I am trying Pilon to polish a genome, but it fails because the default setting " java -Xmx16G" does not allocate enough memory for the java heap space. Is there a way to change the default value?
Thanks in advance for your help.
I am trying Pilon to polish a genome, but it fails because the default setting " java -Xmx16G" does not allocate enough memory for the java heap space. Is there a way to change the default value?
Thanks in advance for your help.
Welcome, @matteo_rucco
It sounds like the tool is running out of working memory during execution. FAQ: Understanding 'exceeds memory allocation' error messages
Computational resource are fixed at the public Galaxy servers. (“Job” resources are different from data storage memory in your account). Public Galaxy Servers
All that said, we could confirm that is what is actually going on with your job.
If you would like help exploring exactly why the job is failing, and what you can do, we’ll need more details about it. A shared history would be best for this type of error. Please see the banner at this forum for how to generate and post back the link, or here directly. → How to get faster help with your question. You can post the share link back here, then unshare your history once we are done.
Let’s start there, thanks!
Dear @jennaj ,
Thanks a lot for your reply. I tested Pilon (the same version installed on the public Galaxy servers) with the same input files and input parameters but increased the memory (Xmx100G) on a different machine, and it worked. So, I would conclude that it is not an issue with the tool or the files; it is about the allocation of the memory. I will investigate a non-public Galaxy server for future experiments.