Pilon - Custom heap size for the Java Virtual Machine

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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.

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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.

  1. Input data or parameter settings can lead to jobs that spin out and are killed for resource reasons (you could re-check your data versus tutorials or the tool help).
  2. Sometimes a tool has a minor bug (we would want to squash :beetle:'s!).
  3. Some small fraction of jobs may fail by chance (always try at least one rerun).
  4. We can also maybe suggest a different public Galaxy server to work at since each host different resources, and it is easy to move data between servers.
  5. Finally, you might be using an older version of the tool that has subsequently had a correction (switch to the current version to address this).

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! :slight_smile:

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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.

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