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Old 07-28-2015, 01:49 AM   #1
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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.
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bowtie 2, ubuntu server

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