Any suggestions on the mem set up

[Mao]

Hi Terry or Lynn,

I have about 3,800 Gb of fastQ files that I would like to use to generate a SNP discovery db.

Do you think this will cause any issues and crash the Tassle pipeline with any potential memory issues?

If not, could you suggest on what would be a reasonable number to set up in the GBSSeqToTagDBPlugin for -Xms and -Xmx,

as well as the alignment step for bwa mem -t ?

Thanks

Mao

[Lynn Carol Johnson]

Memory issues will depend on what memory is available on your system.  In terms of TASSEL and GBSvs, the best I can say is give the command a relatively large value for -Xmx that doesn’t exceed what your system has available and test,  You may have to adjust.

In terms of bwa-mem usage, this depends on your genome size and read characteristics.  The base memory requirement for bwa-mem is determined by the size of the reference genome as it loads the index of the ref genome into memory.  While threads make execution faster, threads also have overhead.  I would check bwa-mem documentation or google this on forums to determine what works best for you.

 

 

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