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 - '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/Pas!
te!
> -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.cookies: ( __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: []
> paste.httpexceptions: 0x631c890>
> paste.httpserver.thread_pool: 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.include:
> paste.recursive.include_app_iter:
> paste.recursive.script_name: ''
> paste.throw_errors: True
> webob._parsed_query_vars: (MultiDict([('hda_ldda', 'hda'), ('dataset_id',
> '0f5bae0d7db33d73'), ('chrom', 'chrIII')]),
> 'hda_ldda=hda&datase
