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

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

RAxML-NG was called at 17-Jun-2021 23:40:31 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/2_msa/P49768_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/2_msa/P49768_trimmed_msa.fasta
[00:00:00] Loaded alignment with 629 taxa and 275 sites

WARNING: Sequences tr_B4QRZ4_B4QRZ4_DROSI_7240 and sp_O02194_PSN_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QRZ4_B4QRZ4_DROSI_7240 and tr_B4IAA8_B4IAA8_DROSE_7238 are exactly identical!
WARNING: Sequences tr_F1NGP7_F1NGP7_CHICK_9031 and tr_G1N2Q5_G1N2Q5_MELGA_9103 are exactly identical!
WARNING: Sequences sp_Q4JIM4_PSN1_CHICK_9031 and tr_G1NGN7_G1NGN7_MELGA_9103 are exactly identical!
WARNING: Sequences tr_M3YWN2_M3YWN2_MUSPF_9669 and tr_A0A2Y9K2F5_A0A2Y9K2F5_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2J8T4E5_A0A2J8T4E5_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and sp_Q5R780_PSN1_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_H2Q8K1_H2Q8K1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A287CTD7_A0A287CTD7_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and sp_P49768_PSN1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_F7AGU8_F7AGU8_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_G7PAT1_G7PAT1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2I3LNK2_A0A2I3LNK2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A0D9RK10_A0A0D9RK10_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K5N1F1_A0A2K5N1F1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K6CVX6_A0A2K6CVX6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K5YUS1_A0A2K5YUS1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2R9BSY5_A0A2R9BSY5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3HNF2_G3HNF2_CRIGR_10029 and tr_A0A1U7QI63_A0A1U7QI63_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A2J8U215_A0A2J8U215_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and sp_P49810_PSN2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_F7A2E1_F7A2E1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_F7GCJ5_F7GCJ5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_G7P3N8_G7P3N8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A096MR14_A0A096MR14_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A0D9RUZ9_A0A0D9RUZ9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A2K5NYW1_A0A2K5NYW1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A2K6CMA8_A0A2K6CMA8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and tr_A0A2K5XVZ1_A0A2K5XVZ1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0R3P728_A0A0R3P728_DROPS_46245 and tr_B4H7M0_B4H7M0_DROPE_7234 are exactly identical!
WARNING: Sequences tr_F1PHD2_F1PHD2_CANLF_9615 and tr_M3WQU7_M3WQU7_FELCA_9685 are exactly identical!
WARNING: Sequences tr_F1PHD2_F1PHD2_CANLF_9615 and tr_A0A2U3VVJ2_A0A2U3VVJ2_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F1PHD2_F1PHD2_CANLF_9615 and tr_A0A2Y9JP29_A0A2Y9JP29_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_F1PWY2_F1PWY2_CANLF_9615 and tr_A0A337S513_A0A337S513_FELCA_9685 are exactly identical!
WARNING: Sequences tr_F1PWY2_F1PWY2_CANLF_9615 and tr_A0A2U3VGA1_A0A2U3VGA1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_H2R821_H2R821_PANTR_9598 and tr_A0A2R9A5I7_A0A2R9A5I7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5NTE9_W5NTE9_SHEEP_9940 and sp_Q9XT96_PSN2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5QKL3_A0A3B5QKL3_XIPMA_8083 and tr_A0A096LTC9_A0A096LTC9_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A158NMP7_A0A158NMP7_ATTCE_12957 and tr_A0A151X1I3_A0A151X1I3_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A158NMP7_A0A158NMP7_ATTCE_12957 and tr_A0A195DBK4_A0A195DBK4_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158NMP7_A0A158NMP7_ATTCE_12957 and tr_A0A151I5D9_A0A151I5D9_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NMP7_A0A158NMP7_ATTCE_12957 and tr_A0A151JTA9_A0A151JTA9_9HYME_34720 are exactly identical!
WARNING: Sequences tr_I3N481_I3N481_ICTTR_43179 and tr_A0A1S3AGI8_A0A1S3AGI8_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_I3N481_I3N481_ICTTR_43179 and tr_A0A1U7UNU2_A0A1U7UNU2_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_A0A0E0FK13_A0A0E0FK13_ORYNI_4536 and tr_A0A0E0MUL4_A0A0E0MUL4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GQC9_A0A0E0GQC9_ORYNI_4536 and tr_A0A0E0NY02_A0A0E0NY02_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GQC9_A0A0E0GQC9_ORYNI_4536 and tr_A0A0D9ZAC7_A0A0D9ZAC7_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0GQC9_A0A0E0GQC9_ORYNI_4536 and tr_C7J054_C7J054_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0K0JC50_A0A0K0JC50_BRUMA_6279 and tr_A0A0R3QZ14_A0A0R3QZ14_9BILA_42155 are exactly identical!
WARNING: Sequences tr_H0Z1M3_H0Z1M3_TAEGU_59729 and tr_U3KAI4_U3KAI4_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0Z1M3_H0Z1M3_TAEGU_59729 and tr_A0A218UJM5_A0A218UJM5_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A8X5S7_A8X5S7_CAEBR_6238 and tr_A0A2G5SJB1_A0A2G5SJB1_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_M4DPB3_M4DPB3_BRARP_51351 and tr_A0A078J4P4_A0A078J4P4_BRANA_3708 are exactly identical!
WARNING: Sequences tr_U3JSE4_U3JSE4_FICAL_59894 and tr_A0A087R222_A0A087R222_APTFO_9233 are exactly identical!
WARNING: Sequences tr_U3JSE4_U3JSE4_FICAL_59894 and tr_A0A099ZX37_A0A099ZX37_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A015ICJ2_A0A015ICJ2_9GLOM_1432141 and tr_A0A2I1FXT3_A0A2I1FXT3_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015ICJ2_A0A015ICJ2_9GLOM_1432141 and tr_U9UMQ1_U9UMQ1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A067FHZ3_A0A067FHZ3_CITSI_2711 and tr_A0A2H5QAG8_A0A2H5QAG8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4TFW0_V4TFW0_9ROSI_85681 and tr_A0A2H5PEB7_A0A2H5PEB7_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2LVY9_A0A0D2LVY9_GOSRA_29730 and tr_A0A1U8P253_A0A1U8P253_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2PEP2_A0A0D2PEP2_GOSRA_29730 and tr_A0A1U8I1H6_A0A1U8I1H6_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2PEP2_A0A0D2PEP2_GOSRA_29730 and tr_A0A1U8NMF4_A0A1U8NMF4_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0K0FPP6_A0A0K0FPP6_STRVS_75913 and tr_A0A0N5B409_A0A0N5B409_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A0W8C6W5_A0A0W8C6W5_PHYNI_4790 and tr_A0A0W8CMZ3_A0A0W8CMZ3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A091F513_A0A091F513_CORBR_85066 and tr_A0A091W1P6_A0A091W1P6_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091F513_A0A091F513_CORBR_85066 and tr_A0A093GE51_A0A093GE51_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A091IT10_A0A091IT10_EGRGA_188379 and tr_A0A091WVW2_A0A091WVW2_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091IT10_A0A091IT10_EGRGA_188379 and tr_A0A087RE79_A0A087RE79_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091IT10_A0A091IT10_EGRGA_188379 and tr_A0A091GJT9_A0A091GJT9_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A0L9U7A0_A0A0L9U7A0_PHAAN_3914 and tr_A0A1S3TBJ8_A0A1S3TBJ8_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A091FMF9_A0A091FMF9_9AVES_55661 and tr_A0A2I0MNS4_A0A2I0MNS4_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A091FMF9_A0A091FMF9_9AVES_55661 and tr_A0A091IKP7_A0A091IKP7_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A091FMF9_A0A091FMF9_9AVES_55661 and tr_A0A1V4KEW2_A0A1V4KEW2_PATFA_372326 are exactly identical!
WARNING: Sequences tr_R7VWX4_R7VWX4_COLLI_8932 and tr_A0A1V4JJ63_A0A1V4JJ63_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V0S949_A0A0V0S949_9BILA_6336 and tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0S949_A0A0V0S949_9BILA_6336 and tr_A0A0V0UQH5_A0A0V0UQH5_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0S949_A0A0V0S949_9BILA_6336 and tr_A0A0V1LU29_A0A0V1LU29_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0S949_A0A0V0S949_9BILA_6336 and tr_A0A0V1AGD8_A0A0V1AGD8_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0S949_A0A0V0S949_9BILA_6336 and tr_A0A0V1NV59_A0A0V1NV59_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0S949_A0A0V0S949_9BILA_6336 and tr_A0A0V0TJL5_A0A0V0TJL5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S3XK05_A0A1S3XK05_TOBAC_4097 and tr_A0A1S4AXB7_A0A1S4AXB7_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3XK05_A0A1S3XK05_TOBAC_4097 and tr_A0A314L6V0_A0A314L6V0_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S3XK05_A0A1S3XK05_TOBAC_4097 and tr_A0A1U7VCP0_A0A1U7VCP0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3ZTL3_A0A1S3ZTL3_TOBAC_4097 and tr_A0A1U7VRH0_A0A1U7VRH0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1Y1XJK0_A0A1Y1XJK0_9FUNG_1314790 and tr_A0A1Y1Y376_A0A1Y1Y376_9FUNG_1314790 are exactly identical!
WARNING: Sequences tr_A0A2D0Q228_A0A2D0Q228_ICTPU_7998 and tr_A0A2D0Q3B7_A0A2D0Q3B7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RMH4_A0A2D0RMH4_ICTPU_7998 and tr_A0A2D0RNI1_A0A2D0RNI1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2P5D8X3_A0A2P5D8X3_TREOI_63057 and tr_A0A2P5DB73_A0A2P5DB73_PARAD_3476 are exactly identical!
WARNING: Sequences tr_A0A2U4A8E9_A0A2U4A8E9_TURTR_9739 and tr_A0A2Y9NSH6_A0A2Y9NSH6_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4A8E9_A0A2U4A8E9_TURTR_9739 and tr_A0A2Y9EQM3_A0A2Y9EQM3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4A8E9_A0A2U4A8E9_TURTR_9739 and tr_A0A384AB18_A0A384AB18_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 91

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.reduced.phy

Alignment comprises 1 partitions and 275 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 275 / 275
Gaps: 6.96 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.rba

Parallelization scheme autoconfig: 6 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 629 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 275 / 22000
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -244701.806476] Initial branch length optimization
[00:00:06 -185246.308160] Model parameter optimization (eps = 10.000000)
[00:00:52 -185127.407515] AUTODETECT spr round 1 (radius: 5)
[00:02:35 -133813.175595] AUTODETECT spr round 2 (radius: 10)
[00:05:51 -107174.138902] AUTODETECT spr round 3 (radius: 15)
[00:10:35 -92280.712001] AUTODETECT spr round 4 (radius: 20)
[00:14:02 -85934.170444] AUTODETECT spr round 5 (radius: 25)
[00:17:37 -79122.479964] SPR radius for FAST iterations: 25 (autodetect)
[00:17:37 -79122.479964] Model parameter optimization (eps = 3.000000)
[00:19:44 -78509.710693] FAST spr round 1 (radius: 25)
[00:22:08 -65488.767233] FAST spr round 2 (radius: 25)
[00:24:25 -64912.143864] FAST spr round 3 (radius: 25)
[00:26:00 -64843.063945] FAST spr round 4 (radius: 25)
[00:28:08 -64833.920455] FAST spr round 5 (radius: 25)
[00:29:16 -64833.562291] FAST spr round 6 (radius: 25)
[00:30:23 -64833.560083] Model parameter optimization (eps = 1.000000)
[00:30:56 -64825.551383] SLOW spr round 1 (radius: 5)
[00:33:52 -64799.763242] SLOW spr round 2 (radius: 5)
[00:36:00 -64793.216596] SLOW spr round 3 (radius: 5)
[00:39:01 -64791.194922] SLOW spr round 4 (radius: 5)
[00:40:30 -64791.194405] SLOW spr round 5 (radius: 10)
[00:43:14 -64791.194069] SLOW spr round 6 (radius: 15)
[00:46:57 -64791.193843] SLOW spr round 7 (radius: 20)
[00:51:35 -64791.193682] SLOW spr round 8 (radius: 25)
[00:58:13 -64791.193560] Model parameter optimization (eps = 0.100000)

[00:58:26] [worker #0] ML tree search #1, logLikelihood: -64791.023352

[00:58:26 -241196.616620] Initial branch length optimization
[00:58:41 -185513.733431] Model parameter optimization (eps = 10.000000)
[00:59:50] [worker #5] ML tree search #6, logLikelihood: -65310.949464
[01:01:00 -185402.557044] AUTODETECT spr round 1 (radius: 5)
[01:04:02 -134343.317177] AUTODETECT spr round 2 (radius: 10)
[01:06:20 -105174.654876] AUTODETECT spr round 3 (radius: 15)
[01:09:19 -90480.848811] AUTODETECT spr round 4 (radius: 20)
[01:12:45 -81575.083630] AUTODETECT spr round 5 (radius: 25)
[01:15:43 -79496.427972] SPR radius for FAST iterations: 25 (autodetect)
[01:15:43 -79496.427972] Model parameter optimization (eps = 3.000000)
[01:17:33 -78858.445265] FAST spr round 1 (radius: 25)
[01:23:53 -66198.981803] FAST spr round 2 (radius: 25)
[01:25:38 -64863.760356] FAST spr round 3 (radius: 25)
[01:27:15 -64814.115679] FAST spr round 4 (radius: 25)
[01:28:40 -64811.019577] FAST spr round 5 (radius: 25)
[01:29:50 -64811.018502] Model parameter optimization (eps = 1.000000)
[01:30:06 -64805.583962] SLOW spr round 1 (radius: 5)
[01:31:54 -64791.775665] SLOW spr round 2 (radius: 5)
[01:33:34 -64785.658639] SLOW spr round 3 (radius: 5)
[01:35:08 -64785.657417] SLOW spr round 4 (radius: 10)
[01:36:53] [worker #3] ML tree search #4, logLikelihood: -64790.218309
[01:36:55 -64785.059943] SLOW spr round 5 (radius: 5)
[01:37:28] [worker #4] ML tree search #5, logLikelihood: -64769.425098
[01:39:33 -64785.059263] SLOW spr round 6 (radius: 10)
[01:41:27 -64785.059140] SLOW spr round 7 (radius: 15)
[01:44:04 -64785.059055] SLOW spr round 8 (radius: 20)
[01:45:26] [worker #2] ML tree search #3, logLikelihood: -64767.206650
[01:48:45 -64785.058985] SLOW spr round 9 (radius: 25)
[01:58:01 -64785.058919] Model parameter optimization (eps = 0.100000)

[01:58:15] [worker #0] ML tree search #7, logLikelihood: -64784.414268

[01:58:16 -240510.598524] Initial branch length optimization
[01:58:31 -184832.382763] Model parameter optimization (eps = 10.000000)
[01:59:38 -184685.438641] AUTODETECT spr round 1 (radius: 5)
[02:03:41 -137249.736955] AUTODETECT spr round 2 (radius: 10)
[02:04:23] [worker #1] ML tree search #2, logLikelihood: -64796.324194
[02:06:48] [worker #5] ML tree search #12, logLikelihood: -64786.688657
[02:07:19 -109946.154664] AUTODETECT spr round 3 (radius: 15)
[02:11:57 -87851.603084] AUTODETECT spr round 4 (radius: 20)
[02:16:31 -78076.382763] AUTODETECT spr round 5 (radius: 25)
[02:19:37 -77399.154731] SPR radius for FAST iterations: 25 (autodetect)
[02:19:37 -77399.154731] Model parameter optimization (eps = 3.000000)
[02:20:57 -76655.884744] FAST spr round 1 (radius: 25)
[02:24:19 -65879.177514] FAST spr round 2 (radius: 25)
[02:27:12 -64930.282684] FAST spr round 3 (radius: 25)
[02:30:04 -64843.930395] FAST spr round 4 (radius: 25)
[02:32:04 -64839.749132] FAST spr round 5 (radius: 25)
[02:33:13 -64836.428628] FAST spr round 6 (radius: 25)
[02:35:13 -64836.428562] Model parameter optimization (eps = 1.000000)
[02:35:53 -64825.422311] SLOW spr round 1 (radius: 5)
[02:37:54 -64796.005613] SLOW spr round 2 (radius: 5)
[02:39:29 -64795.747147] SLOW spr round 3 (radius: 5)
[02:41:05 -64795.484172] SLOW spr round 4 (radius: 5)
[02:43:34 -64795.482933] SLOW spr round 5 (radius: 10)
[02:47:16 -64792.569461] SLOW spr round 6 (radius: 5)
[02:50:12 -64785.366588] SLOW spr round 7 (radius: 5)
[02:52:37 -64785.364854] SLOW spr round 8 (radius: 10)
[02:58:06 -64785.364572] SLOW spr round 9 (radius: 15)
[03:01:29 -64785.364466] SLOW spr round 10 (radius: 20)
[03:07:38 -64784.625307] SLOW spr round 11 (radius: 5)
[03:10:23 -64784.625152] SLOW spr round 12 (radius: 10)
[03:13:06 -64784.625083] SLOW spr round 13 (radius: 15)
[03:18:01] [worker #4] ML tree search #11, logLikelihood: -64797.424708
[03:20:34 -64784.625018] SLOW spr round 14 (radius: 20)
[03:23:55] [worker #3] ML tree search #10, logLikelihood: -64802.296823
[03:26:42 -64784.624955] SLOW spr round 15 (radius: 25)
[03:30:11] [worker #1] ML tree search #8, logLikelihood: -64781.002815
[03:32:54] [worker #2] ML tree search #9, logLikelihood: -64788.210761
[03:34:58 -64784.624893] Model parameter optimization (eps = 0.100000)

[03:35:18] [worker #0] ML tree search #13, logLikelihood: -64783.611015

[03:35:18 -242502.253013] Initial branch length optimization
[03:35:27 -185571.106779] Model parameter optimization (eps = 10.000000)
[03:36:54 -185392.769806] AUTODETECT spr round 1 (radius: 5)
[03:40:00 -134569.178233] AUTODETECT spr round 2 (radius: 10)
[03:40:34] [worker #5] ML tree search #18, logLikelihood: -64811.480640
[03:42:25 -111043.739980] AUTODETECT spr round 3 (radius: 15)
[03:45:59 -99512.856043] AUTODETECT spr round 4 (radius: 20)
[03:48:57 -84880.592863] AUTODETECT spr round 5 (radius: 25)
[03:55:58 -78763.056683] SPR radius for FAST iterations: 25 (autodetect)
[03:55:58 -78763.056683] Model parameter optimization (eps = 3.000000)
[03:57:11 -78206.745672] FAST spr round 1 (radius: 25)
[03:59:45 -65622.603106] FAST spr round 2 (radius: 25)
[04:02:49 -64926.662919] FAST spr round 3 (radius: 25)
[04:04:58 -64878.492910] FAST spr round 4 (radius: 25)
[04:07:31 -64854.827124] FAST spr round 5 (radius: 25)
[04:09:53 -64839.511807] FAST spr round 6 (radius: 25)
[04:12:32 -64837.543111] FAST spr round 7 (radius: 25)
[04:14:54 -64837.539599] Model parameter optimization (eps = 1.000000)
[04:15:41 -64816.972294] SLOW spr round 1 (radius: 5)
[04:19:45 -64789.276323] SLOW spr round 2 (radius: 5)
[04:22:41 -64785.401078] SLOW spr round 3 (radius: 5)
[04:24:41 -64784.856116] SLOW spr round 4 (radius: 5)
[04:28:09 -64784.855266] SLOW spr round 5 (radius: 10)
[04:30:42 -64781.117026] SLOW spr round 6 (radius: 5)
[04:33:06 -64778.788396] SLOW spr round 7 (radius: 5)
[04:38:23 -64778.787927] SLOW spr round 8 (radius: 10)
[04:43:27 -64778.787822] SLOW spr round 9 (radius: 15)
[04:43:32] [worker #4] ML tree search #17, logLikelihood: -64777.720742
[04:47:40 -64778.787751] SLOW spr round 10 (radius: 20)
[04:51:48] [worker #2] ML tree search #15, logLikelihood: -64783.511171
[04:52:59 -64778.787687] SLOW spr round 11 (radius: 25)
[05:03:44 -64778.787626] Model parameter optimization (eps = 0.100000)

[05:04:05] [worker #0] ML tree search #19, logLikelihood: -64778.291766

[05:06:49] [worker #3] ML tree search #16, logLikelihood: -64784.754240
[05:36:11] [worker #1] ML tree search #14, logLikelihood: -64788.025071
[07:14:59] [worker #1] ML tree search #20, logLikelihood: -64786.812161

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.373488,0.605306) (0.274919,1.344449) (0.294523,1.004426) (0.057070,1.900898) 
   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: -64767.206650

AIC score: 132056.413299 / AICc score: 3314820.413299 / BIC score: 136617.161653
Free parameters (model + branch lengths): 1261

WARNING: Number of free parameters (K=1261) is larger than alignment size (n=275).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 139 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P49768/3_mltree/P49768.raxml.log

Analysis started: 17-Jun-2021 23:40:31 / finished: 18-Jun-2021 06:55:31

Elapsed time: 26099.898 seconds