OutOfMemoryError: Java heap space

[lczech]

Hi there!

I am using DamageProfiler 1.1 via the conda package, which means that the call to run the command line version simply is

damageprofiler [options]

instead of the call

java -jar DamageProfiler-VERSION.jar [options]

that is given in the documentation.

Now, for some large datasets, I am getting

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

and my guess after a bit of searching is that I need to provide Java with

-Xmx<amount of memory>

for this to work (NB: WTF Java?! Just use the available memory!).

My questions here are: Is that indeed the solution to the issue? And if so, how do I provide this with the conda version? Trying to locate the jar file within the conda env directory does not seem like a robust idea - what is the canonical way of solving this?

Thanks in advance and so long
Lucas

[JudithNeukamm]

Hi Lucas,
sorry for the late reply.
Actually, that's the way I usually solve this issue ;)

However, you can try to increase the general JVM heap space used for java applications (However, I'm not sure if this also works for the conda package): export _JAVA_OPTIONS="-Xms512m -Xmx1024m"

Let me know if that works!
I'll try to find another/an additional solution. Or @jfy133 do you have any idea?

[jfy133]

I'm pretty sure I've done it somehow inthe past but can't remember atm.

At least the python script used with the damageprofiler variable, that calls the jar includes the following line:

https://github.com/bioconda/bioconda-recipes/blob/73395171feca2b41f495c660b91964d5e70f7d1e/recipes/damageprofiler/damageprofiler.py#L16

I guess 'default' would imply it's changeable, but won't be able to check until tomorrow. @apeltzer has more bioconda experience though!

[jfy133]

Quickly looking at the script, maybe try damageprofiler -Xm 000g?

Regardless, congrats on having so many read s;) b

[apeltzer]

Linking to an issue in one of my other pipelines for bacterial assembly, where we had similar issues: nf-core/bacass#28

Recommendation was to simply replace it - see here bioconda/bioconda-recipes#24749

e.g. a damageprofiler -Xmx64g could already do the trick maybe?

[JudithNeukamm]

Hi @lczech
could this solve your problem?

[lczech]

Hi @JudithNeukamm,

thanks for the follow up. Unfortunately, I did not yet get back to that project, so as of now, I don't know whether that solution works. I'll post here once I know.

Thank you and all the best
Lucas