This job failed for reasons that could not be determined.
Hi all Certain jobs fail on my cloud Galaxy instance with the error message in the subject line. No stderr or stdout is produced by the tool, at least it's not accessible from Galaxy. However the data seems to be there, in so far that I can view it (clicking on the eye) and download it using the floppy disk icon. The only thing I see (repeatedly) in my Galaxy logs is this: ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 46619) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/usr/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/usr/lib/python2.7/socket.py", line 283, in close self.flush() File "/usr/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- Does this look familiar to anyone? Thanks very much for any input Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
Hi Ulf I don't think the two things are connected which each other. In the logs of our local installation we see once in a while, lines like: File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe but without any errors or failed jobs associated. We consider those as harmless, temporary glitches in the web server part of galaxy. Sorry, not much help... Just one question for clarification, which might help others (with more cloud experience) to jump in: do the failed jobs occur randomly with any tool? or are they all coming from the same tool? Regards, Hans-Rudolf On 07/25/2016 12:48 PM, Ulf Schaefer wrote:
Hi all
Certain jobs fail on my cloud Galaxy instance with the error message in the subject line. No stderr or stdout is produced by the tool, at least it's not accessible from Galaxy. However the data seems to be there, in so far that I can view it (clicking on the eye) and download it using the floppy disk icon.
The only thing I see (repeatedly) in my Galaxy logs is this:
---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 46619) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/usr/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/usr/lib/python2.7/socket.py", line 283, in close self.flush() File "/usr/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ----------------------------------------
Does this look familiar to anyone?
Thanks very much for any input Ulf
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ 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: https://lists.galaxyproject.org/
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Hi Hans-Rudolf It happens with a number of tools. I will need to do some more testing to see if I can narrow it down further. Thanks for your help Ulf On 26/07/16 07:13, Hans-Rudolf Hotz wrote:
Hi Ulf
I don't think the two things are connected which each other. In the logs of our local installation we see once in a while, lines like:
File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe
but without any errors or failed jobs associated. We consider those as harmless, temporary glitches in the web server part of galaxy.
Sorry, not much help...
Just one question for clarification, which might help others (with more cloud experience) to jump in: do the failed jobs occur randomly with any tool? or are they all coming from the same tool?
Regards, Hans-Rudolf
On 07/25/2016 12:48 PM, Ulf Schaefer wrote:
Hi all
Certain jobs fail on my cloud Galaxy instance with the error message in the subject line. No stderr or stdout is produced by the tool, at least it's not accessible from Galaxy. However the data seems to be there, in so far that I can view it (clicking on the eye) and download it using the floppy disk icon.
The only thing I see (repeatedly) in my Galaxy logs is this:
---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 46619) Traceback (most recent call last): File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/usr/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/usr/lib/python2.7/socket.py", line 283, in close self.flush() File "/usr/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ----------------------------------------
Does this look familiar to anyone?
Thanks very much for any input Ulf
**************************************************************************
The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
participants (2)
-
Hans-Rudolf Hotz -
Ulf Schaefer