Picard MarkDuplicates VM warning: fix the library

[arthurmelo]

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.

[dpryan]

Please don't crosspost on here and biostars.

[arthurmelo]

OK Devon Ryan, So sorry.
But do you know anything about my question?

[dpryan]

Why don't you try doing what the error message says and then mention if it solves the problem.

[trotos]

As I got the same error, I also would like to know the answer to that, because sometimes if it works the best way to do go is not to play arround.
So if anyone knows about JDK could please provide us with an answer!!!
thank you

[arthurmelo]

Hello trotos,
I think I can fix the problem determining a limit for Java memory, with "MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=" option. I'm using the follow script

java -jar /usr/local/picard-tools-1.119/MarkDuplicates.jar \
INPUT=merged.bam \
OUTPUT=dedup.bam \
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 \
METRICS_FILE=metrics.txt


All the best...

[trotos]

thank you for the answer,

[trotos]

still the same
i'm providing a little bit of the error messages:

PROGRAM_RECORD_ID=MarkDuplicates
PROGRAM_GROUP_NAME=MarkDuplicates
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000
SORTING_COLLECTION_SIZE_RATIO=0.25
READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*
OPTICAL_DUPLICATE_PIXEL_DISTANCE=100
VERBOSITY=INFO
QUIET=false
VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
MAX_RECORDS_IN_RAM=500000
CREATE_INDEX=false
CREATE_MD5_FILE=false
OpenJDK 64-Bit Server VM warning: You have loaded library /media/trotos/documents/NGS_programms/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'.

will it really affect the results (the way that parsing the file is done?)