diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java
index 385d8e4f5..9f64cefbc 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java
@@ -105,12 +105,14 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
         // Can only call from UnifiedGenotyper
         if ( !(walker instanceof UnifiedGenotyper) ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                if ( walker != null )
-                    logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getName());
-                else
-                    logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
-                walkerIdentityCheckWarningLogged = true;
+            synchronized (this) {
+                if (!walkerIdentityCheckWarningLogged) {
+                    if (walker != null)
+                        logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getSimpleName());
+                    else
+                        logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
+                    walkerIdentityCheckWarningLogged = true;
+                }
             }
             return null;
         }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java
index 24b393155..709e266ab 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java
@@ -109,12 +109,14 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements RodRequiri
 
         // Can only be called from VariantAnnotator
         if ( !(walker instanceof VariantAnnotator) ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                if ( walker != null )
-                    logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getName());
-                else
-                    logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
-                walkerIdentityCheckWarningLogged = true;
+            synchronized (this) {
+                if (!walkerIdentityCheckWarningLogged) {
+                    if (walker != null)
+                        logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getSimpleName());
+                    else
+                        logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
+                    walkerIdentityCheckWarningLogged = true;
+                }
             }
             return null;
         }
@@ -123,9 +125,11 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements RodRequiri
             // Must have a pedigree file
             trios = ((Walker) walker).getSampleDB().getTrios();
             if ( trios.isEmpty() ) {
-                if ( !pedigreeCheckWarningLogged ) {
-                    logger.warn("Annotation will not be calculated, mendelian violation annotation must provide a valid PED file (-ped) from the command line.");
-                    pedigreeCheckWarningLogged = true;
+                synchronized (this) {
+                    if (!pedigreeCheckWarningLogged) {
+                        logger.warn("Annotation will not be calculated, mendelian violation annotation must provide a valid PED file (-ped) from the command line.");
+                        pedigreeCheckWarningLogged = true;
+                    }
                 }
                 return null;
             }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java
index a56ba0dea..908e7c86d 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java
@@ -112,12 +112,14 @@ public class PossibleDeNovo extends InfoFieldAnnotation implements RodRequiringA
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
 
         if ( !(walker instanceof VariantAnnotator ) ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                if ( walker != null )
-                    logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getName());
-                else
-                    logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
-                walkerIdentityCheckWarningLogged = true;
+            synchronized (this) {
+                if (!walkerIdentityCheckWarningLogged) {
+                    if (walker != null)
+                        logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getSimpleName());
+                    else
+                        logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
+                    walkerIdentityCheckWarningLogged = true;
+                }
             }
             return null;
         }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
index 672f28460..962addd53 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
@@ -95,12 +95,14 @@ public class SpanningDeletions extends InfoFieldAnnotation implements StandardUG
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
         // Can only call from UnifiedGenotyper
         if ( !(walker instanceof UnifiedGenotyper) ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                if ( walker != null )
-                    logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getName());
-                else
-                    logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
-                walkerIdentityCheckWarningLogged = true;
+            synchronized (this) {
+                if (!walkerIdentityCheckWarningLogged) {
+                    if (walker != null)
+                        logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getSimpleName());
+                    else
+                        logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
+                    walkerIdentityCheckWarningLogged = true;
+                }
             }
             return null;
         }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
index db7932330..7eca78775 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
@@ -79,7 +79,6 @@ import java.util.*;
  */
 public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardUGAnnotation, ActiveRegionBasedAnnotation {
     private final static Logger logger = Logger.getLogger(TandemRepeatAnnotator.class);
-    private boolean walkerIdentityCheckWarningLogged = false;
 
     @Override
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java
index 1c5f02bf3..6542d18a9 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java
@@ -101,12 +101,14 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
 
         // Can only be called from VariantAnnotator
         if ( !(walker instanceof VariantAnnotator) ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                if ( walker != null )
-                    logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getName());
-                else
-                    logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
-                walkerIdentityCheckWarningLogged = true;
+            synchronized (this) {
+                if (!walkerIdentityCheckWarningLogged) {
+                    if (walker != null)
+                        logger.warn("Annotation will not be calculated, must be called from VariantAnnotator, not " + walker.getClass().getSimpleName());
+                    else
+                        logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
+                    walkerIdentityCheckWarningLogged = true;
+                }
             }
             return null;
         }
@@ -115,9 +117,11 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
         if ( trios == null ) {
             trios = ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents();
             if (trios == null || trios.isEmpty()) {
-                if ( !pedigreeCheckWarningLogged ) {
-                    logger.warn("Transmission disequilibrium test annotation requires a valid ped file be passed in.");
-                    pedigreeCheckWarningLogged = true;
+                synchronized (this) {
+                    if (!pedigreeCheckWarningLogged) {
+                        logger.warn("Transmission disequilibrium test annotation requires a valid ped file be passed in.");
+                        pedigreeCheckWarningLogged = true;
+                    }
                 }
                 return null;
             }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java
index 00e16a49a..8829e6a05 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java
@@ -115,12 +115,14 @@ public class BaseQualitySumPerAlleleBySample extends GenotypeAnnotation implemen
 
         // Can only call from MuTect2
         if ( !(walker instanceof MuTect2) ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                if ( walker != null )
-                    logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getName());
-                else
-                    logger.warn("Annotation will not be calculated, can only be called from MuTect2");
-                walkerIdentityCheckWarningLogged = true;
+            synchronized (this) {
+                if (!walkerIdentityCheckWarningLogged) {
+                    if (walker != null)
+                        logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getSimpleName());
+                    else
+                        logger.warn("Annotation will not be calculated, can only be called from MuTect2");
+                    walkerIdentityCheckWarningLogged = true;
+                }
             }
             return;
         }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java
index b12eedc4c..089e79276 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java
@@ -121,12 +121,14 @@ public class OxoGReadCounts extends GenotypeAnnotation {
 
         // Can only call from MuTect2
         if ( !(walker instanceof MuTect2) ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                if ( walker != null )
-                    logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getName());
-                else
-                    logger.warn("Annotation will not be calculated, can only be called from MuTect2");
-                walkerIdentityCheckWarningLogged = true;
+            synchronized (this) {
+                if (!walkerIdentityCheckWarningLogged) {
+                    if (walker != null)
+                        logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getSimpleName());
+                    else
+                        logger.warn("Annotation will not be calculated, can only be called from MuTect2");
+                    walkerIdentityCheckWarningLogged = true;
+                }
             }
             return;
         }