SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Novoalign MPI homopolymer filter jgSoton Bioinformatics 5 10-04-2011 06:18 AM
ClustalW MPI arkal Bioinformatics 2 07-03-2011 08:55 AM
PhD @ MPI for Immunobiology, Freiburg, Germany tmanke Academic/Non-Profit Jobs 0 04-09-2010 01:32 AM
Postdoc @ MPI for Immunobiology, Freiburg tmanke Academic/Non-Profit Jobs 0 04-09-2010 01:28 AM
Titanium software (MPI mode) westerman 454 Pyrosequencing 9 06-24-2009 01:04 AM

Reply
 
Thread Tools
Old 12-13-2011, 04:27 AM   #1
jgSoton
Member
 
Location: UK

Join Date: Sep 2011
Posts: 12
Default novalign MPI

hi,

I'm using novoalignMPI and found this:

Release 2.05.17 - 5th November 2009
----------------------------------
novoalign
1. When running multithreaded default output is now asynchronous with read files. If you need output in sync with reads add option -oSync to the command line.


Should I be using this option? I'm not sure what it means.

Thanks,
Jane
jgSoton is offline   Reply With Quote
Old 12-13-2011, 08:07 AM   #2
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

Hi Jane

This option is only valid for standalone novoalign and not the MPI version. So all this means is that if you want to get the read order the same in the alignment file as in the reads file then you use this option. For the MPI version this is not possible because the message passing and return states are asynchronous and it would require an algorithm change.
zee is offline   Reply With Quote
Old 12-14-2011, 12:09 AM   #3
jgSoton
Member
 
Location: UK

Join Date: Sep 2011
Posts: 12
Default

Thanks for the reply.

Do I understand correctly that there is a multithreaded stand alone version of novoalign which this command should be used for. And a separate MPI version which the -o sync command is not applicable?

I was confused thinking that "multithreaded novalign" and "novoalign MPI" were the same thing.

Thanks,
Jane
jgSoton is offline   Reply With Quote
Old 12-14-2011, 05:37 AM   #4
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

That is correct. The multithreaded version is limited to a single server.
zee is offline   Reply With Quote
Old 01-02-2012, 05:50 AM   #5
dawe
Senior Member
 
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258
Default

BTW, asynchronous data writing should speed up things. The only issue may be that running novoalign twice on the same data will give you two results ordered in different ways. If you are going to check data integrity using some hashing (such as md5), you may have some problems.

d
dawe is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:02 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO