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Added verbose option for mcmc log file printing
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@stephaneguindon
stephaneguindon committed Sep 13, 2024
1 parent 188952e commit ea8e16e
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Showing 4 changed files with 78 additions and 158 deletions.
3 changes: 2 additions & 1 deletion src/init.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -598,7 +598,7 @@ void Set_Defaults_Input(option* io)
io->n_data_set_asked = -1;
io->print_boot_trees = 1;
io->n_part = 1;
io->ratio_test = ABAYES;
io->ratio_test = ABAYES;
io->multigene = 0;
io->config_multigene = 0;
io->curr_interface = 0;
Expand Down Expand Up @@ -3704,6 +3704,7 @@ void MCMC_Init_MCMC_Struct(char *filename, option *io, t_mcmc *mcmc)
mcmc->always_yes = NO;
mcmc->max_lag = 1000;
mcmc->sample_num = 0;
mcmc->out_verbose = 1;

if(filename)
{
Expand Down
218 changes: 62 additions & 156 deletions src/io.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6884,12 +6884,6 @@ void PHYREX_Print_MCMC_Stats(t_tree *tree)
PhyML_Fprintf(fp_stats,"%s\t","lnPSpac");
PhyML_Fprintf(fp_stats,"%s\t","lnPRate");
PhyML_Fprintf(fp_stats,"%s\t","lnPTime");
/* PhyML_Fprintf(fp_stats,"%s\t","lnRateAutoCor"); */
/* PhyML_Fprintf(fp_stats,"%s\t","lnRateClock"); */
/* PhyML_Fprintf(fp_stats,"%s\t","lnRateRoot1"); */
/* PhyML_Fprintf(fp_stats,"%s\t","lnRateRoot2"); */
/* PhyML_Fprintf(fp_stats,"%s\t","lnRater1"); */
/* PhyML_Fprintf(fp_stats,"%s\t","lnRater2"); */
PhyML_Fprintf(fp_stats,"%s\t","substRate");
PhyML_Fprintf(fp_stats,"%s\t","clockRate");
for(int i=0;i<tree->mmod->n_dim;++i) PhyML_Fprintf(fp_stats,"%s%s\t","sigSq",(i==0)?("Lon"):((i==1)?("Lat"):("xx")));
Expand All @@ -6913,27 +6907,13 @@ void PHYREX_Print_MCMC_Stats(t_tree *tree)
PhyML_Fprintf(fp_stats,"%s\t","rootTime");
PhyML_Fprintf(fp_stats,"%s\t","rootLon");
PhyML_Fprintf(fp_stats,"%s\t","rootLat");
/* for(int i=0;i<Scalar_Len(tree->mod->kappa);++i) PhyML_Fprintf(fp_stats,"tstv%d\t",i); */
/* if(tree->mod->ras->free_mixt_rates == NO) PhyML_Fprintf(fp_stats,"alpha\t"); */
/* else */
/* { */
/* for(int i=0;i<tree->mod->ras->n_catg;++i) PhyML_Fprintf(fp_stats,"p(%d)\t",i+1); */
/* for(int i=0;i<tree->mod->ras->n_catg;++i) PhyML_Fprintf(fp_stats,"rr(%d)\t",i+1); */
/* } */
PhyML_Fprintf(fp_stats,"%s\t","nu");
PhyML_Fprintf(fp_stats,"%s\t","rrNormFact");
PhyML_Fprintf(fp_stats,"%s\t","rrRateMult");
PhyML_Fprintf(fp_stats,"%s\t","rrwNormFact");

/* PhyML_Fprintf(fp_stats,"%s\t","treeLen"); */
/* PhyML_Fprintf(fp_stats,"%s\t","speed"); */

/* PhyML_Fprintf(fp_stats,"%s\t","accSigSq"); */
/* PhyML_Fprintf(fp_stats,"%s\t","accSPR"); */
/* PhyML_Fprintf(fp_stats,"%s\t","accSPRsLide"); */
PhyML_Fprintf(fp_stats,"%s\t","accNarrowExchange");
PhyML_Fprintf(fp_stats,"%s\t","accWideExchange");
/* PhyML_Fprintf(fp_stats,"%s\t","accLdskGivenDisk"); */
PhyML_Fprintf(fp_stats,"%s\t","accMoveRootTime");
PhyML_Fprintf(fp_stats,"%s\t","accMoveScaleTime");
PhyML_Fprintf(fp_stats,"%s\t","accNodeTimes");
Expand All @@ -6944,85 +6924,48 @@ void PHYREX_Print_MCMC_Stats(t_tree *tree)
PhyML_Fprintf(fp_stats,"%s\t","accScaleVeloc");
PhyML_Fprintf(fp_stats,"%s\t","tuneRatesShrink");
PhyML_Fprintf(fp_stats,"%s\t","tuneVeloc");
/* PhyML_Fprintf(fp_stats,"%s\t","accLdskTipToRoot"); */

/* PhyML_Fprintf(fp_stats,"%s\t","tuneScale"); */
/* PhyML_Fprintf(fp_stats,"%s\t","tuneLdskGivenDisk"); */
/* PhyML_Fprintf(fp_stats,"%s\t","tuneLdskTipToRoot"); */
/* PhyML_Fprintf(fp_stats,"%s\t","tuneRootTime"); */

/* for(int i=0;i<1;++i) */
/* { */
/* PhyML_Fprintf(fp_stats,"aux%dLocLnL\t",i); */
/* PhyML_Fprintf(fp_stats,"aux%dTimeLnL\t",i); */
/* } */

/* PhyML_Fprintf(fp_stats,"aux0RootTime\t"); */

/* PhyML_Fprintf(fp_stats,"%s\t","auxaccSPR"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxaccSPRsLide"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxaccNarrowExchange"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxaccWideExchange"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxaccLdskGivenDisk"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxaccMoveRootTime"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxaccLdskTipToRoot"); */

/* PhyML_Fprintf(fp_stats,"%s\t","auxtuneScale"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxtuneLdskGivenDisk"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxtuneLdskTipToRoot"); */
/* PhyML_Fprintf(fp_stats,"%s\t","auxtuneRootTime"); */

if(tree->mmod->model_id == RRW_GAMMA ||
tree->mmod->model_id == RRW_LOGNORMAL) for(int i=0;i<2*tree->n_otu-1;++i) PhyML_Fprintf(fp_stats,"sigSq%d\t",i);
/* for(int i=0;i<2*tree->n_otu-1;++i) PhyML_Fprintf(fp_stats,"auxsigSq%d\t",i); */
if (tree->mcmc->out_verbose == 1)
if (tree->mmod->model_id == RRW_GAMMA ||
tree->mmod->model_id == RRW_LOGNORMAL)
for (int i = 0; i < 2 * tree->n_otu - 1; ++i)
PhyML_Fprintf(fp_stats, "sigSq%d\t", i);

PhyML_Fprintf(fp_stats,"sigSqSonLeft\t");
PhyML_Fprintf(fp_stats,"sigSqSonRght\t");

PhyML_Fprintf(fp_stats,"rrSonLeft\t");
PhyML_Fprintf(fp_stats,"rrSonRght\t");

/* for(int i=0;i<2*tree->n_otu-2;++i) PhyML_Fprintf(fp_stats,"rr%d%c\t", */
/* i, */
/* (tree->a_nodes[i] == tree->n_root->v[1] || */
/* tree->a_nodes[i] == tree->n_root->v[2]) ? */
/* '*':' '); */

PhyML_Fprintf(fp_stats, "root_VelocLon\t");
PhyML_Fprintf(fp_stats, "root_VelocLat\t");

for (int i = 0; i < tree->n_otu; ++i)
if(tree->mcmc->out_verbose == 1)
{
PhyML_Fprintf(fp_stats, "%s_VelocLon\t", tree->a_nodes[i]->name);
PhyML_Fprintf(fp_stats, "%s_VelocLat\t", tree->a_nodes[i]->name);
for (int i = 0; i < tree->n_otu; ++i)
{
PhyML_Fprintf(fp_stats, "%s_VelocLon\t", tree->a_nodes[i]->name);
PhyML_Fprintf(fp_stats, "%s_VelocLat\t", tree->a_nodes[i]->name);
}

if (VELOC_Is_Integrated_Velocity(tree->mmod) == YES)
{
for (int i = tree->n_otu; i < 2 * tree->n_otu - 1; ++i)
{
PhyML_Fprintf(fp_stats, "%d_VelocLon%s\t", i, (tree->a_nodes[i] == tree->n_root->v[1] || tree->a_nodes[i] == tree->n_root->v[2]) ? "*" : "");
PhyML_Fprintf(fp_stats, "%d_VelocLat%s\t", i, (tree->a_nodes[i] == tree->n_root->v[1] || tree->a_nodes[i] == tree->n_root->v[2]) ? "*" : "");
}
}
}
for (int i = tree->n_otu; i < 2 * tree->n_otu - 1; ++i)

if (tree->mcmc->out_verbose == 1)
{
PhyML_Fprintf(fp_stats, "%d_%s_VelocLon%s\t", i,"anc",(tree->a_nodes[i] == tree->n_root->v[1] || tree->a_nodes[i] == tree->n_root->v[2]) ? "*" : "");
PhyML_Fprintf(fp_stats, "%d_%s_VelocLat%s\t", i,"anc",(tree->a_nodes[i] == tree->n_root->v[1] || tree->a_nodes[i] == tree->n_root->v[2]) ? "*" : "");
for (int i = tree->n_otu; i < 2 * tree->n_otu - 1; ++i)
{
PhyML_Fprintf(fp_stats, "%d_Lon%s\t", i, (tree->a_nodes[i] == tree->n_root->v[1] || tree->a_nodes[i] == tree->n_root->v[2]) ? "*" : "");
PhyML_Fprintf(fp_stats, "%d_Lat%s\t", i, (tree->a_nodes[i] == tree->n_root->v[1] || tree->a_nodes[i] == tree->n_root->v[2]) ? "*" : "");
}
}

/* for(int i=0;i<tree->n_otu;++i) */
/* { */
/* PhyML_Fprintf(fp_stats,"%s_DispLon\t",tree->a_nodes[i]->name); */
/* PhyML_Fprintf(fp_stats,"%s_DispLat\t",tree->a_nodes[i]->name); */
/* } */

/* for(int i=0;i<tree->n_otu;++i) */
/* { */
/* PhyML_Fprintf(fp_stats,"%s_Disp\t",tree->a_nodes[i]->name); */
/* } */

/* for(int i=0;i<tree->n_otu-1;++i) */
/* { */
/* PhyML_Fprintf(fp_stats,"%d_Lon\t",tree->a_nodes[tree->n_otu+i]->num); */
/* PhyML_Fprintf(fp_stats,"%d_Lat\t",tree->a_nodes[tree->n_otu+i]->num); */
/* } */

/* if(tree->io->mcmc_output_times == YES) */
/* { */
/* for(int i=tree->n_otu;i<2*tree->n_otu-1;++i) PhyML_Fprintf(fp_stats,"%d_Time\t",tree->a_nodes[i]->num); */
/* } */
}
}

Expand Down Expand Up @@ -7079,26 +7022,12 @@ void PHYREX_Print_MCMC_Stats(t_tree *tree)
PhyML_Fprintf(fp_stats,"%g\t",tree->n_root->ldsk->coord->lonlat[0]);
PhyML_Fprintf(fp_stats,"%g\t",tree->n_root->ldsk->coord->lonlat[1]);

/* Output_Scalar_Dbl(tree->mod->kappa,"\t",fp_stats); */
/* if(tree->mod->ras->free_mixt_rates == NO) PhyML_Fprintf(fp_stats,"%g\t",tree->mod->ras->alpha->v); */
/* else */
/* { */
/* for(int i=0;i<tree->mod->ras->n_catg;++i) PhyML_Fprintf(fp_stats,"%g\t",tree->mod->ras->gamma_r_proba->v[i]); */
/* for(int i=0;i<tree->mod->ras->n_catg;++i) PhyML_Fprintf(fp_stats,"%g\t",tree->mod->ras->gamma_rr->v[i]); */
/* } */
PhyML_Fprintf(fp_stats,"%g\t",tree->rates->nu);
PhyML_Fprintf(fp_stats,"%g\t",tree->rates->norm_fact);
PhyML_Fprintf(fp_stats,"%g\t",RATES_Mean_Rate_Multiplier(tree));
PhyML_Fprintf(fp_stats,"%g\t",tree->mmod->sigsq_scale_norm_fact);
/* PhyML_Fprintf(fp_stats,"%g\t",Tree_Length(tree)); */
/* PhyML_Fprintf(fp_stats,"%g\t",difftime(tree->mcmc->time_end,tree->mcmc->time_beg)/(phydbl)tree->mcmc->sample_interval); */

/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_sigsq]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_spr]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_spr_slide]); */
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_narrow_exchange]);
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_wide_exchange]);
/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_ldsk_given_disk]); */
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_root_time]);
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_scale_times]);
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_node_times]);
Expand All @@ -7109,78 +7038,55 @@ void PHYREX_Print_MCMC_Stats(t_tree *tree)
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_all_veloc]);
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->tune_move[tree->mcmc->num_move_rates_shrink]);
PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->tune_move[tree->mcmc->num_move_phyrex_node_veloc]);
/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->acc_rate[tree->mcmc->num_move_phyrex_ldsk_tip_to_root]); */

/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->tune_move[tree->mcmc->num_move_phyrex_scale_times]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->tune_move[tree->mcmc->num_move_phyrex_ldsk_given_disk]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->tune_move[tree->mcmc->num_move_phyrex_ldsk_tip_to_root]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->mcmc->tune_move[tree->mcmc->num_move_root_time]); */


/* for(int i=0;i<1;++i) */
/* { */
/* PhyML_Fprintf(fp_stats,"%.2f\t",tree->aux_tree[i]->mmod->c_lnL); */
/* PhyML_Fprintf(fp_stats,"%.2f\t",tree->aux_tree[i]->times->c_lnL); */
/* } */

/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->times->nd_t[tree->aux_tree[0]->n_root->num]); */


/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->acc_rate[tree->aux_tree[0]->mcmc->num_move_phyrex_spr]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->acc_rate[tree->aux_tree[0]->mcmc->num_move_phyrex_spr_slide]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->acc_rate[tree->aux_tree[0]->mcmc->num_move_phyrex_narrow_exchange]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->acc_rate[tree->aux_tree[0]->mcmc->num_move_phyrex_wide_exchange]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->acc_rate[tree->aux_tree[0]->mcmc->num_move_phyrex_ldsk_given_disk]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->acc_rate[tree->aux_tree[0]->mcmc->num_move_root_time]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->acc_rate[tree->aux_tree[0]->mcmc->num_move_phyrex_ldsk_tip_to_root]); */

/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->tune_move[tree->aux_tree[0]->mcmc->num_move_phyrex_scale_times]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->tune_move[tree->aux_tree[0]->mcmc->num_move_phyrex_ldsk_given_disk]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->tune_move[tree->aux_tree[0]->mcmc->num_move_phyrex_ldsk_tip_to_root]); */
/* PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mcmc->tune_move[tree->aux_tree[0]->mcmc->num_move_root_time]); */

if(tree->mmod->model_id == RRW_GAMMA ||
tree->mmod->model_id == RRW_LOGNORMAL)
for(int i=0;i<2*tree->n_otu-1;++i) PhyML_Fprintf(fp_stats,"%g\t",tree->mmod->sigsq_scale[i]);
/* for(int i=0;i<2*tree->n_otu-1;++i) PhyML_Fprintf(fp_stats,"%g\t",tree->aux_tree[0]->mmod->sigsq_scale[i]); */
if (tree->mcmc->out_verbose == 1)
if (tree->mmod->model_id == RRW_GAMMA ||
tree->mmod->model_id == RRW_LOGNORMAL)
for (int i = 0; i < 2 * tree->n_otu - 1; ++i)
PhyML_Fprintf(fp_stats, "%g\t", tree->mmod->sigsq_scale[i]);

PhyML_Fprintf(fp_stats,"%f\t",tree->mmod->sigsq_scale[tree->n_root->v[1]->num]);
PhyML_Fprintf(fp_stats,"%f\t",tree->mmod->sigsq_scale[tree->n_root->v[2]->num]);

PhyML_Fprintf(fp_stats,"%f\t",tree->rates->br_r[tree->n_root->v[1]->num]);
PhyML_Fprintf(fp_stats,"%f\t",tree->rates->br_r[tree->n_root->v[2]->num]);

/* for(int i=0;i<2*tree->n_otu-2;++i) PhyML_Fprintf(fp_stats,"%f\t",tree->rates->br_r[tree->a_nodes[i]->num]); */

if(VELOC_Is_Integrated_Velocity(tree->mmod) == YES)
{
PhyML_Fprintf(fp_stats,"%g\t",tree->n_root->ldsk->veloc->deriv[0]);
PhyML_Fprintf(fp_stats,"%g\t",tree->n_root->ldsk->veloc->deriv[1]);
if (VELOC_Is_Integrated_Velocity(tree->mmod) == YES)
{
PhyML_Fprintf(fp_stats, "%g\t", tree->n_root->ldsk->veloc->deriv[0]);
PhyML_Fprintf(fp_stats, "%g\t", tree->n_root->ldsk->veloc->deriv[1]);

/* for(int i=0;i<tree->n_otu;++i) */
for(int i=0;i<2*tree->n_otu-1;++i)
{
PhyML_Fprintf(fp_stats,"%g\t",tree->a_nodes[i]->ldsk->veloc->deriv[0]);
PhyML_Fprintf(fp_stats,"%g\t",tree->a_nodes[i]->ldsk->veloc->deriv[1]);
}
}
else if(RRW_Is_Rw(tree->mmod) == YES)
{
if (tree->mcmc->out_verbose == 1)
for (int i = 0; i < 2 * tree->n_otu - 1; ++i)
{
PhyML_Fprintf(fp_stats, "%g\t", tree->a_nodes[i]->ldsk->veloc->deriv[0]);
PhyML_Fprintf(fp_stats, "%g\t", tree->a_nodes[i]->ldsk->veloc->deriv[1]);
}
}
else if (RRW_Is_Rw(tree->mmod) == YES)
{
RRW_Tip_Velocities(tree);

PhyML_Fprintf(fp_stats,"%g\t",-1.);
PhyML_Fprintf(fp_stats,"%g\t",-1);
PhyML_Fprintf(fp_stats, "%g\t", -1.);
PhyML_Fprintf(fp_stats, "%g\t", -1.);

/* for(int i=0;i<tree->n_otu;++i) */
for(int i=0;i<2*tree->n_otu-1;++i)
{
PhyML_Fprintf(fp_stats,"%g\t",tree->a_nodes[i]->ldsk->veloc->deriv[0]);
PhyML_Fprintf(fp_stats,"%g\t",tree->a_nodes[i]->ldsk->veloc->deriv[1]);
}
if (tree->mcmc->out_verbose == 1)
{
for (int i = 0; i < tree->n_otu; ++i)
{
PhyML_Fprintf(fp_stats, "%g\t", tree->a_nodes[i]->ldsk->veloc->deriv[0]);
PhyML_Fprintf(fp_stats, "%g\t", tree->a_nodes[i]->ldsk->veloc->deriv[1]);
}
}
}

}
if (tree->mcmc->out_verbose == 1)
for (int i = tree->n_otu; i < 2 * tree->n_otu - 1; ++i)
{
PhyML_Fprintf(fp_stats, "%g\t", tree->a_nodes[i]->ldsk->coord->lonlat[0]);
PhyML_Fprintf(fp_stats, "%g\t", tree->a_nodes[i]->ldsk->coord->lonlat[1]);
}


/* for(int i=0;i<tree->n_otu;++i) */
/* { */
/* PhyML_Fprintf(fp_stats,"%g\t%g\t", */
Expand Down
13 changes: 13 additions & 0 deletions src/phyrex.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -132,6 +132,19 @@ void PHYREX_XML(char *xml_filename)
else mixt_tree->io->mcmc_output_trees = NO;
}

dum_string = XML_Get_Attribute_Value(xnd,"mcmc.verbose");
if(dum_string != NULL)
{
int select = XML_Validate_Attr_Int(dum_string,6,
"true","yes","y",
"false","no","n");
if(select < 3) mixt_tree->io->mcmc->out_verbose = 1;
else mixt_tree->io->mcmc->out_verbose = 0;
}





dum_string = XML_Get_Attribute_Value(xnd,"ignore.sequences");
if(!dum_string) dum_string = XML_Get_Attribute_Value(xnd,"ignore.seq");
Expand Down
2 changes: 1 addition & 1 deletion src/utilities.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1918,7 +1918,7 @@ typedef struct __Tmcmc {
int always_yes; /* Always accept proposed move (as long as log-likelihood > UNLIKELY) */
int is; /* Importance sampling? Yes or NO */


short int out_verbose;

}t_mcmc;

Expand Down

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