Question: segmentation fault (core dumped) error when using BWA and BOWTIE
0
gravatar for reza
2.6 years ago by
reza230
Iran
reza230 wrote:

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".

bowtie bwa software error • 1.8k views
ADD COMMENTlink modified 2.6 years ago by Devon Ryan96k • written 2.6 years ago by reza230

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

ADD REPLYlink written 2.6 years ago by kloetzl1.1k
0
gravatar for Devon Ryan
2.6 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

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

ADD COMMENTlink written 2.6 years ago by Devon Ryan96k

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

ADD REPLYlink written 2.6 years ago by 5heikki8.9k

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Devon Ryan96k

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

ADD REPLYlink written 2.6 years ago by reza230

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by reza230

No one here can help you with hardware issues.

ADD REPLYlink written 2.6 years ago by Devon Ryan96k

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

ADD REPLYlink written 2.6 years ago by reza230

Yes

ADD REPLYlink written 2.6 years ago by Devon Ryan96k

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.

ADD REPLYlink written 2.6 years ago by kloetzl1.1k
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