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=..." "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&d... '/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' ------------------------------------------------------------