segmentation fault (core dumped) error when using BWA and BOWTIE

Question

[reza]

hi everyone

i got segmentation fault (core dumped) error when using BWA (mem) and BOWTIE (index). anybody know how can i resolve this error? i try with different versions of mentioned programs and get same error. also sometimes i get "bus error".

[kloetzl]

A segfault indicates a programming error. Did you double check your inputs? Maybe they are weirdly formatted.

Answer 1

[Devon Ryan]

You have some sort of file system error. You'll need to fix that, this isn't a problem with bowtie2 or bwa.

[5heikki]

My guess would be that OP is running out of RAM..

[Devon Ryan]

I don't think that'd give you an occasional bus error (though perhaps if you're swapping...).

[reza]

5heikki, i did mapping on my PC previously without any problem on same data but now i have this problem whit it. After the problem occurred, I installed the new Linux, but the problem did not fix

[reza]

Devon, Can you give me more guidance? it is worth to mentioned that i got the segmentation error in my previous linux and after install new linux on my PC, i get same error on new linux.

[Devon Ryan]

No one here can help you with hardware issues.

[reza]

Devon, is your opinion that the problem is related to hardware such as RAM?

[Devon Ryan]

Yes

[kloetzl]

Checking RAM is easy. However, I doubt it is a hardware failure, rather than a simple memory access error. After all, an invalid read is undefined behaviour. Anything can happen.