Question: segmentation fault (core dumped) error when using BWA and BOWTIE
0
gravatar for reza
11 months ago by
reza200
Iran
reza200 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 • 739 views
ADD COMMENTlink modified 11 months ago by Devon Ryan86k • written 11 months ago by reza200

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

ADD REPLYlink written 11 months ago by kloetzl990
0
gravatar for Devon Ryan
11 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k 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 11 months ago by Devon Ryan86k

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

ADD REPLYlink written 11 months ago by 5heikki7.9k

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

ADD REPLYlink modified 11 months ago • written 11 months ago by Devon Ryan86k

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 11 months ago by reza200

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 11 months ago • written 11 months ago by reza200

No one here can help you with hardware issues.

ADD REPLYlink written 11 months ago by Devon Ryan86k

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

ADD REPLYlink written 11 months ago by reza200

Yes

ADD REPLYlink written 11 months ago by Devon Ryan86k

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 11 months ago by kloetzl990
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