It got hung up in cross-talk correction, by the look of it. Odd, that's
usually quite quick, IIRC.
There are no Memstats lines in the output. What's become of them?
--TS
Nava Whiteford wrote:
> Though it says it's not using the reference, it maybe processing a large
> number of smaller contigs. I've corrected this in the latest checkin of
> swift but it would be worth trying this tile with no reference
> specified.
>
> Other than that, it does look like the tile is generating an abnormally
> large number of clusters. If possible can you send me a sample tile?
>
> On Mon, Apr 27, 2009 at 04:41:51PM +0200, Bernd Jagla wrote:
>
>> Here are the associated output-files...
>> The one with the worst times unfortunately hasn't gotten any stdout/err for
>> some odd reason. Here is second "best"...
>>
>>
>> -----Original Message-----
>> From: Nava Whiteford [mailto:ne...@sg...]
>> Sent: Monday, April 27, 2009 4:30 PM
>> To: Bernd Jagla
>> Cc: 'Tom Skelly'; Swi...@li...
>> Subject: Re: long run times
>>
>> How big is dm3_ucsc.fa? Swifts aligner is very slow and only designed to
>> deal with 5000bp sequences.
>>
>> ->Dm3 is not being used (too big)...
>>
>> Are you saying it took 39 hours using the parameters settings in the
>> svn? That would be a bit odd, if you can send me the stdout/err that
>> would be useful.
>>
>> ->See attached
>>
>> Sorry, for the delay in getting back to you on your xml questions. I've
>> not forgotten! Just snowed under.
>>
>> ->no worries... it is cold here in Paris too today, but not that cold ;)...
>> Good luck !!
>>
>> Nav
>>
>> On Mon, Apr 27, 2009 at 04:07:06PM +0200, Bernd Jagla wrote:
>>
>>> Nava,
>>>
>>>
>>>
>>> Here is a list of parameters I tested and associated run-times (143,343.85
>>> sec = 39hrs!!!!) for one tile.
>>>
>>> Could you please comment on where all the time might be spent?
>>>
>>>
>>>
>>> I would like to understand the problem to be able to optimize our
>>>
>> protocols.
>>
>>>
>>>
>>> It doesn't really seem to be possible to reduce the time without loosing
>>>
>> too
>>
>>> many clusters.
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>> Bernd
>>>
>>>
>>>
>>> Time = [sec] user time from time command
>>>
>>> Wc pf = number of lines in *.pf files
>>>
>>> Wc nonpf = numbe of lines in *.nonpf files
>>>
>>> There is only one parameter changed compared to the standard (normal) call
>>> of the program.
>>>
>>>
>>>
>>> idx parameter time wc pf wc nonpf
>>>
>>> 1 normal 143,343.85 182,256 1,720,580
>>>
>>> 2 --ref dm3_ucsc.fa 27,681.68 110,988 1,809,448
>>>
>>> 3 --correlation_cc_subimage_multiplier 20 114,063.20 179,724
>>> 1,695,836
>>>
>>> 4 --correlation_cc_subimage_multiplier 10 34,372.92 154,840
>>> 1,751,684
>>>
>>> 5 --correlation_cc_subimage_multiplier 40 4,732.95 116,920
>>> 1,801,616
>>>
>>> 6 --threshold_window 3 2,311.50 131,260 664,312
>>>
>>> 7 --threshold_window 4 2,226.00 106,416 261,468
>>>
>>> 8 --segment_cycles 2 3,343.96 143,712 1,301,216
>>>
>>> 9 --segment_cycles 1 2,266.62 142,016 772,496
>>>
>>>
>> --
>> Nav
>>
>> Work: 01865 854873
>> Mob : 07518-358405
>>
>
>
>
>
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