seqParallel with BiocParallel::BatchtoolsParam object ?

[ldcato]

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.

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?

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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).

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Thank you for any help! Liam

[davidroberson]

nudging this almost four years later.... I see it is still open.

[zhengxwen]

Sorry! I have forgot this issue during the pandemic. It is on my radar now.

Xiuwen