Question: Bwa mem error: [fread] Unexpected end of file
0
gravatar for bigheiniu
4.4 years ago by
bigheiniu0
bigheiniu0 wrote:

Whenever I using bwa mem command:

bwa mem -t 10 -M ${classpath}/genome.fa 1.fastq > test.sam

or like that:

bwa mem -t 10  ${classpath}/genome.fa 1.fastq 2.fastq >test.sam

it just output the error message:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[fread] Unexpected end of file

Is the problem of bwaIndex file ?

Thank you for your suggestion.

bwa alignment • 4.3k views
ADD COMMENTlink modified 4.4 years ago by ATpoint46k • written 4.4 years ago by bigheiniu0
0
gravatar for lakhujanivijay
4.4 years ago by
lakhujanivijay5.4k
India/Ahmedabad
lakhujanivijay5.4k wrote:

Did you checked this post?

ADD COMMENTlink written 4.4 years ago by lakhujanivijay5.4k
0
gravatar for ATpoint
4.4 years ago by
ATpoint46k
ATpoint46k wrote:

I would rebuild the index and try again. In my experience, errors like this usually come from corrupted files.

ADD COMMENTlink written 4.4 years ago by ATpoint46k
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