Hi Enis,

THANK YOU!!!

I see that my "filter pileup on data" step is running. Is this the same 
analysis that was running before or did it relauch when you restarted Galaxy? I 
just don't know if the analysis would be compromised.

Thanks again to you and the whole Galaxy team.

Best,
Mike

--- On Tue, 4/12/11, Enis Afgan <eaf...@emory.edu> wrote:

From: Enis Afgan <eaf...@emory.edu>
Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
To: "Mike Dufault" <dufau...@yahoo.com>
Cc: "Anton Nekrutenko" <an...@bx.psu.edu>, galaxy-u...@bx.psu.edu
Date: Tuesday, April 12, 2011, 9:16 PM

Ahh, for some reason cloudman is thinking Galaxy is not 'running' but still 
'starting' and has thus not enabled the given button. To access the analysis, 
in your browser, just delete the '/cloud' part of the URL and that should load 
Galaxy.


Sorry about the confusion,Enis

On Tue, Apr 12, 2011 at 9:12 PM, Mike Dufault <dufau...@yahoo.com> wrote:


Hi Enis,

Thanks for looking into this.



>From the Galaxy Cloudman Console, I can see that it was restarted from the log 
>(thanks), but the "Access Galaxy" choice is still grayed out and I don't know 
>how to access the Analysis window.

Is there a way back into my analysis?



Thanks,
Mike



--- On Tue, 4/12/11, Enis Afgan <eaf...@emory.edu> wrote:



From: Enis Afgan <eaf...@emory.edu>
Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
To: "Mike Dufault" <dufau...@yahoo.com>


Cc: "Anton Nekrutenko" <an...@bx.psu.edu>, galaxy-u...@bx.psu.edu
Date: Tuesday, April 12, 2011, 8:55 PM



Hi Mike, Try accessing your Galaxy instance now.
 It should be ok.
The link in your email contained the IP for your instance so I took the liberty 
of restarting Galaxy and that brought it back up. There seems to have been an 
issue with Galaxy accessing its database and that resulted in Galaxy crashing. 
We'll look into why that happened in the first place but should be ok now. 




Let me know if you have any more trouble,Enis

On Tue, Apr 12, 2011 at 2:49 PM, Mike Dufault <dufau...@yahoo.com> wrote:




Hello Galaxy Staff,





My data has been running on the Amazon EC2 for just over 24hrs. I have not 
closed any windows and my Exome analysis made it all the way through to filter 
on Pile up. I have two tabs for this instance. One is the Galaxy Cloudman 
Console and the other is the tab where I perform the analysis, load data, 
history etc.





Anyway, I went to add a step to the work flow and the screen "Welcome Galaxy to 
the Cloud" screen along with the information "There is no Galaxy instance 
running on this host, or the Galaxy instance
 is not responding.  To manage Galaxy on this host, please use the Cloud 
Console."

What happened???

When I go back to the Galaxy Cloudman Console, it shows that my instance is 
still running along with the four cores, the Cluster log is below. AWS also 
shows that my instance is running.





Will the work flow finish? Can I get my data? How? 

I tried to re-access the analysis page by selecting "Access Galaxy" from the 
"Galaxy Cloudman Console" but it sends me to the same "Welcome page." 





Is there a way to get back into the analysis page?

Please help!!!

Thanks,
Mike

The cluster log shows:

        13:05:24 - Master starting13:05:25 - Completed initial cluster 
configuration.13:05:33 - Starting service 'SGE'13:05:48 - Configuring 
SGE...13:05:56 - Successfully setup SGE; configuring SGE



13:05:57 - Saved file 'persistent_data.yaml' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'13:05:57 - Saved file 'cm_boot.py' to 
bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3'



13:05:57 - Saved file 'cm.tar.gz' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'13:05:57 - Problem connecting to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3', attempt 1/513:05:59 - Saved file 
'Fam122261.clusterName' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3'



13:06:24 - Initializing a 'Galaxy' cluster.13:06:24 - Retrieved file 
'snaps.yaml' from bucket 'cloudman' to 'cm_snaps.yaml'.13:06:41 - Adding 3 
instance(s)...



13:07:02 - Saved file 'persistent_data.yaml' to bucket
 'cm-a42f040c55e7519eb63bbaf269fa78d3'13:07:38 - Saved file 
'persistent_data.yaml' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3'13:07:38 
- Saved file 'universe_wsgi.ini.cloud' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'



13:07:38 - Saved file 'tool_conf.xml.cloud' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'13:07:48
 - Error mounting file system '/mnt/galaxyData' from '/dev/sdg3', 
running command '/bin/mount /dev/sdg3 /mnt/galaxyData' returned code 
'32' and following stderr: 'mount: you must specify the filesystem type
'13:07:52 - Saved file 'persistent_data.yaml' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'13:07:52 - Starting service 
'Postgres'13:07:52 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data' 
does not exist (yet?)



13:07:52 - Configuring PostgreSQL with a database for Galaxy...13:08:05 - Saved 
file 'persistent_data.yaml' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'13:08:05 - Starting service 'Galaxy'



13:08:05 -      Galaxy daemon not running.13:08:05 - Galaxy service state 
changed from 'Starting' to 'Error'13:08:05 - Setting up Galaxy 
application13:08:05
 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3' to 
'/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'.13:08:05 - 
Retrieved file 'tool_conf.xml.cloud' from bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3' to 
'/mnt/galaxyTools/galaxy-central/tool_conf.xml'.13:08:05 - 
Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cloudman' 
to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'.13:08:05 - 
Starting Galaxy...13:08:09 - Galaxy service state changed from 'Error' to 
'Starting'13:08:09 - Saved file 'persistent_data.yaml' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'



13:08:09 - Saved file 'tool_data_table_conf.xml.cloud' to bucket 
'cm-a42f040c55e7519eb63bbaf269fa78d3'13:08:28 - Instance 'i-e46f0a8b' reported 
alive13:08:28 - Successfully generated root user's public key.



13:08:28 - Sent master public key to worker instance 'i-e46f0a8b'.13:08:28 - 
Instance 'i-e26f0a8d' reported alive13:08:28 - Sent master public key to worker 
instance 'i-e26f0a8d'.



13:08:33 - Instance 'i-e06f0a8f' reported alive13:08:33 - Sent master public 
key to worker instance 'i-e06f0a8f'.13:08:33 - Adding instance i-e46f0a8b to 
SGE Execution Host list



13:08:44 - Successfully added
 instance 'i-e46f0a8b' to SGE13:08:44 - Waiting on worker instance 'i-e46f0a8b' 
to configure itself...13:08:44 - Instance 'i-e26f0a8d' already in SGE's 
@allhosts13:08:44 - Waiting on worker instance 'i-e26f0a8d' to configure 
itself...



13:08:45 - Instance 'i-e06f0a8f' already in SGE's @allhosts13:08:45 - Waiting 
on worker instance 'i-e06f0a8f' to configure itself...13:08:50 - Instance 
'i-e46f0a8b' ready



13:09:27 - Galaxy service state changed from 'Starting' to 'Running'22:38:18 - 
Found '3' idle instances; trying to remove '2'22:38:18 - Specific termination 
of instance 'i-e26f0a8d' requested.



22:38:18 - Removing instance 'i-e26f0a8d' from SGE22:38:18 - Successfully 
updated @allhosts to remove 'i-e26f0a8d'22:38:19 - Terminating instance 
'i-e26f0a8d'22:38:19 - Initiated requested termination of instance. Terminating
 'i-e26f0a8d'.22:38:19 - Specific termination of instance 'i-e46f0a8b' 
requested.22:38:19 - Removing instance 'i-e46f0a8b' from SGE22:38:19 - 
Successfully initiated termination of instance 'i-e26f0a8d'



22:38:19 - Successfully updated @allhosts to remove 'i-e46f0a8b'22:38:20 - 
Terminating instance 'i-e46f0a8b'22:38:20 - Initiated requested termination of 
instance. Terminating 'i-e46f0a8b'.



22:38:20 - Initiated requested termination of instances. Terminating '2' 
instances.22:38:20 - Successfully initiated termination of instance 
'i-e46f0a8b'22:38:41 - Found '1' idle instances; trying to remove '1'



22:38:41 - Specific termination of instance 'i-e06f0a8f' requested.22:38:41 - 
Removing instance 'i-e06f0a8f' from SGE22:38:41 - Successfully updated 
@allhosts to remove 'i-e06f0a8f'



22:38:42 - Initiated requested termination of instance. Terminating
 'i-e06f0a8f'.22:38:42 - Initiated requested termination of instances. 
Terminating '1' instances.22:38:42 - Terminating instance 'i-e06f0a8f'22:38:42 
- Successfully initiated termination of instance 'i-e06f0a8f'



22:38:47 - Instance 'i-e26f0a8d' successfully terminated.22:38:49 - Instance 
'i-e46f0a8b' successfully terminated.22:38:59 - Adding 3 instance(s)...22:39:07 
- Instance 'i-e06f0a8f' successfully terminated.



22:41:02 - Instance 'i-fa096e95' reported alive22:41:02 - Sent master public 
key to worker instance 'i-fa096e95'.22:41:06 - Adding instance i-fa096e95 to 
SGE Execution Host list



22:41:17 - Successfully added instance 'i-fa096e95' to SGE22:41:17 - Waiting on 
worker instance 'i-fa096e95' to configure itself...22:41:17 - Instance 
'i-fe096e91' reported alive



22:41:17 - Sent master public key to worker instance
 'i-fe096e91'.22:41:22 - Adding instance i-fe096e91 to SGE Execution Host 
list22:41:34 - Successfully added instance 'i-fe096e91' to SGE22:41:34 - 
Waiting on worker instance 'i-fe096e91' to configure itself...



22:41:34 - Instance 'i-fa096e95' ready22:41:52 - Instance 'i-fe096e91' 
ready22:42:28 - Instance 'i-fc096e93' reported alive22:42:28 - Sent master 
public key to worker instance 'i-fc096e93'.



22:42:38 - Adding instance i-fc096e93 to SGE Execution Host list22:42:49 - 
Successfully added instance 'i-fc096e93' to SGE22:42:49 - Waiting on worker 
instance 'i-fc096e93' to configure itself...



22:43:13 - Instance 'i-fc096e93' ready18:29:10 - Failure checking disk usage.  
[Errno 12] Cannot allocate memory18:29:10 - Failure checking disk usage.  
[Errno 12] Cannot allocate memory



18:29:10 - Failure checking disk usage.  [Errno 12] Cannot
 allocate memory
    

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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
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  http://lists.bx.psu.edu/

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