diff --git a/bwamem_pair.c b/bwamem_pair.c
index 06aacff..c218925 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -301,6 +301,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag;
 		mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
 		mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
+		if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
 		free(h[0].cigar); free(h[1].cigar);
 	} else goto no_pairing;
 	return n;
@@ -319,6 +320,7 @@ no_pairing:
 	}
 	mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
 	mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
+	if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
 	free(h[0].cigar); free(h[1].cigar);
 	return n;
 }
diff --git a/bwape.c b/bwape.c
index 08490e7..2c96e06 100644
--- a/bwape.c
+++ b/bwape.c
@@ -706,6 +706,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 			}
 			bwa_print_sam1(bns, p[0], p[1], opt.mode, opt.max_top2);
 			bwa_print_sam1(bns, p[1], p[0], opt.mode, opt.max_top2);
+			if (strcmp(p[0]->name, p[1]->name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", p[0]->name, p[1]->name);
 		}
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
 
diff --git a/fastmap.c b/fastmap.c
index 8b4ae3f..598194b 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -60,7 +60,7 @@ int main_mem(int argc, char *argv[])
 		else return 1;
 	}
 	if (opt->n_threads < 1) opt->n_threads = 1;
-	if (optind + 1 >= argc) {
+	if (optind + 1 >= argc || optind + 3 < argc) {
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\n");
 		fprintf(stderr, "Algorithm options:\n\n");
diff --git a/main.c b/main.c
index 06d24bc..dd60d1c 100644
--- a/main.c
+++ b/main.c
@@ -46,10 +46,11 @@ static int usage()
 	fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
 	fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
 	fprintf(stderr, "\n");
-	fprintf(stderr, "Note: To use BWA, you need to first index the genome with `bwa index'. There are\n");
-	fprintf(stderr, "      three alignment algorithms in BWA: `mem', `bwasw' and `aln/samse/sampe'. If\n");
-	fprintf(stderr, "      you are not sure which to use, try `bwa mem' first. Please `man ./bwa.1' for\n");
-	fprintf(stderr, "      for the manual.\n\n");
+	fprintf(stderr,
+"Note: To use BWA, you need to first index the genome with `bwa index'.\n"
+"      There are three alignment algorithms in BWA: `mem', `bwasw', and\n"
+"      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'\n"
+"      first. Please `man ./bwa.1' for the manual.\n\n");
 	return 1;
 }