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Forum: Bioinformatics 12-23-2011, 11:45 AM
Replies: 0
Views: 437
Posted By dp05yk
Looking to release software to the NGS community

Hi SEQanswers,

First, let me apologize if this is not the right avenue to make this request. I am the author of pBWA - a parallel implementation of a Burrows-Wheeler transform based short read...
Forum: Bioinformatics 12-23-2011, 11:28 AM
Replies: 7
Views: 1,839
Posted By dp05yk
Sometimes insert sizes receive extremely high...

Sometimes insert sizes receive extremely high estimates for certain datasets - you can use the -A parameter to disable isize estimating altogether and enforce your own, IIRC.

And I believe...
Forum: Bioinformatics 09-16-2011, 03:54 AM
Replies: 52
Views: 10,248
Posted By dp05yk
Given it's the same error message in the same...

Given it's the same error message in the same function, I'm going to say RAM again - sampe/samse require more RAM than aln, because sampe/samse require every processor to have the entire suffix array...
Forum: Bioinformatics 09-15-2011, 02:12 PM
Replies: 52
Views: 10,248
Posted By dp05yk
Unfortunately not. This is why running pBWA is...

Unfortunately not. This is why running pBWA is all about finding the right balance between multithreading and parallelism. If you ran (as I suggested) 24 processes across 3 cores each with 3...
Forum: Bioinformatics 09-15-2011, 02:11 PM
Replies: 52
Views: 10,248
Posted By dp05yk
Actually, BWA only has multi-threaded...

Actually, BWA only has multi-threaded functionality for half of the process. sampe/samse is not multithreaded. Moreover, BWA's multithreading was inefficient when I initially released pBWA for...
Forum: Bioinformatics 09-15-2011, 10:05 AM
Replies: 52
Views: 10,248
Posted By dp05yk
It could possibly be a RAM issue... with MPI...

It could possibly be a RAM issue... with MPI applications each instance of the program is completely separate from another. Ie. where threaded applications share global variables, MPI applications...
Forum: Bioinformatics 09-15-2011, 09:46 AM
Replies: 52
Views: 10,248
Posted By dp05yk
Hm... could you answer a couple of questions for...

Hm... could you answer a couple of questions for me?

1. What is your system's nodal information (# nodes, # cores per node, RAM per node).

2. How are you splitting the jobs up (ie. how many...
Forum: Bioinformatics 09-14-2011, 02:21 PM
Replies: 52
Views: 10,248
Posted By dp05yk
That's interesting... as the website for pBWA...

That's interesting... as the website for pBWA notes, gzipped FASTQ files are not supported since we required random file access to split up the input files.
Forum: Bioinformatics 08-23-2011, 05:36 AM
Replies: 52
Views: 10,248
Posted By dp05yk
Hi Sheng, You need to figure out the alias...

Hi Sheng,

You need to figure out the alias to use to call the MPI compiler. On most clusters this will be "mpicc"... you'll have to contact your system administrator to figure out what this is,...
Forum: Bioinformatics 08-23-2011, 03:22 AM
Replies: 52
Views: 10,248
Posted By dp05yk
Hi sheng, These requirements can be broken...

Hi sheng,

These requirements can be broken down as follows. pBWA is a _parallel_ implementation of BWA. This means that unless your computer system has multiple processors, this software will be...
Forum: Bioinformatics 07-25-2011, 11:23 AM
Replies: 6
Views: 2,257
Posted By dp05yk
To his credit, the code is kind of a mess, even...

To his credit, the code is kind of a mess, even if the theory behind it is solid.
Forum: Bioinformatics 07-05-2011, 05:56 AM
Replies: 52
Views: 10,248
Posted By dp05yk
Just to let everyone know, an alternate version...

Just to let everyone know, an alternate version of pBWA is now available (http://sourceforge.net/projects/pbwa) that cleans up the workflow a bit. The user is no longer required to enter the number...
Forum: Bioinformatics 06-22-2011, 06:16 AM
Replies: 5
Views: 1,193
Posted By dp05yk
In my experience BWA won't really ever error out...

In my experience BWA won't really ever error out unless there's a problem with your data or your command (or lack of memory). As long as your data/commands are correct you can just use a shell...
Forum: Bioinformatics 06-21-2011, 08:22 PM
Replies: 5
Views: 1,193
Posted By dp05yk
Just write a shell script that calls your three...

Just write a shell script that calls your three commands in order... unless you are executing BWA on a server with a scheduler, in which case you can just submit all three commands independently with...
Forum: Bioinformatics 06-21-2011, 04:24 AM
Replies: 9
Views: 4,479
Posted By dp05yk
It says in the paper that BWA will find all...

It says in the paper that BWA will find all single-end alignments for each mate and sort them in ascending order of chromosomal coordinates. Then it uses an estimated insert size to determine which...
Forum: Bioinformatics 06-16-2011, 07:34 PM
Replies: 1
Views: 1,211
Posted By dp05yk
If you're getting core dumps, it means your...

If you're getting core dumps, it means your program run is crashing, likely due to an invalid memory access causing a segmentation fault.

Try analysing your core dumps with gdb if your system has...
Forum: Bioinformatics 06-15-2011, 01:14 PM
Replies: 1
Views: 1,187
Posted By dp05yk
sai files contain the suffix array intervals for...

sai files contain the suffix array intervals for each sequence.

If one sequence does not match anywhere, it's suffix array interval will be null, and take up 4 bytes (a 0 integer). However, if...
Forum: Bioinformatics 06-15-2011, 04:16 AM
Replies: 3
Views: 4,476
Posted By dp05yk
Can you give an example of your stderr output? ...

Can you give an example of your stderr output? My guess is it's hanging up on "align unmapped mates". If this is the case, check out this thread:
...
Forum: Bioinformatics 06-14-2011, 07:15 PM
Replies: 1
Views: 696
Posted By dp05yk
Oh, wait, now it looks like the sequence and...

Oh, wait, now it looks like the sequence and reverse sequence (p->seq & p->rseq) in the code are actually identical unless they are SOLiD reads, in which case they are simply complements (but NOT...
Forum: Bioinformatics 06-14-2011, 07:06 PM
Replies: 1
Views: 696
Posted By dp05yk
BWA & Reverse Sequences

Hi all,

Just wanted to clear something up. When BWA reads the input sequences, it generates the reverse sequence for each read. Then, when searching for matches, it will check both the forward...
Forum: Bioinformatics 06-14-2011, 01:48 PM
Replies: 1
Views: 887
Posted By dp05yk
BWA determines the suffix array intervals for...

BWA determines the suffix array intervals for each read during the 'aln' stage. If you're allowing errors (bwa aln -n #oferrors), a read can have many suffix array intervals of varying lengths.
...
Forum: Bioinformatics 06-01-2011, 11:09 AM
Replies: 1
Views: 927
Posted By dp05yk
I also come from a computer science background...

I also come from a computer science background and had to do a lot of self-teaching. Never underestimate the power of wikipedia as a rudimentary educational tool!

I had the advantage of being...
Forum: Bioinformatics 05-27-2011, 10:56 AM
Replies: 25
Views: 7,800
Posted By dp05yk
Yes - for samse, it's not really a big deal, hack...

Yes - for samse, it's not really a big deal, hack up your FASTQs! The problems with FASTQ file mods are when you're pairing, because BWA will take each read from each file in order, and assume that...
Forum: Bioinformatics 05-27-2011, 10:41 AM
Replies: 25
Views: 7,800
Posted By dp05yk
As long as the nth read in each mate file are...

As long as the nth read in each mate file are actually mates for all n, then you're fine.



This is absolutely your problem. If you filter one read that has too many N's, you _need_ to also...
Forum: Bioinformatics 05-27-2011, 10:22 AM
Replies: 25
Views: 7,800
Posted By dp05yk
Yeah, it's a weird feature. Using the -a...

Yeah, it's a weird feature. Using the -a parameter, it should be clear that you want to override the program's estimating process, but for some reason the -a parameter becomes a fallback value.
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