From cefbad85aa35e34df9daba88a6fad75f167ee630 Mon Sep 17 00:00:00 2001
From: Gavin John <>
Date: Thu, 16 May 2024 13:36:21 -0500
Subject: [PATCH] Add helpful error messages to read_fastx.py

---
 metaphlan/utils/read_fastx.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/metaphlan/utils/read_fastx.py b/metaphlan/utils/read_fastx.py
index 5adb3dc..fd47e6f 100755
--- a/metaphlan/utils/read_fastx.py
+++ b/metaphlan/utils/read_fastx.py
@@ -114,10 +114,15 @@ def read_and_write_raw_int(fd, min_len=None, prefix_id=""):
     #         avg_read_length = len(l) + avg_read_length
     #         _ = sys.stdout.write(ignore_spaces(l))
 
+    if not idx:
+        sys.stderr.write('Error: no reads found.\n')
+        sys.exit(1)
+
     nreads = idx - discarded
 
     if not nreads:
-        nreads, avg_read_length = 0, 0
+        sys.stderr.write('Error: no reads longer than {} bp found.\n'.format(min_len))
+        sys.exit(1)
 
     return (nreads, avg_read_length)