diff --git a/genome_grist/conf/Snakefile b/genome_grist/conf/Snakefile
index c68921d..d6760ee 100755
--- a/genome_grist/conf/Snakefile
+++ b/genome_grist/conf/Snakefile
@@ -265,7 +265,10 @@ class Checkpoint_GatherResults:
         genome_idents = []
         for row in load_gather_csv(gather_csv):
             ident = row['name'].split()[0]
+
+            # skip identifiers we've been asked to ignore in 'skip_genomes'
             if ident in IGNORE_IDENTS:
+                print(f"Skipping identifier '{ident}' because it is in 'skip_genomes'")
                 continue
             genome_idents.append(ident)
 
@@ -353,6 +356,11 @@ class ListGatherGenomes(Checkpoint_GatherResults):
         for row in load_csv(gather_csv):
             ident = row['name'].split()[0]
 
+            # skip identifiers we've been asked to ignore in 'skip_genomes'
+            if ident in IGNORE_IDENTS:
+                print(f"Skipping identifier '{ident}' because it is in 'skip_genomes'")
+                continue
+
             # if in local information, use that as genome source.
             if ident in local_info:
                 info = local_info[ident]
diff --git a/tests/test-data/GCF_000020205-is-missing.trim.sig.zip b/tests/test-data/GCF_000020205-is-missing.trim.sig.zip
index 141a601..e7e89ee 100644
Binary files a/tests/test-data/GCF_000020205-is-missing.trim.sig.zip and b/tests/test-data/GCF_000020205-is-missing.trim.sig.zip differ
diff --git a/tests/test-data/conf-missing-skip.yml b/tests/test-data/conf-missing-skip.yml
index 99c77bb..4e8ebb5 100644
--- a/tests/test-data/conf-missing-skip.yml
+++ b/tests/test-data/conf-missing-skip.yml
@@ -3,6 +3,7 @@ samples:
 outdir: outputs.missing
 sourmash_databases:
 - tests/test-data/GCF_000020205.1.sig.zip
+- tests/test-data/SRR5950647.x.gtdb-rs202.matches.zip
 
 prevent_sra_download: true
 
diff --git a/tests/test-data/conf-missing.yml b/tests/test-data/conf-missing.yml
index c8433e1..9fcb1e5 100644
--- a/tests/test-data/conf-missing.yml
+++ b/tests/test-data/conf-missing.yml
@@ -3,6 +3,7 @@ samples:
 outdir: outputs.missing
 sourmash_databases:
 - tests/test-data/GCF_000020205.1.sig.zip
+- tests/test-data/SRR5950647.x.gtdb-rs202.matches.zip
 
 prevent_sra_download: true
 
diff --git a/tests/test_snakemake_errors.py b/tests/test_snakemake_errors.py
index 8e2a00b..530296e 100644
--- a/tests/test_snakemake_errors.py
+++ b/tests/test_snakemake_errors.py
@@ -129,7 +129,7 @@ def test_missing_genbank_genome_skip():
     global _tempdir
 
     conf = utils.relative_file('tests/test-data/conf-missing-skip.yml')
-    extra_args = ["download_genbank_genomes"]
+    extra_args = ["download_genbank_genomes", "retrieve_genomes"]
 
     sigs_dir = os.path.join(_tempdir, "sigs")
     try: