Question: BWA error [bns_restore_core] Parse error reading
1
gravatar for Picasa
2.1 years ago by
Picasa390
Picasa390 wrote:

Hi,

I have downloaded some bacteria genomes on ncbi and then I cat them.

I have built an index with these genome after trying to map my reads I got this error:

[bns_restore_core] Parse error reading db/contaminants.amb

Someone know what is going on ? Thanks

bwa index • 2.1k views
ADD COMMENTlink modified 10 months ago by said342780 • written 2.1 years ago by Picasa390

I have the same problem with bwa-0.7.12 (I tried 0.7.4 and it works). Did you find a solution? my genome file does not contain spaces.

ADD REPLYlink written 21 months ago by lironyoffe0
1
gravatar for Vijay Lakhujani
2.1 years ago by
Vijay Lakhujani3.5k
India
Vijay Lakhujani3.5k wrote:

Based on previous encounters with such issues, please check if your genome file contains any spaces. Remove using sed or tr (if you find any).

ADD COMMENTlink written 2.1 years ago by Vijay Lakhujani3.5k
0
gravatar for tshtatland
18 months ago by
tshtatland20
tshtatland20 wrote:

See the answer from Vijay Lakhujani above. More specifically, remove whitespace from the fasta reference sequences (whitespace in fasta header is okay). See also: Burrows-Wheeler Aligner / Mailing Lists

https://sourceforge.net/p/bio-bwa/mailman/message/33230220/

https://sourceforge.net/p/bio-bwa/mailman/message/34430833/

ADD COMMENTlink written 18 months ago by tshtatland20
0
gravatar for said3427
10 months ago by
said342780
Mexico
said342780 wrote:

sed -i 's/\s*$//g' db/contaminants

bwa index db/contaminants

ADD COMMENTlink modified 10 months ago • written 10 months ago by said342780
1

If you have spaces in your header, use this instead:

sed -i 's/^[^>]\s*$//g' db/contaminants
ADD REPLYlink modified 9 months ago • written 9 months ago by bird7720
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