Question: segmentation fault (core dumped) error when using BWA and BOWTIE
0
gravatar for reza
20 months ago by
reza210
Iran
reza210 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 • 1.3k views
ADD COMMENTlink modified 20 months ago by Devon Ryan92k • written 20 months ago by reza210

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

ADD REPLYlink written 20 months ago by kloetzl1.0k
0
gravatar for Devon Ryan
20 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k 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 20 months ago by Devon Ryan92k

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

ADD REPLYlink written 20 months ago by 5heikki8.5k

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

ADD REPLYlink modified 20 months ago • written 20 months ago by Devon Ryan92k

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 20 months ago by reza210

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 20 months ago • written 20 months ago by reza210

No one here can help you with hardware issues.

ADD REPLYlink written 20 months ago by Devon Ryan92k

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

ADD REPLYlink written 20 months ago by reza210

Yes

ADD REPLYlink written 20 months ago by Devon Ryan92k

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 20 months ago by kloetzl1.0k
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