From f4cc9e54e35e67449b3d7fa381ba52f58588cc88 Mon Sep 17 00:00:00 2001 From: Joseph Lemaitre Date: Thu, 25 Jan 2024 18:44:12 +0100 Subject: [PATCH 1/3] adding log file to inference slot --- flepimop/main_scripts/inference_main.R | 1 + 1 file changed, 1 insertion(+) diff --git a/flepimop/main_scripts/inference_main.R b/flepimop/main_scripts/inference_main.R index aefd5a1ac..ac44fd20b 100644 --- a/flepimop/main_scripts/inference_main.R +++ b/flepimop/main_scripts/inference_main.R @@ -131,6 +131,7 @@ 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="") sep = " ") ) if(err != 0){quit("no")} From fb31b550f11edf6da8ba4f0fb11d775df1f48aed Mon Sep 17 00:00:00 2001 From: Joseph Lemaitre Date: Thu, 25 Jan 2024 18:44:52 +0100 Subject: [PATCH 2/3] fix --- flepimop/main_scripts/inference_main.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/flepimop/main_scripts/inference_main.R b/flepimop/main_scripts/inference_main.R index ac44fd20b..49ddf7e85 100644 --- a/flepimop/main_scripts/inference_main.R +++ b/flepimop/main_scripts/inference_main.R @@ -131,7 +131,7 @@ 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", flepi_slot, ".txt", sep=""), sep = " ") ) if(err != 0){quit("no")} From 62284545199d16f57a1cc1baec883871050bfcf1 Mon Sep 17 00:00:00 2001 From: Alison Hill <34223923+alsnhll@users.noreply.github.com> Date: Fri, 26 Jan 2024 12:59:23 -0500 Subject: [PATCH 3/3] Updated name of output pipe file to include config name/runID --- flepimop/main_scripts/inference_main.R | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/flepimop/main_scripts/inference_main.R b/flepimop/main_scripts/inference_main.R index 49ddf7e85..e402bd6d9 100644 --- a/flepimop/main_scripts/inference_main.R +++ b/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$iterations_per_slot)) { @@ -131,7 +128,9 @@ foreach(flepi_slot = seq_len(opt$slots)) %dopar% { "-R", opt[["is-resume"]], "-I", opt[["is-interactive"]], "-L", opt$reset_chimeric_on_accept, - paste("2>&1 | tee log_inference_slot", flepi_slot, ".txt", sep=""), + #paste("2>&1 | tee log_inference_slot", flepi_slot, ".txt", sep=""), + paste("2>&1 | tee log_inference_slot_",config$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")}