Re: [galaxy-dev] Error Setting BAM Metadata

Yes it is....and my galaxy is up to date.

Thanks, Liisa From: Nate Coraor <nate(a)bx.psu.edu&gt; To: Liisa Koski <liisa.koski(a)dnalandmarks.ca&gt; Cc: galaxy-dev(a)lists.bx.psu.edu Date: 01/30/2012 03:07 PM Subject: Re: [galaxy-dev] Error Setting BAM Metadata 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/ >