Question: segmentation fault (core dumped) error when using BWA and BOWTIE
0
gravatar for reza
8 months ago by
reza190
Iran
reza190 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 • 591 views
ADD COMMENTlink modified 8 months ago by Devon Ryan84k • written 8 months ago by reza190

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

ADD REPLYlink written 8 months ago by kloetzl970
0
gravatar for Devon Ryan
8 months ago by
Devon Ryan84k
Freiburg, Germany
Devon Ryan84k 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 8 months ago by Devon Ryan84k

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

ADD REPLYlink written 8 months ago by 5heikki7.6k

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

ADD REPLYlink modified 8 months ago • written 8 months ago by Devon Ryan84k

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 8 months ago by reza190

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 8 months ago • written 8 months ago by reza190

No one here can help you with hardware issues.

ADD REPLYlink written 8 months ago by Devon Ryan84k

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

ADD REPLYlink written 8 months ago by reza190

Yes

ADD REPLYlink written 8 months ago by Devon Ryan84k

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 8 months ago by kloetzl970
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