diff --git a/minos/etc/minos_config.yaml b/minos/etc/minos_config.yaml
index 9288f72..b0290f5 100644
--- a/minos/etc/minos_config.yaml
+++ b/minos/etc/minos_config.yaml
@@ -28,6 +28,7 @@ params:
     quant: "-b 100"
   blast:
     makeblastdb: "-dbtype prot"
+    chunk_size: 1000
     blastp: "-max_target_seqs 1 -evalue 1e-5"
     blastx: "-max_target_seqs 1 -evalue 1e-5"
     tophit:
@@ -35,6 +36,7 @@ params:
       qcov_threshold: 0.0
   diamond:
     makedb: ""
+    chunk_size: 20000
     blastp: "--max-target-seqs 1 --evalue 1e-5"
     blastx: "--max-target-seqs 1 --evalue 1e-5"
     tophit:
diff --git a/minos/zzz/minos_run.smk b/minos/zzz/minos_run.smk
index 06f4f97..63243a3 100644
--- a/minos/zzz/minos_run.smk
+++ b/minos/zzz/minos_run.smk
@@ -473,7 +473,7 @@ checkpoint minos_chunk_proteins:
 	log:
 		os.path.join(LOG_DIR, os.path.basename(rules.minos_gffread_extract_sequences.output.pep if config["blast-mode"] == "blastp" else rules.minos_gffread_extract_sequences.output.cds) + ".chunk.log")
 	params:
-		chunksize = 1000,
+		chunksize = config["params"]["diamond"]["chunk_size"] if config["use-diamond"] else config["params"]["blast"]["chunk_size"],
 		outdir = os.path.join(TEMP_DIR, "chunked_proteins")
 	threads:
 		HPC_CONFIG.get_cores("minos_chunk_proteins")