Hello Jose,

It sounds as if the job is running out of memory. Since you are already working on a cloud, I am going to make the assumption that you have explored the server options with high-capacity memory there. But if not, that is one place to start, in particular your EC2 Instance type, as described on this wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud/CapacityPlanning


However, even if that was an option, you may want to consider running your in data through in another way - by running smaller jobs, then merging results, to avoid the large jobs. For example, in the last step where you join to the "full BamHI delimited bin file", instead join to groups of bins in that file (perhaps grouped by chromosome), then combine the results to produce the full output.

Hopefully this helps provide some options,

Jen
Galaxy team

On 5/4/12 2:18 PM, Xianrong Wong wrote:
Hello,
         I have binned the mouse genome into fragments based on
restriction enzyme cut sites.  So each bin is a fragment flanked by say
BamHI.  The output file is in the interval format: chr# start and end
coordinates of each bin.  I want to count how many times each bin has
reads that align to it.  I mapped my reads using bowtie and generated a
dataset (interval format) for the aligned reads.  I then used join in
"operate on genomic intervals" and asked it to return intervals that
innerjoin the "bin file".  The subsequent steps involve grouping and
counting and then joining back to the 1st dataset (BamHI delimited
bins).  I have tried this workflow on small datasets and it worked.
However when I subject my full alignment file and full BamHI delimited
bin file, the tool fails.  I am doing this on cloud.  Any advice would
be appreciated!

Jose


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