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&dataset_id=0f5bae0d7db33d73&chrom=chrIIIFile '/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' ------------------------------------------------------------ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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