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&am..." "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 langhorst@neb.commailto:langhorst@neb.com