Question

error displaying bam files

1

Entering edit mode

kamal.fartiyal84 ▴ 10

@kamalfartiyal84-7976

Last seen 5.3 years ago

Cancer Research UK Cambridge Institute

Getting following error on displaying the content of bam file.

> aln <- readGAlignments("sample.bam")

> aln

GAlignments object with 32984922 alignments and 0 metadata columns:

Error in (function (classes, fdef, mtable) :

unable to find an inherited method for function ‘rglist’ for signature ‘"GAlignments"’

> sessionInfo()

R version 3.4.2 (2017-09-28)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS Linux 7 (Core)

Matrix products: default

BLAS: /home/bioinformatics/software/R/R-3.4.2/lib64/R/lib/libRblas.so

LAPACK: /home/bioinformatics/software/R/R-3.4.2/lib64/R/lib/libRlapack.so

locale:

[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8

[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8

[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats4 parallel stats graphics grDevices utils datasets

[8] methods base

other attached packages:

[1] GenomicAlignments_1.12.2 Rsamtools_1.28.0

[3] Biostrings_2.44.2 XVector_0.16.0

[5] SummarizedExperiment_1.6.5 DelayedArray_0.2.7

[7] matrixStats_0.52.2 Biobase_2.36.2

[9] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0

[11] IRanges_2.12.0 S4Vectors_0.16.0

[13] BiocGenerics_0.24.0

loaded via a namespace (and not attached):

[1] lattice_0.20-35 bitops_1.0-6 grid_3.4.2

[4] zlibbioc_1.22.0 Matrix_1.2-11 BiocParallel_1.10.1

[7] tools_3.4.2 RCurl_1.95-4.8 compiler_3.4.2

[10] GenomeInfoDbData_0.99.0

genomicalignments • 1.5k views

ADD COMMENT • link 6.4 years ago kamal.fartiyal84 ▴ 10

score 0 · Answer 1 · 2017-11-16

0

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Martin Morgan 25k

@martin-morgan-1513

Last seen 3 days ago

United States

Usually this type of error occurs when packages are out of sync. Does the result of

BiocInstaller::biocValid()

suggest any problems? Does the simpler example

example(readGAlignments)

work?

ADD COMMENT • link 6.4 years ago Martin Morgan 25k

Martin Morgan · Answer 2 · 2017-11-30

0

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kamal.fartiyal84 ▴ 10

@kamalfartiyal84-7976

Last seen 5.3 years ago

Cancer Research UK Cambridge Institute

Hello Matrin,

Thanks for your reply. Yes, it works now.

ADD COMMENT • link 6.4 years ago kamal.fartiyal84 ▴ 10

0

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Hi, i have a similar issue that i can solve.

bamfile = readGAlignments("/Documents/chr22.sorted.bam")
> stackStringsFromBam(bamfile, param="seq1:1-21")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘readGAlignments’ for signature ‘"GAlignments"’

when i run

> BiocInstaller::biocValid()
Error in loadNamespace(name) : there is no package called ‘BiocInstaller’

when i try to install

package ‘BiocInstaller’ is not available (for R version 3.6.1)

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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  
[9] base     

other attached packages:
 [1] GenomicAlignments_1.20.1    Rsamtools_2.0.1             Biostrings_2.52.0          
 [4] XVector_0.24.0              SummarizedExperiment_1.14.1 DelayedArray_0.10.0        
 [7] BiocParallel_1.18.1         matrixStats_0.55.0          Biobase_2.44.0             
[10] GenomicRanges_1.36.1        GenomeInfoDb_1.20.0         IRanges_2.18.2             
[13] S4Vectors_0.22.1            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] lattice_0.20-38        bitops_1.0-6           grid_3.6.1            
 [4] zlibbioc_1.30.0        Matrix_1.2-17          tools_3.6.1           
 [7] RCurl_1.95-4.12        compiler_3.6.1         BiocManager_1.30.4    
[10] GenomeInfoDbData_1.2.1

Does this mean i cannot use GenomicAlignments with R3.6.1? 3.6.0 does not exist for mac

thanks

ADD REPLY • link updated 4.6 years ago by Martin Morgan 25k • written 4.6 years ago by afadda • 0

0

Entering edit mode

Use BiocManager::valid() to test for whether your installation is correct or not. BiocManager replaces BiocInstaller.

ADD REPLY • link 4.6 years ago Martin Morgan 25k