Re: [galaxy-dev] Empty TopHat output
The same here. Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is "empty" files. Is anyone else having this issue? Does anyone have any suggestions? Many thanks in advance! Cheers, Mo Heydarian On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob <joachim.jacob@vib.be> wrote:
The same here.
Cheers, Joachim
-- Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
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Given that this doesn't seem to be happening on our public server or on local instances, my best guess is that the issue is old code. Are you running the most recent dist? J. On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote:
We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is "empty" files.
Is anyone else having this issue? Does anyone have any suggestions?
Many thanks in advance!
Cheers, Mo Heydarian
On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob <joachim.jacob@vib.be> wrote: The same here.
Cheers, Joachim
-- Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
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___________________________________________________________ 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:
We are running "galaxy-cloudman-2011-03-22 (ami-da58aab3)". Our latest instance was loaded up just last week. Thanks! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Wed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks <jeremy.goecks@emory.edu>wrote:
Given that this doesn't seem to be happening on our public server or on local instances, my best guess is that the issue is old code. Are you running the most recent dist?
J.
On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote:
We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is "empty" files.
Is anyone else having this issue? Does anyone have any suggestions?
Many thanks in advance!
Cheers, Mo Heydarian
On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob <joachim.jacob@vib.be>wrote:
The same here.
Cheers, Joachim
-- Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
______________________________**_____________________________ 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:
___________________________________________________________ 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:
In this case, it's useful to differentiate between (i) the AMI that Galaxy Cloud uses and (ii) the Galaxy code running on the cloud. I suspect that (ii) is out of data for you; this is not (yet) automatically updated, even when starting a new instance. Try using the admin console to update to the most recent Galaxy dist using this URL: https://bitbucket.org/galaxy/galaxy-dist/ (not galaxy-central, as is the default) Best, J. On Oct 31, 2012, at 8:36 PM, Mohammad Heydarian wrote:
We are running "galaxy-cloudman-2011-03-22 (ami-da58aab3)".
Our latest instance was loaded up just last week.
Thanks!
Cheers, Mo Heydarian
PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205
On Wed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: Given that this doesn't seem to be happening on our public server or on local instances, my best guess is that the issue is old code. Are you running the most recent dist?
J.
On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote:
We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is "empty" files.
Is anyone else having this issue? Does anyone have any suggestions?
Many thanks in advance!
Cheers, Mo Heydarian
On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob <joachim.jacob@vib.be> wrote: The same here.
Cheers, Joachim
-- Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
___________________________________________________________ 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:
___________________________________________________________ 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:
Thanks, Jeremy. I updated my instance of Galaxy by the repository you provided ( https://bitbucket.org/galaxy/galaxy-dist/) and re-ran my analysis. I see that TopHat is generating data (by monitoring the disk usage on the Cloudman interface) again, but this time I the output file is in the error state and the message returned is: "Job output not returned from cluster". Any thoughts? Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Wed, Oct 31, 2012 at 9:03 PM, Jeremy Goecks <jeremy.goecks@emory.edu>wrote:
In this case, it's useful to differentiate between (i) the AMI that Galaxy Cloud uses and (ii) the Galaxy code running on the cloud. I suspect that (ii) is out of data for you; this is not (yet) automatically updated, even when starting a new instance.
Try using the admin console to update to the most recent Galaxy dist using this URL:
https://bitbucket.org/galaxy/galaxy-dist/
(not galaxy-central, as is the default)
Best, J.
On Oct 31, 2012, at 8:36 PM, Mohammad Heydarian wrote:
We are running "galaxy-cloudman-2011-03-22 (ami-da58aab3)".
Our latest instance was loaded up just last week.
Thanks!
Cheers, Mo Heydarian
PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205
On Wed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks <jeremy.goecks@emory.edu>wrote:
Given that this doesn't seem to be happening on our public server or on local instances, my best guess is that the issue is old code. Are you running the most recent dist?
J.
On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote:
We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is "empty" files.
Is anyone else having this issue? Does anyone have any suggestions?
Many thanks in advance!
Cheers, Mo Heydarian
On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob <joachim.jacob@vib.be>wrote:
The same here.
Cheers, Joachim
-- Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
______________________________**_____________________________ 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:
___________________________________________________________ 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:
participants (3)
-
Jeremy Goecks -
Joachim Jacob -
Mohammad Heydarian