START OF LOG FILE argv = "/lsweb/josef_sites/selecton/pipeline/selecton.exe" "-i" "/lsweb/josef_results/selecton/1742133720/DNA.msa" "-e0.1" "-q" "1" "-n" "8" #Process_id= 1253357 ------------------------- Reconstructing NJ tree (10:0.040565,(13:0.017573,(1:0.018757,17:0.007920):0.005055):0.022907,(14:0.071488,(((12:0.117571,(3:0.053017,7:0.048795):0.037824):0.010754,((4:0.066285,8:0.057377):0.027575,(6:0.139048,(5:0.059008,11:0.054002):0.042137):0.002942):0.009554):0.356064,((9:0.039907,((19:0.003954,20:0.000001):0.033005,(2:0.016660,18:0.011796):0.018473):0.005697):0.026180,(15:0.020492,16:0.010065):0.009823):0.075168):0.035875):0.003075); Codon frequencies (F3x4) ===================== GCT 0x1.e587c6b69d74bp-7 GCC 0x1.947e1e2ff2641p-7 GCA 0x1.8d0879c993617p-7 GCG 0x1.00d62aeddf0afp-6 CGT 0x1.8c5da51168043p-7 CGC 0x1.4aef2fb4df0d3p-7 CGA 0x1.44e94d9b37215p-7 CGG 0x1.a316bfe690157p-7 AGA 0x1.7e869bfd00689p-7 AGG 0x1.eea5c60b05383p-7 AAT 0x1.cea537b754a0cp-6 AAC 0x1.7fa435c110e77p-6 GAT 0x1.dfcadcd2a2167p-6 GAC 0x1.8dc98be7fe81p-6 TGT 0x1.413915a7746f5p-7 TGC 0x1.0cf18d6e3e513p-7 CAA 0x1.3defe3e9400abp-6 CAG 0x1.9d73751a5089p-6 GAA 0x1.863d1b7cb488ap-6 GAG 0x1.fc456dad39282p-6 GGT 0x1.e48086e169733p-7 GGC 0x1.93a4f1c6a52ddp-7 GGA 0x1.8c338b25a776bp-7 GGG 0x1.004a8ada93531p-6 CAT 0x1.8667ce59a3a01p-6 CAC 0x1.440ba73e3f9bbp-6 ATT 0x1.6bd31ed47c8bcp-6 ATC 0x1.2e1df97a89632p-6 ATA 0x1.286fd80c7fdbap-6 CTT 0x1.336678e2536d5p-6 CTC 0x1.ff2312a64b825p-7 CTA 0x1.f5984197b7da9p-7 CTG 0x1.4566833dd2af9p-6 TTA 0x1.954ce655a9eefp-7 TTG 0x1.0641f69177646p-6 AAA 0x1.785e7e690ef46p-6 AAG 0x1.ea14f70efee46p-6 ATG 0x1.8141289689398p-6 TTT 0x1.efc052efead2bp-7 TTC 0x1.9cecb2ad35c75p-7 CCT 0x1.8d32abb300e15p-7 CCC 0x1.4b9eed4796cf3p-7 CCA 0x1.45959c8e094bdp-7 CCG 0x1.a3f8b957c550bp-7 TCT 0x1.41e34a8ce96d5p-7 TCC 0x1.0d7df7df9c653p-7 TCA 0x1.08ab44e1de243p-7 TCG 0x1.54157978c2d6fp-7 AGT 0x1.d3984d032c3e9p-7 AGC 0x1.85b246dd2769fp-7 ACT 0x1.d495ea7471c77p-7 ACC 0x1.8683809226d91p-7 ACA 0x1.7f53bfa93cdefp-7 ACG 0x1.efb2cde32a543p-7 TGG 0x1.5360ec0edf0fdp-7 TAT 0x1.3a3245e04b5bdp-6 TAC 0x1.052cd303032a1p-6 GTT 0x1.7937bd7f9e7fdp-6 GTC 0x1.392a7de028a1bp-6 GTA 0x1.33451f1d87d2ep-6 GTG 0x1.8f762ea3b75d9p-6 Beginning optimization of parameters Iteration Number= 0 --------------------- current best L= -0x1.a950d941ea54p+12 new L After alpha= -0x1.a7840b5621aedp+12 new alpha = 0x1.4de6b0d86d7cep-3 current best L= -0x1.a7840b5621aedp+12 new L After beta= -0x1.a77f54c77d1c8p+12 new beta = 0x1.4c87b07a3babdp+0 current best L= -0x1.a77f54c77d1c8p+12 new L After kappa= -0x1.a673fa5df3328p+12 new kappa = 0x1.92acc9p+1 current best L= -0x1.a673fa5df3328p+12 new L After additional omega caetgory = -0x1.a571ea978d74bp+12 new additional omega caetgory = 0x1.381cfffe4a6d4p+1 current best L= -0x1.a571ea978d74bp+12 new L After prob(additional omega caetgory)= -0x1.a5543af41a051p+12 new prob(additional omega caetgory)= 0x1.c6b4bd6d487aap-2 ******BEGIN OF BBL EM********* current best L= -0x1.a5543af41a051p+12 last best L= -0x1.a5543af41a051p+12 current best L= -0x1.a4603ce96c6ap+12 last best L= -0x1.a4603ce96c6ap+12 current best L= -0x1.a45df697976dbp+12 ******END OF BBL EM********* current best L= -0x1.a5543af41a051p+12 new L After BL = -0x1.a45df697976dbp+12 Tree after this BBL iteration: (10:0x1.4c4fecbfb1984p-5,(13:0x1.1fea49a223e2p-6,(1:0x1.5301b295f2bdap-6,17:0x1.038907bfc0ab8p-7):0x1.8b1be523b71b6p-8):0x1.77507da5906ecp-6,(14:0x1.4218c10321939p-4,(((12:0x1.e191f71f8b82p-4,(3:0x1.f09df0161a6bep-5,7:0x1.8fbb1cde83f8p-5):0x1.35da8abcbb438p-5):0x1.56b8ced883a8ep-5,((4:0x1.0f80b72ceadb6p-4,8:0x1.292e286d031fep-4):0x1.01741dcd3beb7p-5,(6:0x1.3a8b843ccfcc2p-3,(5:0x1.e36504344471dp-5,11:0x1.ba62ebb8d89abp-5):0x1.97d5f2fa7356ep-5):0x1.ed3d3788a6e51p-8):0x1.3910665772a0bp-7):0x1.d5d23e9e51022p-2,((9:0x1.46eb689377c3ap-5,((19:0x1.031dab55384b1p-8,20:0x1.0c6f7ap-20):0x1.4d525c593e1p-5,(2:0x1.10f68a0f68fdap-6,18:0x1.8284ce0e2dab6p-7):0x1.2eaa57708a9d2p-6):0x1.f987aaf53d624p-7):0x1.15a1b4e8e7a42p-5,(15:0x1.4fbe67565551cp-6,16:0x1.49cea6ab431dep-7):0x1.41e3498182ab2p-7):0x1.52af0b325c6aap-4):0x1.455016eb58183p-5):0x1.92fc9c6be67ep-9); Iteration Number= 1 --------------------- current best L= -0x1.a45df697976dbp+12 new L After alpha= -0x1.a3b69f1f87e0fp+12 new alpha = 0x1.de8a882dba43fp-2 current best L= -0x1.a3b69f1f87e0fp+12 new L After beta= -0x1.a3b51d7103135p+12 new beta = 0x1.8cafd9b1f4d42p+0 current best L= -0x1.a3b69f1f87e0fp+12 new L After kappa= -0x1.a3b269b2d7985p+12 new kappa = 0x1.baf1438036f9cp+1 current best L= -0x1.a3b269b2d7985p+12 new L After additional omega caetgory = -0x1.a38875d7021f3p+12 new additional omega caetgory = 0x1.7be53a1ef0c04p+1 current best L= -0x1.a38875d7021f3p+12 new L After prob(additional omega caetgory)= -0x1.a3325fb1d07d9p+12 new prob(additional omega caetgory)= 0x1.5afc7f7b0726ap-2 ******BEGIN OF BBL EM********* current best L= -0x1.a3325fb1d07d9p+12 last best L= -0x1.a3325fb1d07d9p+12 current best L= -0x1.a32c4535d376p+12 last best L= -0x1.a32c4535d376p+12 current best L= -0x1.a32b8d45cc137p+12 ******END OF BBL EM********* current best L= -0x1.a3325fb1d07d9p+12 new L After BL = -0x1.a32b8d45cc137p+12 Tree after this BBL iteration: (10:0x1.6df0b43644652p-5,(13:0x1.1fea49a223e2p-6,(1:0x1.5301b295f2bdap-6,17:0x1.038907bfc0ab8p-7):0x1.8b1be523b71b6p-8):0x1.77507da5906ecp-6,(14:0x1.4218c10321939p-4,(((12:0x1.0a14985a4c971p-3,(3:0x1.f09df0161a6bep-5,7:0x1.8fbb1cde83f8p-5):0x1.35da8abcbb438p-5):0x1.56b8ced883a8ep-5,((4:0x1.0f80b72ceadb6p-4,8:0x1.292e286d031fep-4):0x1.01741dcd3beb7p-5,(6:0x1.3a8b843ccfcc2p-3,(5:0x1.e36504344471dp-5,11:0x1.e6a00359131a1p-5):0x1.97d5f2fa7356ep-5):0x1.ed3d3788a6e51p-8):0x1.3910665772a0bp-7):0x1.d5d23e9e51022p-2,((9:0x1.46eb689377c3ap-5,((19:0x1.031dab55384b1p-8,20:0x1.0c6f7ap-20):0x1.4d525c593e1p-5,(2:0x1.30b24c6ce5236p-6,18:0x1.8284ce0e2dab6p-7):0x1.2eaa57708a9d2p-6):0x1.f987aaf53d624p-7):0x1.15a1b4e8e7a42p-5,(15:0x1.4fbe67565551cp-6,16:0x1.6ac9b78cf6c7p-7):0x1.41e3498182ab2p-7):0x1.748d5924ab46ep-4):0x1.455016eb58183p-5):0x1.92fc9c6be67ep-9); Iteration Number= 2 --------------------- current best L= -0x1.a32b8d45cc137p+12 new L After alpha= -0x1.a2ea53342862dp+12 new alpha = 0x1.819d5ff114528p-1 current best L= -0x1.a2ea53342862dp+12 new L After beta= -0x1.a2ea53342862dp+12 new beta = 0x1.4c87b07a3babdp+0 current best L= -0x1.a2ea53342862dp+12 new L After kappa= -0x1.a2ea53342862dp+12 new kappa = 0x1.baf1438036f9cp+1 current best L= -0x1.a2ea53342862dp+12 new L After additional omega caetgory = -0x1.a2c87bbfffa3dp+12 new additional omega caetgory = 0x1.c33b2e2360e6fp+1 current best L= -0x1.a2c87bbfffa3dp+12 new L After prob(additional omega caetgory)= -0x1.a2a8e286d26f3p+12 new prob(additional omega caetgory)= 0x1.1e95f40630b64p-2 ******BEGIN OF BBL EM********* current best L= -0x1.a2a8e286d26f3p+12 last best L= -0x1.a2a8e286d26f3p+12 current best L= -0x1.a293e61903871p+12 last best L= -0x1.a293e61903871p+12 current best L= -0x1.a293e61903871p+12 ******END OF BBL EM********* current best L= -0x1.a2a8e286d26f3p+12 new L After BL = -0x1.a293e61903871p+12 Tree after this BBL iteration: (10:0x1.6df0b43644652p-5,(13:0x1.1fea49a223e2p-6,(1:0x1.5301b295f2bdap-6,17:0x1.038907bfc0ab8p-7):0x1.8b1be523b71b6p-8):0x1.77507da5906ecp-6,(14:0x1.4218c10321939p-4,(((12:0x1.0a14985a4c971p-3,(3:0x1.f09df0161a6bep-5,7:0x1.6314cd171e9b6p-5):0x1.35da8abcbb438p-5):0x1.34732081eb41bp-5,((4:0x1.debbf8862576dp-5,8:0x1.292e286d031fep-4):0x1.01741dcd3beb7p-5,(6:0x1.59ffde46542fcp-3,(5:0x1.09ddf58a04dcfp-4,11:0x1.e6a00359131a1p-5):0x1.97d5f2fa7356ep-5):0x1.ed3d3788a6e51p-8):0x1.3910665772a0bp-7):0x1.d5d23e9e51022p-2,((9:0x1.46eb689377c3ap-5,((19:0x1.031dab55384b1p-8,20:0x1.0c6f7ap-20):0x1.4d525c593e1p-5,(2:0x1.30b24c6ce5236p-6,18:0x1.8284ce0e2dab6p-7):0x1.10661b6366473p-6):0x1.f987aaf53d624p-7):0x1.15a1b4e8e7a42p-5,(15:0x1.4fbe67565551cp-6,16:0x1.6ac9b78cf6c7p-7):0x1.e2d4ee424400bp-8):0x1.748d5924ab46ep-4):0x1.65d81943d28a8p-5):0x1.92fc9c6be67ep-9); Iteration Number= 3 --------------------- current best L= -0x1.a293e61903871p+12 new L After alpha= -0x1.a27d0ffbdd4d2p+12 new alpha = 0x1.f21bba2f5707ep-1 current best L= -0x1.a27d0ffbdd4d2p+12 new L After beta= -0x1.a27d0ffbdd4d2p+12 new beta = 0x1.4c87b07a3babdp+0 current best L= -0x1.a27d0ffbdd4d2p+12 new L After kappa= -0x1.a27d0ffbdd4d2p+12 new kappa = 0x1.baf1438036f9cp+1 current best L= -0x1.a27d0ffbdd4d2p+12 new L After additional omega caetgory = -0x1.a270a36ee51a1p+12 new additional omega caetgory = 0x1.f54e33165fe93p+1 current best L= -0x1.a270a36ee51a1p+12 new L After prob(additional omega caetgory)= -0x1.a2692c7018394p+12 new prob(additional omega caetgory)= 0x1.01493ec47a9c6p-2 ******BEGIN OF BBL EM********* current best L= -0x1.a2692c7018394p+12 last best L= -0x1.a2692c7018394p+12 current best L= -0x1.a2653e8d16cccp+12 last best L= -0x1.a2653e8d16cccp+12 current best L= -0x1.a2653e8d16cccp+12 ******END OF BBL EM********* current best L= -0x1.a2692c7018394p+12 new L After BL = -0x1.a2653e8d16cccp+12 Tree after this BBL iteration: (10:0x1.6df0b43644652p-5,(13:0x1.1fea49a223e2p-6,(1:0x1.5301b295f2bdap-6,17:0x1.d329da519a822p-8):0x1.8b1be523b71b6p-8):0x1.77507da5906ecp-6,(14:0x1.4218c10321939p-4,(((12:0x1.0a14985a4c971p-3,(3:0x1.f09df0161a6bep-5,7:0x1.6314cd171e9b6p-5):0x1.35da8abcbb438p-5):0x1.34732081eb41bp-5,((4:0x1.debbf8862576dp-5,8:0x1.292e286d031fep-4):0x1.01741dcd3beb7p-5,(6:0x1.59ffde46542fcp-3,(5:0x1.09ddf58a04dcfp-4,11:0x1.e6a00359131a1p-5):0x1.97d5f2fa7356ep-5):0x1.ed3d3788a6e51p-8):0x1.e62e54a2f67efp-8):0x1.d5d23e9e51022p-2,((9:0x1.46eb689377c3ap-5,((19:0x1.031dab55384b1p-8,20:0x1.0c6f7ap-20):0x1.4d525c593e1p-5,(2:0x1.30b24c6ce5236p-6,18:0x1.8284ce0e2dab6p-7):0x1.10661b6366473p-6):0x1.f987aaf53d624p-7):0x1.15a1b4e8e7a42p-5,(15:0x1.4fbe67565551cp-6,16:0x1.6ac9b78cf6c7p-7):0x1.e2d4ee424400bp-8):0x1.748d5924ab46ep-4):0x1.65d81943d28a8p-5):0x1.92fc9c6be67ep-9); Iteration Number= 4 --------------------- current best L= -0x1.a2653e8d16cccp+12 new L After alpha= -0x1.a25cbc90efa83p+12 new alpha = 0x1.29ff3bfe14c5p+0 current best L= -0x1.a25cbc90efa83p+12 new L After beta= -0x1.a25cbc90efa83p+12 new beta = 0x1.4c87b07a3babdp+0 current best L= -0x1.a25cbc90efa83p+12 new L After kappa= -0x1.a25cbc90efa83p+12 new kappa = 0x1.baf1438036f9cp+1 current best L= -0x1.a25cbc90efa83p+12 new L After additional omega caetgory = -0x1.a25827a16894ap+12 new additional omega caetgory = 0x1.0afb6bebae671p+2 current best L= -0x1.a25827a16894ap+12 new L After prob(additional omega caetgory)= -0x1.a2565feddf0adp+12 new prob(additional omega caetgory)= 0x1.e3e1b5ba6ec4cp-3 ******BEGIN OF BBL EM********* current best L= -0x1.a2565feddf0adp+12 last best L= -0x1.a2565feddf0adp+12 current best L= -0x1.a251d0621a77p+12 last best L= -0x1.a251d0621a77p+12 current best L= -0x1.a24f6823206c4p+12 ******END OF BBL EM********* current best L= -0x1.a2565feddf0adp+12 new L After BL = -0x1.a24e26b354102p+12 Tree after this BBL iteration: (10:0x1.6df0b43644652p-5,(13:0x1.1fea49a223e2p-6,(1:0x1.5301b295f2bdap-6,17:0x1.a4727741e45c2p-8):0x1.8b1be523b71b6p-8):0x1.77507da5906ecp-6,(14:0x1.4218c10321939p-4,(((12:0x1.0a14985a4c971p-3,(3:0x1.f09df0161a6bep-5,7:0x1.6314cd171e9b6p-5):0x1.35da8abcbb438p-5):0x1.34732081eb41bp-5,((4:0x1.debbf8862576dp-5,8:0x1.292e286d031fep-4):0x1.01741dcd3beb7p-5,(6:0x1.59ffde46542fcp-3,(5:0x1.09ddf58a04dcfp-4,11:0x1.e6a00359131a1p-5):0x1.97d5f2fa7356ep-5):0x1.ed3d3788a6e51p-8):0x1.5d5efbfc5be7cp-8):0x1.d5d23e9e51022p-2,((9:0x1.46eb689377c3ap-5,((19:0x1.031dab55384b1p-8,20:0x1.0c6f7ap-20):0x1.4d525c593e1p-5,(2:0x1.30b24c6ce5236p-6,18:0x1.5bddec6f628dcp-7):0x1.10661b6366473p-6):0x1.f987aaf53d624p-7):0x1.15a1b4e8e7a42p-5,(15:0x1.4fbe67565551cp-6,16:0x1.6ac9b78cf6c7p-7):0x1.13a819baf906ep-8):0x1.748d5924ab46ep-4):0x1.65d81943d28a8p-5):0x1.25c6fe0a1584fp-9); Finished optimization of parameters Too many iterations in function optimizeCodonModelAndBBL. The last optimized parameters are used for the calculations. Calculating posterior and expectation of posterior values for all sites Printing selection color bins to file END OF LOG FILE