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 15-Jul-2021 05:52:01 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A5/2_msa/Q9Y3A5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A5/3_mltree/Q9Y3A5 --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/Q9Y3A5/2_msa/Q9Y3A5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 956 taxa and 241 sites

WARNING: Sequences tr_E3S8R0_E3S8R0_PYRTT_861557 and tr_B2WKF0_B2WKF0_PYRTR_426418 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and sp_Q5RAZ2_SBDS_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_H2QUN6_H2QUN6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_F6VQ59_F6VQ59_HORSE_9796 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and sp_Q9Y3A5_SBDS_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_G7MP28_G7MP28_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_G7P1P9_G7P1P9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_A0A0D9S0A2_A0A0D9S0A2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_A0A1U7TID4_A0A1U7TID4_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_A0A2K5N2X7_A0A2K5N2X7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RSB1_G1RSB1_NOMLE_61853 and tr_A0A2K6BTP3_A0A2K6BTP3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_J3KM63_J3KM63_COCIM_246410 and tr_A0A0J7AXZ6_A0A0J7AXZ6_COCIT_404692 are exactly identical!
WARNING: Sequences tr_C0NX45_C0NX45_AJECG_447093 and tr_C6HI24_C6HI24_AJECH_544712 are exactly identical!
WARNING: Sequences tr_C0NX45_C0NX45_AJECG_447093 and tr_F0UH60_F0UH60_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_Q7RXW9_Q7RXW9_NEUCR_367110 and tr_G4UNR3_G4UNR3_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B8NXS8_B8NXS8_ASPFN_332952 and tr_Q2TYA0_Q2TYA0_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NXS8_B8NXS8_ASPFN_332952 and tr_A0A2G7FEW1_A0A2G7FEW1_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A179V006_A0A179V006_BLAGS_559298 and tr_C5GEU7_C5GEU7_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_A0A2I3SXQ2_A0A2I3SXQ2_PANTR_9598 and tr_A0A2I3TN52_A0A2I3TN52_PANTR_9598 are exactly identical!
WARNING: Sequences tr_W5PLQ9_W5PLQ9_SHEEP_9940 and tr_F1RJJ3_F1RJJ3_PIG_9823 are exactly identical!
WARNING: Sequences tr_F9FQA0_F9FQA0_FUSOF_660025 and tr_A0A0D2XDE7_A0A0D2XDE7_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FQA0_F9FQA0_FUSOF_660025 and tr_N4TM31_N4TM31_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FQA0_F9FQA0_FUSOF_660025 and tr_A0A2H3TCM9_A0A2H3TCM9_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FQA0_F9FQA0_FUSOF_660025 and tr_A0A2H3HDI4_A0A2H3HDI4_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_E9F0G3_E9F0G3_METRA_655844 and tr_A0A0B4I4H1_A0A0B4I4H1_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E4USD0_E4USD0_ARTGP_535722 and tr_A0A059J078_A0A059J078_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_J4KLR1_J4KLR1_BEAB2_655819 and tr_A0A0A2VP43_A0A0A2VP43_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4KLR1_J4KLR1_BEAB2_655819 and tr_A0A162JN90_A0A162JN90_9HYPO_1081107 are exactly identical!
WARNING: Sequences tr_J4KLR1_J4KLR1_BEAB2_655819 and tr_A0A2N6NE24_A0A2N6NE24_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A158P3W0_A0A158P3W0_ATTCE_12957 and tr_A0A195BKR1_A0A195BKR1_9HYME_520822 are exactly identical!
WARNING: Sequences tr_G9P7I4_G9P7I4_HYPAI_452589 and tr_A0A2P4Z837_A0A2P4Z837_9HYPO_398673 are exactly identical!
WARNING: Sequences tr_A0A286XSI9_A0A286XSI9_CAVPO_10141 and tr_A0A091DLS2_A0A091DLS2_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_A0A0E0I6D3_A0A0E0I6D3_ORYNI_4536 and tr_B8BA40_B8BA40_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0I6D3_A0A0E0I6D3_ORYNI_4536 and tr_A0A0E0QDE1_A0A0E0QDE1_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0I6D3_A0A0E0I6D3_ORYNI_4536 and tr_A0A0D3GVK2_A0A0D3GVK2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0I6D3_A0A0E0I6D3_ORYNI_4536 and tr_A0A0E0APY3_A0A0E0APY3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0I6D3_A0A0E0I6D3_ORYNI_4536 and tr_Q6ZD69_Q6ZD69_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A5AB22_A5AB22_ASPNC_425011 and tr_A0A319A496_A0A319A496_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7X7A1_G7X7A1_ASPKW_1033177 and tr_A0A100IU23_A0A100IU23_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7X7A1_G7X7A1_ASPKW_1033177 and tr_A0A317W4L5_A0A317W4L5_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_E5SX31_E5SX31_TRISP_6334 and tr_A0A0V0SAU2_A0A0V0SAU2_9BILA_6336 are exactly identical!
WARNING: Sequences tr_F9X2T2_F9X2T2_ZYMTI_336722 and tr_A0A0F4GVZ8_A0A0F4GVZ8_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9X2T2_F9X2T2_ZYMTI_336722 and tr_A0A1X7RJ08_A0A1X7RJ08_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YGS1_G2YGS1_BOTF4_999810 and tr_M7TMF3_M7TMF3_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2T0B6_F2T0B6_TRIRC_559305 and tr_A0A178F9E5_A0A178F9E5_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_D2HW33_D2HW33_AILME_9646 and tr_A0A384CQN4_A0A384CQN4_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G0RF41_G0RF41_HYPJQ_431241 and tr_A0A2T4B7H7_A0A2T4B7H7_9HYPO_58853 are exactly identical!
WARNING: Sequences tr_B3S4K1_B3S4K1_TRIAD_10228 and tr_A0A369S1W6_A0A369S1W6_9METZ_287889 are exactly identical!
WARNING: Sequences tr_W7NHN4_W7NHN4_GIBM7_334819 and tr_A0A2K0UTX2_A0A2K0UTX2_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_W7NHN4_W7NHN4_GIBM7_334819 and tr_A0A365MLE4_A0A365MLE4_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_L0PF44_L0PF44_PNEJ8_1209962 and tr_A0A0W4ZMC9_A0A0W4ZMC9_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_M3X604_M3X604_FELCA_9685 and tr_A0A096NY31_A0A096NY31_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_M4ETR1_M4ETR1_BRARP_51351 and tr_A0A078HUA2_A0A078HUA2_BRANA_3708 are exactly identical!
WARNING: Sequences tr_V2XZ85_V2XZ85_MONRO_1381753 and tr_A0A0W0FAB2_A0A0W0FAB2_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015K541_A0A015K541_9GLOM_1432141 and tr_U9UGB8_U9UGB8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A044V0V6_A0A044V0V6_ONCVO_6282 and tr_A0A182EH74_A0A182EH74_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A094DFU5_A0A094DFU5_9PEZI_1420910 and tr_A0A094EB61_A0A094EB61_9PEZI_1420912 are exactly identical!
WARNING: Sequences tr_A0A094DFU5_A0A094DFU5_9PEZI_1420910 and tr_A0A2P2SWB5_A0A2P2SWB5_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A094DFU5_A0A094DFU5_9PEZI_1420910 and tr_A0A1B8CCQ5_A0A1B8CCQ5_9PEZI_1622147 are exactly identical!
WARNING: Sequences tr_A0A0G0A1T4_A0A0G0A1T4_TRIHA_5544 and tr_A0A2T4APJ0_A0A2T4APJ0_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_A0A0N0DI41_A0A0N0DI41_FUSLA_179993 and tr_I1RRZ0_I1RRZ0_GIBZE_229533 are exactly identical!
WARNING: Sequences tr_A0A0N0DI41_A0A0N0DI41_FUSLA_179993 and tr_A0A2T4H3P2_A0A2T4H3P2_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A0N0DI41_A0A0N0DI41_FUSLA_179993 and tr_A0A366S042_A0A366S042_9HYPO_2109339 are exactly identical!
WARNING: Sequences tr_A0A091JKG9_A0A091JKG9_EGRGA_188379 and tr_A0A087QWJ1_A0A087QWJ1_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A0L9VKR6_A0A0L9VKR6_PHAAN_3914 and tr_A0A1S3TEC0_A0A1S3TEC0_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A093JX18_A0A093JX18_STRCA_441894 and tr_A0A099ZSN7_A0A099ZSN7_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A0G4P4L3_A0A0G4P4L3_PENCA_1429867 and tr_A0A117NRW4_A0A117NRW4_9EURO_48697 are exactly identical!
WARNING: Sequences tr_A0A0G4P4L3_A0A0G4P4L3_PENCA_1429867 and tr_A0A1V6N8L0_A0A1V6N8L0_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A0G4P4L3_A0A0G4P4L3_PENCA_1429867 and tr_A0A1V6RKB4_A0A1V6RKB4_9EURO_60172 are exactly identical!
WARNING: Sequences tr_A0A0V1KYD5_A0A0V1KYD5_9BILA_6335 and tr_A0A0V0U476_A0A0V0U476_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0ZQG5_A0A0V0ZQG5_9BILA_990121 and tr_A0A0V1NU68_A0A0V1NU68_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A164R641_A0A164R641_9HOMO_1314777 and tr_A0A166HL16_A0A166HL16_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S4CR99_A0A1S4CR99_TOBAC_4097 and tr_A0A1U7WF34_A0A1U7WF34_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3SZQ1_A0A1S3SZQ1_SALSA_8030 and tr_B5XEK1_B5XEK1_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1L9UP02_A0A1L9UP02_9EURO_767769 and tr_A0A395H7J3_A0A395H7J3_9EURO_1448316 are exactly identical!
WARNING: Sequences tr_A0A1L9WPK6_A0A1L9WPK6_ASPAC_690307 and tr_A0A319D8J0_A0A319D8J0_9EURO_1448315 are exactly identical!
WARNING: Sequences tr_A0A1L9WPK6_A0A1L9WPK6_ASPAC_690307 and tr_A0A2V5JAM1_A0A2V5JAM1_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A1L9WPK6_A0A1L9WPK6_ASPAC_690307 and tr_A0A2V5HG49_A0A2V5HG49_9EURO_1450538 are exactly identical!
WARNING: Sequences tr_A0A2G5I5V6_A0A2G5I5V6_CERBT_122368 and tr_A0A2S6BW23_A0A2S6BW23_9PEZI_357750 are exactly identical!
WARNING: Sequences tr_A0A2G4ST90_A0A2G4ST90_9FUNG_1340429 and tr_A0A367J4A2_A0A367J4A2_9FUNG_86630 are exactly identical!
WARNING: Duplicate sequences found: 80

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/Q9Y3A5/3_mltree/Q9Y3A5.raxml.reduced.phy

Alignment comprises 1 partitions and 241 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 241 / 241
Gaps: 4.80 %
Invariant sites: 0.41 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A5/3_mltree/Q9Y3A5.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 956 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 241 / 19280
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -339244.494255] Initial branch length optimization
[00:00:06 -291510.136332] Model parameter optimization (eps = 10.000000)
[00:00:51 -289958.962985] AUTODETECT spr round 1 (radius: 5)
[00:03:28 -203683.806333] AUTODETECT spr round 2 (radius: 10)
[00:06:15 -157810.541873] AUTODETECT spr round 3 (radius: 15)
[00:09:20 -131798.761810] AUTODETECT spr round 4 (radius: 20)
[00:12:45 -116822.952104] AUTODETECT spr round 5 (radius: 25)
[00:16:39 -115290.906448] SPR radius for FAST iterations: 25 (autodetect)
[00:16:39 -115290.906448] Model parameter optimization (eps = 3.000000)
[00:17:03 -115254.002259] FAST spr round 1 (radius: 25)
[00:20:21 -99783.224753] FAST spr round 2 (radius: 25)
[00:22:42 -99098.198770] FAST spr round 3 (radius: 25)
[00:24:48 -99056.523358] FAST spr round 4 (radius: 25)
[00:26:42 -99049.693471] FAST spr round 5 (radius: 25)
[00:28:30 -99049.690451] Model parameter optimization (eps = 1.000000)
[00:28:50 -99035.301236] SLOW spr round 1 (radius: 5)
[00:31:19 -99015.747568] SLOW spr round 2 (radius: 5)
[00:33:46 -99014.565541] SLOW spr round 3 (radius: 5)
[00:36:08 -99014.348062] SLOW spr round 4 (radius: 5)
[00:38:28 -99014.159827] SLOW spr round 5 (radius: 5)
[00:40:46 -99014.158564] SLOW spr round 6 (radius: 10)
[00:43:10 -99011.394599] SLOW spr round 7 (radius: 5)
[00:46:04 -99011.058362] SLOW spr round 8 (radius: 5)
[00:48:37 -99011.058167] SLOW spr round 9 (radius: 10)
[00:51:06 -99011.058157] SLOW spr round 10 (radius: 15)
[00:55:09 -99010.104523] SLOW spr round 11 (radius: 5)
[00:57:35] [worker #1] ML tree search #2, logLikelihood: -98987.811567
[00:58:17 -99009.134187] SLOW spr round 12 (radius: 5)
[01:00:56 -99009.134069] SLOW spr round 13 (radius: 10)
[01:03:27 -99009.134066] SLOW spr round 14 (radius: 15)
[01:07:29 -99009.134065] SLOW spr round 15 (radius: 20)
[01:12:54 -99009.134065] SLOW spr round 16 (radius: 25)
[01:18:50] [worker #4] ML tree search #5, logLikelihood: -98990.398329
[01:19:13 -99009.134065] Model parameter optimization (eps = 0.100000)

[01:19:24] [worker #0] ML tree search #1, logLikelihood: -99008.891624

[01:19:25 -339588.856542] Initial branch length optimization
[01:19:30 -292558.941264] Model parameter optimization (eps = 10.000000)
[01:20:10 -290911.624016] AUTODETECT spr round 1 (radius: 5)
[01:20:50] [worker #3] ML tree search #4, logLikelihood: -98978.398529
[01:22:51 -201510.164240] AUTODETECT spr round 2 (radius: 10)
[01:25:41 -154071.958532] AUTODETECT spr round 3 (radius: 15)
[01:28:55 -128152.969391] AUTODETECT spr round 4 (radius: 20)
[01:32:38 -118258.111550] AUTODETECT spr round 5 (radius: 25)
[01:36:52 -116688.030205] SPR radius for FAST iterations: 25 (autodetect)
[01:36:52 -116688.030205] Model parameter optimization (eps = 3.000000)
[01:37:18 -116655.679784] FAST spr round 1 (radius: 25)
[01:39:55] [worker #2] ML tree search #3, logLikelihood: -98970.054765
[01:40:41 -99669.709019] FAST spr round 2 (radius: 25)
[01:43:12 -99132.265415] FAST spr round 3 (radius: 25)
[01:45:24 -99080.600813] FAST spr round 4 (radius: 25)
[01:47:17 -99080.581675] Model parameter optimization (eps = 1.000000)
[01:47:36 -99048.363532] SLOW spr round 1 (radius: 5)
[01:50:15 -99002.252592] SLOW spr round 2 (radius: 5)
[01:52:45 -98997.569744] SLOW spr round 3 (radius: 5)
[01:55:13 -98993.759305] SLOW spr round 4 (radius: 5)
[01:57:32 -98993.757936] SLOW spr round 5 (radius: 10)
[01:58:59] [worker #1] ML tree search #7, logLikelihood: -98993.262842
[01:59:55 -98991.255631] SLOW spr round 6 (radius: 5)
[02:02:55 -98990.174761] SLOW spr round 7 (radius: 5)
[02:05:34 -98990.173775] SLOW spr round 8 (radius: 10)
[02:08:03 -98989.661719] SLOW spr round 9 (radius: 5)
[02:11:02 -98984.111501] SLOW spr round 10 (radius: 5)
[02:13:42 -98983.787942] SLOW spr round 11 (radius: 5)
[02:16:07 -98983.787067] SLOW spr round 12 (radius: 10)
[02:18:31 -98978.709070] SLOW spr round 13 (radius: 5)
[02:21:26 -98974.980343] SLOW spr round 14 (radius: 5)
[02:24:05 -98970.135322] SLOW spr round 15 (radius: 5)
[02:26:35 -98964.663043] SLOW spr round 16 (radius: 5)
[02:28:54 -98964.662106] SLOW spr round 17 (radius: 10)
[02:29:42] [worker #3] ML tree search #9, logLikelihood: -98982.045078
[02:31:16 -98964.662099] SLOW spr round 18 (radius: 15)
[02:34:51] [worker #4] ML tree search #10, logLikelihood: -98999.458528
[02:35:18 -98963.030376] SLOW spr round 19 (radius: 5)
[02:38:25 -98961.151673] SLOW spr round 20 (radius: 5)
[02:41:07 -98960.371780] SLOW spr round 21 (radius: 5)
[02:43:32 -98960.371682] SLOW spr round 22 (radius: 10)
[02:45:56 -98960.371677] SLOW spr round 23 (radius: 15)
[02:49:56 -98960.371676] SLOW spr round 24 (radius: 20)
[02:55:10 -98960.371676] SLOW spr round 25 (radius: 25)
[02:55:54] [worker #2] ML tree search #8, logLikelihood: -98984.133556
[02:57:04] [worker #1] ML tree search #12, logLikelihood: -98969.560771
[03:01:09 -98960.371676] Model parameter optimization (eps = 0.100000)

[03:01:26] [worker #0] ML tree search #6, logLikelihood: -98958.606370

[03:01:27 -338050.648494] Initial branch length optimization
[03:01:31 -289543.374974] Model parameter optimization (eps = 10.000000)
[03:02:13 -287902.753886] AUTODETECT spr round 1 (radius: 5)
[03:04:52 -206986.549130] AUTODETECT spr round 2 (radius: 10)
[03:07:38 -162856.372624] AUTODETECT spr round 3 (radius: 15)
[03:10:43 -130101.902436] AUTODETECT spr round 4 (radius: 20)
[03:14:21 -113952.648073] AUTODETECT spr round 5 (radius: 25)
[03:17:58 -112771.077201] SPR radius for FAST iterations: 25 (autodetect)
[03:17:58 -112771.077201] Model parameter optimization (eps = 3.000000)
[03:18:20 -112737.990751] FAST spr round 1 (radius: 25)
[03:21:30 -99849.506192] FAST spr round 2 (radius: 25)
[03:23:55 -99115.322322] FAST spr round 3 (radius: 25)
[03:26:06 -99063.244611] FAST spr round 4 (radius: 25)
[03:28:01 -99057.564773] FAST spr round 5 (radius: 25)
[03:29:50 -99053.777758] FAST spr round 6 (radius: 25)
[03:31:36 -99052.422842] FAST spr round 7 (radius: 25)
[03:33:19 -99052.422536] Model parameter optimization (eps = 1.000000)
[03:33:41 -99024.988468] SLOW spr round 1 (radius: 5)
[03:34:04] [worker #4] ML tree search #15, logLikelihood: -98984.375496
[03:36:09 -98994.588066] SLOW spr round 2 (radius: 5)
[03:38:16] [worker #3] ML tree search #14, logLikelihood: -98997.954084
[03:38:38 -98979.031391] SLOW spr round 3 (radius: 5)
[03:41:03 -98973.644793] SLOW spr round 4 (radius: 5)
[03:43:23 -98973.529048] SLOW spr round 5 (radius: 5)
[03:45:40 -98973.528427] SLOW spr round 6 (radius: 10)
[03:48:04 -98971.246634] SLOW spr round 7 (radius: 5)
[03:51:01 -98966.935097] SLOW spr round 8 (radius: 5)
[03:53:37 -98960.890700] SLOW spr round 9 (radius: 5)
[03:56:00 -98960.890075] SLOW spr round 10 (radius: 10)
[03:58:24 -98960.793905] SLOW spr round 11 (radius: 15)
[04:02:24 -98960.793307] SLOW spr round 12 (radius: 20)
[04:07:43] [worker #1] ML tree search #17, logLikelihood: -98993.843412
[04:07:46 -98960.792710] SLOW spr round 13 (radius: 25)
[04:14:00 -98960.792114] Model parameter optimization (eps = 0.100000)

[04:14:09] [worker #0] ML tree search #11, logLikelihood: -98960.763936

[04:14:09 -341812.396818] Initial branch length optimization
[04:14:10] [worker #2] ML tree search #13, logLikelihood: -99004.255159
[04:14:16 -292979.185535] Model parameter optimization (eps = 10.000000)
[04:15:17 -291380.906814] AUTODETECT spr round 1 (radius: 5)
[04:17:52 -202546.326473] AUTODETECT spr round 2 (radius: 10)
[04:20:56 -149617.428834] AUTODETECT spr round 3 (radius: 15)
[04:23:55 -129965.004307] AUTODETECT spr round 4 (radius: 20)
[04:27:16 -116893.269105] AUTODETECT spr round 5 (radius: 25)
[04:31:24 -113867.733210] SPR radius for FAST iterations: 25 (autodetect)
[04:31:24 -113867.733210] Model parameter optimization (eps = 3.000000)
[04:31:51 -113813.345027] FAST spr round 1 (radius: 25)
[04:35:10 -100087.190623] FAST spr round 2 (radius: 25)
[04:37:39 -99159.909837] FAST spr round 3 (radius: 25)
[04:39:44 -99078.955551] FAST spr round 4 (radius: 25)
[04:41:40 -99048.457382] FAST spr round 5 (radius: 25)
[04:43:27 -99047.238775] FAST spr round 6 (radius: 25)
[04:45:11 -99046.523316] FAST spr round 7 (radius: 25)
[04:46:54 -99046.523291] Model parameter optimization (eps = 1.000000)
[04:47:09 -99032.938652] SLOW spr round 1 (radius: 5)
[04:49:38 -98994.969670] SLOW spr round 2 (radius: 5)
[04:52:03 -98989.980305] SLOW spr round 3 (radius: 5)
[04:54:20] [worker #3] ML tree search #19, logLikelihood: -98973.703261
[04:54:21 -98987.456516] SLOW spr round 4 (radius: 5)
[04:56:37 -98987.455665] SLOW spr round 5 (radius: 10)
[04:59:00 -98985.221671] SLOW spr round 6 (radius: 5)
[05:02:01 -98984.722234] SLOW spr round 7 (radius: 5)
[05:04:36 -98984.722220] SLOW spr round 8 (radius: 10)
[05:07:06 -98984.722216] SLOW spr round 9 (radius: 15)
[05:11:16 -98984.179180] SLOW spr round 10 (radius: 5)
[05:14:18 -98984.178941] SLOW spr round 11 (radius: 10)
[05:17:06 -98984.178900] SLOW spr round 12 (radius: 15)
[05:21:01 -98984.178892] SLOW spr round 13 (radius: 20)
[05:26:52 -98979.991979] SLOW spr round 14 (radius: 5)
[05:28:11] [worker #4] ML tree search #20, logLikelihood: -98980.058653
[05:30:04 -98977.703970] SLOW spr round 15 (radius: 5)
[05:32:45 -98977.703601] SLOW spr round 16 (radius: 10)
[05:35:16 -98977.703599] SLOW spr round 17 (radius: 15)
[05:37:42] [worker #2] ML tree search #18, logLikelihood: -98982.805883
[05:39:11 -98977.703599] SLOW spr round 18 (radius: 20)
[05:44:51 -98977.703599] SLOW spr round 19 (radius: 25)
[05:51:38 -98977.703599] Model parameter optimization (eps = 0.100000)

[05:51:48] [worker #0] ML tree search #16, logLikelihood: -98977.553753


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.284539,0.463668) (0.178464,0.889546) (0.316648,0.875569) (0.220348,1.960844) 
   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: -98958.606370

AIC score: 201747.212741 / AICc score: 7540027.212741 / BIC score: 208420.598869
Free parameters (model + branch lengths): 1915

WARNING: Number of free parameters (K=1915) is larger than alignment size (n=241).
         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/Q9Y3A5/3_mltree/Q9Y3A5.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A5/3_mltree/Q9Y3A5.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A5/3_mltree/Q9Y3A5.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A5/3_mltree/Q9Y3A5.raxml.log

Analysis started: 15-Jul-2021 05:52:01 / finished: 15-Jul-2021 11:43:50

Elapsed time: 21109.096 seconds

Consumed energy: 1744.099 Wh (= 9 km in an electric car, or 44 km with an e-scooter!)