Picard MarkDuplicates VM warning: fix the library
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.
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3 answers
Hi you can try this "execstack -c /usr/local/picard-tools-1.119/libIntelDeflater.so" to solve your problem
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Hello arthurmelobio!
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