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Question: error when I use groHMM on data outside of the tutorial
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gravatar for simonalsager
12 days ago by
simonalsager0 wrote:

Hi,

When I tried the groHMM package tutorial, I was able to get everything to work. When I try it with real data, I keep getting this error "the score must be numeric, without any NA's". I appreciate any help because I have been searching the internet and trying to figure this out on my own for several days. 

For data processing, I used cutadapt to remove adapters and low quality reads. I aligned to hg19 with bwa, and coverted the resulting sam file to a bam file with samtools. When I load it into R for groHMM analysis, this is what happens:

 

> SRR5364056 <- as(readGAlignments("SRR5364056.bam"), "GRanges")
> writeWiggle(reads=SRR5364056, file="SRR5364056_Plus.wig", fileType="wig", strand="+",
+ reverse=FALSE)
Error in .local(object, con, format, ...) : 
  The score must be numeric, without any NA's
In addition: Warning messages:
1: In mclapply(readsList, function(x) { :
  all scheduled cores encountered errors in user code
2: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion
> writeWiggle(reads=SRR5364056, file="SRR5364056_Minus.wig", fileType="wig", strand="-",
+ reverse=TRUE)
Error in .local(object, con, format, ...) : 
  The score must be numeric, without any NA's
In addition: Warning messages:
1: In mclapply(readsList, function(x) { :
  all scheduled cores encountered errors in user code
2: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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] groHMM_1.14.0               rtracklayer_1.40.6         
 [3] GenomicAlignments_1.16.0    Rsamtools_1.32.3           
 [5] Biostrings_2.48.0           XVector_0.20.0             
 [7] SummarizedExperiment_1.10.1 DelayedArray_0.6.5         
 [9] BiocParallel_1.14.2         matrixStats_0.54.0         
[11] Biobase_2.40.0              GenomicRanges_1.32.6       
[13] GenomeInfoDb_1.16.0         IRanges_2.14.11            
[15] S4Vectors_0.18.3            BiocGenerics_0.26.0        
[17] MASS_7.3-50                

loaded via a namespace (and not attached):
 [1] zlibbioc_1.26.0        lattice_0.20-35        tools_3.5.1           
 [4] grid_3.5.1             Matrix_1.2-14          GenomeInfoDbData_1.1.0
 [7] bitops_1.0-6           RCurl_1.95-4.11        compiler_3.5.1        
[10] XML_3.98-1.16         
> SRR5364056
GRanges object with 18253707 ranges and 0 metadata columns:
             seqnames            ranges strand
                <Rle>         <IRanges>  <Rle>
         [1]    chr10       67286-67336      +
         [2]    chr10       82341-82391      +
         [3]    chr10       84427-84477      +
         [4]    chr10       84434-84484      +
         [5]    chr10       84564-84614      +
         ...      ...               ...    ...
  [18253703]     chrY 59360648-59360698      +
  [18253704]     chrY 59360705-59360755      +
  [18253705]     chrY 59360705-59360755      +
  [18253706]     chrY 59360705-59360755      +
  [18253707]     chrY 59360706-59360756      +
  -------
  seqinfo: 93 sequences from an unspecified genome
> 

 

Thanks a million! 

ADD COMMENTlink modified 11 days ago • written 12 days ago by simonalsager0
2

Hello,

Can you try including just the standard chromosomes and then execute the writeWiggle step

gr <- keepStandardChromosomes(SRR5364056)

or if you are using  R 3.4.4

gr <- keepStandardChromosomes(SRR5364056, pruning.mode="coarse")

 

 

 

ADD REPLYlink written 11 days ago by anusha.nagari20

THANK YOU!!!!!!!

ADD REPLYlink written 11 days ago by simonalsager0
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