Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

2015-12-01 Thread Dannon Baker 
You're currently seeing 91% usage?  I just checked again and your disk
calculation should have been up to date (the recalc procedure did not
change anything), and I'm seeing 50% usage on your account.

On Tue, Dec 1, 2015 at 3:45 AM, Felix Mayr  wrote:
> The login emailaddress I use is felix.m...@gmail.com.
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
> On 01 Jan 2015, at 09:44, Felix Mayr  wrote:
>
> Dear Galaxy dev,
>
> I have two problems, which might be related to each other.
>
> 1) For a long time already, I continuously have ‘left over’ data allocation
> after deleting and purging histories. Someone from your team has repeatedly
> resolved that problem, but it root of the problem still persists. I know
> have 91% allocation, when only having two histories of 67.48 and 59.45 GB.
> The fix for automatic recalculation doesn’t seem to work…?
>
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The
> problem: the SNP mapping plots shows the exact same mapping/plots of the
> SNPs. They can not be the same. What is not the problem: the input files, as
> they are different in size, first and last lines of the files, and they
> produce very different SNP mapping mutation tables. Therefore, I think there
> might be a problem that the workflow somehow uses the same intermediate file
> for generating the SNP mapping plots. I already re-uploaded and rerun the
> workflows in new histories multiple times, but the same result each time. I
> would upload and run another data set for which I already have SNP mapping
> plots to see whether I again get the same plots or not, but that is now not
> possible as I am close to the data quota.
>
> I hope you can help solve these problems.
>
> All best,
>
> Felix
>
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
>
>
> ___
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Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

2015-12-01 Thread Jennifer Hillman-Jackson 
Hi Felix,

I have recalculated disk for you again. Our team is aware of this problem
and is working on a more permanent solution.

We will take a look at your workflow/histories to rule out a tool or
workflow function problem. If this does turn out to be a method issue
instead, then contacting the authors of the Cloudman pipeline would be
recommended as the next step. https://usegalaxy.org/u/gm2123/p/cloudmap

Thanks for using Galaxy and we will get back to you in a bit about the
workflow,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Tue, Dec 1, 2015 at 12:45 AM, Felix Mayr  wrote:

> The login emailaddress I use is felix.m...@gmail.com.
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
> On 01 Jan 2015, at 09:44, Felix Mayr  wrote:
>
> Dear Galaxy dev,
>
> I have two problems, which might be related to each other.
>
> 1) For a long time already, I continuously have ‘left over’ data
> allocation after deleting and purging histories. Someone from your team has
> repeatedly resolved that problem, but it root of the problem still
> persists. I know have 91% allocation, when only having two histories of
> 67.48 and 59.45 GB.  The fix for automatic recalculation doesn’t seem to
> work…?
>
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The
> problem: the SNP mapping plots shows the exact same mapping/plots of the
> SNPs. They can not be the same. What is not the problem: the input files,
> as they are different in size, first and last lines of the files, and they
> produce very different SNP mapping mutation tables. Therefore, I think
> there might be a problem that the workflow somehow uses the same
> intermediate file for generating the SNP mapping plots. I already
> re-uploaded and rerun the workflows in new histories multiple times, but
> the same result each time. I would upload and run another data set for
> which I already have SNP mapping plots to see whether I again get the same
> plots or not, but that is now not possible as I am close to the data quota.
>
> I hope you can help solve these problems.
>
> All best,
>
> Felix
>
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
>
>
> ___
> 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/
>
___
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:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

2015-12-01 Thread Felix Mayr 
The login emailaddress I use is felix.m...@gmail.com 
.


˜
Felix Mayr, MSc.
Max Planck Institute for Biology of Ageing
Research Group of Dr. Martin Denzel
Metabolic and Genetic Regulation of Ageing
Joseph-Stelzmann-Str. 9b
D-50931 Cologne
Germany
+49.221.3797.0465
www.age.mpg.de/science/research-labs/denzel/

> On 01 Jan 2015, at 09:44, Felix Mayr  wrote:
> 
> Dear Galaxy dev,
> 
> I have two problems, which might be related to each other. 
> 
> 1) For a long time already, I continuously have ‘left over’ data allocation 
> after deleting and purging histories. Someone from your team has repeatedly 
> resolved that problem, but it root of the problem still persists. I know have 
> 91% allocation, when only having two histories of 67.48 and 59.45 GB.  The 
> fix for automatic recalculation doesn’t seem to work…? 
> 
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The 
> problem: the SNP mapping plots shows the exact same mapping/plots of the 
> SNPs. They can not be the same. What is not the problem: the input files, as 
> they are different in size, first and last lines of the files, and they 
> produce very different SNP mapping mutation tables. Therefore, I think there 
> might be a problem that the workflow somehow uses the same intermediate file 
> for generating the SNP mapping plots. I already re-uploaded and rerun the 
> workflows in new histories multiple times, but the same result each time. I 
> would upload and run another data set for which I already have SNP mapping 
> plots to see whether I again get the same plots or not, but that is now not 
> possible as I am close to the data quota. 
> 
> I hope you can help solve these problems. 
> 
> All best,
> 
> Felix
> 
> 
> 
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/ 
> 

___
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:
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