Workers don't locate BAM files in parallel mode

[franciscodavid]

Hi,

When running CopywriteR with BiocParallel with a bp.param like this one:

bp.param <- SnowParam(workers= 5, type= "SOCK")

I'm getting errors regarding BAM files not found in the workers

Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: failed to open BamFile: file(s) do not exist:

These errors are not occurring in multicore or singlecore runs and seem to be caused by using the basename of BAM paths instead of the full BAM paths.

Here is the traceback() output of the error

4: stop(.error_bplist(res))
3: bplapply(sample.files, Stats.2, BPPARAM = bp.param)
2: bplapply(sample.files, Stats.2, BPPARAM = bp.param)
1: CopywriteR(sample.control = data.frame(samples, controls), destination.folder = outpF,
reference.folder = binref, capture.regions.file = roi, bp.param = bp.param)

I hope that helps.

[breezyzhao]

Hi,

I met the same problem here... if I only use one sample for the test, then everything looks good, however, the error happens when I try to use the parallel methods....

Any idea how to solve this?

Many thanks in advance