gmapR failure to build TP53Genome in osx
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jls2282 • 0
@jls2282-7127
Last seen 7.3 years ago
United States

Unable to follow examples with gmapR failing at the stage of gmapR::TP53Which()

 

 

.libPaths('~/Dropbox/R_packages/library/')
library(gmapR)
gmapR::TP53Genome()

Fails with following message:

'select()' returned 1:1 mapping between keys and columns
-b flag not specified, so building with default base size of 12
Running /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//fa_coords   -o ./TP53_demo_3.2.2.coords "/var/folders/v0/1n6fvj6n2m5dc8hys1fgjbkw0000gn/T//RtmpyTdJ6p/file9dead7804d4"
Opening file /var/folders/v0/1n6fvj6n2m5dc8hys1fgjbkw0000gn/T//RtmpyTdJ6p/file9dead7804d4
  Contig TP53: concatenated at chromosome end: TP53:1..2025772 (length = 2025772 nt)

============================================================
Contig mapping information has been written to file ./TP53_demo_3.2.2.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmap_process  -c ./TP53_demo_3.2.2.coords "/var/folders/v0/1n6fvj6n2m5dc8hys1fgjbkw0000gn/T//RtmpyTdJ6p/file9dead7804d4" | /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmapindex  -d TP53_demo_3.2.2 -D . -A -s none
Reading coordinates from file ./TP53_demo_3.2.2.coords
Logging contig TP53 at TP53:1..2025772 in genome TP53_demo_3.2.2
Total genomic length = 2025772 bp
Chromosome TP53 has universal coordinates 1..2025772
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Running /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmap_process  -c ./TP53_demo_3.2.2.coords "/var/folders/v0/1n6fvj6n2m5dc8hys1fgjbkw0000gn/T//RtmpyTdJ6p/file9dead7804d4" | /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmapindex  -d TP53_demo_3.2.2 -F . -D . -G
Genome length is 2025772 nt
Trying to allocate 189918*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./TP53_demo_3.2.2.coords
Writing contig TP53 to universal coordinates 1..2025772 in genome TP53_demo_3.2.2
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./TP53_demo_3.2.2.genomecomp | /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmapindex -d TP53_demo_3.2.2 -U > ./TP53_demo_3.2.2.genomebits
Running cat ./TP53_demo_3.2.2.genomecomp | /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmapindex -b 12 -k 15 -q 3  -d TP53_demo_3.2.2 -F . -D . -O 
Offset compression types: gamma bitpack
Allocating 1073741825*4 bytes for offsets
Indexing offsets of oligomers in genome TP53_demo_3.2.2 (15 bp every 3 bp), position 0
Writing 1073741825 offsets compressed via gammas to file with total of 675253 k-mers...Checking gammas...done
Writing 1073741825 offsets compressed via bitpack to file with total of 675253 k-mers...sh: line 1: 40483 Done                    cat ./TP53_demo_3.2.2.genomecomp
     40484 Illegal instruction: 4  | /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmapindex -b 12 -k 15 -q 3 -d TP53_demo_3.2.2 -F . -D . -O
cat ./TP53_demo_3.2.2.genomecomp | /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin//gmapindex -b 12 -k 15 -q 3  -d TP53_demo_3.2.2 -F . -D . -O  failed with return code 33792 at /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin/gmap_build line 249.
Error in .gmap_build(db = genome(genome), dir = path(directory(genome)),  : 
  system call returned a non-0 status: /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin/gmap_build --db=TP53_demo_3.2.2 --dir=/Users/JS/.local/share/gmap --kmer=15 --sort=none -B /Users/JS/Dropbox/R_packages/library/gmapR/usr/bin/ /var/folders/v0/1n6fvj6n2m5dc8hys1fgjbkw0000gn/T//RtmpyTdJ6p/file9dead7804d4

 

sessionInfo()

 

R version 3.3.1 (2016-06-21)
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] gmapR_1.16.0         Rsamtools_1.26.1     Biostrings_2.42.1    XVector_0.14.0       GenomicRanges_1.26.1 GenomeInfoDb_1.10.1  IRanges_2.8.1       
[8] S4Vectors_0.12.1     BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8                             AnnotationDbi_1.36.0                    GenomicAlignments_1.10.0               
 [4] zlibbioc_1.20.0                         BiocParallel_1.8.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [7] BSgenome_1.42.0                         lattice_0.20-34                         BSgenome.Hsapiens.UCSC.hg19_1.4.0      
[10] org.Hs.eg.db_3.4.0                      tools_3.3.1                             grid_3.3.1                             
[13] SummarizedExperiment_1.4.0              Biobase_2.34.0                          DBI_0.5-1                              
[16] digest_0.6.10                           Matrix_1.2-7.1                          rtracklayer_1.34.1                     
[19] bitops_1.0-6                            RCurl_1.95-4.8                          biomaRt_2.30.0                         
[22] memoise_1.0.0                           RSQLite_1.1                             GenomicFeatures_1.26.0                 
[25] XML_3.98-1.5                            VariantAnnotation_1.20.2               

 

 

Thanks for any help!

 

 

 

gmapR • 1.2k views
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Did you compile it on a different machine or something? GMAP is very sensitive to the architecture, because it uses a lot of assembly.

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Thanks for the info. In fact the same R library (shared on Dropbox) is used by two different machines. But I tried to uninstall gmapR and reinstall it on the same machine and did not fix the problem.

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Are you using the binary version of the package? There may be an incompatibility between the Bioc build machine and your computer. Please try installing it from source.

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That did it, thanks!

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