Question: Picard MarkDuplicates VM warning: fix the library
0
gravatar for Arthur Melo
4.4 years ago by
Brazil
Arthur Melo0 wrote:

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 mensage 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.

 

software error • 2.4k views
ADD COMMENTlink modified 2.7 years ago by Aamiralizai0 • written 4.4 years ago by Arthur Melo0

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.

ADD REPLYlink written 4.4 years ago by Devon Ryan88k
0
gravatar for Aamiralizai
2.7 years ago by
Aamiralizai0 wrote:

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

ADD COMMENTlink written 2.7 years ago by Aamiralizai0
0
gravatar for Aamiralizai
2.7 years ago by
Aamiralizai0 wrote:

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

ADD COMMENTlink written 2.7 years ago by Aamiralizai0
-1
gravatar for Aamiralizai
2.7 years ago by
Aamiralizai0 wrote:

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

ADD COMMENTlink written 2.7 years ago by Aamiralizai0
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