Question: Local Galaxy error in Create DBKey and Reference Genome
0
gravatar for Seongmin Choi
5 months ago by
South Korea
Seongmin Choi20 wrote:

Hi all,

I've setup a local galaxy container using docker, using https://github.com/bgruening/docker-galaxy-stable.
When I used "Create DBKey and Reference Genome" (Galaxy version 0.0.2), it was killed with the following error:

An error occurred with this dataset:
Fatal error: Exit code 137 ()
/export/galaxy-central/database/job_working_directory/000/8/tool_script.sh: line 9:  3222 Killed                  python '/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bb

My memory usage soared as I was using this, so I am currently assuming that it's a memory problem. However, because the memory of my PC (32G) was enough to run almost all tools except for STAR, I thought I'll have no problems using Galaxy.

I ran the tool using an existing dbkey (hg_g1k_b37), and all I changed was sorting the chromosome names by "GATK".

Am I doing something wrong here? I'll appreciate any help you guys could give me. Thanks. :)

error galaxy local • 264 views
ADD COMMENTlink modified 5 months ago by Bjoern Gruening5.1k • written 5 months ago by Seongmin Choi20
1
gravatar for Bjoern Gruening
5 months ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

I would also recommend to not sort with the GATK option. Also try a very tiny genome if you can. It all sounds to me that you are running out of memory. Have you looked at using the CVMFS reference genome, which the community is offering?

ADD COMMENTlink written 5 months ago by Bjoern Gruening5.1k

FAQ for CVMFS https://galaxyproject.org/admin/reference-data-repo/

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

Avoid the GATK sorting option - it is known to be problematic and uses much more memory.

Try using just the formatting from the source. If that works, you can test the other options and if they fail, then you'll know the tool is hitting a memory problem. This is a very large genome.

If you need special sorting or reformatting in the fasta (to be GATK format compliant), you can always do that yourself first, then upload the custom fasta to Galaxy and create an index from it directly from the history. The currently wrapped GATK tools for Galaxy are considered deprecated, but updates are being developed again now.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
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