BWA aln - failed to locate the index

Question

[m.wekking]

So I have a lot of paired-end sequence samples in the format sample_x_fw.fastq and sample_x_rv.fastq and want to align these with the BWA sampe command

So I downloaded the hg19.fasta and ran:

bwa index -p bwa_hg19 -a bwtsw hg19.fa

This resulted in:

• bwa_hg19.amb
• bwa_hg19.ann
• bwa_hg19.bwt
• bwa_hg19.pac
• bwa_hg19.sa

after this I tried to run:

bwa aln bwa_hg19.fa sample_1_fw.fastq > aln_sa1.sai

and I get the error:

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln] fail to locate the index

Does anyone have any idea what goes wrong?

[Nicolas Rosewick]

quick question : why bwa aln and not the more recent bwa mem ? Are your reads small ( < 50bp ? )

Answer 1

[ATpoint]

It is bwa aln bwa_hg19 sample_1_fw.fastq > aln_sa1.sai as the prefix you gave for indexing is bwa_hg19, not bwa_hg19.fa

[m.wekking]

That's it! thank you very much!

Answer 2

[Pierre Lindenbaum]

try

bwa aln bwa_hg19 sample_1_fw.fastq > aln_sa1.sai

or

bwa index -a bwtsw hg19.fa
bwa aln hg19.fa sample_1_fw.fastq > aln_sa1.sai

[m.wekking]

That's it! thank you very much!