SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error during bowtie2-align run , (ERR): bowtie2-align exited with value 139 harijay Bioinformatics 2 02-08-2017 01:24 AM
Expected bowtie2 to be in same directory with bowtie2-align nimrod337 Bioinformatics 4 04-11-2015 01:54 PM
Using Bowtie2 for to align paired end reads sewellh Bioinformatics 5 06-05-2014 10:50 AM
Bowtie2 is unable to align query sequences that contain an intervening stretch of N's quokka Bioinformatics 2 10-03-2013 12:18 PM
How to align reads to multiple index in bowtie2 ssharma Bioinformatics 3 07-16-2013 03:13 AM

Reply
 
Thread Tools
Old 07-28-2015, 01:49 AM   #1
harijay
Junior Member
 
Location: Cambridge, MA

Join Date: Feb 2015
Posts: 4
Red face bowtie2-align dided with the signal 11 (SEGV) (core dumped) with bowtie2

I am running bowtie2 to map 300 bp reads to a fixed set of amplicons.

I always get a "bowtie2-align died with the signal 11 (SEGV) (core dumped)" error regardless of whether I use the ubuntu version of bowtie2 or a self compiled version of bowtie2 ( ver 2.2.5)

The error is Ubuntu specific as I have tested it with self and ubuntu compiled versions on Ubuntu servers , running both 12.04 and 14.04 on my personal hardware and on Amazon EC2 ( controlling for hardware issues) with both 16 GB and 98 GB of memory ( all 8 combinations gave the error )

When I switched the same workload to a server running SUSE Linux on Amazon EC2 or ran it on my dev laptop running OS X with 32 and 16 GB of RAM respectively, I never get the "bowtie2-align dided with the signal 11 (SEGV) (core dumped)" error.

I don't know how to run bowtie2 in debug mode to troubleshoot this error . Any help understanding why this error occurs will be greatly appreciated.
harijay is offline   Reply With Quote
Reply

Tags
bowtie 2, ubuntu server

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:07 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO