(Sorry about the delay in replying. Had been busy on other tasks of the 
project.)
This problem happened again today, i.e. there is only schema/ under 
data/databases/graph.db/ and no other files or directories.

There are no error on neo4j.log. 

After I kill -9 <neo4j_pid>  (kill <neo4j_pid> didn't kill neo4j, nor did 
neo4j/bin/neo4j stop), neo4j was able to restarted normally (2nd time), 
i.e. there are files and directory index/. I restarted neo4j again (3rd 
time). While case1 (first time, failed case) and case 2 have some 
differences, but case 1 has exactly the same debug.log output as case 3.

Thanks,
Ray

On Thursday, October 20, 2016 at 5:25:42 PM UTC-7, Michael Hunger wrote:
>
> can you share your logfiles?
>
> On Fri, Oct 21, 2016 at 1:24 AM, Ray Chengr <[email protected] 
> <javascript:>> wrote:
>
>> We are using Neo4j community edition 3.0.3 for a few months. After 
>> re-installed Neo4j and applications to a new system, Neo4j was able to 
>> start. After inserted a few hundred thousand Nodes and Relationships, we 
>> found:
>>
>> There are no files or directories created except schema/ under 
>> data/databases/graph.db
>>
>> From the browser,
>>
>> match(n) return count(n)
>> returns 431117
>>
>> match ()-[r]->() return count(r)
>> returns 0
>>
>> merge (n:People {name: "Bob"})
>> returns this following error: 
>>
>> org.neo4j.kernel.api.exceptions.TransactionFailureException: Could not apply 
>> the transaction to the store after written to log
>>
>> But node count will increase by one after this failure. There are still 
>> no other files and directories except schema/ under data/databases/graph.db
>>
>> create (n:People {name: "Bob"}) return n
>> doesn't return at all. 
>>
>> create (n:People {name: "Mary"})
>> returns 
>>
>> org.neo4j.kernel.api.exceptions.TransactionFailureException: Could not apply 
>> the transaction to the store after written to log
>>
>>
>> Any idea?
>>
>> Thanks,
>> Ray
>>
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