Yes it is....and my galaxy is up to date.
Thanks, Liisa
From: Nate Coraor nate@bx.psu.edu To: Liisa Koski liisa.koski@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 ___________________________________________________________ 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: