Problems to create GmapGenome - gmapR
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@lelemraposo-7775
Last seen 6.7 years ago
Brazil

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.

gmapR GmapGenome error create • 1.6k views
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@steve-lianoglou-2771
Last seen 19 hours ago
United States

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.

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@lelemraposo-7775
Last seen 6.7 years ago
Brazil

Thanks for your answer.

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

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I think it's just the amount of RAM your machine (virtual or real) has access to

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