[Bioc-devel] readGAlignmentPairs Fails if Used Inside mclapply Loop

[Dario Strbenac]

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