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/
The login emailaddress I use is felix.mayr@gmail.com mailto:felix.mayr@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 FMayr@age.mpg.de wrote:
Dear Galaxy dev,
I have two problems, which might be related to each other.
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…?
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/ http://www.age.mpg.de/science/research-labs/denzel/
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 fmayr@age.mpg.de wrote:
The login emailaddress I use is felix.mayr@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 FMayr@age.mpg.de wrote:
Dear Galaxy dev,
I have two problems, which might be related to each other.
- 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…?
- 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/
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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 fmayr@age.mpg.de wrote:
The login emailaddress I use is felix.mayr@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 FMayr@age.mpg.de wrote:
Dear Galaxy dev,
I have two problems, which might be related to each other.
- 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…?
- 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/
galaxy-dev@lists.galaxyproject.org
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Jennifer Hillman-Jackson