diff --git a/alphafold/data/tools/hhblits.py b/alphafold/data/tools/hhblits.py
index 1d8c180d8..0962c7a6d 100644
--- a/alphafold/data/tools/hhblits.py
+++ b/alphafold/data/tools/hhblits.py
@@ -127,7 +127,7 @@ def query(self, input_fasta_path: str) -> List[Mapping[str, Any]]:
 
       logging.info('Launching subprocess "%s"', ' '.join(cmd))
       process = subprocess.Popen(
-          cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+          cmd, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
       with utils.timing('HHblits query'):
         stdout, stderr = process.communicate()
diff --git a/alphafold/data/tools/hhsearch.py b/alphafold/data/tools/hhsearch.py
index 696d42d87..08b64189f 100644
--- a/alphafold/data/tools/hhsearch.py
+++ b/alphafold/data/tools/hhsearch.py
@@ -84,7 +84,7 @@ def query(self, a3m: str) -> str:
 
       logging.info('Launching subprocess "%s"', ' '.join(cmd))
       process = subprocess.Popen(
-          cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+          cmd, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
       with utils.timing('HHsearch query'):
         stdout, stderr = process.communicate()
         retcode = process.wait()
diff --git a/alphafold/data/tools/hmmbuild.py b/alphafold/data/tools/hmmbuild.py
index f8f331da0..0af389d10 100644
--- a/alphafold/data/tools/hmmbuild.py
+++ b/alphafold/data/tools/hmmbuild.py
@@ -119,7 +119,7 @@ def _build_profile(self, msa: str, model_construction: str = 'fast') -> str:
       ])
 
       logging.info('Launching subprocess %s', cmd)
-      process = subprocess.Popen(cmd, stdout=subprocess.PIPE,
+      process = subprocess.Popen(cmd, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE)
 
       with utils.timing('hmmbuild query'):
diff --git a/alphafold/data/tools/hmmsearch.py b/alphafold/data/tools/hmmsearch.py
index 08f0b8d47..b7391d802 100644
--- a/alphafold/data/tools/hmmsearch.py
+++ b/alphafold/data/tools/hmmsearch.py
@@ -102,7 +102,7 @@ def query_with_hmm(self, hmm: str) -> str:
 
       logging.info('Launching sub-process %s', cmd)
       process = subprocess.Popen(
-          cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+          cmd, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
       with utils.timing(
           f'hmmsearch ({os.path.basename(self.database_path)}) query'):
         stdout, stderr = process.communicate()
diff --git a/alphafold/data/tools/jackhmmer.py b/alphafold/data/tools/jackhmmer.py
index 68997f857..df63c0c22 100644
--- a/alphafold/data/tools/jackhmmer.py
+++ b/alphafold/data/tools/jackhmmer.py
@@ -132,7 +132,7 @@ def _query_chunk(self,
 
       logging.info('Launching subprocess "%s"', ' '.join(cmd))
       process = subprocess.Popen(
-          cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+          cmd, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
       with utils.timing(
           f'Jackhmmer ({os.path.basename(database_path)}) query'):
         _, stderr = process.communicate()
diff --git a/alphafold/data/tools/kalign.py b/alphafold/data/tools/kalign.py
index 21ce1a361..80ebde9c7 100644
--- a/alphafold/data/tools/kalign.py
+++ b/alphafold/data/tools/kalign.py
@@ -85,7 +85,7 @@ def align(self, sequences: Sequence[str]) -> str:
       ]
 
       logging.info('Launching subprocess "%s"', ' '.join(cmd))
-      process = subprocess.Popen(cmd, stdout=subprocess.PIPE,
+      process = subprocess.Popen(cmd, stdin=subprocess.DEVNULL, stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE)
 
       with utils.timing('Kalign query'):