Error Setting BAM Metadata
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? Thanks in advance, Liisa
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:
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
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: previously uploaded with no problems.
Traceback (most recent call last): File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py",
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 126, in run_job 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:
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@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:
participants (2)
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Liisa Koski -
Nate Coraor