Question: BWA error [bns_restore_core] Parse error reading
1
gravatar for Picasa
3.8 years ago by
Picasa560
Picasa560 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 • 4.1k views
ADD COMMENTlink modified 2.6 years ago by said342790 • written 3.8 years ago by Picasa560

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 3.5 years ago by lironyoffe0
1
gravatar for lakhujanivijay
3.8 years ago by
lakhujanivijay5.3k
India/Ahmedabad
lakhujanivijay5.3k 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 3.8 years ago by lakhujanivijay5.3k
0
gravatar for tshtatland
3.3 years ago by
tshtatland60
United States
tshtatland60 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 3.3 years ago by tshtatland60
0
gravatar for said3427
2.6 years ago by
said342790
Mexico
said342790 wrote:

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

bwa index db/contaminants

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by said342790
1

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

sed -i 's/^[^>]\s*$//g' db/contaminants
ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by bird7760
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