172.17.130.203 - - [19/Apr/2013:10:31:20 -0400] "GET /api/datasets/dd61915e24aa3fd0?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr1 HTTP/1.1" 200 - "http://galaxy.neb.com/visualization/trackster?dataset_id=b8edc02014d74add&hda_ldda=hda"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_3) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.65 Safari/537.31" galaxy.webapps.galaxy.api.datasets ERROR 2013-04-19 10:31:21,775 Error in dataset API at listing contents: unpack requires a string argument of length 4: unpack requires a string argument of length 4 Traceback (most recent call last): File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 41, in show is_true( kwd.get( 'retry', False ) ) ) File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 1037, in has_data f, bbi = self._get_dataset() File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 1170, in _get_dataset return f, BigWigFile(file=f) File "bigwig_file.pyx", line 127, in bx.bbi.bigwig_file.BigWigFile.__init__ (lib/bx/bbi/bigwig_file.c:3011) File "bbi_file.pyx", line 119, in bx.bbi.bbi_file.BBIFile.__init__ (lib/bx/bbi/bbi_file.c:3508) File "bbi_file.pyx", line 129, in bx.bbi.bbi_file.BBIFile.open (lib/bx/bbi/bbi_file.c:3660) File "/mnt/ngswork/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg/bx/misc/binary_file.py", line 30, in __init__ if struct.unpack( ">I", bytes )[0] == magic: error: unpack requires a string argument of length 4
Is this a bug or have I done something unexpected? I'm trying to use the trackbrowser to visualize some bam files that I aligned to a genome that I had to install manually (Zea_mays_B73_RefGen_v2), maybe i've screwed something up. I was initially able to see some reads, but after reverting to the sample datatypes file and restarting galaxy i can't see anything anymore. I also added a .2bit file to twobit.locs Zea_mays_AGPv2 /mnt/ngswork/galaxy/galaxy-dist/tool-data/genome/Zea_mays_AGPv2/seq/Zea_mays_AGPv2.2bit maybe that's related... I've tried copying the bams to a new history - and they seem to be reindexing as a result, but I still see no reads. Any ideas? Brad -- Brad Langhorst [email protected]<mailto:[email protected]>
___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
