If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
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.