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Question: Preparation of summarizedExperiment for dexSeq
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gravatar for A
5 weeks ago by
A0
A0 wrote:

Hi all, 

 

I am running in to a problem I have not had before and was wondering if somebody might be able to help. I am processing a summarized experiment object for exonic regions to looks for differential exon usage with the dexseq package. Preprocessing before has always worked, however, I have just run in to this problem now (reason for carrying out code again is because of more BAM files after sequencing of more samples)... I do not understand this error as I following the dexseq vignette, however looking at the error itself, makes sense to me, however it doesnt make sense in the context of the code I am carrying out here as I can put my finger on the specific source:

 

hse <- makeTxDbFromBiomart(biomart="ensembl", dataset="mmusculus_gene_ensembl")

exonicParts = disjointExons( hse, aggregateGenes=FALSE )

bamDir<- file.path(file= "pathtofile/")
fls <-list.files( bamDir, pattern="bam$", full=TRUE )

bamlst = BamFileList( fls, index=character(), yieldSize=100000,
obeyQname=TRUE )

SE<-summarizeOverlaps( exonicParts, bamlst, mode="Union",
singleEnd=FALSE, ignore.strand=TRUE, inter.feature=FALSE,
fragments=TRUE )

This code produces the following error (which it never did before):

Warning: stop worker failed:
  'clear_cluster' receive data failed:
  reached elapsed time limit
Error in names(res) <- nms : 
  'names' attribute [143] must be the same length as the vector [48]

I am not sure what the names(res) refers to and not sure which the vector is? Is it it the bamlst itself? Which is weird as there 143 objects inside it and therefore the length should be correct?

 

Any help would be greatly appreciated as this is frustrating! 

 

Many thanks!

ADD COMMENTlink written 5 weeks ago by A0

You should probably include the output from both traceback() and sessionInfo() (in that order) after you get the error.

ADD REPLYlink written 4 weeks ago by James W. MacDonald48k

Many thanks!! please see below for that order! 

 

Traceback:

8.
bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
7.
bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
6.
bplapply(setNames(seq_along(reads), names(reads)), function(i, FUN, reads, features, mode, ignore.strand, inter.feature, param, preprocess.reads, ...) { bf <- reads[[i]] ...
5.
bplapply(setNames(seq_along(reads), names(reads)), function(i, FUN, reads, features, mode, ignore.strand, inter.feature, param, preprocess.reads, ...) { bf <- reads[[i]] ...
4.
.dispatchBamFiles(features, reads, mode, ignore.strand, inter.feature = inter.feature, singleEnd = singleEnd, fragments = fragments, param = param, preprocess.reads = preprocess.reads, ...)
3.
.local(features, reads, mode, ignore.strand, ...)
2.
summarizeOverlaps(exonicParts, bamlst, mode = "Union", singleEnd = FALSE, ignore.strand = TRUE, inter.feature = FALSE, fragments = TRUE)
1.
summarizeOverlaps(exonicParts, bamlst, mode = "Union", singleEnd = FALSE, ignore.strand = TRUE, inter.feature = FALSE, fragments = TRUE)

 

sessioninfo:

R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenomicFeatures_1.30.3     AnnotationDbi_1.40.0       GenomicAlignments_1.14.2  
 [4] Rsamtools_1.30.0           Biostrings_2.46.0          XVector_0.18.0            
 [7] SummarizedExperiment_1.8.1 DelayedArray_0.4.1         matrixStats_0.54.0        
[10] Biobase_2.38.0             GenomicRanges_1.30.3       GenomeInfoDb_1.14.0       
[13] IRanges_2.12.0             S4Vectors_0.16.0           BiocGenerics_0.24.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19           compiler_3.4.2         prettyunits_1.0.2      bitops_1.0-6          
 [5] tools_3.4.2            zlibbioc_1.24.0        progress_1.2.0         biomaRt_2.34.2        
 [9] digest_0.6.18          bit_1.1-14             RSQLite_2.1.1          memoise_1.1.0         
[13] lattice_0.20-35        pkgconfig_2.0.2        rlang_0.2.2            Matrix_1.2-11         
[17] DBI_1.0.0              rstudioapi_0.8         curl_3.2               GenomeInfoDbData_1.0.0
[21] knitr_1.20             rtracklayer_1.38.3     httr_1.3.1             stringr_1.3.1         
[25] hms_0.4.2              bit64_0.9-7            grid_3.4.2             R6_2.3.0              
[29] snow_0.4-3             XML_3.98-1.16          RMySQL_0.10.15         BiocParallel_1.12.0   
[33] magrittr_1.5           blob_1.1.1             assertthat_0.2.0       stringi_1.1.7        

 

Apologies for the delay in replying: really hope this can be solved!

Many thanks!

 

ADD REPLYlink written 4 weeks ago by A0
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