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magicblast can't parse the header of database #56

Closed Rinoahu closed 1 year ago

Rinoahu commented 1 year ago

hello, I used magicblast to map short reads to a fasta with >20000 reference sequences. I found that magicblast couldn't parse the header of the reference sequences. Instead, it turned the header into numbers. Is there any way to solve this? thanks

boratyng commented 1 year ago

Hi @Rinoahu, I am sorry you ran into problems. I suspect that you created a BLAST database for your reference sequences and did not include the -parse_seqids flag. Please include it when running makeblastdb:

makeblastdb -in reference.fa -out reference -dbtype nucl -parse_seqids

If this does not help or you did not use makeblastdb before running magicblast, the please post your magicblast command line and an example of your reference sequence. Thanks.

Rinoahu commented 1 year ago

Hi @Rinoahu, I am sorry you ran into problems. I suspect that you created a BLAST database for your reference sequences and did not include the -parse_seqids flag. Please include it when running makeblastdb:

makeblastdb -in reference.fa -out reference -dbtype nucl -parse_seqids

If this does not help or you did not use makeblastdb before running magicblast, the please post your magicblast command line and an example of your reference sequence. Thanks.

Works. Thank you!