Re: [galaxy-user] More help neeeded

2012-10-19 Thread Jennifer Jackson 

Hello Kshama,

I went into your account and examined your data. Starting with "Saved 
Histories", the default view is all active histories in the center 
panel. In your case right now, none of these have hidden or deleted 
datasets.


Next, I clicked on "Advanced Search" in this same view in the middle 
panel, then selected "status: all". (This is covered in the wiki link I 
shared - and in the screencast). This brings up many datasets that have 
been deleted and/or permanently deleted. The far right column will note 
which. Some of these contain error datasets and some do not. I did not 
go through each to check to see which datasets in the individual 
histories are deleted, purged, hidden, etc., I will leave this for you 
to examine.


I suggested checking in this group to see if your missing workflow 
output wrote to one of these histories, although if you cannot execute a 
test run that has it write to the same history as the inputs, then there 
is most likely something wrong with the workflow itself that needs to be 
examined first by you.


I would also suggest reviewing these deleted histories and permanently 
deleting those you no longer need. This will free up disc space in your 
account.


Good luck,

Jen
Galaxy team

On 10/19/12 5:25 AM, Kshama Aswath wrote:

Hello ,
I tried everything possible according to the reply I got from Jen ,
helping me fix my problem but is not working.Please see below .
Is it possible that because the usage shows 91% I am not able to
retrieve anything back to display? Might sound ridiculous but
have no clue !! I still have no output back and none of the hidden
datasets or deleted datasets are showing so I can purge them.
When I chose the "purge deleted datasets" from the gear icon , I got
back a message indicating "0 datasets purged". Please hlep as this is
tremendously delaying my analysis process.
I have answered some of the steps Jen asked me to take ,please see below:
here is what Jen wrote to help me with my problem on galaxy :
We would like to help. I looked for an account under your email address
"kasw...@masonlive.gmu.edu " on the
public Main Galaxy instance at
http://main.g2.bx.psu.edu 
(http://usegalaxy.org ), and did not find one,
so I will tell you how to check for the data yourself, then you can
share your account email address if you are still stuck.
I am registered under compug...@gmail.com ,
that is why u could not find me on my school ID.
1 - For unexplained data counting towards your quota: Check for datasets
in histories that are deleted, but not permanently deleted. Inside a
history, select "Options (gear icon) -> View Deleted Datasets" to bring
up those that were deleted. Each will note if permanently deleted or not
and give the option to purge.
I tried this and it did not show the deleted datasets
Also check for complete histories that may be deleted, but also not
permanently deleted (or purged). Select "Options (gear icon) -> Saved
Histories", then view "all" to see active and deleted. The table will
note if the data is deleted, but not purged. The option to
purge/permanently delete will also be given.
The show all option showed what I currenlty have bt not the deleted datasets
2 - To locate the output of workflow that seems to be missing: Check for
hidden datasets. From within a history (the history that launched the
job, if no other history was created), select "Options (gear icon) ->
View Hidden Datasets" to bring up those that were hidden by the
workflow. (Hiding intermediate datasets is a workflow option). Perhaps
there was an error early on in the workflow, before the stage where a
result would be written to a new history. I would also recommended that
you experiment with a test run where the output is not written to a new
history (if you have not already done so), just to rule out any problems
central to the workflow (or the inputs), independent of the new history
issue.
Tried this but the hidden datasets did not show up !

Help is also in this wiki:

http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets

See Hidden & Delete_vs_Delete_Permanently

Hopefully this helps, but please let us know if you need more assistance,

Jen
Galaxy team


On 10/17/12 7:20 PM, kaswath wrote:
 > Hello Galaxy,
 >
 > I have a dataset about *20.8GB *to work with using the NGS analysis. I
 > FTPd the dataset and created a workflow for the analysis and ran the job
 > on the entire 20.8GB on Galaxy main around september 27th.
 >
 > I waited on about two to four days .no output of any sort !
 > I had requested the results be saved in a different history. I checked ,
 > but no new history with results was created !
 >
 > I reran the job again after a week or so and still no results !
 >
 > I had tried running this on small dataset and it had worked earlier !
 > Anyhow, getting back to this proble,m I have NOT receive any error
 > message however , my U

[galaxy-user] More help neeeded

2012-10-19 Thread Kshama Aswath 
 Hello ,
I tried everything possible according to the reply I got from Jen , helping
me fix my problem but is not working.Please see below .
Is it possible that because the usage shows 91% I am not able to retrieve
anything back to display? Might sound ridiculous but
have no clue !! I still have no output back and none of the hidden datasets
or deleted datasets are showing so I can purge them.
When I chose the "purge deleted datasets" from the gear icon , I got back a
message indicating "0 datasets purged". Please hlep as this is tremendously
delaying my analysis process.
I have answered some of the steps Jen asked me to take ,please see below:

here is what Jen wrote to help me with my problem on galaxy :

We would like to help. I looked for an account under your email address
"kasw...@masonlive.gmu.edu" on the public Main Galaxy instance at
http://main.g2.bx.psu.edu (http://usegalaxy.org), and did not find one,
so I will tell you how to check for the data yourself, then you can
share your account email address if you are still stuck.

I am registered under compug...@gmail.com, that is why u could not find me
on my school ID.
1 - For unexplained data counting towards your quota: Check for datasets
in histories that are deleted, but not permanently deleted. Inside a
history, select "Options (gear icon) -> View Deleted Datasets" to bring
up those that were deleted. Each will note if permanently deleted or not
and give the option to purge.
I tried this and it did not show the deleted datasets
Also check for complete histories that may be deleted, but also not
permanently deleted (or purged). Select "Options (gear icon) -> Saved
Histories", then view "all" to see active and deleted. The table will
note if the data is deleted, but not purged. The option to
purge/permanently delete will also be given.
The show all option showed what I currenlty have bt not the deleted datasets
2 - To locate the output of workflow that seems to be missing: Check for
hidden datasets. From within a history (the history that launched the
job, if no other history was created), select "Options (gear icon) ->
View Hidden Datasets" to bring up those that were hidden by the
workflow. (Hiding intermediate datasets is a workflow option). Perhaps
there was an error early on in the workflow, before the stage where a
result would be written to a new history. I would also recommended that
you experiment with a test run where the output is not written to a new
history (if you have not already done so), just to rule out any problems
central to the workflow (or the inputs), independent of the new history
issue.

Tried this but the hidden datasets did not show up !


Help is also in this wiki:

http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets

See Hidden & Delete_vs_Delete_Permanently

Hopefully this helps, but please let us know if you need more assistance,

Jen
Galaxy team


On 10/17/12 7:20 PM, kaswath wrote:
> Hello Galaxy,
>
> I have a dataset about *20.8GB *to work with using the NGS analysis. I
> FTPd the dataset and created a workflow for the analysis and ran the job
> on the entire 20.8GB on Galaxy main around september 27th.
>
> I waited on about two to four days .no output of any sort !
> I had requested the results be saved in a different history. I checked ,
> but no new history with results was created !
>
> I reran the job again after a week or so and still no results !
>
> I had tried running this on small dataset and it had worked earlier !
> Anyhow, getting back to this proble,m I have NOT receive any error
> message however , my USAGE bar on the top right is at 90% !! So I went
> back and deleted the old copies of my history I had , even so the usage
> bar is still at 90%!
> Before I ran my workflow I had the usage bar being way less !
>
> Please can u let me know what is happening? Why I have not received any
> results on my analysis yet? I really need to get this done ASAP !
>
> Thanks so much for all your help !
>
> Regards
>
> Kshama.
>
>
>
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>



--
Jennifer Jackson
http://galaxyproject.org



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