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Also I would suggest looking into Geneious Map Reader, it allows for 1 reads: http://www.geneious.com/assets/docum...ReadMapper.pdf
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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,
SLComment
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is that a typeo in your command? '--phred 33' instead of '--phred33' ?/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */Comment
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Sorry, yes it is. I accidentally put a space in when posting to the thread.Comment
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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 managementComment
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