Possible some threads are not complete due to bug?

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+Date: Sun, 13 Sep 2015 00:03:20 -0400\r
+Message-ID:\r
+ <CAJhTkNh7_hXDLsAGyD7nwkXV4ca6ymkLtFG945USvfqK4ZJEdQ@mail.gmail.com>\r
+Subject: Possible some threads are not complete due to bug?\r
+From: Xu Wang <xuwang762@gmail.com>\r
+To: notmuch@notmuchmail.org\r
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+\r
+Hi,\r
+\r
+Sometimes I need to do:\r
+\r
+$ notmuch search --output=threads "id:MYMSGID"\r
+thread:000000000000a125\r
+$ notmuch search --output=messages "thread:000000000000a125"\r
+\r
+In theory, this should output the message that responded to message ID\r
+"MYMSGID". Sometimes it works. But sometimes it does not work. That\r
+is, there exists an email where I am sure (I checked the raw email)\r
+that there is a header\r
+In-Reply-To: <MYMSGID>\r
+but that email does not show when I do the two commands above.\r
+Indeed, that mail belongs to a different thread ID.\r
+\r
+I am just curious if the above is due to:\r
+\r
+1. My missing of understanding of how notmuch deals with threads\r
+2. A bug or missing feature in notmuch causes some threads to be incomplete\r
+\r
+By the way, my goal is to use Suvayu's script to check if a message\r
+was responded to.\r
+\r
+Kind regards,\r
+\r
+Xu\r