gmapR fills my tmp directory
1
0
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@seantaylor-7638
Last seen 3.4 years ago
United States

I am attempting to create a GmapGenome index for hg19. Here is the code I am using:

library(BSgenome.Hsapiens.UCSC.hg19)
gmapGenomePath <- '/data/staylo/ref/ucsc/hg19/genome/gsnap/'
gmapGenomeDirectory <- GmapGenomeDirectory(gmapGenomePath, create=TRUE)
hg19 <- GmapGenome(genome=Hsapiens,
                   directory=gmapGenomeDirectory,
                   name='hg19',
                   create=TRUE, k=12L
                   )

The code exits with non-0 status: 

Writing 16777217 offsets to file with total of 965773859 k-mers...done
Running cat ./hg19.genomecomp | /home/staylo/R/x86_64-redhat-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d hg19 -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is hg19.ref123offsets
  Positions file is hg19.ref123positions
cat: write error: Broken pipe
sh: line 1:  9040 Done(1)                 cat ./hg19.genomecomp
      9041 Segmentation fault      (core dumped) | /home/staylo/R/x86_64-redhat-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3 -d hg19 -F . -D . -P
cat ./hg19.genomecomp | /home/staylo/R/x86_64-redhat-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d hg19 -F . -D . -P failed with return code 35584 at /home/staylo/R/x86_64-redhat-linux-gnu-library/3.2/gmapR/usr/bin/gmap_build line 259.
Error in .gmap_build(db = genome(genome), dir = path(directory(genome)),  : 
  system call returned a non-0 status: /home/staylo/R/x86_64-redhat-linux-gnu-library/3.2/gmapR/usr/bin/gmap_build --db=hg19 --dir=/data/staylo/ref/ucsc/hg19/genome/gsnap --kmer=12 --sort=none --circular=chrM -B /home/staylo/R/x86_64-redhat-linux-gnu-library/3.2/gmapR/usr/bin/ /tmp/RtmpsJnTvJ/gmap_build_fasta1efb63a8be94

 

I believe this is because it has filled up my tmp directory which is currently only 5GB on the system I am using. If I index something smaller, say chrX or even chr2, the code completes. I am currently working with our IT to increase the size of tmp. But in the mean time, I was wondering if there was an argument I could pass that would allow me to specify a different location for tmp, for instance to a larger data partition. 

Thanks,

Sean

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.38.0                   rtracklayer_1.30.1                dplyr_0.4.3                      
 [5] Rbowtie_1.10.0                    ShortRead_1.28.0                  GenomicAlignments_1.6.1           BiocParallel_1.4.3               
 [9] sangerseqR_1.6.0                  seqTools_1.4.1                    zlibbioc_1.16.0                   sagenhaft_1.40.0                 
[13] SparseM_1.7                       gmapR_1.12.0                      VariantAnnotation_1.16.4          Rsamtools_1.22.0                 
[17] SummarizedExperiment_1.0.1        Biobase_2.30.0                    GenomicRanges_1.22.2              GenomeInfoDb_1.6.1               
[21] msa_1.2.1                         Biostrings_2.38.2                 XVector_0.10.0                    IRanges_2.4.6                    
[25] S4Vectors_0.8.5                   BiocGenerics_0.16.1              

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2            RColorBrewer_1.1-2     futile.logger_1.4.1    GenomicFeatures_1.22.7 bitops_1.0-6           futile.options_1.0.0  
 [7] tools_3.2.2            biomaRt_2.26.1         digest_0.6.8           lattice_0.20-33        RSQLite_1.0.0          shiny_0.12.2          
[13] DBI_0.3.1              hwriter_1.3.2          grid_3.2.2             R6_2.1.1               AnnotationDbi_1.32.3   XML_3.98-1.3          
[19] latticeExtra_0.6-26    magrittr_1.5           lambda.r_1.1.7         htmltools_0.2.6        assertthat_0.1         xtable_1.8-0          
[25] mime_0.4               httpuv_1.3.3           RCurl_1.95-4.7     
gmapr gmapgenome • 834 views
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@michael-lawrence-3846
Last seen 7 weeks ago
United States

Should be able to set your TMPDIR environment variable.

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Thought of that and checked with my IT support, but that environment variable is shared globally by the other users, so it would reroute more than I bargained for. If that is the only solution, then I can work with our IT support to setup a bigger tmp location. I was hoping there might be a software solution where I could specify it as a one-off for just this command. 

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You can set that variable at the process level with Sys.setenv()

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Tried that too and kept getting the old tmp directory. I guess I will have to wait for IT to build a bigger tmp.

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Sorry, it looks like you need to set that when R is started. So just start R at the shell with:

TMPDIR="/my/tmp/dir" R
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Aha! I had tried that as well with no luck, but I think I may have been pointing it to a directory that was not writable. Once I pointed it to a valid location it started to work and I was able to complete the indexing. Thanks for the help!

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