BWA sampe runs 'forever'

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

BWA sampe runs 'forever'

Assaf Gordon-2
Hello,

Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ?

A little digging shows that it's the "bwa sampe" step, and SEQanswers thread mention it's somewhat common:
http://seqanswers.com/forums/showthread.php?t=11652
http://seqanswers.com/forums/showthread.php?t=6340

One suggested work-around is to add "-A" to "bwa sampe", but there's no way to do it in the current BWA wrapper.
(On the command-line with the same input files it does make things much faster).

I'm wondering if this is common enough to justify adding "-A" to the wrapper, or is it rare enough and can be ignored.

-gordon
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: BWA sampe runs 'forever'

Fields, Christopher J
On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:

> Hello,
>
> Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ?
>
> A little digging shows that it's the "bwa sampe" step, and SEQanswers thread mention it's somewhat common:
> http://seqanswers.com/forums/showthread.php?t=11652
> http://seqanswers.com/forums/showthread.php?t=6340
>
> One suggested work-around is to add "-A" to "bwa sampe", but there's no way to do it in the current BWA wrapper.
> (On the command-line with the same input files it does make things much faster).
>
> I'm wondering if this is common enough to justify adding "-A" to the wrapper, or is it rare enough and can be ignored.
>
> -gordon

Can it be added as an optional argument?  So that if it is selected, the setting is passed to the tool, otherwise not.

chris


___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: BWA sampe runs 'forever'

Assaf Gordon-2
Chris Fields wrote, On 07/29/2011 12:35 PM:
> On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:
>> Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ?
>>...
>> I'm wondering if this is common enough to justify adding "-A" to the wrapper, or is it rare enough and can be ignored.
>>
>
> Can it be added as an optional argument?  So that if it is selected, the setting is passed to the tool, otherwise not.
>
Obviously, it can be added to the XML wrapper.

I'm asking if other people encountered this situation with Paired-end mapping, and whether it's rare or not.

>From a user's perspective, this kind of parameter makes no sense:
it basically tells the user: "run BWA without this parameter, and if after 24 hours the job is still running, kill it and re-run with this parameter".
That's not the way to build user-friendly tools :(

-gordon
___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: BWA sampe runs 'forever'

Fields, Christopher J
On Jul 29, 2011, at 12:44 PM, Assaf Gordon wrote:

> Chris Fields wrote, On 07/29/2011 12:35 PM:
>> On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:
>>> Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ?
>>> ...
>>> I'm wondering if this is common enough to justify adding "-A" to the wrapper, or is it rare enough and can be ignored.
>>>
>>
>> Can it be added as an optional argument?  So that if it is selected, the setting is passed to the tool, otherwise not.
>>
> Obviously, it can be added to the XML wrapper.
>
> I'm asking if other people encountered this situation with Paired-end mapping, and whether it's rare or not.

If there are cases where this does occur (as you have pointed out), then the XML wrapper should have the option and maybe even a bit of documentation pointing this out (even if it is a rare event).  I wouldn't want this running on a cluster where users are charged, for instance.

>> From a user's perspective, this kind of parameter makes no sense:
> it basically tells the user: "run BWA without this parameter, and if after 24 hours the job is still running, kill it and re-run with this parameter".
> That's not the way to build user-friendly tools :(
>
> -gordon

It's definitely not intuitive and violates least surprise.  If I explicitly set any parameter, I don't expect the application to possibly (and silently) assume I am wrong and change it anyway.

chris
___________________________________________________________
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/