Question: BWA error [bns_restore_core] Parse error reading
0
gravatar for Picasa
19 months ago by
Picasa350
Picasa350 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 • 1.4k views
ADD COMMENTlink modified 4 months ago by said342770 • written 19 months ago by Picasa350

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 15 months ago by lironyoffe0
1
gravatar for Vijay Lakhujani
19 months ago by
Vijay Lakhujani2.8k
India
Vijay Lakhujani2.8k 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 19 months ago by Vijay Lakhujani2.8k
0
gravatar for tshtatland
12 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 12 months ago by tshtatland20
0
gravatar for said3427
4 months ago by
said342770
Mexico
said342770 wrote:

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

bwa index db/contaminants

ADD COMMENTlink modified 4 months ago • written 4 months ago by said342770
1

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

sed -i 's/^[^>]\s*$//g' db/contaminants
ADD REPLYlink modified 3 months ago • written 4 months ago by bird7710
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