On Jan 25, 2012, at 2:43 PM, Liisa Koski wrote: > Hello, > I am trying to upload BAM files (by pasting a URL) to my history(or > DataLibrary) and get the following error. These are bam files which I had > previously uploaded with no problems. > > Traceback (most recent call last): > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line > 126, in run_job > job_wrapper.finish( stdout, stderr ) > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 618, > in finish > dataset.set_meta( overwrite = False ) > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 874, > in set_meta > return self.datatype.set_meta( self, **kwd ) > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/datatypes/binary.py", line > 179, in set_meta > raise Exception, "Error Setting BAM Metadata: %s" % stderr > Exception: Error Setting BAM Metadata: [bam_header_read] EOF marker is > absent. The input is probably truncated. > [bam_header_read] invalid BAM binary header (this is not a BAM file) > > I ran bamtools on the unix command line to see if there was anything wrong > with the file(s) but nothing. I tried uploading different bam files from > other projects and get the same error. > > I did do an update to the latest release yesterday...if that helps?
Hi Liisa, Is this a regular upload via a browser? --nate > > Thanks in advance, > Liisa > ___________________________________________________________ > 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/ > ___________________________________________________________ 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/
