bwa_sai2sam_pe fail to locate the index

[alig]

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

[GenoMax]

The BWA index format was changed in 0.6.0 to integrate the BWT and
reverse BWT into the same file.

Ref: https://github.com/lh3/bwa/blob/master/NEWS

Release 0.5.10 and 0.6.0 (12 November, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The 0.6.0 release comes with two major changes. Firstly, the index data
structure has been changed to support genomes longer than 4GB. The forward
and reverse backward genome is now integrated in one index.

[alig]

BWA0.6.2 indexes

Thank you for the information re the new BWA indexes,

All seems to be running now, think my problem was an error in my script.

alig

[Nowlan Freese]

Alig,

I'm getting the same error:

[bwa_sai2sam_pe] fail to locate the index

What was the error that you encountered in your script, as I might be doing the same thing.

Thanks!

Nowlan

[GenoMax]

Can you provide the command you are using?

[Nowlan Freese]

bwa index S_lycopersicum_chromosomes.fa

gunzip 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R1_001.fastq.gz
gunzip 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R2_001.fastq.gz

bwa aln S_lycopersicum_chromosomes.fa 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R1_001.fastq > L002_R1_001.sai

bwa aln S_lycopersicum_chromosomes.fa 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R2_001.fastq > L002_R2_001.sai


bwa sampe S_lycopersicum_chromosomes.fa L002_R1_001.sai L002_R2_001.sai 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R1_001.fastq 141217HiSeq_Run_Sample_Sample_3_TTAGGC_L002_R2_001.fastq > mutant002.sam

[bwa_sai2sam_pe] fail to locate the index

[GenoMax]

Which version of bwa are you using? Are all these files (and the index files) in the same directory and are not empty (i.e. they are non-zero bytes)? For future reference you do not need to uncompress the sequence files.

[Nowlan Freese]

The index and .sai files all have data, and we're using the most recent version of BWA (0.7.12).

We're going to try and rerun with -a bwtsw as an option while indexing, and we'll make sure all of the files are in the same directory. I'll let you know how it turns out.

Thanks!

Nowlan

[Nowlan Freese]

We were able to get BWA to run correctly.

The only thing we had to change was to use -a bwtsw when indexing the genome.

This was a little unexpected as we were using the tomato genome, which has a moderately sized genome at just under 1Gb.