Question: GENESIS pcrelate() to load gds file and continue where the function broke
0
gravatar for roll
10 months ago by
roll0
United Kingdom
roll0 wrote:

Hi,
I was running pc-relate on a very large set. pcrelate() step was running for days  with the option, write.to.gds=TRUE and just before it finished the job was killed.

The function ran up to:

...

Creating GDS file for PC-Relate Results
Computing Relatedness Estimates for Scan Block Pair (11,4)...

...


Is there a way to load the *pcrelate.gds file and continue the analysis rather than doing everything all over again?

Alternatively is there a way to run this job in parallel so that it does not take so much time?

Many Thanks

gds genesis pcrrelate • 213 views
ADD COMMENTlink modified 10 months ago by Stephanie M. Gogarten680 • written 10 months ago by roll0
Answer: GENESIS pcrelate() to load gds file and continue where the function broke
1
gravatar for Stephanie M. Gogarten
10 months ago by
University of Washington
Stephanie M. Gogarten680 wrote:

We are actively working on a version of pcrelate that can run in parallel. We hope to have this available in the devel branch of GENESIS by the end of the year.

Unfortunately there is no automated way to restart a failed job, but you could try opening the file that was created and seeing which sample pairs still have missing values, then re-running on those pairs only. You would need to use the gdsfmt package to interact with the GDS file.

ADD COMMENTlink written 10 months ago by Stephanie M. Gogarten680
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