Question: Local Galaxy job delays: This job is waiting to run
1
gravatar for marp.p
8 days ago by
marp.p20
marp.p20 wrote:

Hi, I have been trying to run job(s) for all the day on Galaxy and they just hang with the "waiting to run" status. I did not have other jobs queued and form my admin log I found the error:

  Exception happened during processing of request from ('127.0.0.1', 46175) Traceback (most recent call last):   File "/mnt/galaxy/galaxy-app/.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 651, in __init__
    self.finish()   File "/usr/lib/python2.7/SocketServer.py", line 710, in finish
    self.wfile.close()   File "/usr/lib/python2.7/socket.py", line 279, in close
    self.flush()   File "/usr/lib/python2.7/socket.py", line 303, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe
ADD COMMENTlink modified 7 days ago • written 8 days ago by marp.p20
1

A few more details will help to troubleshoot the problem.

  • Are you running the most current release of Galaxy? Version 17.09?
  • What was the source? Github https://getgalaxy.org or ?
  • Have any advanced admin changes been made? (A cluster is in use, etc)
  • Have jobs ever run successfully or are these the first jobs to be run?
  • Do all tools stall at the queued stage or just some? Have you checked to make certain the tools and dependencies are installed correctly and completely?
ADD REPLYlink written 8 days ago by Jennifer Hillman Jackson23k

Hi, thanks for your answer!

I'm running my own instance of Galaxy on Amazon web Services EC2, managed by CloudMan (the most current release I can select is 17.05). I found that error message in the Galaxy log file in the CloudMan Admin panel. The jobs run successfully until two days ago, I hadn't similar problem before. Actually I'm trying to run FastQC, but I also made some tests with other tools (Trim Galore, Text manipulation... ). The tools I'm using and dependencies seems to be installed correctly and completely.

Thanks again

ADD REPLYlink modified 7 days ago • written 7 days ago by marp.p20
0
gravatar for marp.p
7 days ago by
marp.p20
marp.p20 wrote:

Update:

All the jobs are running successfully now, after I simply launched an instance with more memory (m4.2xlarge instead of m4.xlarge). The "Error" is still present in the log file, but it seems to not affect the jobs!

ADD COMMENTlink written 7 days ago by marp.p20
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