Hi all, I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why. Here's the workflow: input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course). And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data: Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values. Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either. Any ideas? Let me know if you need more info! Thanks! Marijn
Marijn, Are there any other actions on this first step? Has the input dataset been modified previously by a set datatype workflow action? And, lastly, what revision are you working with? 'hg tip' will show this. -Dannon On Aug 9, 2010, at 4:58 AM, Marijn Vandevoorde wrote:
Hi all,
I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why.
Here's the workflow:
input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course).
And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data:
Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.
Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either.
Any ideas? Let me know if you need more info!
Thanks!
Marijn _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Dannon, Thanks for getting back to me. Dataset hasn't been modified, I've just uploaded the files and gave it a go. Revision is 4084:a8ef6a46d622 (i'm using galaxy central. maybe i should give the galaxy-dist trunk a try?) Thanks! Marijn On 08/09/2010 02:45 PM, Dannon Baker wrote:
Marijn,
Are there any other actions on this first step? Has the input dataset been modified previously by a set datatype workflow action?
And, lastly, what revision are you working with? 'hg tip' will show this.
-Dannon
On Aug 9, 2010, at 4:58 AM, Marijn Vandevoorde wrote:
Hi all,
I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why.
Here's the workflow:
input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course).
And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data:
Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.
Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either.
Any ideas? Let me know if you need more info!
Thanks!
Marijn _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
gave it a try with the dist version, but no luck. Any help would be greatly appreciated. Marijn On 08/09/2010 02:56 PM, Marijn Vandevoorde wrote:
Hi Dannon,
Thanks for getting back to me.
Dataset hasn't been modified, I've just uploaded the files and gave it a go.
Revision is 4084:a8ef6a46d622 (i'm using galaxy central. maybe i should give the galaxy-dist trunk a try?)
Thanks! Marijn
On 08/09/2010 02:45 PM, Dannon Baker wrote:
Marijn,
Are there any other actions on this first step? Has the input dataset been modified previously by a set datatype workflow action?
And, lastly, what revision are you working with? 'hg tip' will show this.
-Dannon
On Aug 9, 2010, at 4:58 AM, Marijn Vandevoorde wrote:
Hi all,
I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why.
Here's the workflow:
input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course).
And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data:
Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.
Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either.
Any ideas? Let me know if you need more info!
Thanks!
Marijn _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
Marijn and Shaun, We're tracking down what might be causing the issue, but in the meantime, setting the following line in your universe_wsgi.ini should get things going again: track_jobs_in_database = True Let me know if this doesn't resolve the problem you're seeing. -Dannon On Aug 10, 2010, at 9:26 AM, Marijn Vandevoorde wrote:
gave it a try with the dist version, but no luck.
Any help would be greatly appreciated.
Marijn
On 08/09/2010 02:56 PM, Marijn Vandevoorde wrote:
Hi Dannon,
Thanks for getting back to me.
Dataset hasn't been modified, I've just uploaded the files and gave it a go.
Revision is 4084:a8ef6a46d622 (i'm using galaxy central. maybe i should give the galaxy-dist trunk a try?)
Thanks! Marijn
On 08/09/2010 02:45 PM, Dannon Baker wrote:
Marijn,
Are there any other actions on this first step? Has the input dataset been modified previously by a set datatype workflow action?
And, lastly, what revision are you working with? 'hg tip' will show this.
-Dannon
On Aug 9, 2010, at 4:58 AM, Marijn Vandevoorde wrote:
Hi all,
I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why.
Here's the workflow:
input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course).
And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data:
Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.
Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either.
Any ideas? Let me know if you need more info!
Thanks!
Marijn _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Marijn Vandevoorde
Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde@psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
I am experiencing a similar problem. If I use a running dataset as input for a new tool, the job will remain in queuing status even after the first job has finished. I am running revision 4134:e2577b117dd1 Shaun Quoting Dannon Baker <dannonbaker@me.com>:
Marijn,
Are there any other actions on this first step? Has the input dataset been modified previously by a set datatype workflow action?
And, lastly, what revision are you working with? 'hg tip' will show this.
-Dannon
On Aug 9, 2010, at 4:58 AM, Marijn Vandevoorde wrote:
Hi all,
I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why.
Here's the workflow:
input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course).
And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data:
Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.
Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either.
Any ideas? Let me know if you need more info!
Thanks!
Marijn _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
participants (4)
-
Dannon Baker -
Marijn Vandevoorde -
Marijn Vandevoorde -
SHAUN WEBB