src/obikmer/src/cmd/index/mod.rs

@@ -225,7 +225,7 @@ pub fn run(args: IndexArgs) {
             }
             info
         });
-        KmerIndex::create(&output, config, genome_info, false).unwrap_or_else(|e| {
+        KmerIndex::create(&output, config, genome_info, args.force).unwrap_or_else(|e| {
             eprintln!("error creating index: {e}");
             std::process::exit(1);
         })

src/obikpartitionner/src/partition/kmer_partition.rs

@@ -59,7 +59,11 @@ impl KmerPartition {
         force: bool,
     ) -> SKResult<Self> {
         let root_path = path.as_ref().to_owned();
-        if root_path.exists() {
+        // `root_path` itself may already exist as a bare directory: callers
+        // typically hold an index-level lock file there before creating the
+        // partition layout. What actually signals a pre-existing partition
+        // set is the `PARTITIONS_SUBDIR` subdirectory, not the root itself.
+        if root_path.join(PARTITIONS_SUBDIR).exists() {
             if force {
                 remove_dir_all(&root_path)?;
             } else {