Question: BWA error [bns_restore_core] Parse error reading
0
gravatar for Picasa
16 months ago by
Picasa340
Picasa340 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 • 1.1k views
ADD COMMENTlink modified 5 weeks ago by said342760 • written 16 months ago by Picasa340

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 12 months ago by lironyoffe0
1
gravatar for Vijay Lakhujani
16 months ago by
Vijay Lakhujani1.9k
India
Vijay Lakhujani1.9k 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 16 months ago by Vijay Lakhujani1.9k
0
gravatar for tshtatland
9 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 9 months ago by tshtatland20
0
gravatar for said3427
5 weeks ago by
said342760
Mexico
said342760 wrote:

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

bwa index db/contaminants

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by said342760
1

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

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