Question: Failed in fetching reference genome in local instance
gravatar for chumho
4.0 years ago by
United States
chumho0 wrote:

Hi all,

(This question is for Centos 6.5 server, python 2.7, November 2014 version of Galaxy)

I've been trying to fetch mouse mm9 genome from UCSC through data manager without success. I'd followed Daniel's video demo "Managing Galaxy's built-in data" (Thank you Dan :)). So I installed data manager accordingly. In the reference genome data manager form, I selected mouse mm9 and UCSC's dbkey = mm9, and click "execute".

But I didn't see the job in history as mentioned in the video. Then I went to Admin/Data/Manage local data/view data manager jobs/reference genome fetching. I saw the job with status 'running'

The command line box showed this:

python /mnt/drive2/home/galaxy/shed_tools/ "/mnt/drive2/home/galaxy/galaxy-dist/database/files/000/dataset_33.dat" --dbkey_description 'Mouse July 2007 (NCBI37/mm9) (mm9)

I did 'ps -ef | grep galaxy", I saw these two jobs:

galaxy   20191 20128  0 13:40 ?        00:00:00 /bin/sh /mnt/drive2/home/galaxy/galaxy-dist/database/job_working_directory/000/25/

galaxy   20192 20191  0 13:40 ?        00:00:01 python /mnt/drive2/home/galaxy/shed_tools/ /mnt/drive2/home/galaxy/galaxy-dist/database/files/000/dataset_33.dat --dbkey_description Mouse July 2007 (NCBI37/mm9) (mm9)

I ran forever without producing anything as I checked database/files/000/dataset_33_files, only a zero-byte mm9.fa was created.

I also checked the i icon for the job detail. Both stdout and stderr showed 'none'.

Since the job is basically a python program, then I killed the above two tasks and ran directly at terminal as below:

$ cd galaxy/shed_tools/

$ python /mnt/drive2/home/galaxy/galaxy-dist/database/files/000/dataset_33.dat --dbkey_description 'Mouse July 2007 (NCBI37/mm9) (mm9)'

But I encountered import error

Traceback (most recent call last):

  File "", line 17, in <module>

    from galaxy.util.json import from_json_string, to_json_string

ImportError: No module named galaxy.util.json


I checked is in /mnt/drive2/home/galaxy/galaxy-dist/lib/galaxy/util/

So, would it be due to path problem?

Any idea? Appreciated.





software error galaxy • 1.2k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by chumho0
gravatar for chumho
4.0 years ago by
United States
chumho0 wrote:


Don't worry about it I figured out myself. The download process took incredible long time to complete (12 hours) which was unusual in my campus (ftp of the mouse genome normally takes <1hr). Also, I didn't know that I need to switch to other history in the history pane.

Thanks for everyone that had spent time in thinking about this issue.

ADD COMMENTlink written 4.0 years ago by chumho0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour