Hello,

I have a piece of code that have worked on three vcf files but failed on fourth. For the files the reference, samples and gff3 files are the same, only SNP calling algorithm is different.

The error I'm getting is:

Error in relist(v, part) :
  shape of 'skeleton' is not compatible with 'NROW(flesh)'

What does this error mean? Do you know what could be causing this? I just need to know what to look for. 

Best wishes,

Agnieszka

Piece of code:

compressVcf <- bgzip("all.vcf.h.sgs.flt", tempfile())
idx <- indexTabix(compressVcf, "vcf")
tab <- TabixFile(compressVcf, idx)
c <- "C1"
fn <- paste(c,".fasta", sep="")
gn <- paste(c,".gff3", sep="")
fltF <- paste("contig.info.",c, sep="")
fltT <- read.csv(fltF, sep=",", header=TRUE)
fltG <- with(fltT, GRanges(chr, IRanges(start, end)))
param <- ScanVcfParam(which=fltG)
txdb <- makeTxDbFromGFF(gn)
Prepare the 'metadata' data frame ... metadata: OK
Warning message:
In matchCircularity(seqlevels(gr), circ_seqs) :
  None of the strings in your circ_seqs argument match your seqnames.
vcf2<-readVcf(tab, paste("bolep", c), param=param)
Error in relist(v, part) :
  shape of 'skeleton' is not compatible with 'NROW(flesh)'

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)

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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] VariantAnnotation_1.14.3 Rsamtools_1.20.4         Biostrings_2.36.1
 [4] XVector_0.8.0            GenomicFeatures_1.20.1   AnnotationDbi_1.30.1
 [7] Biobase_2.28.0           GenomicRanges_1.20.5     GenomeInfoDb_1.4.1
[10] IRanges_2.2.4            S4Vectors_0.6.0          BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] zlibbioc_1.14.0         GenomicAlignments_1.4.1 BiocParallel_1.2.3
 [4] BSgenome_1.36.1         tools_3.2.1             DBI_0.3.1
 [7] lambda.r_1.1.7          futile.logger_1.4.1     rtracklayer_1.28.5
[10] futile.options_1.0.0    bitops_1.0-6            RCurl_1.95-4.6
[13] biomaRt_2.24.0          RSQLite_1.0.0           XML_3.98-1.2

Hi Agnieszka,

I'm not sure what is causing that error. You could try using scanVcf() to see if it gives the same error. I'll use a sample file from VariantAnnotation:

> scn <- scanVcf(fl, param=param)
> names(scn[[1]])
[1] "rowRanges" "REF"       "ALT"       "QUAL"      "FILTER"    "INFO"     
[7] "GENO"  

It's possible one of these elements has a character that's not being parsed correctly and causing the dimensions to be off. Take a look at the length of the fields with lapply():

> lapply(scn[[1]], length)
$rowRanges
[1] 103

$REF
[1] 103

$ALT
[1] 103

$QUAL
[1] 103

$FILTER
[1] 103

$INFO
[1] 22

$GENO
[1] 3

INFO and GENO are lists of fields so we have to look at those separately. Check the dim in GENO (vs the length):

> lapply(scn[[1]]$GENO, dim)
$GT
[1] 103   5

$DS
[1] 103   5

$GL
[1] 103   5

If that doesn't help identify the problem I can take a look at the file.

Valerie