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 14-Jul-2021 16:20:34 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/2_msa/P25490_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/3_mltree/P25490.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/4_raxmlng_ancestral/P25490 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626268834 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/2_msa/P25490_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 414 sites WARNING: Sequences sp_O70230_ZN143_MOUSE_10090 and sp_Q5XIU2_ZN143_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XWP2_M3XWP2_MUSPF_9669 and tr_A0A2Y9K0G1_A0A2Y9K0G1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_G1RLW0_G1RLW0_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_H2N7X4_H2N7X4_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_H2R0J1_H2R0J1_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_I3N1E6_I3N1E6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A1D5QTP0_A0A1D5QTP0_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_G5C6H8_G5C6H8_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_G7NUB1_G7NUB1_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_M3WEC6_M3WEC6_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A096N999_A0A096N999_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A0D9S7Q6_A0A0D9S7Q6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A1U7TIG8_A0A1U7TIG8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A2K6D1A4_A0A2K6D1A4_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A2R9ASU3_A0A2R9ASU3_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A2U3ZI42_A0A2U3ZI42_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A2Y9IVA3_A0A2Y9IVA3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YSW8_M3YSW8_MUSPF_9669 and tr_A0A384CDR4_A0A384CDR4_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Z8Z2_M3Z8Z2_MUSPF_9669 and tr_A0A2U3W9V0_A0A2U3W9V0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z8Z2_M3Z8Z2_MUSPF_9669 and tr_A0A2Y9IH32_A0A2Y9IH32_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I2Y6M6_A0A2I2Y6M6_GORGO_9595 and tr_H2R6F0_H2R6F0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y6M6_A0A2I2Y6M6_GORGO_9595 and tr_A0A2R8ZED3_A0A2R8ZED3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YXR8_A0A2I2YXR8_GORGO_9595 and tr_H2PX48_H2PX48_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2YXR8_A0A2I2YXR8_GORGO_9595 and tr_A0A2I3TA29_A0A2I3TA29_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YXR8_A0A2I2YXR8_GORGO_9595 and sp_A6NM28_ZFP92_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YXR8_A0A2I2YXR8_GORGO_9595 and tr_A0A2R9A217_A0A2R9A217_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QT22_G3QT22_GORGO_9595 and tr_A0A2J8L7X1_A0A2J8L7X1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QT22_G3QT22_GORGO_9595 and tr_A0A2R8ZF78_A0A2R8ZF78_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S7S5_G3S7S5_GORGO_9595 and sp_P25490_TYY1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8UPS8_A0A2J8UPS8_PONAB_9601 and tr_A0A2I3SCF5_A0A2I3SCF5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8UPS8_A0A2J8UPS8_PONAB_9601 and sp_P52747_ZN143_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8UPS8_A0A2J8UPS8_PONAB_9601 and tr_A0A337SAB0_A0A337SAB0_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2J8UPS8_A0A2J8UPS8_PONAB_9601 and tr_A0A2R9CAZ1_A0A2R9CAZ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PXS7_H2PXS7_PONAB_9601 and tr_H0WVA2_H0WVA2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2PXS7_H2PXS7_PONAB_9601 and tr_A0A2K5YVK2_A0A2K5YVK2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1MVN8_G1MVN8_MELGA_9103 and tr_A0A226NGS4_A0A226NGS4_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q29EF2_Q29EF2_DROPS_46245 and tr_B4H1Y2_B4H1Y2_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RHE9_E2RHE9_CANLF_9615 and tr_A0A337SDD4_A0A337SDD4_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RHE9_E2RHE9_CANLF_9615 and tr_A0A2U3VKW8_A0A2U3VKW8_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RTL0_E2RTL0_CANLF_9615 and tr_M3XFP4_M3XFP4_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2R7D7_H2R7D7_PANTR_9598 and tr_A0A2R9B6W2_A0A2R9B6W2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6XY85_F6XY85_ORNAN_9258 and tr_G3WPK5_G3WPK5_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5PSE2_W5PSE2_SHEEP_9940 and tr_A0A2U4CEK6_A0A2U4CEK6_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PSE2_W5PSE2_SHEEP_9940 and tr_A0A2U4CEL0_A0A2U4CEL0_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PSE2_W5PSE2_SHEEP_9940 and tr_A0A2Y9LWH2_A0A2Y9LWH2_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5PSE2_W5PSE2_SHEEP_9940 and tr_A0A2Y9MIK2_A0A2Y9MIK2_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5PSE2_W5PSE2_SHEEP_9940 and tr_A0A2Y9SFU9_A0A2Y9SFU9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5PSE2_W5PSE2_SHEEP_9940 and tr_A0A383ZCR3_A0A383ZCR3_BALAS_310752 are exactly identical! WARNING: Sequences tr_F9FIB4_F9FIB4_FUSOF_660025 and tr_W7MFB3_W7MFB3_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FIB4_F9FIB4_FUSOF_660025 and tr_S0DHT2_S0DHT2_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FIB4_F9FIB4_FUSOF_660025 and tr_X0CHB4_X0CHB4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FIB4_F9FIB4_FUSOF_660025 and tr_A0A2H3SV07_A0A2H3SV07_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FIB4_F9FIB4_FUSOF_660025 and tr_A0A2H3I3C4_A0A2H3I3C4_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FIB4_F9FIB4_FUSOF_660025 and tr_A0A2K0WA08_A0A2K0WA08_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F9FIB4_F9FIB4_FUSOF_660025 and tr_A0A366RJP2_A0A366RJP2_9HYPO_2109339 are exactly identical! WARNING: Sequences tr_A0A158NG25_A0A158NG25_ATTCE_12957 and tr_A0A151I1H9_A0A151I1H9_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NK84_A0A158NK84_ATTCE_12957 and tr_A0A151X727_A0A151X727_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NK84_A0A158NK84_ATTCE_12957 and tr_A0A195B9Z8_A0A195B9Z8_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NK84_A0A158NK84_ATTCE_12957 and tr_A0A195FBS0_A0A195FBS0_9HYME_34720 are exactly identical! WARNING: Sequences tr_I3LW91_I3LW91_ICTTR_43179 and tr_M3W4X4_M3W4X4_FELCA_9685 are exactly identical! WARNING: Sequences tr_H0XIR8_H0XIR8_OTOGA_30611 and tr_A0A1D5QGJ5_A0A1D5QGJ5_MACMU_9544 are exactly identical! WARNING: Sequences tr_H0XIR8_H0XIR8_OTOGA_30611 and tr_A0A287AW01_A0A287AW01_PIG_9823 are exactly identical! WARNING: Sequences tr_H0XIR8_H0XIR8_OTOGA_30611 and tr_A0A0A0MU01_A0A0A0MU01_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H0XIR8_H0XIR8_OTOGA_30611 and tr_A0A0D9SE62_A0A0D9SE62_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H0XIR8_H0XIR8_OTOGA_30611 and tr_A0A2K5NER9_A0A2K5NER9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0E0G832_A0A0E0G832_ORYNI_4536 and tr_B8AJE1_B8AJE1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0G832_A0A0E0G832_ORYNI_4536 and tr_I1P176_I1P176_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0G832_A0A0E0G832_ORYNI_4536 and tr_A0A0E0CLU4_A0A0E0CLU4_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0G832_A0A0E0G832_ORYNI_4536 and tr_A0A0D3F699_A0A0D3F699_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A1D5QYJ1_A0A1D5QYJ1_MACMU_9544 and tr_G7PQR4_G7PQR4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QYJ1_A0A1D5QYJ1_MACMU_9544 and tr_A0A096N6I6_A0A096N6I6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QYJ1_A0A1D5QYJ1_MACMU_9544 and tr_A0A0D9QWW6_A0A0D9QWW6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QYJ1_A0A1D5QYJ1_MACMU_9544 and tr_A0A2K5MG14_A0A2K5MG14_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QYJ1_A0A1D5QYJ1_MACMU_9544 and tr_A0A2K6DDC1_A0A2K6DDC1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QYJ1_A0A1D5QYJ1_MACMU_9544 and tr_A0A2K5ZZE5_A0A2K5ZZE5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A2XZG9_A2XZG9_ORYSI_39946 and tr_I1PRP8_I1PRP8_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2XZG9_A2XZG9_ORYSI_39946 and tr_A0A0E0PGF4_A0A0E0PGF4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2XZG9_A2XZG9_ORYSI_39946 and tr_A0A0D3G2B7_A0A0D3G2B7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2XZG9_A2XZG9_ORYSI_39946 and tr_A0A0D9ZT65_A0A0D9ZT65_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2XZG9_A2XZG9_ORYSI_39946 and tr_A0A0E0KXJ2_A0A0E0KXJ2_ORYPU_4537 are exactly identical! WARNING: Sequences tr_A2XZG9_A2XZG9_ORYSI_39946 and tr_Q65XI2_Q65XI2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H0ZR87_H0ZR87_TAEGU_59729 and tr_A0A087R576_A0A087R576_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZR87_H0ZR87_TAEGU_59729 and tr_A0A093HRE7_A0A093HRE7_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0ZR87_H0ZR87_TAEGU_59729 and tr_A0A099ZD15_A0A099ZD15_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0E0NGA5_A0A0E0NGA5_ORYRU_4529 and tr_Q0E0H1_Q0E0H1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0Q9WY04_A0A0Q9WY04_DROVI_7244 and tr_D0Z777_D0Z777_DROVI_7244 are exactly identical! WARNING: Sequences tr_G7P2U9_G7P2U9_MACFA_9541 and tr_A0A096NHN0_A0A096NHN0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7P2U9_G7P2U9_MACFA_9541 and tr_A0A0D9RC55_A0A0D9RC55_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7P2U9_G7P2U9_MACFA_9541 and tr_A0A2K5KJL6_A0A2K5KJL6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P2U9_G7P2U9_MACFA_9541 and tr_A0A2K5ZY72_A0A2K5ZY72_MANLE_9568 are exactly identical! WARNING: Sequences tr_L0PHI9_L0PHI9_PNEJ8_1209962 and tr_A0A0W4ZJS6_A0A0W4ZJS6_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_L5KF60_L5KF60_PTEAL_9402 and tr_A0A1S3GNZ2_A0A1S3GNZ2_DIPOR_10020 are exactly identical! WARNING: Sequences tr_L5KF60_L5KF60_PTEAL_9402 and tr_A0A2Y9FYL9_A0A2Y9FYL9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_U3JE20_U3JE20_FICAL_59894 and tr_A0A218UQM1_A0A218UQM1_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3JJ42_U3JJ42_FICAL_59894 and tr_A0A218V2T1_A0A218V2T1_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A3B6NR40_A0A3B6NR40_WHEAT_4565 and tr_A0A3B6QH50_A0A3B6QH50_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015LX92_A0A015LX92_9GLOM_1432141 and tr_A0A2H5RMH1_A0A2H5RMH1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2I3LSU0_A0A2I3LSU0_PAPAN_9555 and tr_A0A2K5MX30_A0A2K5MX30_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MUS0_A0A2I3MUS0_PAPAN_9555 and tr_A0A0D9SBV6_A0A0D9SBV6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3MUS0_A0A2I3MUS0_PAPAN_9555 and tr_A0A2K5N1E4_A0A2K5N1E4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RJQ3_A0A0D9RJQ3_CHLSB_60711 and tr_A0A2K5YXK9_A0A2K5YXK9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0N0DFY5_A0A0N0DFY5_FUSLA_179993 and tr_A0A1B8B4C0_A0A1B8B4C0_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0N0DFY5_A0A0N0DFY5_FUSLA_179993 and tr_A0A2T4HBR4_A0A2T4HBR4_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0N0DFY5_A0A0N0DFY5_FUSLA_179993 and tr_A0A2L2TIN0_A0A2L2TIN0_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A0Q3XAV6_A0A0Q3XAV6_AMAAE_12930 and tr_A0A091JDP2_A0A091JDP2_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A0Q3XAV6_A0A0Q3XAV6_AMAAE_12930 and tr_A0A091VK86_A0A091VK86_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0Q3XAV6_A0A0Q3XAV6_AMAAE_12930 and tr_A0A087RCL8_A0A087RCL8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0Q3XAV6_A0A0Q3XAV6_AMAAE_12930 and tr_A0A093HWT2_A0A093HWT2_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A0Q3XAV6_A0A0Q3XAV6_AMAAE_12930 and tr_A0A093H7K0_A0A093H7K0_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0Q3XAV6_A0A0Q3XAV6_AMAAE_12930 and tr_A0A091IH91_A0A091IH91_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0W8DR41_A0A0W8DR41_PHYNI_4790 and tr_W2LLL3_W2LLL3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A091JPB5_A0A091JPB5_EGRGA_188379 and tr_A0A087R4T7_A0A087R4T7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JPB5_A0A091JPB5_EGRGA_188379 and tr_A0A0A0ALL4_A0A0A0ALL4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0L9TIJ7_A0A0L9TIJ7_PHAAN_3914 and tr_A0A1S3UIW5_A0A1S3UIW5_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A091V9L8_A0A091V9L8_NIPNI_128390 and tr_A0A091G185_A0A091G185_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091W4N6_A0A091W4N6_OPIHO_30419 and tr_A0A0A0AY49_A0A0A0AY49_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091WA60_A0A091WA60_OPIHO_30419 and tr_A0A0A0AW39_A0A0A0AW39_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1D0G8_A0A0V1D0G8_TRIBR_45882 and tr_A0A0V0ZB26_A0A0V0ZB26_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A194VTK6_A0A194VTK6_9PEZI_105487 and tr_A0A194V484_A0A194V484_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A1S3Y2F2_A0A1S3Y2F2_TOBAC_4097 and tr_Q9ZQT8_Q9ZQT8_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S3Y2F2_A0A1S3Y2F2_TOBAC_4097 and tr_A0A314KMZ6_A0A314KMZ6_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3Y2F2_A0A1S3Y2F2_TOBAC_4097 and tr_A0A1U7W192_A0A1U7W192_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3IRE2_A0A1S3IRE2_LINUN_7574 and tr_A0A1S3JYX2_A0A1S3JYX2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3SLN1_A0A1S3SLN1_SALSA_8030 and tr_A0A060XWT4_A0A060XWT4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MBR8_A0A226MBR8_CALSU_9009 and tr_A0A226MBN3_A0A226MBN3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2G2ZZU5_A0A2G2ZZU5_CAPAN_4072 and tr_A0A2G3CX49_A0A2G3CX49_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U4A7N1_A0A2U4A7N1_TURTR_9739 and tr_A0A2Y9NSC4_A0A2Y9NSC4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A7N1_A0A2U4A7N1_TURTR_9739 and tr_A0A2Y9EU01_A0A2Y9EU01_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4A7N1_A0A2U4A7N1_TURTR_9739 and tr_A0A384AB29_A0A384AB29_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4B441_A0A2U4B441_TURTR_9739 and tr_A0A2Y9M1S8_A0A2Y9M1S8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CJH4_A0A2U4CJH4_TURTR_9739 and tr_A0A2Y9P5F9_A0A2Y9P5F9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CJH4_A0A2U4CJH4_TURTR_9739 and tr_A0A2Y9EWR6_A0A2Y9EWR6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4CJH4_A0A2U4CJH4_TURTR_9739 and tr_A0A384BEE3_A0A384BEE3_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3ZA19_A0A2U3ZA19_ODORO_9708 and tr_A0A2U3XAQ3_A0A2U3XAQ3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3ZA19_A0A2U3ZA19_ODORO_9708 and tr_A0A2Y9D861_A0A2Y9D861_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A2U3ZA19_A0A2U3ZA19_ODORO_9708 and tr_A0A2Y9L8Q9_A0A2Y9L8Q9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3ZA19_A0A2U3ZA19_ODORO_9708 and tr_A0A384BIN3_A0A384BIN3_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2U3YC90_A0A2U3YC90_LEPWE_9713 and tr_A0A2Y9JI76_A0A2Y9JI76_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A367J023_A0A367J023_9FUNG_86630 and tr_A0A367KCW2_A0A367KCW2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A369GM01_A0A369GM01_9HYPO_2039875 and tr_A0A369HHT8_A0A369HHT8_9HYPO_2039874 are exactly identical! WARNING: Sequences tr_A0A369GM01_A0A369GM01_9HYPO_2039875 and tr_A0A367LBG7_A0A367LBG7_9HYPO_1330021 are exactly identical! WARNING: Duplicate sequences found: 141 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/P25490/4_raxmlng_ancestral/P25490.raxml.reduced.phy Alignment comprises 1 partitions and 414 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 414 Gaps: 46.12 % Invariant sites: 0.97 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/4_raxmlng_ancestral/P25490.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/3_mltree/P25490.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 104 / 8320 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -144440.357248 [00:00:00 -144440.357248] Initial branch length optimization [00:00:01 -121746.228104] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -121498.634154 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.063953,0.119512) (0.050627,0.174316) (0.321420,0.562473) (0.564000,1.423300) 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 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/4_raxmlng_ancestral/P25490.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/4_raxmlng_ancestral/P25490.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/4_raxmlng_ancestral/P25490.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P25490/4_raxmlng_ancestral/P25490.raxml.log Analysis started: 14-Jul-2021 16:20:34 / finished: 14-Jul-2021 16:21:16 Elapsed time: 41.909 seconds