You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I have a question regarding the seqParallel function. I can see the cl arguement takes a BiocParallelParam object. I attempted to use it with a BatchtoolsParam object within the BiocParallel package, I don't get error messages but it doesn't scale and just runs 1 chunk on one node.
Submitting 1 jobs in 1 chunks using cluster functions 'SGE' ...
Waiting (Q:0 R:1 D:0 E:0 ?:0) [--------------------------------] 0% eta: ?s
Are there any ambitions to include BatchtoolsParam support? Am I missing something that would allow this to work in the first place?
This all came about because I wanted to use the seqVCF2GDS() function with large VCF files, and set the parallel argument equal to my BatchtoolsParam object. seqVCF2GDS(vcf.fn='an_examplefile.vcf', out.fn='test.gds', header=NULL, storage.option="LZMA_RA", info.import=NULL, fmt.import=NULL, genotype.var.name="GT", ignore.chr.prefix="chr", scenario="general", reference='GRCh38', start=1L, count=-1L, optimize=TRUE, raise.error=TRUE, digest=TRUE, **parallel=param**, verbose=TRUE)
^ my BatchtoolsParam object is named param.
In case it's important:
Running R version 4.0.0 (2020-04-24), x86_64 RedHat. With package versions: SeqArray_1.29.3, gdsfmt_1.26.1, BiocParallel_1.22.0, batchtools_0.9.14.
I'm on an SGE cluster
BatchtoolsParam works well, everything registered and works with the example provided at the end of the documentation (that I've linked above).
Thank you for any help!
Liam
The text was updated successfully, but these errors were encountered:
Hi, amazing resource of tools built here!
I have a question regarding the seqParallel function. I can see the
cl
arguement takes a BiocParallelParam object. I attempted to use it with a BatchtoolsParam object within the BiocParallel package, I don't get error messages but it doesn't scale and just runs 1 chunk on one node.Are there any ambitions to include BatchtoolsParam support? Am I missing something that would allow this to work in the first place?
This all came about because I wanted to use the seqVCF2GDS() function with large VCF files, and set the parallel argument equal to my BatchtoolsParam object.
seqVCF2GDS(vcf.fn='an_examplefile.vcf', out.fn='test.gds', header=NULL, storage.option="LZMA_RA", info.import=NULL, fmt.import=NULL, genotype.var.name="GT", ignore.chr.prefix="chr", scenario="general", reference='GRCh38', start=1L, count=-1L, optimize=TRUE, raise.error=TRUE, digest=TRUE, **parallel=param**, verbose=TRUE)
^ my BatchtoolsParam object is named param.
In case it's important:
Thank you for any help!
Liam
The text was updated successfully, but these errors were encountered: