diff --git a/.gitmodules b/.gitmodules
index 6656ad3..1e07742 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,22 +1,28 @@
 [submodule "repos/nim-DAZZ_DB"]
 	path = repos/nim-DAZZ_DB
 	url = https://github.com/bio-nim/nim-DAZZ_DB
+	ignore=dirty
 	branch = dev
 [submodule "repos/nim-htslib"]
 	path = repos/nim-htslib
 	url = https://github.com/bio-nim/nim-htslib
+	ignore=dirty
 [submodule "repos/nim-DALIGNER"]
 	path = repos/nim-DALIGNER
 	url = https://github.com/bio-nim/nim-DALIGNER
+	ignore=dirty
 	branch = dev
 [submodule "repos/nim-heap"]
 	path = repos/nim-heap
 	url = https://github.com/bio-nim/nim-heap
+	ignore=dirty
 [submodule "repos/cligen"]
 	path = repos/cligen
 	url = https://github.com/c-blake/cligen
+	ignore=dirty
 	branch = master
 [submodule "repos/msgpack4nim"]
 	path = repos/msgpack4nim
 	url = https://github.com/jangko/msgpack4nim
+	ignore=dirty
 	#branch = master
diff --git a/repos/cligen b/repos/cligen
index 292723b..533f940 160000
--- a/repos/cligen
+++ b/repos/cligen
@@ -1 +1 @@
-Subproject commit 292723b044424c20e3a7dde9598f3dfd18d47a60
+Subproject commit 533f9401fb9d45bd6eaab6f9784432fe798dda03
diff --git a/repos/msgpack4nim b/repos/msgpack4nim
index 82de886..c95e495 160000
--- a/repos/msgpack4nim
+++ b/repos/msgpack4nim
@@ -1 +1 @@
-Subproject commit 82de8867d63e6641989ff0dfdff7fac75e61fe6b
+Subproject commit c95e495aeb134509e9ca5beaaef890472e891258
diff --git a/src/falcon/rr_hctg_track.nim b/src/falcon/rr_hctg_track.nim
index 340620b..93c5ac5 100644
--- a/src/falcon/rr_hctg_track.nim
+++ b/src/falcon/rr_hctg_track.nim
@@ -1,6 +1,7 @@
 # vim: sw=2 ts=2 sts=2 tw=80 et:
 # Nim re-write of FALCON_unzip/falcon_unzip/rr_hctg_track.py
 import "../msgpack4nim/msgpack4nim.nim"
+import "../msgpack4nim/msgpack4collection.nim"
 from "../nim-heap/binaryheap" import nil
 from sys import log
 
@@ -499,8 +500,10 @@ proc run_stage2*(
       let infile = streams.newFileStream(fn_rtn, system.fmRead)
       defer:
         infile.close()
+      var msgss = msgpack4nim.initMsgStream()
+      msgss.data = infile.readAll()
       var res: mytable
-      msgpack4nim.unpack(infile, res)
+      msgpack4nim.unpack(msgss, res)
       log("  Updating bread_to_areads table with ", len(res), " breads.")
       for k,v in res.pairs:
         if not bread_to_areads.contains(k):