Picard MarkDuplicates VM warning: fix the library

Question

[Arthur Melo]

Dears, I'm running Picard to MarkDuplicates in a _merged.sorted.bam file from RNA-seq data. My script is:

java -Xmx5g \
  -jar /usr/local/picard-tools-1.119/MarkDuplicates.jar \
  INPUT=merged.sorted.bam \
  OUTPUT= merged.sorted.deduped.bam \
  METRICS_FILE=metrics_duplicates.txt \
  REMOVE_DUPLICATES=TRUE \
  VALIDATION_STRINGENCY=LENIENT \
  ASSUME_SORTED=TRUE \
  CREATE_INDEX=TRUE

So, a strange message show:

OpenJDK 64-Bit Server VM warning: You have loaded library /usr/local/picard-tools-1.119/libIntelDeflater.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c <libfile>', or link it with '-z noexecstack'.

I don't have idea about this problem...

I would be extremely grateful to some help.

Thank you.

[Devon Ryan]

Hello arthurmelobio!

It appears that your post has been cross-posted to another site: SEQanswers.

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Aamiralizai]

Hi you can try this "execstack -c /usr/local/picard-tools-1.119/libIntelDeflater.so" to solve your problem

Answer 2

[Aamiralizai]

https://www.raspberrypi.org/forums/viewtopic.php?f=81&t=146784

Answer 3

[Aamiralizai]

https://www.raspberrypi.org/forums/viewtopic.php?f=81&t=146784