Error running getBamCounts from ExomeDepth
Hi all, I have a problem when running Exomedepth when executing getBamCounts:
> require(ExomeDepth)
> data(exons.hg19)
> options(stringsAsFactors=FALSE)
> bamlist = read.table('bam.list')$V1
> counts = getBamCounts(bed.frame = exons.hg19, bam.files = bamlist)
The output error is:
Error in as.vector(x, mode) :
'.SigArgs' is shorter than '.SigLength' says it should be
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ExomeDepth_1.1.10 optparse_1.3.2
loaded via a namespace (and not attached):
[1] lattice_0.20-24 IRanges_2.8.1
[3] Rsamtools_1.26.1 Biostrings_2.42.0
[5] bitops_1.0-6 GenomicAlignments_1.10.0
[7] grid_3.3.2 GenomeInfoDb_1.10.1
[9] stats4_3.3.2 zlibbioc_1.20.0
[11] XVector_0.14.0 getopt_1.20.0
[13] S4Vectors_0.12.0 Matrix_1.1-2
[15] aod_1.3 BiocParallel_1.8.1
[17] tools_3.3.2 Biobase_2.34.0
[19] parallel_3.3.2 BiocGenerics_0.20.0
[21] GenomicRanges_1.26.1 SummarizedExperiment_1.4.0
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Could you print the bamlist variable?
The bamlist variable looks like this
The vignette says that bam.files argument has to be "character, list of BAM files to extract read count data from". I have also tried using a list, but it still not working.
Is the chromosome notation in your bam files the same as in exons.hg19?
Both bam files have the chromosome notation without 'chr', e.g. "1", "2"...
And you bamfiles are indexed, i.e. file1.bam.bai?
(If this doesn't explain it I have no idea what's wrong)
Yes, they are indexed in the same dir than the bam files are located as fileX.bam.bai
Well I'm out of ideas, you could try
traceback()after getting the error to trace the error. Besides that, perhaps your best guess is contacting the author of the package.The
traceback()output is:17: as.vector(x, mode)
16: as.vector(x, mode = "integer")
15: .local(x, ...)
14: as.integer(seqnames(x))
13: as.integer(seqnames(x))
12: get_out_of_bound_index(x)
11: valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE)
10: valid.func(object)
9: validityMethod(as(object, superClass))
8: anyStrings(validityMethod(as(object, superClass)))
7: validObject(.Object)
6: initialize(value, ...)
5: initialize(value, ...)
4: new(Class, seqnames = seqnames, ranges = ranges, strand = strand, elementMetadata = mcols, seqinfo = seqinfo)
3: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = mcols, seqlengths = seqlengths, seqinfo = seqinfo)
2: GenomicRanges::GRanges(seqnames = bed.frame$seqnames, IRanges::IRanges(start = bed.frame$start + 1, end = bed.frame$end))
1: getBamCounts(bed.frame = exons.hg19, bam.files = bamlist)
Anyway, I am contacting the author of the package. Thanks for replying.
Well I am not sure. Definitely something to do with the chromosome names, as it's a seqnames pbm. What reference genome did you use exactly?