Question: Trackster Error On Dbkeys
0
Aarthi Mohan • 10 wrote:
Hi all,
I am setting up galaxy on a server running CentOS 6.5.
I found that Trackster application hits me with an error
"Could not load chroms for this dbkey: PF3D7", when I try "add new
track"
from Visualization.
I am working with Plasmodium falciparum (PF3d7) genome, and I followed
the
instruction for setting visualization from "
https://wiki.galaxyproject.org/Visualization%20Setup" and placed the
2bit,
len files in the appropriate path.
I have also made sure the genome build is present in the builds.txt
under
tool-data/shared/ucsc.
For a test, I have the human chromosomes len files and Trackster loads
it
without any problem.
Any suggestion would greatly help me.
Thanks
RT
Log file:
127.0.0.1 - - [10/Apr/2014:12:29:44 +0800] "GET
/visualization/trackster
HTTP/1.1" 200 - "http://127.0.0.1:8081/" "Mozilla/5.0 (X11; Linux
x86_64;
rv:24.0) Gecko/20100101 Firefox/24.0"
127.0.0.1 - - [10/Apr/2014:12:29:45 +0800] "GET
/api/genomes?chrom_info=True HTTP/1.1" 200 - "
http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11;
Linux
x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
127.0.0.1 - - [10/Apr/2014:12:29:51 +0800] "GET
/api/genomes/PF3D7?low=0&num=100 HTTP/1.1" 500 - "
http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11;
Linux
x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
Error - <type 'exceptions.indexerror'="">: list index out of range
URL: http://127.0.0.1:8081/api/genomes/PF3D7?low=0&num=100
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
return self.handle_request( environ, start_response )
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
body = method( trans, **kwargs )
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/lib/galaxy/web/framework/__init__.py',
line 78 in decorator
return to_json_string( func( self, trans, *args, **kwargs ) )
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/lib/galaxy/webapps/galaxy/api/genomes.py',
line 42 in show
rval = self.app.genomes.chroms( trans, dbkey=id, num=num,
chrom=chrom,
low=low )
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/lib/galaxy/visualization/genomes.py',
line 292 in chroms
rval = genome.to_dict( num=num, chrom=chrom, low=low )
File
'/data/maarthi/Galaxy/Test/galaxy-
dist/lib/galaxy/visualization/genomes.py',
line 153 in to_dict
chroms[ fields[0] ] = int( fields[1] )
IndexError: list index out of range
CGI Variables
CONTENT_LENGTH: '0'
HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_COOKIE:
'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d
9de0824b221b12b4bbc465351'
HTTP_HOST: '127.0.0.1:8081'
HTTP_REFERER: 'http://127.0.0.1:8081/visualization/trackster'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:24.0)
Gecko/20100101
Firefox/24.0'
HTTP_X_REQUESTED_WITH: 'XMLHttpRequest'
PATH_INFO: '/api/genomes/PF3D7'
QUERY_STRING: 'low=0&num=100'
REMOTE_ADDR: '127.0.0.1'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8081'
SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
application: <paste.recursive.recursivemiddleware object="" at="" 0x6b37cd0="">
is_api_request: True
paste.cookies: (<simplecookie: galaxysession="c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d
9de0824b221b12b4bbc465351">,
'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d
9de0824b221b12b4bbc465351')
paste.expected_exceptions: [<class 'paste.httpexceptions.httpexception'="">]
paste.httpexceptions: <paste.httpexceptions.httpexceptionhandler object="" at="" 0x748eed0="">
paste.httpserver.thread_pool: <paste.httpserver.threadpool object="" at="" 0x795c310="">
paste.parsed_querystring: ([('low', '0'), ('num', '100')],
'low=0&num=100')
paste.recursive.forward: <paste.recursive.forwarder from=""/>
paste.recursive.include: <paste.recursive.includer from=""/>
paste.recursive.include_app_iter: <paste.recursive.includerappiter from=""/>
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'c1be491ec06811e39ed60025905a9e10'
webob._parsed_query_vars: (MultiDict([('low', '0'), ('num',
'100')]),
'low=0&num=100')
wsgi process: 'Multithreaded'