diff --git a/dadi_cli/GenerateFs.py b/dadi_cli/GenerateFs.py
index dc22363..0fa8b60 100644
--- a/dadi_cli/GenerateFs.py
+++ b/dadi_cli/GenerateFs.py
@@ -59,8 +59,6 @@ def generate_fs(
         If the VCF file does not contain the AA INFO field and `polarized` is True.
 
     """
-    if len(pop_ids) != len(projections):
-        raise ValueError("The lengths of `pop_ids` and `projections` must match.")
 
     if polarized:
         try:
@@ -89,6 +87,11 @@ def generate_fs(
         print(projections, ploidy, subsample)
     else:
         dd = dadi.Misc.make_data_dict_vcf(vcf_filename=vcf, popinfo_filename=pop_info, calc_coverage=calc_coverage)
+
+    # Moved this lower, since using subsamples make projections not required
+    if len(pop_ids) != len(projections):
+        raise ValueError("The lengths of `pop_ids` and `projections` must match.")
+
     if calc_coverage:    
         import pickle
         coverage_dd = {chrom_pos:{'coverage':dd[chrom_pos]['coverage']} for chrom_pos in dd}
diff --git a/dadi_cli/parsers/generate_fs_parsers.py b/dadi_cli/parsers/generate_fs_parsers.py
index 9f096f9..212944e 100644
--- a/dadi_cli/parsers/generate_fs_parsers.py
+++ b/dadi_cli/parsers/generate_fs_parsers.py
@@ -108,11 +108,15 @@ def add_generate_fs_parsers(subparsers: argparse.ArgumentParser) -> None:
         dest="pop_info",
     )
 
+    # Check if subsamples are being requested to determin if --projections needed
+    proj_req = True
+    if "--subsample" in sys.argv:
+        proj_req = False
     parser.add_argument(
         "--projections",
         type=positive_int,
         nargs="+",
-        required=True,
+        required=proj_req,
         help="Sample sizes after projection; If you do not want to project down your data, please input the original sample sizes of your data.",
     )