On 25/11/2013 20:01, stylz2k wrote: > Hi everyone, Hello
> 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 would try the tool service rather than the beanshell. So create a tool service where the command is java -Xms256m -Xmx512m -jar /path/to/Programm.jar %%input1%% %%input2%% %%input3%% %%output%% and have three input ports and one output. Also, how are you passing around the data? Once it gets large then it is better to pass it as files rather than data. So (assuming input1 is the large file), have a command that says java -Xms256m -Xmx512m -jar /path/to/Programm.jar input1 %%input2%% %%input3%% %%output%% > I'm really thankful for any help on this topic. > > Best Regards, > > Julian Alan ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
