greenepipe run error about grenepipe HOT 5 CLOSED

Thank you

osp

from grenepipe.

Hi Octávio @ospfsg,

thanks for posting this here again! :-)

This seems like an error in one of the tools (picard MarkDuplicates), which will need a bit of detective work to find. The first clue:

    log: logs/picard/dedup/PN1.log (check log file(s) for error message)

So could you please check that file and upload it here? It might already contain the error description we are looking for.

Also, please follow the steps of the troubleshooting part of the documentation. If you are not running this on a cluster, not all steps might be as described there (the job ID for instance), but it will give you a general idea which files to investigate to figure out where the error is coming from! Any log files that you find through this, you can also post here.

Cheers and so long
Lucas

from grenepipe.

Hi Lucas

When I open the log file

MarkDuplicates -REMOVE_DUPLICATES true -INPUT mapped/PN1.merged.bam -OUTPUT dedup/PN1.bam -METRICS_FILE qc/dedup/PN1.metrics.txt

and no output file is present and qc/dedup folder is not there!

PN1.log

In the log file:

[Wed Mar 20 20:38:55 WET 2024] Executing as dau1@frey on Linux 6.5.0-26-generic amd64; OpenJDK 64-Bit Server VM 21.0.2-internal-adhoc.conda.src; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.27.4-SNAPSHOT

It seems this the problem? ..... Provider GCS is not available

cheers
osp

from grenepipe.

Hi Octávio @ospfsg,

thanks for proving the log file. The error usually is the last thing to be logged, which is also the case here. At the end of the file, there is a log entry:

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

which is the issue here: You are running out of memory for Java. Java is a bit weird, and limits itself in terms of memory unless specified otherwise. So, in order to increase the amount of memory that Java will use, grenepipe provides an option to set Java-specific settings for each Java-based tool.

In your case, this is this line in the config file. By setting this to

MarkDuplicates-java-opts: "-Xmx10g"

you should give Java enough memory to work with.

Let me know if that works, and so long
Lucas

from grenepipe.

Closed as per #44 (comment)

from grenepipe.