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Search: Posts Made By: pallo
Forum: Bioinformatics 04-11-2011, 05:45 AM
Replies: 1
Views: 3,532
Posted By pallo
samtools vs picard index

I just stumbled upon something weird. I have a library specific bam file, with several illumina lanes of PE data merged. The file is coordinate sorted and I wanted to index it, like I have past...
Forum: Bioinformatics 12-17-2010, 05:11 AM
Replies: 278
Views: 115,639
Posted By pallo
hi drio, Nope, I dont have any benchmarks......

hi drio,

Nope, I dont have any benchmarks...
Its just SOP here to try to compile with the "native" intel and then gcc if intel binaries fail.
Forum: Bioinformatics 12-17-2010, 01:19 AM
Replies: 278
Views: 115,639
Posted By pallo
Hi seb567 Good news, looks like it works...

Hi seb567

Good news, looks like it works with gcc 4.4 + openmpi 1.4.2 (still ran out of memory though, but I will try a bigger set of nodes next time).

I dont think we need to debug the Intel...
Forum: Bioinformatics 12-15-2010, 10:45 PM
Replies: 278
Views: 115,639
Posted By pallo
Hi, Ray 1.2.0 crashes here, and I mean...

Hi,

Ray 1.2.0 crashes here, and I mean segfaults:

ray.err:



I have 16 lanes of illumina data (about 500M 90bp PE reads).
I call Ray simply with:
Forum: Bioinformatics 11-23-2010, 11:29 PM
Replies: 278
Views: 115,639
Posted By pallo
@seb567: You are right, trying to run on a bigger...

@seb567: You are right, trying to run on a bigger set of nodes (20x8cores) as well as a smaller set of larger memory cores made no difference - the jobs hang within 24hrs of startup and do so using...
Forum: Bioinformatics 11-08-2010, 10:09 PM
Replies: 278
Views: 115,639
Posted By pallo
Hi, The job had to be killed for other...

Hi,

The job had to be killed for other reasons, but here are the last lines of ray.out:



The interconnections are Infiniband.

Im rerunning the job on a bigger set of nodes, Ill post the...
Forum: Bioinformatics 11-07-2010, 11:44 PM
Replies: 278
Views: 115,639
Posted By pallo
First of all: thanks for providing Ray. I am...

First of all: thanks for providing Ray. I am reading the paper and it sounds very promising.

I am testing version 0.1.0 (openMPI 1.4.2, compiled with intel11.1) on 8 X 8 core/48GB nodes. The data...
Forum: Bioinformatics 12-02-2009, 01:33 AM
Replies: 26
Views: 13,929
Posted By pallo
I believe this is a manifestation of the "bug" I...

I believe this is a manifestation of the "bug" I mentioned above. As the script never actually scans through the bam file, the stats it is supposed to produce never get produced, and therefore some...
Forum: Bioinformatics 11-20-2009, 04:53 AM
Replies: 26
Views: 13,929
Posted By pallo
Just started playing with BreakDancer and ran...

Just started playing with BreakDancer and ran into the same problem with bam2cfg.pl, that is, it returned nothing, when run on a single lane bam of my solexa results.

I think I have found the...
Forum: Introductions 10-22-2009, 03:12 AM
Replies: 0
Views: 1,280
Posted By pallo
Hi from Iceland

Hi everybody,

My name is Pall Olason, I am a bioinformatician at Decode Genetics.

We have had two Illumina GA-1s since summer 2007. We have mostly been running pooled samples for variation...
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