RealignerTargetCreator issue : not provide enough memory to run this program
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Comments (13)

Hi,

I want to run RealignerTargetCreator with this command line :

qsub -b Y -N RTC -q bigmem.q "/usr/local/java/latest/bin/java -Xmx36g -jar /home/sabotf/sources/GenomeAnalysisTK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /data/projects/assembling-glab/PacBio_test/XL/filtered_subreads_XL.fasta -o /data/projects/assembling-glab/mappingResults/Tog5681Clean_vs_CG14_XL/output.intervals -I /data/projects/assembling-glab/mappingResults/Tog5681Clean_vs_CG14_XL/rmdup.bam" but this return this error :

`##### ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 2.3-9-ge5ebf34):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java
ERROR ------------------------------------------------------------------------------------------`

I tried with -Xmx4g, then,-Xmx12g, then -Xmx48g, and always the same error. I don't know what to do ... any idea ? thanks


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