Good day,
I found that readGAlignmentPairs fails when used inside an mclapply loop but
not an sapply loop. I haven't had such problems with other functions when using
mclapply.
> class(mappedToGenomeFiles)
[1] "character"
> length(mappedToGenomeFiles)
[1] 13
> mappedReadsGenome <- sapply(mappedToGenomeFiles, function(bamFile)
{
readGAlignmentPairs(bamFile, strandMode = 2)
})
# No error. Each item is of GAlignmentPairs class.
But, with mclapply:
> mappedReadsGenome <- mclapply(mappedToGenomeFiles, function(bamFile)
{
readGAlignmentPairs(bamFile, strandMode = 2)
}, mc.cores = 7)
Warning message:
In mclapply(mappedToGenomeFiles, function(bamFile) { :
scheduled cores 6, 5, 3, 1, 4, 2 encountered errors in user code, all values
of the jobs will be affected
> mappedReadsGenome
[[1]]
[1] "fatal error in wrapper code"
attr(,"class")
[1] "try-error"
[[2]]
[1] "fatal error in wrapper code"
attr(,"class")
[1] "try-error"
.
.
.
[[7]]
GAlignmentPairs object with 41860576 pairs, strandMode=2, and 0 metadata
columns:
seqnames strand : ranges --
ranges
<Rle> <Rle> : <IRanges> --
<IRanges>
[1] chr14 + : [19010525, 19010623] -- [19010414,
19010513]
[2] chr14 + : [19010543, 19010612] -- [19010505,
19010604]
[3] chr14 + : [19010608, 19010707] -- [19010577,
19010676]
[4] chr14 + : [19011187, 19011286] -- [19011142,
19011241]
[5] chr14 + : [19011318, 19011415] -- [19011187,
19011286]
... ... ... ... ... ...
...
[41860572] chr4 + : [190972787, 190972886] -- [190972685,
190972784]
[41860573] chr4 - : [190974302, 190974385] -- [190974302,
190974385]
[41860574] chr4 - : [190978480, 190978579] -- [190978542,
190978641]
[41860575] chr4 - : [190982116, 190982215] -- [190982125,
190982224]
[41860576] chr4 + : [191031678, 191031776] -- [191031630,
191031729]
-------
seqinfo: 25 sequences from an unspecified genome
.
.
.
[[13]]
[1] "fatal error in wrapper code"
attr(,"class")
[1] "try-error"
Interestingly, reading in from one of the thirteen file paths worked.
In contrast, a simple test case of the same length works:
X=1:13
mclapply(X, function(x) x + 1, mc.cores = 7) # Prints 2:14.
The BAM file import also works with blapply and BPPARAM =
MulticoreParam(workers = 7)
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] GenomicAlignments_1.10.0 SummarizedExperiment_1.4.0
GenomicFeatures_1.26.0 AnnotationDbi_1.36.0 Biobase_2.34.0
[6] Rsamtools_1.26.1 Biostrings_2.42.0 XVector_0.14.0
GenomicRanges_1.26.1 GenomeInfoDb_1.10.1
[11] IRanges_2.8.1 S4Vectors_0.12.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.20.0 BiocParallel_1.8.1 lattice_0.20-34 tools_3.3.2
grid_3.3.2 DBI_0.5-1 Matrix_1.2-7.1
[8] rtracklayer_1.34.1 bitops_1.0-6 RCurl_1.95-4.8 biomaRt_2.30.0
RSQLite_1.0.0 XML_3.98-1.5
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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