bwa index error : Floating point exception

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7.2 years ago

comma1993 ▴ 20

I have one sequence with size of 2.4G. And I built index with bwa using the following command: bwa index -a bwtsw test.fa But it stoppped with the error : [bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 303: Success And I changed the latest version BWA and it returned a different error : Floating point exception

Does anyone know the reason why the error come about? Thanks a lot!

bwa alignment software error • 4.0k views

ADD COMMENT • link 7.2 years ago by comma1993 ▴ 20

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I would suspect that it's an issue with RAM. How much have you available? The RAM filled up and then the OS was unable to allocate any more.

Edit: the function at that line number in the C file is realloc (https://www.tutorialspoint.com/c_standard_library/c_function_realloc.htm), which is indeed an attempt to allocate memory.

ADD REPLY • link 7.2 years ago by Kevin Blighe 88k

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Try to run it on a subset of the large sequence dump.

ADD REPLY • link 7.2 years ago by Bioaln ▴ 360

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