On Feb 3, 2012, at 3:14 PM, Liisa Koski wrote:
> Yes it is....and my galaxy is up to date.
Sorry for not getting back to you. Did you ever figure out what was up with
this? Since you're pasting a URL, I'm wondering if the URL fetch is failing.
> From: Nate Coraor <n...@bx.psu.edu>
> To: Liisa Koski <liisa.ko...@dnalandmarks.ca>
> Cc: email@example.com
> 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?
> > Thanks in advance,
> > Liisa
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