Hello everybody,

can anybody help me?

I'm trying to create a GmapGenome but I always receive this error:

> fastaFile <- rtracklayer::FastaFile("/home/less/Downloads/HXB2_LosAlamos.fasta")
> seqref<- GmapGenome(fastaFile, create=TRUE)
-b flag not specified, so building with default base size of 12
Running /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//fa_coords   -o ./HXB2_LosAlamos.coords "/home/less/Downloads/HXB2_LosAlamos.fasta"
Opening file /home/less/Downloads/HXB2_LosAlamos.fasta
  Processed short contigs (<1000000 nt): .
============================================================
Contig mapping information has been written to file ./HXB2_LosAlamos.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//gmap_process  -c ./HXB2_LosAlamos.coords "/home/less/Downloads/HXB2_LosAlamos.fasta" | /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex  -d HXB2_LosAlamos -D . -A -s none
Reading coordinates from file ./HXB2_LosAlamos.coords
Logging contig K03455|HIVHXB2CG at K03455|HIVHXB2CG:1..9719 in genome HXB2_LosAlamos
Total genomic length = 9719 bp
Chromosome K03455|HIVHXB2CG has universal coordinates 1..9719
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 /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//gmap_process  -c ./HXB2_LosAlamos.coords "/home/less/Downloads/HXB2_LosAlamos.fasta" | /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex  -d HXB2_LosAlamos -F . -D . -G
Genome length is 9719 nt
Trying to allocate 912*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./HXB2_LosAlamos.coords
Writing contig K03455|HIVHXB2CG to universal coordinates 1..9719 in genome HXB2_LosAlamos
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./HXB2_LosAlamos.genomecomp | /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex -d HXB2_LosAlamos -U > ./HXB2_LosAlamos.genomebits
Running cat ./HXB2_LosAlamos.genomecomp | /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex -b 12 -k 15 -q 3  -d HXB2_LosAlamos -F . -D . -O
Offset compression types: gamma bitpack
Allocating 1073741825*4 bytes for offsets
Failed attempt to calloc 1073741825 x 4 bytes
Exception:  Allocation Failed  raised at indexdb-write.c:2890
Uncaught exception:  Allocation Failed  raised at indexdb-write.c:2890
Aborted (core dumped)
cat ./HXB2_LosAlamos.genomecomp | /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin//gmapindex -b 12 -k 15 -q 3  -d HXB2_LosAlamos -F . -D . -O  failed with return code 34304 at /home/less/R/x86_64-pc-linux-gnu-library/3.2/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: /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin/gmap_build --db=HXB2_LosAlamos --dir=/home/less/.local/share/gmap --kmer=15 --sort=none -B /home/less/R/x86_64-pc-linux-gnu-library/3.2/gmapR/usr/bin/ /home/less/Downloads/HXB2_LosAlamos.fasta

What's the problem?
Thanks so much!

Leticia.

If I had to guess -- burried in the errors you reported is this little nugget:

Failed attempt to calloc 1073741825 x 4 bytes
Exception:  Allocation Failed  raised at indexdb-write.c:2890
Uncaught exception:  Allocation Failed  raised at indexdb-write.c:2890
Aborted (core dumped)

Which suggests to me that the machine has ran out of RAM while trying to build the genome index.

Thanks for your answer.

I'm using Linux in a virtual machine. Do you think this could be influencing?