Hi,
I'm trying to run BWA.0.6.2 I notice that when I index my reference file it is missing some indexes. This seems to be fine if I align single end sequence.
However when I want to run paired end sequence I get an error.
It will do the 2 alignments fine - bwa aln etc
But when I try to run bwa sampe I get this error.
[bwa_sai2sam_pe] fail to locate the index
Now I'm using the same path as when I ran bwa aln
So I'm thinking it's complaining about the missing indexes - .rbwt, rpac & rsa
Why does bwa0.6.2 not make these when you index the reference?
Any help greatly appreciated,
thanks alig
I'm trying to run BWA.0.6.2 I notice that when I index my reference file it is missing some indexes. This seems to be fine if I align single end sequence.
However when I want to run paired end sequence I get an error.
It will do the 2 alignments fine - bwa aln etc
But when I try to run bwa sampe I get this error.
[bwa_sai2sam_pe] fail to locate the index
Now I'm using the same path as when I ran bwa aln
So I'm thinking it's complaining about the missing indexes - .rbwt, rpac & rsa
Why does bwa0.6.2 not make these when you index the reference?
Any help greatly appreciated,
thanks alig
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