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'Cannot allocate memory' when I try to run gatk4-data-processing use whole genome data of one person
I have tried to run gatk4-data-processing with the test data you provide, with no error tips, finally I got the outputs.
Then ,I tried to run this workflow with whole genome data of one person,however,it always reported some error like this:
OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x000000079af80000, 1695023104, 0) failed; error='Cannot allocate memory'
I read the processing-for-variant-discovery-gatk4.wdl, and guess that the reason may be I do not have enough memory to support it.
However, I can not get more memory or change another better mechine, may I do something else to run this workflow with my data?
When It call this task:BaseRecalibrator,it will been shut down:
Is there any method to change the scatter function?
Thank u very much to give me some suggestions,I will be appricate for your suggestions.