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 09-Jul-2021 23:55:05 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/2_msa/Q8N3L3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/2_msa/Q8N3L3_trimmed_msa.fasta [00:00:00] Loaded alignment with 638 taxa and 261 sites WARNING: Sequences tr_B4QVF6_B4QVF6_DROSI_7240 and tr_Q9VBL3_Q9VBL3_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QVF6_B4QVF6_DROSI_7240 and tr_B4ICE8_B4ICE8_DROSE_7238 are exactly identical! WARNING: Sequences tr_F1P0Q4_F1P0Q4_CHICK_9031 and sp_Q9I969_TXLNB_CHICK_9031 are exactly identical! WARNING: Sequences sp_Q8BHN1_TXLNG_MOUSE_10090 and tr_F6ZQV4_F6ZQV4_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q8BHN1_TXLNG_MOUSE_10090 and tr_A0A0G2QC39_A0A0G2QC39_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BHN1_TXLNG_MOUSE_10090 and tr_I3M142_I3M142_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q8BHN1_TXLNG_MOUSE_10090 and tr_H0XCB9_H0XCB9_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q8BHN1_TXLNG_MOUSE_10090 and tr_A0A1U7TZ72_A0A1U7TZ72_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q8BHN1_TXLNG_MOUSE_10090 and tr_A0A3Q0CYB2_A0A3Q0CYB2_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XUM9_M3XUM9_MUSPF_9669 and tr_D2HDU3_D2HDU3_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XUM9_M3XUM9_MUSPF_9669 and tr_A0A337RXY1_A0A337RXY1_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XUM9_M3XUM9_MUSPF_9669 and tr_A0A2U3XZB4_A0A2U3XZB4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XUM9_M3XUM9_MUSPF_9669 and tr_A0A2Y9KJT2_A0A2Y9KJT2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XUM9_M3XUM9_MUSPF_9669 and tr_A0A384CIQ2_A0A384CIQ2_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_J9PA47_J9PA47_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_I3NH54_I3NH54_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_H0X0M0_H0X0M0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_G3TW95_G3TW95_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_D2HI61_D2HI61_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_M3WW86_M3WW86_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_A0A1S3WW91_A0A1S3WW91_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_A0A2U3ZLT8_A0A2U3ZLT8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_A0A2Y9QI28_A0A2Y9QI28_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_A0A2Y9J322_A0A2Y9J322_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YV34_M3YV34_MUSPF_9669 and tr_A0A384CD00_A0A384CD00_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_G3QGT7_G3QGT7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_K7BNC6_K7BNC6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and sp_P40222_TXLNA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_G7MI83_G7MI83_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_F7EWF4_F7EWF4_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_G8F3T7_G8F3T7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_A0A096N233_A0A096N233_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_A0A0D9S7X8_A0A0D9S7X8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_A0A2K6DUA2_A0A2K6DUA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QPJ4_G1QPJ4_NOMLE_61853 and tr_A0A2R8Z7Q5_A0A2R8Z7Q5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1REH4_G1REH4_NOMLE_61853 and tr_A0A1D5RC87_A0A1D5RC87_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1REH4_G1REH4_NOMLE_61853 and tr_G7Q2B0_G7Q2B0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1REH4_G1REH4_NOMLE_61853 and tr_A0A096N4L1_A0A096N4L1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1REH4_G1REH4_NOMLE_61853 and tr_A0A0D9RQM7_A0A0D9RQM7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1REH4_G1REH4_NOMLE_61853 and tr_A0A2K5LVL4_A0A2K5LVL4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1REH4_G1REH4_NOMLE_61853 and tr_A0A2K6A5Z4_A0A2K6A5Z4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RYF8_G1RYF8_NOMLE_61853 and tr_G3QLE7_G3QLE7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RYF8_G1RYF8_NOMLE_61853 and tr_H2QTU4_H2QTU4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RYF8_G1RYF8_NOMLE_61853 and sp_Q8N3L3_TXLNB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3H949_G3H949_CRIGR_10029 and tr_A0A3Q0D595_A0A3Q0D595_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A0E1RUZ9_A0A0E1RUZ9_COCIM_246410 and tr_E9DGL8_E9DGL8_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0E1RUZ9_A0A0E1RUZ9_COCIM_246410 and tr_A0A0J7B7K7_A0A0J7B7K7_COCIT_404692 are exactly identical! WARNING: Sequences tr_G3QIX7_G3QIX7_GORGO_9595 and tr_H2PV06_H2PV06_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QIX7_G3QIX7_GORGO_9595 and tr_H2QYC7_H2QYC7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QIX7_G3QIX7_GORGO_9595 and sp_Q9NUQ3_TXLNG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1N007_G1N007_MELGA_9103 and tr_A0A226NFX5_A0A226NFX5_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A179UCC5_A0A179UCC5_BLAGS_559298 and tr_A0A179U1P9_A0A179U1P9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A179UCC5_A0A179UCC5_BLAGS_559298 and tr_A0A2B7X8M4_A0A2B7X8M4_9EURO_2060905 are exactly identical! WARNING: Sequences tr_W5NQQ4_W5NQQ4_SHEEP_9940 and tr_A0A287BAM9_A0A287BAM9_PIG_9823 are exactly identical! WARNING: Sequences tr_W5NQQ4_W5NQQ4_SHEEP_9940 and tr_E1BGS4_E1BGS4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5NQQ4_W5NQQ4_SHEEP_9940 and tr_A0A2U4BKQ2_A0A2U4BKQ2_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5NQQ4_W5NQQ4_SHEEP_9940 and tr_A0A2Y9FJV8_A0A2Y9FJV8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5NSX8_W5NSX8_SHEEP_9940 and tr_F1N4G3_F1N4G3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M4AHE0_M4AHE0_XIPMA_8083 and tr_A0A087XHB8_A0A087XHB8_POEFO_48698 are exactly identical! WARNING: Sequences tr_H0VKE9_H0VKE9_CAVPO_10141 and tr_G5BU95_G5BU95_HETGA_10181 are exactly identical! WARNING: Sequences tr_H0VKE9_H0VKE9_CAVPO_10141 and tr_A0A091DQL6_A0A091DQL6_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A0E0GL12_A0A0E0GL12_ORYNI_4536 and tr_A0A0E0NTM5_A0A0E0NTM5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GL12_A0A0E0GL12_ORYNI_4536 and tr_A0A0D3FH57_A0A0D3FH57_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GL12_A0A0E0GL12_ORYNI_4536 and tr_A0A0D9Z5R3_A0A0D9Z5R3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F6T062_F6T062_MACMU_9544 and tr_G7P317_G7P317_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T062_F6T062_MACMU_9544 and tr_A0A096NQC8_A0A096NQC8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6T062_F6T062_MACMU_9544 and tr_A0A2K5LU47_A0A2K5LU47_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6T062_F6T062_MACMU_9544 and tr_A0A2K6D771_A0A2K6D771_MACNE_9545 are exactly identical! WARNING: Sequences tr_B8ALK6_B8ALK6_ORYSI_39946 and tr_I1PA97_I1PA97_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8ALK6_B8ALK6_ORYSI_39946 and tr_Q84VE3_Q84VE3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G9MGY9_G9MGY9_HYPVG_413071 and tr_A0A0F9XL80_A0A0F9XL80_TRIHA_5544 are exactly identical! WARNING: Sequences tr_G9MGY9_G9MGY9_HYPVG_413071 and tr_A0A2T4AL57_A0A2T4AL57_TRIHA_983964 are exactly identical! WARNING: Sequences tr_F4PCM0_F4PCM0_BATDJ_684364 and tr_A0A177WY15_A0A177WY15_BATDE_403673 are exactly identical! WARNING: Sequences tr_H0ZBZ6_H0ZBZ6_TAEGU_59729 and tr_U3JP10_U3JP10_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZBZ6_H0ZBZ6_TAEGU_59729 and tr_A0A091EGI8_A0A091EGI8_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZBZ6_H0ZBZ6_TAEGU_59729 and tr_A0A093SA39_A0A093SA39_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZBZ6_H0ZBZ6_TAEGU_59729 and tr_A0A218UN72_A0A218UN72_9PASE_299123 are exactly identical! WARNING: Sequences tr_F9XER8_F9XER8_ZYMTI_336722 and tr_A0A1X7RXX6_A0A1X7RXX6_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YPG4_G2YPG4_BOTF4_999810 and tr_M7UGH2_M7UGH2_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A017SD46_A0A017SD46_9EURO_1388766 and tr_A0A1E3BU42_A0A1E3BU42_9EURO_573508 are exactly identical! WARNING: Sequences tr_A0A015LAU8_A0A015LAU8_9GLOM_1432141 and tr_A0A2H5SY31_A0A2H5SY31_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067EBZ8_A0A067EBZ8_CITSI_2711 and tr_V4VB46_V4VB46_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067EBZ8_A0A067EBZ8_CITSI_2711 and tr_A0A2H5PB29_A0A2H5PB29_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078I4K9_A0A078I4K9_BRANA_3708 and tr_A0A0D3B429_A0A0D3B429_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094EJ95_A0A094EJ95_9PEZI_1420912 and tr_A0A1B8EGK9_A0A1B8EGK9_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_A0A094EJ95_A0A094EJ95_9PEZI_1420912 and tr_A0A1B8GDV0_A0A1B8GDV0_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094EJ95_A0A094EJ95_9PEZI_1420912 and tr_A0A1B8CFW8_A0A1B8CFW8_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A094EJ95_A0A094EJ95_9PEZI_1420912 and tr_A0A1B8FAS1_A0A1B8FAS1_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A0D2TY92_A0A0D2TY92_GOSRA_29730 and tr_A0A1U8JB09_A0A1U8JB09_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A151MN30_A0A151MN30_ALLMI_8496 and tr_A0A3Q0G4Q6_A0A3Q0G4Q6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0S7DZP8_A0A0S7DZP8_9EURO_293939 and tr_A0A2I1C5Y1_A0A2I1C5Y1_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A0A091VSB9_A0A091VSB9_OPIHO_30419 and tr_A0A091GS00_A0A091GS00_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A099ZMB1_A0A099ZMB1_TINGU_94827 and tr_A0A091HRB7_A0A091HRB7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2I0LNI8_A0A2I0LNI8_COLLI_8932 and tr_A0A1V4JIW7_A0A1V4JIW7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MLT6_A0A2I0MLT6_COLLI_8932 and tr_A0A1V4JCW9_A0A1V4JCW9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A194W532_A0A194W532_9PEZI_105487 and tr_A0A194UM82_A0A194UM82_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A1S3XDQ1_A0A1S3XDQ1_TOBAC_4097 and tr_A0A1U7Y7A5_A0A1U7Y7A5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1L9X5W6_A0A1L9X5W6_ASPAC_690307 and tr_A0A319BZY9_A0A319BZY9_9EURO_1448315 are exactly identical! WARNING: Sequences tr_A0A1L9X5W6_A0A1L9X5W6_ASPAC_690307 and tr_A0A2V5HVC4_A0A2V5HVC4_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A2I4AIH2_A0A2I4AIH2_9TELE_52670 and tr_A0A2I4CR69_A0A2I4CR69_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A2I4AIH2_A0A2I4AIH2_9TELE_52670 and tr_A0A2I4CUC8_A0A2I4CUC8_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A1Z5SXN3_A0A1Z5SXN3_HORWE_1157616 and tr_A0A1Z5T0Y5_A0A1Z5T0Y5_HORWE_1157616 are exactly identical! WARNING: Sequences tr_A0A226NDB0_A0A226NDB0_CALSU_9009 and tr_A0A226PLG9_A0A226PLG9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RRR7_A0A2D0RRR7_ICTPU_7998 and tr_A0A2D0RTA8_A0A2D0RTA8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G5HE53_A0A2G5HE53_CERBT_122368 and tr_A0A2S6CED3_A0A2S6CED3_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2U4AJV3_A0A2U4AJV3_TURTR_9739 and tr_A0A2Y9M872_A0A2Y9M872_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AJV3_A0A2U4AJV3_TURTR_9739 and tr_A0A2Y9RWU4_A0A2Y9RWU4_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 107 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3.raxml.reduced.phy Alignment comprises 1 partitions and 261 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 261 / 261 Gaps: 4.92 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3.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 638 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 261 / 20880 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -273327.633722] Initial branch length optimization [00:00:04 -214956.848342] Model parameter optimization (eps = 10.000000) [00:00:44 -213772.300417] AUTODETECT spr round 1 (radius: 5) [00:02:18 -142681.814156] AUTODETECT spr round 2 (radius: 10) [00:04:01 -107410.475537] AUTODETECT spr round 3 (radius: 15) [00:06:00 -87683.839940] AUTODETECT spr round 4 (radius: 20) [00:08:26 -76341.898323] AUTODETECT spr round 5 (radius: 25) [00:11:26 -73701.002246] SPR radius for FAST iterations: 25 (autodetect) [00:11:26 -73701.002246] Model parameter optimization (eps = 3.000000) [00:11:50 -73547.915905] FAST spr round 1 (radius: 25) [00:13:37 -61501.818710] FAST spr round 2 (radius: 25) [00:15:08 -60151.155619] FAST spr round 3 (radius: 25) [00:16:24 -60093.618476] FAST spr round 4 (radius: 25) [00:17:29 -60092.276818] FAST spr round 5 (radius: 25) [00:18:32 -60092.276719] Model parameter optimization (eps = 1.000000) [00:18:45 -60085.392594] SLOW spr round 1 (radius: 5) [00:20:18 -60077.579485] SLOW spr round 2 (radius: 5) [00:21:50 -60077.577203] SLOW spr round 3 (radius: 10) [00:23:32 -60077.558318] SLOW spr round 4 (radius: 15) [00:25:55 -60077.557594] SLOW spr round 5 (radius: 20) [00:29:14 -60077.557496] SLOW spr round 6 (radius: 25) [00:33:00 -60077.557445] Model parameter optimization (eps = 0.100000) [00:33:05] [worker #0] ML tree search #1, logLikelihood: -60077.535111 [00:33:05 -267295.139430] Initial branch length optimization [00:33:09 -212918.003177] Model parameter optimization (eps = 10.000000) [00:33:42 -211734.352920] AUTODETECT spr round 1 (radius: 5) [00:34:46] [worker #3] ML tree search #4, logLikelihood: -60089.095724 [00:35:16 -137004.807208] AUTODETECT spr round 2 (radius: 10) [00:35:48] [worker #1] ML tree search #2, logLikelihood: -60084.303257 [00:36:01] [worker #2] ML tree search #3, logLikelihood: -60172.203812 [00:36:58 -105086.069069] AUTODETECT spr round 3 (radius: 15) [00:38:53 -89231.458869] AUTODETECT spr round 4 (radius: 20) [00:41:00 -82858.510662] AUTODETECT spr round 5 (radius: 25) [00:43:36 -80139.159636] SPR radius for FAST iterations: 25 (autodetect) [00:43:37 -80139.159636] Model parameter optimization (eps = 3.000000) [00:43:38] [worker #4] ML tree search #5, logLikelihood: -60126.685990 [00:44:00 -80015.488474] FAST spr round 1 (radius: 25) [00:46:04 -62057.765890] FAST spr round 2 (radius: 25) [00:47:30 -60376.475914] FAST spr round 3 (radius: 25) [00:48:48 -60167.056575] FAST spr round 4 (radius: 25) [00:49:56 -60159.452156] FAST spr round 5 (radius: 25) [00:50:59 -60159.452096] Model parameter optimization (eps = 1.000000) [00:51:15 -60145.745567] SLOW spr round 1 (radius: 5) [00:52:48 -60138.500764] SLOW spr round 2 (radius: 5) [00:54:23 -60131.597402] SLOW spr round 3 (radius: 5) [00:55:55 -60128.576371] SLOW spr round 4 (radius: 5) [00:57:22 -60128.575578] SLOW spr round 5 (radius: 10) [00:58:58 -60128.462365] SLOW spr round 6 (radius: 5) [01:00:52 -60128.462310] SLOW spr round 7 (radius: 10) [01:02:43 -60128.462292] SLOW spr round 8 (radius: 15) [01:05:02 -60128.462274] SLOW spr round 9 (radius: 20) [01:08:25 -60128.462256] SLOW spr round 10 (radius: 25) [01:08:48] [worker #1] ML tree search #7, logLikelihood: -60084.862587 [01:12:17 -60128.462239] Model parameter optimization (eps = 0.100000) [01:12:32] [worker #0] ML tree search #6, logLikelihood: -60128.321497 [01:12:32 -269622.092299] Initial branch length optimization [01:12:35 -212807.171961] Model parameter optimization (eps = 10.000000) [01:13:16 -211568.503027] AUTODETECT spr round 1 (radius: 5) [01:14:48 -139371.338601] AUTODETECT spr round 2 (radius: 10) [01:15:25] [worker #2] ML tree search #8, logLikelihood: -60090.110273 [01:16:30 -103937.611646] AUTODETECT spr round 3 (radius: 15) [01:17:53] [worker #4] ML tree search #10, logLikelihood: -60092.959424 [01:18:23 -80194.248329] AUTODETECT spr round 4 (radius: 20) [01:20:41 -71981.066714] AUTODETECT spr round 5 (radius: 25) [01:23:47 -71559.496507] SPR radius for FAST iterations: 25 (autodetect) [01:23:47 -71559.496507] Model parameter optimization (eps = 3.000000) [01:23:48] [worker #3] ML tree search #9, logLikelihood: -60113.626752 [01:24:12 -71378.749367] FAST spr round 1 (radius: 25) [01:26:08 -60769.940003] FAST spr round 2 (radius: 25) [01:27:34 -60131.919239] FAST spr round 3 (radius: 25) [01:28:53 -60114.613244] FAST spr round 4 (radius: 25) [01:29:58 -60113.268166] FAST spr round 5 (radius: 25) [01:31:01 -60113.268025] Model parameter optimization (eps = 1.000000) [01:31:14 -60107.387078] SLOW spr round 1 (radius: 5) [01:32:47 -60091.411977] SLOW spr round 2 (radius: 5) [01:34:22 -60090.645189] SLOW spr round 3 (radius: 5) [01:35:56 -60090.645112] SLOW spr round 4 (radius: 10) [01:37:36 -60090.645112] SLOW spr round 5 (radius: 15) [01:40:06 -60090.645111] SLOW spr round 6 (radius: 20) [01:43:16 -60090.645111] SLOW spr round 7 (radius: 25) [01:44:31] [worker #1] ML tree search #12, logLikelihood: -60085.219775 [01:47:01 -60090.645111] Model parameter optimization (eps = 0.100000) [01:47:07] [worker #0] ML tree search #11, logLikelihood: -60090.583877 [01:47:08 -273086.055558] Initial branch length optimization [01:47:11 -214214.508790] Model parameter optimization (eps = 10.000000) [01:48:00 -212991.913841] AUTODETECT spr round 1 (radius: 5) [01:48:47] [worker #2] ML tree search #13, logLikelihood: -60112.823790 [01:49:33 -146581.195432] AUTODETECT spr round 2 (radius: 10) [01:51:13 -113164.158812] AUTODETECT spr round 3 (radius: 15) [01:53:19 -94006.436921] AUTODETECT spr round 4 (radius: 20) [01:55:41 -72729.152641] AUTODETECT spr round 5 (radius: 25) [01:58:12 -70737.520558] SPR radius for FAST iterations: 25 (autodetect) [01:58:12 -70737.520558] Model parameter optimization (eps = 3.000000) [01:58:29] [worker #4] ML tree search #15, logLikelihood: -60086.544647 [01:58:35 -70628.373253] FAST spr round 1 (radius: 25) [02:00:19 -60696.816452] FAST spr round 2 (radius: 25) [02:01:37 -60146.116313] FAST spr round 3 (radius: 25) [02:02:14] [worker #3] ML tree search #14, logLikelihood: -60122.729132 [02:02:53 -60101.953223] FAST spr round 4 (radius: 25) [02:03:59 -60099.154137] FAST spr round 5 (radius: 25) [02:05:03 -60098.730535] FAST spr round 6 (radius: 25) [02:06:06 -60098.729461] Model parameter optimization (eps = 1.000000) [02:06:17 -60096.402889] SLOW spr round 1 (radius: 5) [02:07:49 -60084.024367] SLOW spr round 2 (radius: 5) [02:09:19 -60083.798570] SLOW spr round 3 (radius: 5) [02:10:46 -60083.798551] SLOW spr round 4 (radius: 10) [02:12:25 -60083.798550] SLOW spr round 5 (radius: 15) [02:14:55 -60083.798549] SLOW spr round 6 (radius: 20) [02:18:17 -60083.798549] SLOW spr round 7 (radius: 25) [02:21:32] [worker #1] ML tree search #17, logLikelihood: -60140.036921 [02:22:14 -60083.798549] Model parameter optimization (eps = 0.100000) [02:22:23] [worker #0] ML tree search #16, logLikelihood: -60083.658108 [02:25:32] [worker #2] ML tree search #18, logLikelihood: -60169.156648 [02:35:23] [worker #4] ML tree search #20, logLikelihood: -60155.964596 [02:36:35] [worker #3] ML tree search #19, logLikelihood: -60082.366568 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.150553,0.465650) (0.100942,1.313861) (0.413778,0.684300) (0.334726,1.535949) 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: -60077.535111 AIC score: 122713.070221 / AICc score: 3396953.070221 / BIC score: 127272.091822 Free parameters (model + branch lengths): 1279 WARNING: Number of free parameters (K=1279) is larger than alignment size (n=261). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 154 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8N3L3/3_mltree/Q8N3L3.raxml.log Analysis started: 09-Jul-2021 23:55:05 / finished: 10-Jul-2021 02:31:40 Elapsed time: 9395.429 seconds