On Feb 3, 2012, at 3:14 PM, Liisa Koski wrote:
Yes it is....and my galaxy is up to date.
Hi Liisa,
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.
--nate
Thanks,
Liisa
From: Nate Coraor <nate(a)bx.psu.edu>
To: Liisa Koski <liisa.koski(a)dnalandmarks.ca>
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
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