I see you have got several pointers to other ways to do it. Personally I
would go for the Tool activity if the jar in question might otherwise cause
Taverna to crash.
Have you checked if the outofmemory happens Taverna-side (possibly making
Taverna unstable) or with your subprocess? You are only allowing it 512 MB
with your command below.
Also try to look at the end of taverna.log, click Advanced -> Show logs and
folders.
On 25 Nov 2013 20:06, "stylz2k" <[email protected]> wrote:
> Hi everyone,
>
> I'm trying to create a workflow for processing data from next generation
> sequencing data. So i have big files.
>
> Input ~ 15 GB.
>
>
> Basically I'm trying to use a beanshell script that looks like the
> following:
>
> String command = "java -Xms256m -Xmx512m -jar /path/to/Programm.jar";
> Process proc = null;
> Runtime rt = Runtime.getRuntime();
> proc = rt.exec(command
> + input1
> + input2
> + input3
> + output);
> int exitVal = proc.waitFor();
>
> When running the workflow I get the following error:
> java.lang.OutOfMemoryError: Requested array size exceeds VM limit
>
> My linux machine has 16 gb of memory and I have already tried to give taverna
> more memory at the start.
>
> On gnome-terminal the command runs without any errors. Are there any
> suggestions?
>
> I'm really thankful for any help on this topic.
>
> Best Regards,
>
> Julian
>
>
>
>
>
>
>
>
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