From 45d4baf15356d8db10d7ea6367247ff4366cdc14 Mon Sep 17 00:00:00 2001
From: Robert Syme <rob.syme@gmail.com>
Date: Wed, 4 Jun 2025 00:29:59 +0000
Subject: [PATCH 1/2] Resolve race condition with FIFO cleanup and child
 process termination

---
 source/Parameters_closeReadsFiles.cpp | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/source/Parameters_closeReadsFiles.cpp b/source/Parameters_closeReadsFiles.cpp
index f3a22ab3..b577081c 100644
--- a/source/Parameters_closeReadsFiles.cpp
+++ b/source/Parameters_closeReadsFiles.cpp
@@ -2,11 +2,32 @@
 #include "ErrorWarning.h"
 #include <fstream>
 #include <sys/stat.h>
+#include <sys/wait.h>
 void Parameters::closeReadsFiles() {
     for (uint imate=0; imate<readFilesIn.size(); imate++) {//open readIn files
         if ( inOut->readIn[imate].is_open() )
             inOut->readIn[imate].close();
-        if (readFilesCommandPID[imate]>0)
-            kill(readFilesCommandPID[imate],SIGKILL);
+        if (readFilesCommandPID[imate]>0) {
+            kill(readFilesCommandPID[imate],SIGTERM);  // Use SIGTERM for graceful shutdown
+            int status;
+            waitpid(readFilesCommandPID[imate], &status, 0);  // Wait for process to terminate
+            
+            // Check if process had issues (but don't fail - this is cleanup)
+            if (WIFEXITED(status)) {
+                int exit_code = WEXITSTATUS(status);
+                if (exit_code != 0) {
+                    warningMessage("readFilesCommand process for mate " + to_string(imate+1) + 
+                                 " exited with non-zero code: " + to_string(exit_code), 
+                                 std::cerr, inOut->logMain, *this);
+                }
+            } else if (WIFSIGNALED(status)) {
+                int signal_num = WTERMSIG(status);
+                if (signal_num != SIGTERM) {  // Don't warn about our own SIGTERM
+                    warningMessage("readFilesCommand process for mate " + to_string(imate+1) + 
+                                 " was terminated by signal: " + to_string(signal_num), 
+                                 std::cerr, inOut->logMain, *this);
+                }
+            }
+        }
     };
 };
\ No newline at end of file

From 296e4dbd2bee2a45563bee9a266bc23f5fdf72cf Mon Sep 17 00:00:00 2001
From: Robert Syme <rob.syme@gmail.com>
Date: Wed, 4 Jun 2025 00:52:34 +0000
Subject: [PATCH 2/2] Clean up processes BEFORE removing files

---
 source/STAR.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/source/STAR.cpp b/source/STAR.cpp
index f9b84b3e..fbdc1fca 100755
--- a/source/STAR.cpp
+++ b/source/STAR.cpp
@@ -292,6 +292,8 @@ int main(int argInN, char *argIn[])
     *P.inOut->logStdOut << timeMonthDayTime(g_statsAll.timeFinish) << " ..... finished successfully\n"
                         << flush;
 
+    P.closeReadsFiles(); // Clean up processes BEFORE removing files
+
     P.inOut->logMain << "ALL DONE!\n"
                      << flush;
     if (P.outTmpKeep == "None")
@@ -299,7 +301,6 @@ int main(int argInN, char *argIn[])
         sysRemoveDir(P.outFileTmp);
     };
 
-    P.closeReadsFiles(); // this will kill the readFilesCommand processes if necessary
     // genomeMain.~Genome(); //need explicit call because of the 'delete P.inOut' below, which will destroy P.inOut->logStdOut
     if (genomeMain.sharedMemory != NULL)
     { // need explicit call because this destructor will write to files which are deleted by 'delete P.inOut' below