diff --git a/src/graph_based_model_construction.py b/src/graph_based_model_construction.py
index 6b56789d..f2cd4a36 100644
--- a/src/graph_based_model_construction.py
+++ b/src/graph_based_model_construction.py
@@ -136,13 +136,6 @@ def process(self, read_assignment_storage):
         self.assign_reads_to_models(read_assignment_storage)
         self.forward_counts()
 
-        # FIXME: remove asserts below
-        if len(set([x.read_id for x in read_assignment_storage])) != len(self.read_assignment_counts):
-            logger.warning("Some reads were not assigned %d %d" % (len(set([x.read_id for x in read_assignment_storage])), len(self.read_assignment_counts)))
-        # FIXME: remove asserts below
-        if any(value < 0 for value in self.read_assignment_counts.values()):
-            logger.warning("Negative values in read assignment counts")
-
         transcript_joiner = TranscriptToGeneJoiner(self.transcript_model_storage, self.gene_info)
         self.transcript_model_storage = transcript_joiner.join_transcripts()