Question

BWA error [bns_restore_core] Parse error reading

2

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7.9 years ago

Picasa ▴ 650

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 • 9.2k views

ADD COMMENT • link updated 6.7 years ago by said3427 ▴ 120 • written 7.9 years ago by Picasa ▴ 650

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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 REPLY • link 7.6 years ago by lironyoffe • 0

score 2 · Answer 1 · 2016-12-26

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7.9 years ago

lakhujanivijay 5.9k

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 COMMENT • link 7.9 years ago by lakhujanivijay 5.9k

score 2 · Answer 2 · 2018-03-19

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6.7 years ago

said3427 ▴ 120

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

bwa index db/contaminants

ADD COMMENT • link 6.7 years ago by said3427 ▴ 120

2

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

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

ADD REPLY • link 6.7 years ago by bird77 ▴ 80

score 1 · Answer 3 · 2017-07-07

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/