diff --git a/doc/source/faq.rst b/doc/source/faq.rst
index 0170b65..6bedb78 100644
--- a/doc/source/faq.rst
+++ b/doc/source/faq.rst
@@ -8,7 +8,9 @@ Can KAT handle compressed sequence files?
 -----------------------------------------
 
 Yes, as of V2.4.0, KAT has native support for gzip decompression, so just treat
-gzipped files as regular uncompressed fastq or fasta files.
+gzipped files as regular uncompressed fastq or fasta files. The exceptions are
+``kat sect`` and ``kat filter`` which use a different fastq parser. For these
+modules, use process substitution as described below.
 
 If you wish to decompress other files such as bzip (or if you are using a pre V2.4.0 KAT), then
 this is supported via named pipes.  Anonymous named pipes (process substitution)
diff --git a/lib/include/kat/pyhelper.hpp b/lib/include/kat/pyhelper.hpp
index f076912..e5ddccc 100644
--- a/lib/include/kat/pyhelper.hpp
+++ b/lib/include/kat/pyhelper.hpp
@@ -75,6 +75,8 @@ private:
             cout << " - Interpreter path: " << fpp << endl;
         }
 
+        Py_Initialize();
+
         vector<string> ppaths;
 
         wchar_t* wtppath2 = Py_GetPath();
@@ -97,7 +99,7 @@ private:
             cout << " - PYTHONPATH set"  << endl;
         }
 
-        Py_Initialize();
+
         if (this->verbose) {
             cout << "Python interpretter initialised" << endl << endl;
         }
