Local Galaxy error in Create DBKey and Reference Genome

Question: Local Galaxy error in Create DBKey and Reference Genome

6 months ago by

South Korea

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 • 283 views

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modified 5 months ago by Bjoern Gruening ♦ 5.1k • written 6 months ago by Seongmin Choi • 20

5 months ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k 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 COMMENT • link written 5 months ago by Bjoern Gruening ♦ 5.1k

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

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

5 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k

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