Re: [svtoolkit-help] problem running genome strip

[Bob H. <han...@br...>]

Can you send me more of the output, including the stack trace and 
anything coming before this?
Also, what version are you using (e.g. what's the output of "java -jar 
SVToolkit.jar") ?
Thanks,
-Bob

On 9/6/11 10:10 AM, Linda Hughes wrote:
> Hi,
>
> Im trying to run genome strip SVdiscovery on 9 bam files to look for 
> deletions in a particular region of chromosome 14. However when I run 
> the program I get the following error:
>
> INFO 11:45:57,665 SVDiscovery - Processing cluster 
> chr14:106783666-106786180 chr14:106810874-106812753 LR 35
> #DBG: RC Cache fill chr14:106776181-106876180 100000 9 0.349954 sec
> Error: Exception processing cluster: Permitted to write any record 
> upstream of position 106788832, but a record at chr14:106786183 was 
> just added.
> Cluster: chr14:106783666-106786180 chr14:106810874-106812753 LR 35
> INFO 11:45:59,342 GATKRunReport - Aggregating data for run report
> [GC 309491K->25036K(819712K), 0.0030080 secs]
> [Full GC 25036K->24617K(819712K), 0.0708550 secs]
> ##### ERROR 
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
>
> Do you have any idea what could be causing the error?
>
> many thanks,
>
> Linda
>
>
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