bplapply memory issue when running scone(run=TRUE)
ckmah opened this issue · 3 comments
I came across an error running the following call to scone(run=TRUE)
while running through the Bioc2016 workshop vignette (added verbose = TRUE
flag):
res <- scone(expr = as.matrix(fcounts),scaling = c(none = identity, deseq = DESEQ_FN, tmm = TMM_FN, uqp = UQ_FN_POS, fq = FQT_FN),
+ ruv_negcon = fhk, k_ruv = 3,
+ qc = as.matrix(fqc), k_qc = 3,
+ bio = fbio,adjust_bio = "yes",
+ batch = fbatch,adjust_batch = "yes",
+ run = TRUE,params = params,
+ eval_poscon = fde, eval_kclust = 2:3, verbose = TRUE)
Output:
Imputation step...
Scaling step...
Computing RUV factors...
Error: 'bplapply' receive data failed:
error reading from connection
Some details:
fcounts
is a 10610 x 91 expression matrix using the data from the vignette. I ran this through RStudio with R default memory settings on OSX with 16GB RAM. @mbcole advised me to post this issue as a potential memory bug.
Hi Clarence,
Thanks for posting this error. I'm actually quite surprised this is occurring for so few cells (91, correct?). I run SCONE on larger data sets using a laptop with less memory. I'm curious whether the error occurs in serial mode. This may be specified by calling
`BiocParallel::register(BiocParallel::SerialParam())`
prior to the scone()
call.
I just tried it in serial mode and the error seems to have gone away. I'll keep you updated and let you know when I get a chance to try it on a larger dataset.
I have the same issue when I run DESeq2 with the parallel option