I'm trying to run bowtie2 in galaxy on my own centos installation to align paired end data to the hg19 reference. I get an out of memory error:
bowtie2 -p ${GALAXY_SLOTS:-4} -x /home/leon/ref_data/bowtie2/hg19/hg19 -1 /home/leon/genome_data/sra/ERR010982/ERR010982_1.fastq -2 /home/leon/genome_data/sra/ERR010982/ERR010982_2.fastq -I 0 -X 250 | samtools view -Su - | samtools sort -o - - > /home/leon/galaxy-dist/database/files/000/dataset_29.dat
Out of memory allocating the ebwt[] array for the Bowtie index. Please try again on a computer with more memory. Error: Encountered internal Bowtie 2 exception (#1) Command: /home/leon/galaxy-dist/dependency_dir/bowtie2/2.1.0/devteam/package_bowtie2_2_1
There is about 2 GB of free memory in the system, and virtual memory is disabled. Why is this happening? It seems like plenty of memory is available.
Thanks Jen! I took it up to 13GB of memory and it worked very well.
Please accept the answer so others can find it easily.