Also I would suggest looking into Geneious Map Reader, it allows for 1 reads: http://www.geneious.com/assets/docum...ReadMapper.pdf
-
-
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
-
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
-
Sorry, yes it is. I accidentally put a space in when posting to the thread.Comment
-
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
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment