Dear GATK team,
Recently, I have got data with whole exon sequence data with longer read length (150bp now VS 75bp before) and bigger data size (4 to 6 GB fastq file for paired end reads together VS 2 GB fastq file before). I can run IndelRealigner smoothly on earlier smaller dataset, but now, it always give me error message as below even though I put argument -Xmx1000G.
ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
......
ERROR MESSAGE: An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument (before the -jar argument) to adjust the maximum heap size provided to Java. Note that this is a JVM argument, not a GATK argument.
ERROR --
I tried to use gatk-4.beta.5, it shows 'IndelRealigner' is not a valid command.
May I ask is there any solution? Thanks.