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Question: RIPSeeker error Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript contains NAs or out-of-bounds indices
1
gravatar for xfwang
22 months ago by
xfwang10
United States
xfwang10 wrote:

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    

ADD COMMENTlink modified 19 months ago • written 22 months ago by xfwang10
0
gravatar for xfwang
19 months ago by
xfwang10
United States
xfwang10 wrote:

Just in case people got same issue as mine:

The issue is that it has to be “NULL” for option “strandType”, if it is non-strand specific sequencing. If use “*”, the error happens.

ADD COMMENTlink written 19 months ago by xfwang10
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