Am 26.11.2013 14:56, schrieb Stian Soiland-Reyes:
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]
<mailto:[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
Hi,
I'm now going for the external Tool activity, and it works! Thanks to
everyone who answered this question. You are great!
Unfortunately there are new questions. (Who guessed...)
I successfully created a tool activity, which runs perfectly.
Now i want to use the created output files with a second tool activity
(and more to come...) in the same workflow.
I discovered that Taverna saves the output files to:
folder1 =/a/directoy/i/can/choose/usecase2041533162701613279dir
In my attemps the second tool activity creates a new folder and creates
a softlink to the files from folder1.
Of course this will work but is it possible to run a different tool
activity in the same folder?
I'm asking because i need the output files from every tool activity. Is
there any way of collecting all output files in one folder?
Or is it possible to execute the complete workflow on folder1 ?
Thanks for any suggestions.
Best,
Julian
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