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 <nate(a)bx.psu.edu>
To: Liisa Koski <liisa.koski(a)dnalandmarks.ca>
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:
> 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
> 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
> I did do an update to the latest release yesterday...if that helps?
Is this a regular upload via a browser?
> Thanks in advance,
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