Merge branch 'breaking-improvments_inference_log' into breaking-impro…

…vments

flepimop/main_scripts/inference_main.R

@@ -41,9 +41,6 @@ print(paste('Running ',opt$j,' jobs in parallel'))
 
 config <- flepicommon::load_config(opt$config)
 
-
-
-
 # Run Specifics -----------------------------------------------------------
 
 if(is.na(opt$iterations_per_slot)) {
@@ -131,6 +128,9 @@ foreach(flepi_slot = seq_len(opt$slots)) %dopar% {
         "-R", opt[["is-resume"]],
         "-I", opt[["is-interactive"]],
         "-L", opt$reset_chimeric_on_accept,
+      #paste("2>&1 | tee log_inference_slot", flepi_slot, ".txt", sep=""),
+      paste("2>&1 | tee log_inference_slot_",config$name,"_",opt$run_id, "_", flepi_slot, ".txt", sep=""),
+      #paste("2>&1 | tee model_output/",config$name,"/",opt$run_id,"/log/log_inference_slot", flepi_slot, ".txt", sep=""), # doesn't work because config$name needs to be combined with scenarios to generate the folder name, and, because this command seems to only be able to pipe output to pre-existing folders
       sep = " ")
     )
   if(err != 0){quit("no")}