CNVPanelizer package error
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Entering edit mode
@sbpatel2009-14018
Last seen 14 months ago

I need help debugging an error from the CNVPanelizer package.  The code, output, traceback, and sessioninfo are shown below.  The version of R is 3.3.3, and the version of R studio is 1.0.136.  ScanBam does read in the bam files, so I know that these files are valid.  I can also visualize the files in IGV. 

I am certain that my packages have been loaded and are up-to-date:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> library("CNVPanelizer")
> BiocInstaller::biocValid()
[1] TRUE

I have read in my bed file and converted it to a GRanges object (partially printed out to confirm):

> bed = read.table("CNS panel/BEDv3.bed",sep = "", skip = 1, header = FALSE)
> colnames(bed) = c("chr", "start", "end", "amplicon", "na1", "na2", "na3", "gene")
> bed[, c("na1", "na2", "na3")] = NULL
> gene = sub(pattern = "GENE_ID=", replacement = "", x = bed$gene)
> gene = sub(pattern = ";Pool=1", replacement = "", x = gene)
> gene = sub(pattern = ";Pool=2", replacement = "", x = gene)
> bed$gene = as.factor(gene)
> ampliconNames = bed$amplicon
> GRbed = makeGRangesFromDataFrame(bed, keep.extra.columns = TRUE)
> head(GRbed)
GRanges object with 6 ranges and 2 metadata columns:
      seqnames               ranges strand |       amplicon     gene
         <Rle>            <IRanges>  <Rle> |       <factor> <factor>
  [1]     chr1 [78414940, 78415056]      * | AMPL7161868567    FUBP1
  [2]     chr1 [78420965, 78421056]      * | AMPL7161219286    FUBP1
  [3]     chr1 [78422278, 78422398]      * | AMPL7161868565    FUBP1
  [4]     chr1 [78425840, 78425944]      * | AMPL7161219288    FUBP1
  [5]     chr1 [78426079, 78426195]      * | AMPL7160313815    FUBP1
  [6]     chr1 [78428430, 78428520]      * | AMPL7161868564    FUBP1
  -------
  seqinfo: 20 sequences from an unspecified genome; no seqlengths

I have specified the correct file directories and have correctly obtained the bam file names:

> controlDirectory = "C:/Users/patelsb/Desktop/Control"
> sampleDirectory = "C:/Users/patelsb/Desktop/Samples"
> (controlFileNames = list.files(path = controlDirectory, pattern = ".bam", full.names = TRUE))
 [1] "C:/Users/patelsb/Desktop/Control/AF1.bam"  "C:/Users/patelsb/Desktop/Control/AF2.bam" 
 [3] "C:/Users/patelsb/Desktop/Control/AM1.bam"  "C:/Users/patelsb/Desktop/Control/AM2.bam" 
 [5] "C:/Users/patelsb/Desktop/Control/CEPH.bam" "C:/Users/patelsb/Desktop/Control/EA1.bam" 
 [7] "C:/Users/patelsb/Desktop/Control/EA2.bam"  "C:/Users/patelsb/Desktop/Control/EU1.bam" 
 [9] "C:/Users/patelsb/Desktop/Control/EU2.bam"  "C:/Users/patelsb/Desktop/Control/NT05.bam"
[11] "C:/Users/patelsb/Desktop/Control/NT06.bam" "C:/Users/patelsb/Desktop/Control/NT11.bam"
[13] "C:/Users/patelsb/Desktop/Control/NT13.bam" "C:/Users/patelsb/Desktop/Control/NT14.bam"
[15] "C:/Users/patelsb/Desktop/Control/NT15.bam" "C:/Users/patelsb/Desktop/Control/NT17.bam"
[17] "C:/Users/patelsb/Desktop/Control/NT18.bam" "C:/Users/patelsb/Desktop/Control/NT25.bam"
[19] "C:/Users/patelsb/Desktop/Control/NT26.bam" "C:/Users/patelsb/Desktop/Control/SA1.bam" 
[21] "C:/Users/patelsb/Desktop/Control/SA2.bam" 
> (sampleFileNames = list.files(path = sampleDirectory, pattern = ".bam", full.names = TRUE))
 [1] "C:/Users/patelsb/Desktop/Samples/E697.bam" "C:/Users/patelsb/Desktop/Samples/M217.bam"
 [3] "C:/Users/patelsb/Desktop/Samples/M448.bam" "C:/Users/patelsb/Desktop/Samples/M533.bam"
 [5] "C:/Users/patelsb/Desktop/Samples/N629.bam" "C:/Users/patelsb/Desktop/Samples/N637.bam"
 [7] "C:/Users/patelsb/Desktop/Samples/N651.bam" "C:/Users/patelsb/Desktop/Samples/N973.bam"
 [9] "C:/Users/patelsb/Desktop/Samples/P270.bam" "C:/Users/patelsb/Desktop/Samples/P308.bam"
[11] "C:/Users/patelsb/Desktop/Samples/P443.bam" "C:/Users/patelsb/Desktop/Samples/P454.bam"
[13] "C:/Users/patelsb/Desktop/Samples/P515.bam" "C:/Users/patelsb/Desktop/Samples/P682.bam"
[15] "C:/Users/patelsb/Desktop/Samples/P792.bam" "C:/Users/patelsb/Desktop/Samples/P794.bam"
[17] "C:/Users/patelsb/Desktop/Samples/P916.bam" "C:/Users/patelsb/Desktop/Samples/P918.bam"
[19] "C:/Users/patelsb/Desktop/Samples/P979.bam" "C:/Users/patelsb/Desktop/Samples/Q059.bam"
[21] "C:/Users/patelsb/Desktop/Samples/Q104.bam"

When I attempt to obtain the reference counts, I get an error:

> referenceReadCounts <- ReadCountsFromBam(bamFilenames = controlFileNames, gr = GRbed, sampleNames = controlFileNames, ampliconNames = ampliconNames, removeDup = FALSE)
Error in { : 
  task 1 failed - "failed to open BamFile: failed to load BAM index
  file: C:/Users/patelsb/Desktop/Control/AF1.bam"
In addition: There were 21 warnings (use warnings() to see them)

Warnings:

> warnings()
Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
2: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
3: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
4: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
5: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
6: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
7: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
8: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
9: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
10: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
11: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
12: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
13: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
14: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
15: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
16: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
17: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
18: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
19: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
20: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
21: In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.

Traceback:

> traceback()
4: stop(simpleError(msg, call = expr))
3: e$fun(obj, substitute(ex), parent.frame(), e$data)
2: foreach(i = seq_along(bamFilenames), .combine = cbind) %do% {
       countBamInGRanges(bamFilenames[i], gr, remove.dup = removeDup, 
           min.mapq = 20, get.width = TRUE)
   }
1: ReadCountsFromBam(bamFilenames = controlFileNames, gr = GRbed, 
       sampleNames = controlFileNames, ampliconNames = ampliconNames, 
       removeDup = FALSE)

session information:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] CNVPanelizer_1.6.0   GenomicRanges_1.28.5 GenomeInfoDb_1.12.2  IRanges_2.10.3      
[5] S4Vectors_0.14.4     BiocGenerics_0.22.0  BiocInstaller_1.26.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12            exomeCopy_1.22.0        XVector_0.16.0         
 [4] splines_3.4.1           zlibbioc_1.22.0         BiocParallel_1.10.1    
 [7] munsell_0.4.3           colorspace_1.3-2        lattice_0.20-35        
[10] rlang_0.1.2             foreach_1.4.3           plyr_1.8.4             
[13] tools_3.4.1             grid_3.4.1              Biobase_2.36.2         
[16] gtable_0.2.0            NOISeq_2.20.0           iterators_1.0.8        
[19] lazyeval_0.2.0          tibble_1.3.4            Matrix_1.2-11          
[22] GenomeInfoDbData_0.99.0 ggplot2_2.2.1           bitops_1.0-6           
[25] codetools_0.2-15        RCurl_1.95-4.8          openxlsx_4.0.17        
[28] compiler_3.4.1          Biostrings_2.44.2       Rsamtools_1.28.0       
[31] scales_0.5.0   

 

This is my first post to this forum, so I apologize in advance if I failed to conform to any aspect of the posting guidelines.

Thank you,

Snehal Patel, MD, PhD

National Institutes of Health, National Cancer Center

 

CNVPanelizer failed to open BamFile failed to load BAM index file • 377 views
ADD COMMENT
0
Entering edit mode
@sbpatel2009-14018
Last seen 14 months ago

Nevermind.  After creating an index, I was able to get it to work.  

controlDirectory = "C:/Users/patelsb/Desktop/Control"
sampleDirectory = "C:/Users/patelsb/Desktop/Samples"
(controlFileNames = list.files(path = controlDirectory, pattern = ".bam", full.names = TRUE))
(sampleFileNames = list.files(path = sampleDirectory, pattern = ".bam", full.names = TRUE))

IndexMultipleBams(controlFileNames)
IndexMultipleBams(sampleFileNames)

Thanks,

Snehal

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