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 01-Jul-2021 13:08:18 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/2_msa/Q6XUX3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/3_mltree/Q6XUX3 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/2_msa/Q6XUX3_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 281 sites

WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and sp_Q4VSN5_DUSTY_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_F7BH26_F7BH26_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_G7NVD5_G7NVD5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_A0A096MT06_A0A096MT06_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_A0A0D9RQ46_A0A0D9RQ46_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_A0A2K5MWD9_A0A2K5MWD9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_A0A2K6DRZ1_A0A2K6DRZ1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_A0A2K5Z4A5_A0A2K5Z4A5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2N406_H2N406_PONAB_9601 and tr_A0A2R9AWM3_A0A2R9AWM3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K4BKS3_K4BKS3_SOLLC_4081 and tr_M1CAB1_M1CAB1_SOLTU_4113 are exactly identical!
WARNING: Sequences sp_Q1L6Q1_DUSTY_APIME_7460 and tr_A0A2A3EDW5_A0A2A3EDW5_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158ND34_A0A158ND34_ATTCE_12957 and tr_F4X0G5_F4X0G5_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A0E0GQW9_A0A0E0GQW9_ORYNI_4536 and tr_A2XJY2_A2XJY2_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0GQW9_A0A0E0GQW9_ORYNI_4536 and tr_I1PDS2_I1PDS2_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GQW9_A0A0E0GQW9_ORYNI_4536 and tr_A0A0E0D3Z8_A0A0E0D3Z8_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0GQW9_A0A0E0GQW9_ORYNI_4536 and tr_A0A0E0NYN0_A0A0E0NYN0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GQW9_A0A0E0GQW9_ORYNI_4536 and tr_A0A0D3FLL4_A0A0D3FLL4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0GQW9_A0A0E0GQW9_ORYNI_4536 and tr_A0A0D9ZAU8_A0A0D9ZAU8_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0GQW9_A0A0E0GQW9_ORYNI_4536 and tr_Q75J49_Q75J49_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0GTK8_A0A0E0GTK8_ORYNI_4536 and tr_I1PFE7_I1PFE7_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HIX4_A0A0E0HIX4_ORYNI_4536 and tr_A2Y7U2_A2Y7U2_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HIX4_A0A0E0HIX4_ORYNI_4536 and tr_I1PY82_I1PY82_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HIX4_A0A0E0HIX4_ORYNI_4536 and tr_A0A0D3GB69_A0A0D3GB69_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0HIX4_A0A0E0HIX4_ORYNI_4536 and tr_Q6L5F3_Q6L5F3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2WT32_A2WT32_ORYSI_39946 and tr_A0A0E0MZU9_A0A0E0MZU9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A2WT32_A2WT32_ORYSI_39946 and tr_Q8LQ53_Q8LQ53_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1NQ10_I1NQ10_ORYGL_4538 and tr_A0A0D9YC79_A0A0D9YC79_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0PRM9_A0A0E0PRM9_ORYRU_4529 and tr_A0A0E0A366_A0A0E0A366_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0R0ERG6_A0A0R0ERG6_SOYBN_3847 and tr_I1M016_I1M016_SOYBN_3847 are exactly identical!
WARNING: Sequences tr_F2E112_F2E112_HORVV_112509 and tr_A0A3B5Z5X1_A0A3B5Z5X1_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_M4C8S7_M4C8S7_BRARP_51351 and tr_A0A078G9L9_A0A078G9L9_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4C8S7_M4C8S7_BRARP_51351 and tr_W8RGQ3_W8RGQ3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4C8S7_M4C8S7_BRARP_51351 and tr_A0A0D3B7N9_A0A0D3B7N9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4CU44_M4CU44_BRARP_51351 and tr_A0A078IX70_A0A078IX70_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4E4V7_M4E4V7_BRARP_51351 and tr_A0A078J0M8_A0A078J0M8_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4E4V7_M4E4V7_BRARP_51351 and tr_A0A0D3ABI1_A0A0D3ABI1_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4EYM9_M4EYM9_BRARP_51351 and tr_V9LY60_V9LY60_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4EYM9_M4EYM9_BRARP_51351 and tr_A0A0D3CH42_A0A0D3CH42_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4F7U1_M4F7U1_BRARP_51351 and tr_A0A078J1L3_A0A078J1L3_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4FDE3_M4FDE3_BRARP_51351 and tr_A0A078HI79_A0A078HI79_BRANA_3708 are exactly identical!
WARNING: Sequences tr_W2PW01_W2PW01_PHYPN_761204 and tr_W2KRX8_W2KRX8_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A077RY41_A0A077RY41_WHEAT_4565 and tr_A0A3B6EH77_A0A3B6EH77_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A077RY41_A0A077RY41_WHEAT_4565 and tr_A0A3B6GRQ5_A0A3B6GRQ5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B6KP76_A0A3B6KP76_WHEAT_4565 and tr_A0A3B6LSV2_A0A3B6LSV2_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B6KP76_A0A3B6KP76_WHEAT_4565 and tr_A0A3B6MW69_A0A3B6MW69_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A015I8D0_A0A015I8D0_9GLOM_1432141 and tr_A0A2H5RR30_A0A2H5RR30_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015ICU0_A0A015ICU0_9GLOM_1432141 and tr_A0A2H5RIX2_A0A2H5RIX2_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015IFM8_A0A015IFM8_9GLOM_1432141 and tr_A0A2H5TXF6_A0A2H5TXF6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015IL66_A0A015IL66_9GLOM_1432141 and tr_A0A2H5RGP3_A0A2H5RGP3_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015IRF2_A0A015IRF2_9GLOM_1432141 and tr_A0A2H5SKZ0_A0A2H5SKZ0_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015J3P8_A0A015J3P8_9GLOM_1432141 and tr_A0A2H5UIA6_A0A2H5UIA6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015J3R3_A0A015J3R3_9GLOM_1432141 and tr_A0A2H5R2R8_A0A2H5R2R8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JCS0_A0A015JCS0_9GLOM_1432141 and tr_A0A2H5TX81_A0A2H5TX81_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JEG5_A0A015JEG5_9GLOM_1432141 and tr_A0A2H5R2Z1_A0A2H5R2Z1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JEH0_A0A015JEH0_9GLOM_1432141 and tr_A0A2H5R2Z4_A0A2H5R2Z4_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JQ81_A0A015JQ81_9GLOM_1432141 and tr_A0A2H5SB47_A0A2H5SB47_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JS95_A0A015JS95_9GLOM_1432141 and tr_A0A2H5RGR6_A0A2H5RGR6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JTA5_A0A015JTA5_9GLOM_1432141 and tr_A0A2H5RQV9_A0A2H5RQV9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JTM1_A0A015JTM1_9GLOM_1432141 and tr_A0A2H5RGZ9_A0A2H5RGZ9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015JW51_A0A015JW51_9GLOM_1432141 and tr_A0A2H5SFT2_A0A2H5SFT2_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015K0W5_A0A015K0W5_9GLOM_1432141 and tr_A0A2H5TF15_A0A2H5TF15_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015K8N5_A0A015K8N5_9GLOM_1432141 and tr_A0A2H5U175_A0A2H5U175_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015K8Q8_A0A015K8Q8_9GLOM_1432141 and tr_A0A2H5RJ13_A0A2H5RJ13_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015KBU3_A0A015KBU3_9GLOM_1432141 and tr_A0A2H5U5G8_A0A2H5U5G8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015KQL9_A0A015KQL9_9GLOM_1432141 and tr_A0A2H5SFW8_A0A2H5SFW8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015L4X5_A0A015L4X5_9GLOM_1432141 and tr_A0A2H5S6A0_A0A2H5S6A0_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015L7T6_A0A015L7T6_9GLOM_1432141 and tr_U9SQU7_U9SQU7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LEK6_A0A015LEK6_9GLOM_1432141 and tr_A0A2H5TAA0_A0A2H5TAA0_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LF03_A0A015LF03_9GLOM_1432141 and tr_A0A2H5QZE9_A0A2H5QZE9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LFU7_A0A015LFU7_9GLOM_1432141 and tr_A0A2H5TCH8_A0A2H5TCH8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LLN3_A0A015LLN3_9GLOM_1432141 and tr_A0A2H5R906_A0A2H5R906_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LMQ0_A0A015LMQ0_9GLOM_1432141 and tr_A0A2H5RDM9_A0A2H5RDM9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015LZ87_A0A015LZ87_9GLOM_1432141 and tr_A0A2H5R2U8_A0A2H5R2U8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015M1L6_A0A015M1L6_9GLOM_1432141 and tr_A0A2H5TB01_A0A2H5TB01_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015MDB2_A0A015MDB2_9GLOM_1432141 and tr_A0A2H5SQH6_A0A2H5SQH6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015MMH9_A0A015MMH9_9GLOM_1432141 and tr_A0A2H5U509_A0A2H5U509_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015N4G0_A0A015N4G0_9GLOM_1432141 and tr_A0A2H5R2D0_A0A2H5R2D0_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015N738_A0A015N738_9GLOM_1432141 and tr_A0A2H5T601_A0A2H5T601_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A067G7A6_A0A067G7A6_CITSI_2711 and tr_A0A2H5Q133_A0A2H5Q133_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A078IJ07_A0A078IJ07_BRANA_3708 and tr_A0A0D3CND5_A0A0D3CND5_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_V4U6L8_V4U6L8_9ROSI_85681 and tr_A0A2H5P2Y6_A0A2H5P2Y6_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2P4R3_A0A0D2P4R3_GOSRA_29730 and tr_A0A1U8JY54_A0A1U8JY54_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2QSC7_A0A0D2QSC7_GOSRA_29730 and tr_A0A1U8L2W6_A0A1U8L2W6_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A091JAZ1_A0A091JAZ1_EGRGA_188379 and tr_A0A091W6H1_A0A091W6H1_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JAZ1_A0A091JAZ1_EGRGA_188379 and tr_A0A091VKR8_A0A091VKR8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091JAZ1_A0A091JAZ1_EGRGA_188379 and tr_A0A0A0APL1_A0A0A0APL1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091JAZ1_A0A091JAZ1_EGRGA_188379 and tr_A0A091J0B4_A0A091J0B4_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A0L9VNY1_A0A0L9VNY1_PHAAN_3914 and tr_A0A1S3VB44_A0A1S3VB44_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A2I0LZV0_A0A2I0LZV0_COLLI_8932 and tr_A0A1V4J1Q1_A0A1V4J1Q1_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3YCC6_A0A1S3YCC6_TOBAC_4097 and tr_A0A1U7YH29_A0A1U7YH29_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3ZGY5_A0A1S3ZGY5_TOBAC_4097 and tr_A0A1U7YPC1_A0A1U7YPC1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4A4B3_A0A1S4A4B3_TOBAC_4097 and tr_A0A1U7YIU1_A0A1U7YIU1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4AGA3_A0A1S4AGA3_TOBAC_4097 and tr_A0A1S4ATC7_A0A1S4ATC7_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S4AGA3_A0A1S4AGA3_TOBAC_4097 and tr_A0A1J6ICX3_A0A1J6ICX3_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S4BYJ1_A0A1S4BYJ1_TOBAC_4097 and tr_A0A1U7XC99_A0A1U7XC99_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A226NHM6_A0A226NHM6_CALSU_9009 and tr_A0A226PXT9_A0A226PXT9_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A1U8H4L3_A0A1U8H4L3_CAPAN_4072 and tr_A0A2G3C9N3_A0A2G3C9N3_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2U3ZYL8_A0A2U3ZYL8_TURTR_9739 and tr_A0A384A671_A0A384A671_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 98

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/Q6XUX3/3_mltree/Q6XUX3.raxml.reduced.phy

Alignment comprises 1 partitions and 281 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 281 / 281
Gaps: 6.76 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/3_mltree/Q6XUX3.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 281 / 22480
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -482420.761976] Initial branch length optimization
[00:00:06 -382630.174618] Model parameter optimization (eps = 10.000000)
[00:01:09 -381555.441911] AUTODETECT spr round 1 (radius: 5)
[00:05:00 -244047.896483] AUTODETECT spr round 2 (radius: 10)
[00:09:20 -189830.531327] AUTODETECT spr round 3 (radius: 15)
[00:13:53 -157730.525684] AUTODETECT spr round 4 (radius: 20)
[00:18:50 -146779.742041] AUTODETECT spr round 5 (radius: 25)
[00:24:52 -140336.837617] SPR radius for FAST iterations: 25 (autodetect)
[00:24:52 -140336.837617] Model parameter optimization (eps = 3.000000)
[00:25:05 -140328.403500] FAST spr round 1 (radius: 25)
[00:30:46 -111299.692165] FAST spr round 2 (radius: 25)
[00:34:38 -109787.241179] FAST spr round 3 (radius: 25)
[00:37:52 -109702.252773] FAST spr round 4 (radius: 25)
[00:40:41 -109688.085526] FAST spr round 5 (radius: 25)
[00:43:17 -109685.500942] FAST spr round 6 (radius: 25)
[00:45:43 -109685.500907] Model parameter optimization (eps = 1.000000)
[00:46:15 -109569.842409] SLOW spr round 1 (radius: 5)
[00:49:49 -109524.127657] SLOW spr round 2 (radius: 5)
[00:53:19 -109513.948326] SLOW spr round 3 (radius: 5)
[00:56:42 -109512.665864] SLOW spr round 4 (radius: 5)
[01:00:02 -109512.476076] SLOW spr round 5 (radius: 5)
[01:03:16 -109512.475968] SLOW spr round 6 (radius: 10)
[01:06:36 -109507.855307] SLOW spr round 7 (radius: 5)
[01:10:36 -109506.743685] SLOW spr round 8 (radius: 5)
[01:14:11 -109505.601797] SLOW spr round 9 (radius: 5)
[01:17:33 -109505.601675] SLOW spr round 10 (radius: 10)
[01:20:56 -109504.979751] SLOW spr round 11 (radius: 5)
[01:24:59 -109501.597603] SLOW spr round 12 (radius: 5)
[01:28:36 -109500.031223] SLOW spr round 13 (radius: 5)
[01:31:57 -109500.031163] SLOW spr round 14 (radius: 10)
[01:35:18 -109500.031162] SLOW spr round 15 (radius: 15)
[01:37:34] [worker #2] ML tree search #3, logLikelihood: -109488.107591
[01:39:28] [worker #1] ML tree search #2, logLikelihood: -109543.260944
[01:39:36] [worker #3] ML tree search #4, logLikelihood: -109495.958342
[01:41:15 -109497.620452] SLOW spr round 16 (radius: 5)
[01:44:04] [worker #5] ML tree search #6, logLikelihood: -109554.378805
[01:45:00 -109496.857697] SLOW spr round 17 (radius: 5)
[01:48:20 -109496.857518] SLOW spr round 18 (radius: 10)
[01:51:33 -109496.857517] SLOW spr round 19 (radius: 15)
[01:56:49 -109496.857517] SLOW spr round 20 (radius: 20)
[02:04:31 -109496.857517] SLOW spr round 21 (radius: 25)
[02:13:14 -109494.873456] SLOW spr round 22 (radius: 5)
[02:17:11 -109493.842140] SLOW spr round 23 (radius: 5)
[02:20:38 -109493.841982] SLOW spr round 24 (radius: 10)
[02:23:57 -109493.841979] SLOW spr round 25 (radius: 15)
[02:28:29] [worker #4] ML tree search #5, logLikelihood: -109518.197343
[02:29:06 -109493.841979] SLOW spr round 26 (radius: 20)
[02:36:41 -109493.841979] SLOW spr round 27 (radius: 25)
[02:45:16 -109493.841979] Model parameter optimization (eps = 0.100000)

[02:45:33] [worker #0] ML tree search #1, logLikelihood: -109492.621482

[02:45:33 -478708.237682] Initial branch length optimization
[02:45:38 -379413.224673] Model parameter optimization (eps = 10.000000)
[02:46:41 -378386.613463] AUTODETECT spr round 1 (radius: 5)
[02:50:14 -250687.472109] AUTODETECT spr round 2 (radius: 10)
[02:54:05 -194872.233673] AUTODETECT spr round 3 (radius: 15)
[02:58:13 -163842.159895] AUTODETECT spr round 4 (radius: 20)
[02:58:37] [worker #3] ML tree search #10, logLikelihood: -109609.504800
[03:02:59 -148838.117151] AUTODETECT spr round 5 (radius: 25)
[03:08:13 -138537.562302] SPR radius for FAST iterations: 25 (autodetect)
[03:08:13 -138537.562302] Model parameter optimization (eps = 3.000000)
[03:08:27 -138529.090433] FAST spr round 1 (radius: 25)
[03:13:32 -110707.171006] FAST spr round 2 (radius: 25)
[03:16:59 -109830.880197] FAST spr round 3 (radius: 25)
[03:19:54 -109773.041622] FAST spr round 4 (radius: 25)
[03:22:25 -109760.361803] FAST spr round 5 (radius: 25)
[03:24:41] [worker #2] ML tree search #9, logLikelihood: -109506.909315
[03:24:42 -109760.360705] Model parameter optimization (eps = 1.000000)
[03:25:13 -109605.515381] SLOW spr round 1 (radius: 5)
[03:28:28 -109548.770195] SLOW spr round 2 (radius: 5)
[03:31:38 -109536.721084] SLOW spr round 3 (radius: 5)
[03:34:46 -109532.494621] SLOW spr round 4 (radius: 5)
[03:37:44 -109532.494146] SLOW spr round 5 (radius: 10)
[03:37:44] [worker #5] ML tree search #12, logLikelihood: -109480.348292
[03:40:48 -109528.312640] SLOW spr round 6 (radius: 5)
[03:41:13] [worker #1] ML tree search #8, logLikelihood: -109516.225528
[03:44:28 -109524.625496] SLOW spr round 7 (radius: 5)
[03:47:43 -109524.625415] SLOW spr round 8 (radius: 10)
[03:50:58 -109522.419299] SLOW spr round 9 (radius: 5)
[03:54:36 -109521.042867] SLOW spr round 10 (radius: 5)
[03:57:50 -109521.042816] SLOW spr round 11 (radius: 10)
[04:01:03 -109521.042771] SLOW spr round 12 (radius: 15)
[04:06:35 -109520.270655] SLOW spr round 13 (radius: 5)
[04:10:23 -109520.270605] SLOW spr round 14 (radius: 10)
[04:14:13 -109520.270604] SLOW spr round 15 (radius: 15)
[04:19:23 -109520.270604] SLOW spr round 16 (radius: 20)
[04:25:32] [worker #4] ML tree search #11, logLikelihood: -109629.824175
[04:26:55 -109520.270604] SLOW spr round 17 (radius: 25)
[04:29:30] [worker #3] ML tree search #16, logLikelihood: -109507.514551
[04:35:28 -109520.270604] Model parameter optimization (eps = 0.100000)

[04:35:35] [worker #0] ML tree search #7, logLikelihood: -109520.221523

[04:35:35 -480072.945935] Initial branch length optimization
[04:35:40 -379822.368300] Model parameter optimization (eps = 10.000000)
[04:36:39 -378770.451925] AUTODETECT spr round 1 (radius: 5)
[04:40:14 -252526.656150] AUTODETECT spr round 2 (radius: 10)
[04:44:04 -196661.679143] AUTODETECT spr round 3 (radius: 15)
[04:48:21 -158646.880229] AUTODETECT spr round 4 (radius: 20)
[04:52:51 -144166.650568] AUTODETECT spr round 5 (radius: 25)
[04:58:04 -142298.791062] SPR radius for FAST iterations: 25 (autodetect)
[04:58:04 -142298.791062] Model parameter optimization (eps = 3.000000)
[04:58:31 -142197.207159] FAST spr round 1 (radius: 25)
[05:03:24 -113021.898830] FAST spr round 2 (radius: 25)
[05:06:52 -109676.385435] FAST spr round 3 (radius: 25)
[05:09:39 -109548.775231] FAST spr round 4 (radius: 25)
[05:10:15] [worker #1] ML tree search #14, logLikelihood: -109609.755094
[05:11:27] [worker #5] ML tree search #18, logLikelihood: -109594.413456
[05:12:11 -109529.448325] FAST spr round 5 (radius: 25)
[05:14:28 -109522.882336] FAST spr round 6 (radius: 25)
[05:16:39 -109522.368641] FAST spr round 7 (radius: 25)
[05:18:47 -109522.368164] Model parameter optimization (eps = 1.000000)
[05:19:06 -109515.399743] SLOW spr round 1 (radius: 5)
[05:22:17 -109492.920619] SLOW spr round 2 (radius: 5)
[05:25:17 -109491.211419] SLOW spr round 3 (radius: 5)
[05:27:47] [worker #2] ML tree search #15, logLikelihood: -109464.468769
[05:28:12 -109491.211397] SLOW spr round 4 (radius: 10)
[05:31:15 -109490.667125] SLOW spr round 5 (radius: 5)
[05:34:53 -109489.290558] SLOW spr round 6 (radius: 5)
[05:38:07 -109489.290558] SLOW spr round 7 (radius: 10)
[05:41:19 -109489.290558] SLOW spr round 8 (radius: 15)
[05:46:35 -109487.898448] SLOW spr round 9 (radius: 5)
[05:50:25 -109481.630915] SLOW spr round 10 (radius: 5)
[05:53:44 -109481.630910] SLOW spr round 11 (radius: 10)
[05:56:58 -109481.630910] SLOW spr round 12 (radius: 15)
[06:02:08 -109481.630910] SLOW spr round 13 (radius: 20)
[06:09:25 -109481.630910] SLOW spr round 14 (radius: 25)
[06:18:06 -109481.630910] Model parameter optimization (eps = 0.100000)

[06:18:13] [worker #0] ML tree search #13, logLikelihood: -109481.603628

[06:18:14] [worker #4] ML tree search #17, logLikelihood: -109512.560957
[06:18:14 -483058.064672] Initial branch length optimization
[06:18:19 -380996.439407] Model parameter optimization (eps = 10.000000)
[06:19:08 -379848.864952] AUTODETECT spr round 1 (radius: 5)
[06:22:38 -246784.589573] AUTODETECT spr round 2 (radius: 10)
[06:26:26 -195772.993084] AUTODETECT spr round 3 (radius: 15)
[06:30:34 -163550.631731] AUTODETECT spr round 4 (radius: 20)
[06:34:58 -145631.854860] AUTODETECT spr round 5 (radius: 25)
[06:39:54 -136010.563038] SPR radius for FAST iterations: 25 (autodetect)
[06:39:55 -136010.563038] Model parameter optimization (eps = 3.000000)
[06:40:05 -136000.162055] FAST spr round 1 (radius: 25)
[06:42:46] [worker #1] ML tree search #20, logLikelihood: -109530.755469
[06:44:49 -110364.293848] FAST spr round 2 (radius: 25)
[06:48:13 -109741.268814] FAST spr round 3 (radius: 25)
[06:51:04 -109667.708895] FAST spr round 4 (radius: 25)
[06:53:29 -109659.037441] FAST spr round 5 (radius: 25)
[06:55:40 -109659.037426] Model parameter optimization (eps = 1.000000)
[06:55:45 -109658.628765] SLOW spr round 1 (radius: 5)
[06:58:58 -109632.912967] SLOW spr round 2 (radius: 5)
[07:02:01 -109626.138637] SLOW spr round 3 (radius: 5)
[07:04:59 -109626.138515] SLOW spr round 4 (radius: 10)
[07:08:00 -109619.984314] SLOW spr round 5 (radius: 5)
[07:11:35 -109614.849453] SLOW spr round 6 (radius: 5)
[07:14:47 -109613.961692] SLOW spr round 7 (radius: 5)
[07:17:39 -109613.961633] SLOW spr round 8 (radius: 10)
[07:20:26 -109613.961632] SLOW spr round 9 (radius: 15)
[07:25:31 -109613.961632] SLOW spr round 10 (radius: 20)
[07:32:34 -109613.961632] SLOW spr round 11 (radius: 25)
[07:40:43 -109613.961632] Model parameter optimization (eps = 0.100000)

[07:40:48] [worker #0] ML tree search #19, logLikelihood: -109613.955818


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.118624,0.273813) (0.241880,0.368348) (0.412721,0.995165) (0.226774,2.062390) 
   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: -109464.468769

AIC score: 222938.937537 / AICc score: 8266998.937537 / BIC score: 230233.838649
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=281).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 101 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/3_mltree/Q6XUX3.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/3_mltree/Q6XUX3.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/3_mltree/Q6XUX3.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/3_mltree/Q6XUX3.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XUX3/3_mltree/Q6XUX3.raxml.log

Analysis started: 01-Jul-2021 13:08:18 / finished: 01-Jul-2021 20:49:07

Elapsed time: 27648.312 seconds

Consumed energy: 2510.853 Wh (= 13 km in an electric car, or 63 km with an e-scooter!)