diff --git a/bseq.c b/bseq.c
index f68b11d..e499dda 100644
--- a/bseq.c
+++ b/bseq.c
@@ -53,7 +53,7 @@ bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
 		size += seqs[n++].l_seq;
 		if (size >= chunk_size) break;
 	}
-	if (n == 0) fp->is_eof = 1;
+	if (size < chunk_size) fp->is_eof = 1;
 	*n_ = n;
 	return seqs;
 }
diff --git a/index.c b/index.c
index 6dc1f76..066a891 100644
--- a/index.c
+++ b/index.c
@@ -279,7 +279,7 @@ mm_idx_t *mm_idx_gen(bseq_file_t *fp, int w, int k, int b, int is_hpc, int mini_
 {
 	pipeline_t pl;
 	memset(&pl, 0, sizeof(pipeline_t));
-	pl.mini_batch_size = mini_batch_size;
+	pl.mini_batch_size = mini_batch_size < batch_size? mini_batch_size : batch_size;
 	pl.keep_name = keep_name;
 	pl.batch_size = batch_size;
 	pl.fp = fp;
diff --git a/main.c b/main.c
index 3c312f1..dea1204 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r129-pre"
+#define MM_VERSION "2.0-r131-pre"
 
 void liftrlimit()
 {