BWA error [bns_restore_core] Parse error reading

Question

[Picasa]

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

[lironyoffe]

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.

Answer 1

[lakhujanivijay]

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).

Answer 2

[said3427]

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

bwa index db/contaminants

[bird77]

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

sed -i 's/^[^>]\s*$//g' db/contaminants

Answer 3

[tshtatland]

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/