The problem was a lack of memory to execute the join function
of bx.intervals.operations.join.
I tested the joining dataset in several machines with different memory
sizes. It was only succeeded on the 16gb memory system.
Also I observed that the joining two datasets,
galaxy-dist/tools/new_operations/gops_join.py, used around 10gb memory for
the computation.
I used 37 mega bytes exons and 185 mega bytes repeats.
Other than 16gb memory system, it was terminated like 'Killed' when it was
running of memory. I suspect the join function might have a memory 'leak'.
I just wanted to update what I found out.
Thanks,
Hyungro
On Mon, Jul 1, 2013 at 10:57 AM, Hyungro Lee wrote:
> Hi,
>
> I am new here and trying to use the Galaxy toolkit for my project on the
> Windows Azure cloud environment. The thing is I got errors when I tested
> the 101 example on my local machine, so I looked 'stderr' via View details
> and it only showed 'Killed' which is not much information to do debugging.
> I looked web logs and found out the execution is : 'python
> /home/.../galaxy-dist/tools/new_operations/gops_join.py
> /home/.../galaxy-dist/database/files/000/dataset_1.dat
> /home/.../galaxy-dist/database/files/000/dataset_2.dat
> /home/.../galaxy-dist/database/files/000/dataset_3.dat -1 1,2,3,6 -2
> 1,2,3,6 -m 1 -f none' which is about joining two datasets. I believe the
> input data sets and the parameters are okay since I tested it on the galaxy
> public server.
>
> To get more debugging information, I tried to run the job on shell but got
> same results, Killed. I was wondering is there a way that I can get more
> information about the execution of the tool other than looking into the
> source code line by line? That might be helpful to figure out what I am
> doing wrong for this test.
>
> Thanks,
> Hyungro
>
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