bowtie2: no stderr output

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

bowtie2: no stderr output

elchia
Dear all


Usually the alignment statistics from bowtie2 will be printed to the stderr file, however, on the local instance, the stderr file is empty after alignment. It still does the alignment, but the statistics are not printed out.

This is my hg summary:
parent: 13802:f7dd0060c296 latest_2014.06.02
 Merged in dannon/galaxy-central-prmaker/stable (pull request #404)
branch: stable
commit: 288 modified, 357 added, 18 unknown (new branch head)
update: 27 new changesets (update)

Will updating to the latest version help?

Or are there any patches available?

Thanks.


Regards
liz

___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: bowtie2: no stderr output

John Chilton-4
It looks like this was a problem for awhile but isn't anymore on main
https://trello.com/c/yFeXvhUg.

It doesn't look like there has been any changes to the bowtie2 wrapper
since it was migrated to the tool shed so I am not sure why it isn't
working for you?

As an admin can you open a successful bowtie2 dataset and see what the
standard error and standard output are saved as - maybe copying them
into pastebin or gist. It might help illuminate the problem.

-John

On Mon, Oct 27, 2014 at 4:31 AM, Elizabeth Chia <[hidden email]> wrote:

> Dear all
>
>
> Usually the alignment statistics from bowtie2 will be printed to the stderr
> file, however, on the local instance, the stderr file is empty after
> alignment. It still does the alignment, but the statistics are not printed
> out.
>
> This is my hg summary:
> parent: 13802:f7dd0060c296 latest_2014.06.02
>  Merged in dannon/galaxy-central-prmaker/stable (pull request #404)
> branch: stable
> commit: 288 modified, 357 added, 18 unknown (new branch head)
> update: 27 new changesets (update)
>
> Will updating to the latest version help?
>
> Or are there any patches available?
>
> Thanks.
>
>
> Regards
> liz
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: bowtie2: no stderr output

elchia
Dear John

Thank you for responding.

Not too sure why I can't see your link unfortunately, but did you mean this?

I've tried modifying the command but doesn't seem to work either.

And I can't use the wrapper too?

I've just updated galaxy as well but doesn't fix it. Any ideas?

Many thanks!


Liz

On Mon, Nov 3, 2014 at 6:59 AM, John Chilton <[hidden email]> wrote:
It looks like this was a problem for awhile but isn't anymore on main
https://trello.com/c/yFeXvhUg.

It doesn't look like there has been any changes to the bowtie2 wrapper
since it was migrated to the tool shed so I am not sure why it isn't
working for you?

As an admin can you open a successful bowtie2 dataset and see what the
standard error and standard output are saved as - maybe copying them
into pastebin or gist. It might help illuminate the problem.

-John

On Mon, Oct 27, 2014 at 4:31 AM, Elizabeth Chia <[hidden email]> wrote:
> Dear all
>
>
> Usually the alignment statistics from bowtie2 will be printed to the stderr
> file, however, on the local instance, the stderr file is empty after
> alignment. It still does the alignment, but the statistics are not printed
> out.
>
> This is my hg summary:
> parent: 13802:f7dd0060c296 latest_2014.06.02
>  Merged in dannon/galaxy-central-prmaker/stable (pull request #404)
> branch: stable
> commit: 288 modified, 357 added, 18 unknown (new branch head)
> update: 27 new changesets (update)
>
> Will updating to the latest version help?
>
> Or are there any patches available?
>
> Thanks.
>
>
> Regards
> liz
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/