6:06 p.m.
Hello,
I am getting consistent breakage for a C. Cerevisiae reference and mapped dataset when
trying to visualize the mapped data in Trackster. I'm running the latest galaxy-dist
and Trackster appears to be generally working since I added a couple of reference genomes
and users were able to visualize their data. I just rebuilt all relevant references for
the sacCer3 (dbkey) genome by concatenating the UCSC chromosome fasta files and building
both 2bit file and the bowtie index from the resulting fasta file. The reference genome
comes up in the Trackster as I can see the sequence. However, adding a track from the
bowtie-mapped data freezes at the "building index" stage and selecting a
chromosome in Trackster produces an immediate traceback. Logs are below.
Thanks,
Alex
10.25.137.177 - - [01/Mar/2012:12:56:50 -0400] "GET
/tracks/converted_datasets_state?hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII
HTTP/1.1" 500 -
"http://galaxy.hpc.ufl.edu/tracks/browser?dataset_id=0f5bae0d7db33d73&id=9b03f356ffec3bf6"
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_3) AppleWebKit/535.11 (KHTML, like
Gecko) Chrome/17.0.963.56 Safari/535.11"Error - <type
'exceptions.EOFError'>:URL:
http://galaxy.hpc.ufl.edu/tracks/converted_datasets_state?hda_ldda=hda&am...
'/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__ app_iter = self.application(environ, start_response)File
'/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in
__call__ return self.application(environ, start_response)File
'/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in
__call__ return self.app( environ, start_response )File
'/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in
__call__ return self.application(environ, start_response)File
'/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__ body =
method( trans, **kwargs )File
'/galaxy/run/prod/lib/galaxy/web/framework/__init__.py', line 67 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )File
'/galaxy/run/prod/lib/galaxy/web/controllers/tracks.py', line 546 in
converted_datasets_state if not indexer.has_data( chrom ):File
'/galaxy/run/prod/lib/galaxy/visualization/tracks/data_providers.py', line 566 in
has_data st = summary_tree_from_file( self.converted_dataset.file_name )File
'/galaxy/run/prod/lib/galaxy/visualization/tracks/summary.py', line 92 in
summary_tree_from_file return cPickle.load(open(filename, "rb"))EOFError:
CGI Variables
-------------
QUERY_STRING: 'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0x6323cd0>
paste.cookies: (<SimpleCookie:
__utma='239163719.1605318534.1329425338.1330006360.1330438487.6'
__utmc='239163719'
__utmz='239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)'
auth_probe='1'
auth_tkt='ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D'
galaxysession='86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe'>,
'galaxysession=86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe;
auth_probe=1; __utma=239163719.1605318534.1329425338.1330006360.1330438487.6;
__utmc=239163719;
__utmz=239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided);
auth_tkt=ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
0x631c890>
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x1314b10>
paste.parsed_querystring: ([('hda_ldda', 'hda'), ('dataset_id',
'0f5bae0d7db33d73'), ('chrom', 'chrIII')],
'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII')
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
webob._parsed_query_vars: (MultiDict([('hda_ldda', 'hda'),
('dataset_id', '0f5bae0d7db33d73'), ('chrom', 'chrIII')]),
'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII')
wsgi process: 'Multithreaded'
------------------------------------------------------------
6:28 p.m.
Alex,
Generally cPickle errors when loading summary trees are a result of indexing gone bad.
Here are a couple notes that should save you some work:
*your bowtie indices and 2bit files do not need to be rebuilt; they are not generating
these errors;
*converting your SAM files to BAM may provide a short-term solution; Trackster SAM support
is new and not well tested yet.
Finally, there are many Trackster fixes in galaxy-central, and I believe some of them may
solve your issues. For SAM datasets, your best bet is to either (a) try visualizing the
datasets with -central or (b) wait for the upcoming (planned for next week) -dist update.
If you're still getting errors with the new code base, let us know.
Thanks,
J.
I'm running the latest galaxy-dist and Trackster appears to be
generally working since I added a couple of reference genomes and users were able to
visualize their data. I just rebuilt all relevant references for the sacCer3 (dbkey)
genome by concatenating the UCSC chromosome fasta files and building both 2bit file and
the bowtie index from the resulting fasta file. The reference genome comes up in the
Trackster as I can see the sequence. However, adding a track from the bowtie-mapped data
freezes at the "building index" stage and selecting a chromosome in Trackster
produces an immediate traceback. Logs are below.
Thanks,
Alex
10.25.137.177 - - [01/Mar/2012:12:56:50 -0400] "GET
/tracks/converted_datasets_state?hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII
HTTP/1.1" 500 -
"http://galaxy.hpc.ufl.edu/tracks/browser?dataset_id=0f5bae0d7db33d73&id=9b03f356ffec3bf6"
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_3) AppleWebKit/535.11 (KHTML, like
Gecko) Chrome/17.0.963.56 Safari/535.11"Error - <type
'exceptions.EOFError'>:URL:
http://galaxy.hpc.ufl.edu/tracks/converted_datasets_state?hda_ldda=hda&am...
'/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__ app_iter = self.application(environ, start_response)File
'/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in
__call__ return self.application(environ, start_response)File
'/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in
__call__ return self.app( environ, start_response )File
'/galaxy/run/prod/eggs/Paste!
-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return
self.application(environ, start_response)File
'/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__ body =
method( trans, **kwargs )File
'/galaxy/run/prod/lib/galaxy/web/framework/__init__.py', line 67 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )File
'/galaxy/run/prod/lib/galaxy/web/controllers/tracks.py', line 546 in
converted_datasets_state if not indexer.has_data( chrom ):File
'/galaxy/run/prod/lib/galaxy/visualization/tracks/data_providers.py', line 566 in
has_data st = summary_tree_from_file( self.converted_dataset.file_name )File
'/galaxy/run/prod/lib/galaxy/visualization/tracks/summary.py', line 92 in
summary_tree_from_file return cPickle.load(open(filename, "rb"))EOFError:
CGI Variables
-------------
QUERY_STRING: 'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0x6323cd0>
paste.cookies: (<SimpleCookie:
__utma='239163719.1605318534.1329425338.1330006360.1330438487.6'
__utmc='239163719'
__utmz='239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)'
auth_probe='1'
auth_tkt='ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D'
galaxysession='86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe'>,
'galaxysession=86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe;
auth_probe=1; __utma=239163719.1605318534.1329425338.1330006360.1330438487.6;
__utmc=239163719;
__utmz=239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided);
auth_tkt=ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
0x631c890>
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x1314b10>
paste.parsed_querystring: ([('hda_ldda', 'hda'), ('dataset_id',
'0f5bae0d7db33d73'), ('chrom', 'chrIII')],
'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII')
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
webob._parsed_query_vars: (MultiDict([('hda_ldda', 'hda'),
('dataset_id', '0f5bae0d7db33d73'), ('chrom', 'chrIII')]),
'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII')
wsgi process: 'Multithreaded'
------------------------------------------------------------
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3777
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3777
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galaxy-dev@lists.galaxyproject.org
1 comments
2 participants
participants (2)
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Jeremy Goecks -
Oleksandr Moskalenko