Dear RIPSeeker people,
Since I did not get any response for added-comment to my previous question, I open this error as new question. Actually, I tried to dig into this error by different version of genome build, different version of tophat, and upgrading the bioconductor package. But, the error is still not figured out.
Here is the code that I used:
binSize <- NULL # automatically determine bin size
minBinSize <- 10000
maxBinSize <- 10100
multicore <- TRUE
strandType <- "*"
biomaRt_dataset <- "hsapiens_gene_ensembl" # human dataset id name
goAnno <- "org.Hs.eg.db"
seekOut.HuR <- ripSeek(bamPath = bamFiles, cNAME = ctrl, reverseComplement = FALSE, genomeBuild = "hg19", strandType = strandType, uniqueHit = TRUE, assignMultihits = TRUE, rerunWithDisambiguatedMultihits = TRUE, binSize=binSize, minBinSize = minBinSize, maxBinSize = maxBinSize, biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", goAnno = goAnno, biomaRt_dataset = biomaRt_dataset, multicore=multicore, outDir=outDir)
Here is the error:
*I. Collect alignment files
RIP alignment files:
/Users/.../tophat1_out_UCSChg19/HuR_S1_accepted_hits_chrX.bam
/Users/.../tophat1_out_UCSChg19/HuR_S2_accepted_hits_chrX.bam
Control alignment files:
/Users/.../tophat1_out_UCSChg19/IgG_S1_accepted_hits_chrX.bam
/Users/.../tophat1_out_UCSChg19/IgG_S2_accepted_hits_chrX.bam
*II. Analyzing RIP library:
**A. Process and combine alignment files
Processing /Users/.../tophat1_out_UCSChg19/HuR_S1_accepted_hits_chrX.bam ... All hits are returned with flags.
Processing /Users/.../tophat1_out_UCSChg19/HuR_S2_accepted_hits_chrX.bam ... All hits are returned with flags.
2 BAM files are combined
*** Only reads from strand * will be considered.
*** Only unique hits are used to compute read count.
*** chr1 do not have any alignment.
*** chr10 do not have any alignment.
*** chr11 do not have any alignment.
*** chr12 do not have any alignment.
*** chr13 do not have any alignment.
*** chr14 do not have any alignment.
*** chr15 do not have any alignment.
*** chr16 do not have any alignment.
*** chr17 do not have any alignment.
*** chr18 do not have any alignment.
*** chr19 do not have any alignment.
*** chr2 do not have any alignment.
*** chr20 do not have any alignment.
*** chr21 do not have any alignment.
*** chr22 do not have any alignment.
*** chr3 do not have any alignment.
*** chr4 do not have any alignment.
*** chr5 do not have any alignment.
*** chr6 do not have any alignment.
*** chr7 do not have any alignment.
*** chr8 do not have any alignment.
*** chr9 do not have any alignment.
*** chrM do not have any alignment.
*** chrX do not have any alignment.
*** chrY do not have any alignment.
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains NAs or out-of-bounds indices
Here is my sessionInfo:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.20.1 RIPSeekerData_1.6.0 RIPSeeker_1.10.0 rtracklayer_1.30.1
[5] GenomicAlignments_1.6.3 Rsamtools_1.22.0 Biostrings_2.38.3 XVector_0.10.0
[9] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.6 S4Vectors_0.8.11
[13] BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] XML_3.98-1.3 bitops_1.0-6 futile.options_1.0.0 zlibbioc_1.16.0 futile.logger_1.4.1
[6] BiocParallel_1.4.3 lambda.r_1.1.7 tools_3.2.3 RCurl_1.95-4.7
