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Indel Realignment die for no enough memory in RNAseq
I have 2 samples of RNAseq with 10 million PE reads for each and read length of 81 bp.
indelRealigner gave me this 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
I increased the heap size to 78g. One sample was done successful but the 2nd sample are still giving the same error.
I tried to use down sampling but still the same error
Here is my code:
java -Xmx78g -jar $GATK/GenomeAnalysisTK.jar \
-T IndelRealigner \
-R $gatk_ref \
-I $sample \
-targetIntervals gatk.intervals \
-nWayOut '.realigned.bam' \
-known $indels \
-model USE_SW \
-LOD 0.4 \
Any advice will be truly appreciated.