)
[12:38:38 -153398.609593] FAST spr round 4 (radius: 25)
[12:41:48 -153380.969978] FAST spr round 5 (radius: 25)
[12:42:34] [worker #4] ML tree search #20, logLikelihood: -153380.258586
[12:44:37 -153379.291824] FAST spr round 6 (radius: 25)
[12:47:19 -153374.176147] FAST spr round 7 (radius: 25)
[12:49:53 -153374.174084] Model parameter optimization (eps = 1.000000)
[12:50:20 -153370.534786] SLOW spr round 1 (radius: 5)
[12:53:55 -153335.776976] SLOW spr round 2 (radius: 5)
[12:57:28 -153329.811526] SLOW spr round 3 (radius: 5)
[13:00:57 -153328.873987] SLOW spr round 4 (radius: 5)
[13:01:23] [worker #1] ML tree search #12, logLikelihood: -153281.648642
[13:04:20 -153328.873718] SLOW spr round 5 (radius: 10)
[13:08:00 -153320.155718] SLOW spr round 6 (radius: 5)
[13:12:16 -153318.772059] SLOW spr round 7 (radius: 5)
[13:16:08 -153318.771311] SLOW spr round 8 (radius: 10)
[13:20:35 -153318.351115] SLOW spr round 9 (radius: 5)
[13:25:39 -153315.976049] SLOW spr round 10 (radius: 5)
[13:30:10 -153315.865912] SLOW spr round 11 (radius: 5)
[13:34:24 -153315.865857] SLOW spr round 12 (radius: 10)
[13:38:49 -153309.920349] SLOW spr round 13 (radius: 5)
[13:43:49 -153308.252750] SLOW spr round 14 (radius: 5)
[13:48:17 -153305.206136] SLOW spr round 15 (radius: 5)
[13:52:31 -153305.206135] SLOW spr round 16 (radius: 10)
[13:55:25] [worker #2] ML tree search #18, logLikelihood: -153283.277392
[13:56:48 -153305.206134] SLOW spr round 17 (radius: 15)
[14:05:01 -153304.451290] SLOW spr round 18 (radius: 5)
[14:10:07 -153304.451289] SLOW spr round 19 (radius: 10)
[14:15:11 -153304.451288] SLOW spr round 20 (radius: 15)
[14:22:50 -153304.451287] SLOW spr round 21 (radius: 20)
[14:33:47 -153304.451286] SLOW spr round 22 (radius: 25)
[14:46:39 -153303.566658] SLOW spr round 23 (radius: 5)
[14:51:56 -153303.566411] SLOW spr round 24 (radius: 10)
[14:57:23 -153303.566411] SLOW spr round 25 (radius: 15)
[15:05:00 -153303.566410] SLOW spr round 26 (radius: 20)
[15:15:57 -153303.566409] SLOW spr round 27 (radius: 25)
[15:28:49 -153303.566408] Model parameter optimization (eps = 0.100000)

[15:29:28] [worker #0] ML tree search #16, logLikelihood: -153302.401082

[15:47:56] [worker #3] ML tree search #19, logLikelihood: -153260.207205
[16:41:40] [worker #1] ML tree search #17, logLikelihood: -153676.113857

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.146388,0.285255) (0.094950,0.700237) (0.492015,0.939472) (0.266647,1.610821) 
   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: -153260.207205

AIC score: 310530.414409 / AICc score: 8354590.414409 / BIC score: 318098.390258
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=322).
         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/Q9BXA9/3_mltree/Q9BXA9.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXA9/3_mltree/Q9BXA9.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXA9/3_mltree/Q9BXA9.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXA9/3_mltree/Q9BXA9.raxml.log

Analysis started: 02-Jul-2021 00:32:17 / finished: 02-Jul-2021 17:13:57

Elapsed time: 60100.711 seconds

Consumed energy: 5213.103 Wh (= 26 km in an electric car, or 130 km with an e-scooter!)