The case you describe sounds suspect and might be a JanusGraph issue. Your last remark ("If i add some delay b/w two operations then vertices are getting removed correctly.") gives an important clue as to what is going on.
A few additional questions:
- Do have the JanusGraph database cache disabled? (This is the default setting for JanusGraph-0.5+)?
- See the tunability section of https://hbase.apache.org/acid-semantics.html. Did you enable any HBase client settings that impact the HBase visibility guarantees (https://hbase.apache.org/book.html#arch.timelineconsistent.reads )? Note that you may have a CLASSPATH that picks up hbase-site.xml configs from your cluster.
If this turns out to be a JanusGraph issue, is it possible for you do the graph operations in a single transaction (workaround)?
Best wishes, Marc