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