diff --git a/modules/bindings/pymod/hhblits2.py b/modules/bindings/pymod/hhblits2.py
index ff08319a4319cc562f6182df296ed20b7b92fe8b..da3ac474fda26e49b05a2fc78cf24009efcee1f8 100644
--- a/modules/bindings/pymod/hhblits2.py
+++ b/modules/bindings/pymod/hhblits2.py
@@ -499,8 +499,8 @@ class HHblits:
                 if self.filename != os.path.abspath(query):
                     shutil.copy(query, self.filename)
             else:
-                self.filename = os.path.join(self.working_dir,
-                                             '%s.fasta' % HHblits.OUTPUT_PREFIX)
+                self.filename = os.path.abspath(os.path.join(self.working_dir,
+                                             '%s.fasta' % HHblits.OUTPUT_PREFIX))
                 ost.io.SaveSequence(query, self.filename)
         else:
             self.needs_cleanup = True
diff --git a/modules/bindings/pymod/hhblits3.py b/modules/bindings/pymod/hhblits3.py
index 8309d1eecf19ee19c6f62aca62b3cd4ea1a76ee9..06b4bcc27c21cc3e7d1f33b6c22923a8861aa47f 100644
--- a/modules/bindings/pymod/hhblits3.py
+++ b/modules/bindings/pymod/hhblits3.py
@@ -505,8 +505,8 @@ class HHblits:
                 if self.filename != os.path.abspath(query):
                     shutil.copy(query, self.filename)
             else:
-                self.filename = os.path.join(self.working_dir,
-                                             '%s.fasta' % HHblits.OUTPUT_PREFIX)
+                self.filename = os.path.abspath(os.path.join(self.working_dir,
+                                             '%s.fasta' % HHblits.OUTPUT_PREFIX))
                 ost.io.SaveSequence(query, self.filename)
         else:
             self.needs_cleanup = True