PHG addHapsFromGVCF restart after memory error

Question

[matt.shenton]

HI there,

Thanks for providing this great tool.

I'm trying to add Haplotypes using

singularity and CreateHaplotypesFromGVCF.groovy

Maybe my memory settings are not ideal, after around 100 gvcfs were processed, the script failed because of an out of memory error.

Is there a good way to restart without recreating the DB from scratch? (It took a few days to get this far).

Should I just edit the keyfile and delete the samples already in the DB? how about the ones that were partially loaded.

Any advice is welcome.

thanks in advance Matt Shenton

Answer 1

[matt.shenton]

I edited the keyfile. For those gvcfs that had been partially loaded into the DB, I had to change the method name in the contig file.

I hope this has solved my issue. Moving onto the consensus step.

Cheers Matt Shenton