diff --git a/src/lib/run.rs b/src/lib/run.rs
index 55ea6c5..f9c8350 100644
--- a/src/lib/run.rs
+++ b/src/lib/run.rs
@@ -90,6 +90,14 @@ pub fn run(opts: Opts) -> Result<(), anyhow::Error> {
                 filenames(s, &opts.output_dir, &opts.read_structures, &output_types_to_write)
                     .into_iter()
                     .map(|name| {
+                        // Create the output directory. This is important if the output is being written
+                        // to a project-specific directory
+                        if let Some(parent) = name.parent() {
+                            std::fs::create_dir_all(parent).with_context(|| {
+                                format!("Could not create output directory: {:?}", parent)
+                            })?;
+                        }
+                        // Now create the output file
                         File::create(&name)
                             .with_context(|| {
                                 format!("Unable to create file: {}", name.to_string_lossy())
diff --git a/src/lib/sample_metadata.rs b/src/lib/sample_metadata.rs
index 417c9e5..5f445e1 100644
--- a/src/lib/sample_metadata.rs
+++ b/src/lib/sample_metadata.rs
@@ -43,7 +43,7 @@ pub struct SampleMetadata {
 
     /// The project associated with this the sample
     #[serde(alias = "Project", rename(serialize = "Project"))]
-    pub project: Option<BString>,
+    pub project: Option<String>,
 
     /// The sanitized `raw_barcode` used for demultiplexing.
     #[serde(skip)]
diff --git a/src/lib/utils.rs b/src/lib/utils.rs
index b484086..f583935 100644
--- a/src/lib/utils.rs
+++ b/src/lib/utils.rs
@@ -76,7 +76,6 @@ pub fn filenames<P: AsRef<Path>>(
         Some(project) => output_dir.as_ref().join(project.to_string()),
         None => output_dir.as_ref().to_path_buf(),
     };
-    std::fs::create_dir_all(&output_dir).unwrap();
 
     for structure in read_structures.iter() {
         for kind in structure.iter().map(|segment| segment.kind).sorted().dedup() {
@@ -367,7 +366,6 @@ mod test {
         vec::IntoIter,
     };
 
-    use bstr::BString;
     use gzp::{BgzfSyncWriter, Compression, MgzipSyncWriter};
     use read_structure::{ReadStructure, SegmentType};
 
@@ -418,7 +416,7 @@ mod test {
         .unwrap();
 
         // Sample with project
-        sample.project = Some(BString::from("Project1"));
+        sample.project = Some(String::from("Project1"));
         let output_fastqs =
             filenames(&sample, output_dir, &read_structures, &output_types_to_write);
         let expected = vec![