diff --git a/bwape.c b/bwape.c
index f2d3d8e..fa4f7f7 100644
--- a/bwape.c
+++ b/bwape.c
@@ -624,7 +624,8 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
 void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt, const char *rg_line)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
-	int i, j, n_seqs, tot_seqs = 0;
+	int i, j, n_seqs;
+	long long tot_seqs = 0;
 	bwa_seq_t *seqs[2];
 	bwa_seqio_t *ks[2];
 	clock_t t;
@@ -711,7 +712,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 
 		for (j = 0; j < 2; ++j)
 			bwa_free_read_seq(n_seqs, seqs[j]);
-		fprintf(stderr, "[bwa_sai2sam_pe_core] %d sequences have been processed.\n", tot_seqs);
+		fprintf(stderr, "[bwa_sai2sam_pe_core] %lld sequences have been processed.\n", tot_seqs);
 		last_ii = ii;
 	}
 
diff --git a/bwase.c b/bwase.c
index 37e4274..18e8671 100644
--- a/bwase.c
+++ b/bwase.c
@@ -507,7 +507,8 @@ void bwase_initialize()
 void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
-	int i, n_seqs, tot_seqs = 0, m_aln;
+	int i, n_seqs, m_aln;
+	long long tot_seqs = 0;
 	bwt_aln1_t *aln = 0;
 	bwa_seq_t *seqs;
 	bwa_seqio_t *ks;
@@ -565,7 +566,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 
 		bwa_free_read_seq(n_seqs, seqs);
-		fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
+		fprintf(stderr, "[bwa_aln_core] %lld sequences have been processed.\n", tot_seqs);
 	}
 
 	// destroy
diff --git a/bwtaln.c b/bwtaln.c
index 20b01cd..a348fdf 100644
--- a/bwtaln.c
+++ b/bwtaln.c
@@ -158,7 +158,8 @@ bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa)
 
 void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 {
-	int i, n_seqs, tot_seqs = 0;
+	int i, n_seqs;
+	long long tot_seqs = 0;
 	bwa_seq_t *seqs;
 	bwa_seqio_t *ks;
 	clock_t t;
@@ -218,7 +219,7 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
 
 		bwa_free_read_seq(n_seqs, seqs);
-		fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
+		fprintf(stderr, "[bwa_aln_core] %lld sequences have been processed.\n", tot_seqs);
 	}
 
 	// destroy