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!
Did you compile it on a different machine or something? GMAP is very sensitive to the architecture, because it uses a lot of assembly.
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.
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.
That did it, thanks!