bwa error

Question

[amahdi779]

When I run bwa in my VM based on github:

git clone https://github.com/lh3/bwa.git

cd bwa; make
./bwa index ref.fa
./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz

I face with yhis error:

[E::bwa_idx_load_from_disk] fail to locate the index files

What exactly can I do to fix this error? I made index file but I don't know what the problem is

Answer 1

[Pierre Lindenbaum]

as you can see in the file directory https://github.com/lh3/bwa , there is no 'ref.fa' in the list . The doc is somehow outdated. There is not any more example file here, if there was ever any.

[amahdi779]

thank you pierre i create an index