Why am I getting the BLAST option error: file does not match input format type
COMMAND USED: makeblastdb -in sorted_alu_seq.fasta -dbtype 'nucl' -out alu
BLAST option error: sorted_alu_seq.fasta does not match input format type, default input type is FASTA.
>gi|26791|27053|(249223568)|SINE/Alu|1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA GGCGGGCGGATCACCTGAGGTCGGGAGTTCGAGACCAGCCTGACCAACAT GGAGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT TGAACCCGGGAGGCGGAGGTTGCGGTGAGCCGAGATCGCGCCATTGCACT CCAGCCTGGGCAAC
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ankita0007 •
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Is this the complete file? There is nothing obviously wrong with this entry and makeblastdb works. Are you probably making a simple mistake, e.g. trying to use the wrong file?
I second this comment. It is possible that you have 1 or more Fastq sequences in your Fasta file.
It's likely. In my experience, the program cd-hit is pretty great for fasta validation (in the output we get info if sequences were discarded and what they were). Maybe others could suggest other methods..
similar error!!