segmentation fault (core dumped) error when using BWA and BOWTIE
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3.9 years ago
reza ▴ 290

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".

bwa bowtie software error • 2.9k views
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A segfault indicates a programming error. Did you double check your inputs? Maybe they are weirdly formatted.

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3.9 years ago

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

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

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

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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

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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.

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No one here can help you with hardware issues.

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

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Yes

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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.

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