diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index f2e0b5d0c..7cc8e9e29 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -280,8 +280,24 @@ public class GenomeAnalysisEngine {
      */
     private void determineThreadAllocation() {
         Tags tags = parsingEngine.getTags(argCollection.numberOfThreads);
-        Integer numCPUThreads = tags.containsKey("cpu") ? Integer.parseInt(tags.getValue("cpu")) : null;
-        Integer numIOThreads = tags.containsKey("io") ? Integer.parseInt(tags.getValue("io")) : null;
+
+        // TODO: Kill this complicated logic once Queue supports arbitrary tagged parameters.
+        Integer numCPUThreads = null;
+        if(tags.containsKey("cpu") && argCollection.numberOfCPUThreads != null)
+            throw new UserException("Number of CPU threads specified both directly on the command-line and as a tag to the nt argument.  Please specify only one or the other.");
+        else if(tags.containsKey("cpu"))
+            numCPUThreads = Integer.parseInt(tags.getValue("cpu"));
+        else if(argCollection.numberOfCPUThreads != null)
+            numCPUThreads = argCollection.numberOfCPUThreads;
+
+        Integer numIOThreads = null;
+        if(tags.containsKey("io") && argCollection.numberOfIOThreads != null)
+            throw new UserException("Number of IO threads specified both directly on the command-line and as a tag to the nt argument.  Please specify only one or the other.");
+        else if(tags.containsKey("io"))
+            numIOThreads = Integer.parseInt(tags.getValue("io"));
+        else if(argCollection.numberOfIOThreads != null)
+            numIOThreads = argCollection.numberOfIOThreads;
+
         this.threadAllocation = new ThreadAllocation(argCollection.numberOfThreads,numCPUThreads,numIOThreads);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 64b63dcd2..08d2c1ad1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -198,6 +198,17 @@ public class GATKArgumentCollection {
     @Argument(fullName = "num_threads", shortName = "nt", doc = "How many threads should be allocated to running this analysis.", required = false)
     public Integer numberOfThreads = 1;
 
+    /**
+     * The following two arguments (num_cpu_threads, num_io_threads are TEMPORARY since Queue cannot currently support arbitrary tagged data types.
+     * TODO: Kill this when I can do a tagged integer in Queue.
+     */
+    @Argument(fullName="num_cpu_threads", shortName = "nct", doc="How many of the given threads should be allocated to the CPU", required = false)
+    @Hidden
+    public Integer numberOfCPUThreads = null;
+    @Argument(fullName="num_io_threads", shortName = "nit", doc="How many of the given threads should be allocated to IO", required = false)
+    @Hidden
+    public Integer numberOfIOThreads = null;
+
     @Argument(fullName = "num_bam_file_handles", shortName = "bfh", doc="The total number of BAM file handles to keep open simultaneously", required=false)
     public Integer numberOfBAMFileHandles = null;
 
@@ -369,6 +380,14 @@ public class GATKArgumentCollection {
         if (!other.numberOfThreads.equals(this.numberOfThreads)) {
             return false;
         }
+        if ((this.numberOfCPUThreads == null && other.numberOfCPUThreads != null) ||
+             this.numberOfCPUThreads.equals(other.numberOfCPUThreads) ) {
+            return false;
+        }
+        if ((this.numberOfIOThreads == null && other.numberOfIOThreads != null) ||
+             this.numberOfIOThreads.equals(other.numberOfIOThreads) ) {
+            return false;
+        }
         if ((other.numberOfBAMFileHandles == null && this.numberOfBAMFileHandles != null) ||
                 (other.numberOfBAMFileHandles != null && !other.numberOfBAMFileHandles.equals(this.numberOfBAMFileHandles))) {
             return false;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index 0a1eb0563..0ace6fde2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -242,8 +242,10 @@ public class SAMDataSource {
 
         this.threadAllocation = threadAllocation;
         // TODO: Consider a borrowed-thread dispatcher implementation.
-        if(this.threadAllocation.getNumIOThreads() > 0)
+        if(this.threadAllocation.getNumIOThreads() > 0) {
+            logger.info("Running in asynchronous I/O mode; number of threads = " + this.threadAllocation.getNumIOThreads());
             dispatcher = new BGZFBlockLoadingDispatcher(this.threadAllocation.getNumIOThreads(), numFileHandles != null ? numFileHandles : 1);
+        }
         else
             dispatcher = null;