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

Thanks,
Liisa




From:
Nate Coraor <n...@bx.psu.edu>
To:
Liisa Koski <liisa.ko...@dnalandmarks.ca>
Cc:
galaxy-dev@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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