makeblastdb error: Error: (803.7) [makeblastdb] Blast-def-line-set.E.seqid.E.local.str Bad char [0xC3] in string at byte 45

Question

[m.rhodes]

I'm trying to make a blastdb out of fungal ITS sequences from UNITE (https://unite.ut.ee/index.php). I downloaded the general fasta file and edited the fasta headers so they look like this:

GQ280590|Calonectria_leucothoës

DQ675574|Epichloë_sibirici

e.t.c.

However, when I run this makeblastdb command:

./makeblastdb -in unite_fungi.fasta -out UNITE_ITS.fasta -dbtype nucl -parse_seqids

I am getting the following error for all entries:

Error: (803.7) [makeblastdb] Blast-def-line-set.E.seqid.E.local.str

Bad char [0xAB] in string at byte 46.

Initially I thought it could be something to do with tabs/spaces at the end of the header, so I tried removing them using (please correct me if I'm wrong):

sed 's/[[:blank:]]*$//'

However, this did not work either.

Does anyone know why this might be happening?

Thanks in advance.

[GenoMax]

Wonder if the issue is using non-US character set.

[m.rhodes]

could you please elaborate?

[GenoMax]

Do you know what unicode character set you are using on this machine? The error you have posted above seems to be referring to this character.

[m.rhodes]

No, but that link helped solve my problem! Turns out it was the 'ë' characters in the fasta headers that were causing the problem. Thanks for the help!

Answer 1

[flyingfinger]

I had the same error but with a different special char.

You can get rid of any/all non-ascii chars by doing something like this:

cat my_file.fasta | perl -ne 's/[^\x00-\x7F]+/ /g; print;' > tmp.fasta

Running makeblastdb on the temp file ran without the errors for me.