Dear all,

I have used CopywriteR package with sequencing data and got an error.

Because I previously got a successful result with a different set of bam files, I think the problem would be the bam list (or some of the bam files), but I don't figure out what exactly is the problem.

My script, error messages and sessionInfo() are attached below.

Script:

library(CopywriteR)

BAMlist="PATH/TO/BAMlist.txt"

ref="PATH/TO/CONTROL.bam"

data.folder="PATH/TO/DATAFOLDER"
bin.size=50000
preCopywriteR(output.folder=file.path(data.folder),bin.size=bin.size,ref.genome="hg19")

bp.param=SnowParam(workers=10, type="SOCK")

samples=readLines(BAMlist)

samples=c(samples,ref)
controls=c(rep(ref,length(samples)))

sample.control=data.frame(samples, controls)

CopywriteR(sample.control=sample.control,
           destination.folder=file.path(data.folder),
           reference.folder=file.path(data.folder, "hg19_50kb"), bp.param=bp.param)

Error messages:

Error in .Method(..., deparse.level = deparse.level) : 
  number of rows of matrices must match (see arg 2)
Calls: CopywriteR ... f -> standardGeneric -> eval -> eval -> eval -> .Method
In addition: Warning messages:
1: In .Method(..., deparse.level = deparse.level) :
  number of columns of result is not a multiple of vector length (arg 2)
2: In `[<-.data.frame`(`*tmp*`, , "total.properreads", value = list( :
  provided 174 variables to replace 1 variables
3: In Ops.factor(res$all.reads, res$chrom.reads) :
  '-' not meaningful for factors
Execution halted

SessionInfo:

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux ComputeNode release 6.7 (Santiago)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] CopywriteR_2.2.0   BiocParallel_1.2.7

loaded via a namespace (and not attached):
 [1] DNAcopy_1.44.0             chipseq_1.20.0            
 [3] XVector_0.10.0             GenomicRanges_1.22.4      
 [5] BiocGenerics_0.16.1        zlibbioc_1.14.0           
 [7] GenomicAlignments_1.6.3    IRanges_2.4.8             
 [9] lattice_0.20-33            hwriter_1.3.2             
[11] GenomeInfoDb_1.6.3         SummarizedExperiment_1.0.2
[13] parallel_3.2.1             grid_3.2.1                
[15] Biobase_2.28.0             data.table_1.9.6          
[17] latticeExtra_0.6-28        lambda.r_1.1.7            
[19] futile.logger_1.4.1        gtools_3.5.0              
[21] matrixStats_0.50.2         RColorBrewer_1.1-2        
[23] S4Vectors_0.8.11           futile.options_1.0.0      
[25] bitops_1.0-6               CopyhelpeR_1.2.0          
[27] Biostrings_2.38.4          Rsamtools_1.22.0          
[29] stats4_3.2.1               ShortRead_1.26.0          
[31] chron_2.3-47              

Best,

Tom

I looked inside the Copywriter.log file and it ended with:

INFO [2016-07-12 14:35:29] remote-error in value[[3L]](cond): failed to open BamFile: file(s) do not exist:
  ‘XXX(one of my bam files).bam’
I corrected the wrong path and then CopywriteR() ended successfully.