diff --git a/cram/cram_io.c b/cram/cram_io.c
index 5e5891114..ce549b728 100644
--- a/cram/cram_io.c
+++ b/cram/cram_io.c
@@ -2473,6 +2473,9 @@ static refs_t *refs_create(void) {
 static BGZF *bgzf_open_ref(char *fn, char *mode, int is_md5) {
     BGZF *fp;
 
+    if (strncmp(fn, "file://", 7) == 0)
+        fn += 7;
+
     if (!is_md5 && !hisremote(fn)) {
         char fai_file[PATH_MAX];
 
@@ -2934,30 +2937,6 @@ static void mkdir_prefix(char *path, int mode) {
     *cp = '/';
 }
 
-/*
- * Return the cache directory to use, based on the first of these
- * environment variables to be set to a non-empty value.
- */
-static const char *get_cache_basedir(const char **extra) {
-    char *base;
-
-    *extra = "";
-
-    base = getenv("XDG_CACHE_HOME");
-    if (base && *base) return base;
-
-    base = getenv("HOME");
-    if (base && *base) { *extra = "/.cache"; return base; }
-
-    base = getenv("TMPDIR");
-    if (base && *base) return base;
-
-    base = getenv("TEMP");
-    if (base && *base) return base;
-
-    return "/tmp";
-}
-
 /*
  * Queries the M5 string from the header and attempts to populate the
  * reference from this using the REF_PATH environment.
@@ -2971,31 +2950,12 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
     sam_hrec_tag_t *tag;
     char path[PATH_MAX];
     kstring_t path_tmp = KS_INITIALIZE;
-    char cache[PATH_MAX], cache_root[PATH_MAX];
     char *local_cache = getenv("REF_CACHE");
     mFILE *mf;
     int local_path = 0;
 
     hts_log_info("Running cram_populate_ref on fd %p, id %d", (void *)fd, id);
 
-    cache_root[0] = '\0';
-
-    if (!ref_path || *ref_path == '\0') {
-        /*
-         * If we have no ref path, we use the EBI server.
-         * However to avoid spamming it we require a local ref cache too.
-         */
-        ref_path = "https://www.ebi.ac.uk/ena/cram/md5/%s";
-        if (!local_cache || *local_cache == '\0') {
-            const char *extra;
-            const char *base = get_cache_basedir(&extra);
-            snprintf(cache_root, PATH_MAX, "%s%s/hts-ref", base, extra);
-            snprintf(cache,PATH_MAX, "%s%s/hts-ref/%%2s/%%2s/%%s", base, extra);
-            local_cache = cache;
-            hts_log_info("Populating local cache: %s", local_cache);
-        }
-    }
-
     if (!r->name)
         return -1;
 
@@ -3009,7 +2969,10 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
 
     /* Use cache if available */
     if (local_cache && *local_cache) {
-        if (expand_cache_path(path, local_cache, tag->str+3) == 0)
+        struct stat sb;
+        if (expand_cache_path(path, local_cache, tag->str+3) == 0 &&
+            stat(path, &sb) == 0)
+            // Found it in the local cache
             local_path = 1;
     }
 
@@ -3053,7 +3016,8 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
 
 
     /* Otherwise search full REF_PATH; slower as loads entire file */
-    if ((mf = open_path_mfile(tag->str+3, ref_path, NULL))) {
+    int is_local = 0;
+    if ((mf = open_path_mfile(tag->str+3, ref_path, NULL, &is_local))) {
         size_t sz;
         r->seq = mfsteal(mf, &sz);
         if (r->seq) {
@@ -3069,15 +3033,22 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
     } else {
         refs_t *refs;
         const char *fn;
+        sam_hrec_tag_t *UR_tag;
 
     no_M5:
         /* Failed to find in search path or M5 cache, see if @SQ UR: tag? */
-        if (!(tag = sam_hrecs_find_key(ty, "UR", NULL)))
+        if (!(UR_tag = sam_hrecs_find_key(ty, "UR", NULL)))
+            return -1;
+
+        if (strncmp(UR_tag->str+3, "file:", 5) != 0) {
+            // Documented as omitted, but accidentally supported until now
+            hts_log_error("UR tags pointing to remote files are not supported");
             return -1;
+        }
 
-        fn = (strncmp(tag->str+3, "file:", 5) == 0)
-            ? tag->str+8
-            : tag->str+3;
+        fn = (strncmp(UR_tag->str+3, "file:", 5) == 0)
+            ? UR_tag->str+8
+            : UR_tag->str+3;
 
         if (fd->refs->fp) {
             if (bgzf_close(fd->refs->fp) != 0)
@@ -3108,15 +3079,9 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
     }
 
     /* Populate the local disk cache if required */
-    if (local_cache && *local_cache) {
+    if (!is_local && local_cache && *local_cache) {
         hFILE *fp;
 
-        if (*cache_root && !is_directory(cache_root)) {
-            hts_log_warning("Creating reference cache directory %s\n"
-                            "This may become large; see the samtools(1) manual page REF_CACHE discussion",
-                            cache_root);
-        }
-
         if (expand_cache_path(path, local_cache, tag->str+3) < 0) {
             return 0; // Not fatal - we have the data already so keep going.
         }
diff --git a/cram/open_trace_file.c b/cram/open_trace_file.c
index 4d617b736..31f450cd7 100644
--- a/cram/open_trace_file.c
+++ b/cram/open_trace_file.c
@@ -324,14 +324,21 @@ static mFILE *find_file_dir(const char *file, char *dirname) {
  * all of the locations listed in 'path' (which is a colon separated list).
  * If 'path' is NULL it uses the RAWDATA environment variable instead.
  *
+ * If non-NULL *local is filled out to 1 for a local file and 0 for a remote
+ * URL.
+ *
  * Returns a mFILE pointer when found.
  *           NULL otherwise.
  */
-mFILE *open_path_mfile(const char *file, char *path, char *relative_to) {
+mFILE *open_path_mfile(const char *file, char *path, char *relative_to,
+                       int *local) {
     char *newsearch;
     char *ele;
     mFILE *fp;
 
+    if (local)
+        *local = 1;
+
     /* Use path first */
     if (!path)
         path = getenv("RAWDATA");
@@ -361,14 +368,16 @@ mFILE *open_path_mfile(const char *file, char *path, char *relative_to) {
 
         if (0 == strncmp(ele2, "URL=", 4)) {
             if ((fp = find_file_url(file, ele2+4))) {
+                if (local)
+                    *local = strncmp(ele2+4, "file:", 5) == 0 ? 1 : 0;
                 free(newsearch);
                 return fp;
             }
-        } else if (!strncmp(ele2, "http:", 5) ||
-                   !strncmp(ele2, "https:", 6) ||
-                   !strncmp(ele2, "ftp:", 4)) {
+        } else if (hisremote(ele2)) {
             if ((fp = find_file_url(file, ele2))) {
                 free(newsearch);
+                if (local)
+                    *local = 0;
                 return fp;
             }
         } else if ((fp = find_file_dir(file, ele2))) {
diff --git a/cram/open_trace_file.h b/cram/open_trace_file.h
index 45860980d..b7b6a4a7c 100644
--- a/cram/open_trace_file.h
+++ b/cram/open_trace_file.h
@@ -96,10 +96,14 @@ char *tokenise_search_path(const char *searchpath);
  * all of the locations listed in 'path' (which is a colon separated list).
  * If 'path' is NULL it uses the RAWDATA environment variable instead.
  *
+ * If non-NULL *local is filled out to 1 for a local file and 0 for a remote
+ * URL.
+ *
  * Returns a mFILE pointer when found.
  *           NULL otherwise.
  */
-mFILE *open_path_mfile(const char *file, char *path, char *relative_to);
+mFILE *open_path_mfile(const char *file, char *path, char *relative_to,
+                       int *local);
 
 /*
  * Returns a mFILE containing the entire contents of the url;