[Zapages]

Also I would suggest looking into Geneious Map Reader, it allows for 1 reads: http://www.geneious.com/assets/docum...ReadMapper.pdf

[slengyel]

Bowtie2 segv

Greetings,

I've been having trouble find the proper post, but I'll see what everyone thinks here. I've been trying to run Bowtie2 on a set of Illumina reads. The command I used after running bowtie-build (There seem to have been no issues building the index) is :

bowtie2 -a --no-mixed -p 16 --phred 33 -q -x <prefix> -1 <1.fastq> -2 <2.fastq> -S <.sam>

I specify the paths to each fastq file and for the same output.

The error I'm recieving is the following:

bowtie2-align dided with the signal 11 (SEGV) (core dumped)

When compiling, I used make BITS=64 to pass the -m64 option to g++, so I don't think it is a compiler issue. The server is has 256gb of RAM, and 51.9gb of swap memory, so I don't think memory is an issue.

Any and all help is appreciated.

Best,
SL

[sdriscoll]

is that a typeo in your command? '--phred 33' instead of '--phred33' ?

[slengyel]

Sorry, yes it is. I accidentally put a space in when posting to the thread.

[harijay]

I am seeing the error :
"bowtie2-align dided with the signal 11 (SEGV) (core dumped)"

a lot on an Ubuntu 14.04 machine with 98GB of RAM in a routine bowtie2 (2.2.5 version) run. I can get this error almost reproducibly .

When I switched OS to SUSE Linux. The same error never occurs.

Any ideas how to troubleshoot this issue. It seems to be due to the application messing up the memory management