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https://issues.apache.org/jira/browse/CHUKWA-4?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=12853475#action_12853475
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Jerome Boulon commented on CHUKWA-4:
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the exception will be on this line "while (seqFileReader.next(key, evt)){ 
seqFileWriter.append(key, evt); } "
so you can add a 1st try/catch block around this line, then add another one 
around rename/delete.
Also, don't delete the .chukwa file in the first place.

Steps:
1- Rename .recover to .recoverDone
2- delete .chukwa
3- rename .recoverDone to .done

At startup time, you should:
1- delete any .recover files
2.0- if you have a .recoverDone and .chukwa with the same name, then delete the 
.chukwa file (Repeat until there's no more .chukwa file that matches this rule)
2.1- Rename all .recoverDone to .done
3- process .chukwa files
4- send .done files



> Collectors don't finish writing .done datasink from last .chukwa datasink 
> when stopped using bin/stop-collectors
> ----------------------------------------------------------------------------------------------------------------
>
>                 Key: CHUKWA-4
>                 URL: https://issues.apache.org/jira/browse/CHUKWA-4
>             Project: Hadoop Chukwa
>          Issue Type: Bug
>          Components: data collection
>         Environment: I am running on our local cluster. This is a linux 
> machine that I also run Hadoop cluster from.
>            Reporter: Andy Konwinski
>            Priority: Minor
>
> When I use start-collectors, it creates the datasink as expected, writes to 
> it as per normal, i.e. writes to the .chukwa file, and roll overs work fine 
> when it renames the .chukwa file to .done. However, when I use 
> bin/stop-collectors to shut down the running collector it leaves a .chukwa 
> file in the HDFS file system. Not sure if this is a valid sink or not, but I 
> think that the collector should gracefully clean up the datasink and rename 
> it .done before exiting.

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