More help neeeded
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 "kaswath@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 compugene@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.
___________________________________________________________ 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, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org Reply Reply to all Forward Click here to Reply, Reply to all, or Forward Why this ad?Ads – Business Analytics Guide Simple Interactive Visualization. Visual Drag & Drop UI. Quick & Easy Pentaho.com/Business-Analytics 128 22% full Using 2.2 GB of your 10.1 GB ©2012 Google - Terms & Privacy Last account activity: 19 minutes ago DetailsPeople (3)Jennifer Jackson jen@bx.psu.edu Show details Ads – Why these ads? The Hartfordhartfordauto.com Save on Car Insurance You Could Save $443* on Car Insurance from The Hartford. Save more when you also insure your home. 17408 More Promotions (3) Data Loss Protect Your Info with the Intel® Core™ vPro™ Processor Technology! intel.com/pcsecurity 128 SPSS Modeler Demo Dig Out The Secrets In Your Data. Learn How In This Free Modeler Demo www.IBM.com/SPSS_Modeler_Demo <http://www.ibm.com/SPSS_Modeler_Demo> 128 Analytics Solution Tools Powerful Tools for Data Artisans. Increase Sales - Free Whitepaper! www.Alteryx.com/Analytics_Tools <http://www.alteryx.com/Analytics_Tools> 16512 Fast Big Data Analysis Make Big Data Decisions in Minutes! Learn More Now. BigData.Pervasive.com 128 SAS + MSA = Opportunity Become a highly sought-after Analytics professional in 10 months analytics.ncsu.edu 512 Hadoop™ Training Flexible training from UMBC. Online on-site and classroom. Start Now! www.umbc.edu/hadoop 128 More about... SAS Datasets » SAS Programming » SAS Job Opportunities » SAS Data Analysis » Business Analytics Guide Simple Interactive Visualization.22% fullUsing 2.2 GB of your 10.1 GB ©2012 Google - Terms & Privacy Last account activity: 19 minutes agoDetailsYou have one new message. -- Kshama Aswath Graduate Student-(PhD) Bioinformatics and computational Biology Prince Williams Campus George Mason University Manasses,VA-20110
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 "kaswath@masonlive.gmu.edu <mailto:kaswath@masonlive.gmu.edu>" on the public Main Galaxy instance at http://main.g2.bx.psu.edu <http://main.g2.bx.psu.edu/> (http://usegalaxy.org <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 compugene@gmail.com <mailto:compugene@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
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.
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://usegalaxy.org>. Please keep all replies on
On 10/17/12 7:20 PM, kaswath wrote: 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, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org <http://galaxyproject.org/>
Reply Reply to all Forward
Click here to Reply, Reply to all, or Forward
Why this ad?Ads – Business Analytics Guide Simple Interactive Visualization. Visual Drag & Drop UI. Quick & Easy Pentaho.com/Business-Analytics 128 22% full Using 2.2 GB of your 10.1 GB ©2012 Google - Terms & Privacy Last account activity: 19 minutes ago DetailsPeople (3)Jennifer Jackson jen@bx.psu.edu <mailto:jen@bx.psu.edu>
Show details Ads – Why these ads? The Hartfordhartfordauto.com Save on Car Insurance You Could Save $443* on Car Insurance from The Hartford. Save more when you also insure your home.
17408 More Promotions (3) Data Loss Protect Your Info with the Intel® Core™ vPro™ Processor Technology! intel.com/pcsecurity <http://intel.com/pcsecurity> 128 SPSS Modeler Demo Dig Out The Secrets In Your Data. Learn How In This Free Modeler Demo www.IBM.com/SPSS_Modeler_Demo <http://www.ibm.com/SPSS_Modeler_Demo> 128 Analytics Solution Tools Powerful Tools for Data Artisans. Increase Sales - Free Whitepaper! www.Alteryx.com/Analytics_Tools <http://www.alteryx.com/Analytics_Tools> 16512 Fast Big Data Analysis Make Big Data Decisions in Minutes! Learn More Now. BigData.Pervasive.com <http://BigData.Pervasive.com> 128 SAS + MSA = Opportunity Become a highly sought-after Analytics professional in 10 months analytics.ncsu.edu <http://analytics.ncsu.edu> 512 Hadoop™ Training Flexible training from UMBC. Online on-site and classroom. Start Now! www.umbc.edu/hadoop <http://www.umbc.edu/hadoop> 128 More about... SAS Datasets »
SAS Programming »
SAS Job Opportunities »
SAS Data Analysis »
Business Analytics Guide Simple Interactive Visualization.22% fullUsing 2.2 GB of your 10.1 GB ©2012 Google - Terms & Privacy Last account activity: 19 minutes agoDetailsYou have one new message.
-- Kshama Aswath Graduate Student-(PhD) Bioinformatics and computational Biology Prince Williams Campus George Mason University Manasses,VA-20110
___________________________________________________________ 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, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
participants (2)
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Jennifer Jackson -
Kshama Aswath