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FASTA parser issue #64

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cgps-admin opened this issue Sep 28, 2022 · 1 comment
Open

FASTA parser issue #64

cgps-admin opened this issue Sep 28, 2022 · 1 comment

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@cgps-admin
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One of our users has managed to trigger a bug in the Kleborate FASTA parsing. If the headers take the following format, Kleborate falls over fairly quickly (I'm not sure of the error as it is swallowed by our wrapper):

>genome_id #1
ATATAT...
>genome_id #2
ATATATTT...
>genome_id #3
CGTACG...

Presumably, the unique part of the header is discarded during parsing, and only the part before the space is being used to identify the contigs. Running `sed -i 's/ /_/g' was enough to "fix" the files and get them running.

@katholt
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katholt commented Sep 28, 2022

Thanks, should be possible for us to fix in a future update. But in the meantime sounds like there's a simple solution on user side, so I'll leave this issue open for easy visibility to other users in case they encounter the same issue.

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