BLAST: can't find reference file in db -
i trying run standalone ncbi-blast-2.2.29+ on machine (mac) error message when running blastx (or blastn) database:
no alias or index file found nucleotide database [db/viral.1.1.genomic] in search path [~/users/kk/ncbi-blast-2.3.0+/virus::]
the way run it:
blastn -query input.fasta -out out.blast.txt -db db/viral.1.1.genomic
my working directory ~/users/kk/ncbi-blast-2.3.0+/virus , there sub-directory db (~/users/kk/ncbi-blast-2.3.0+/virus/db) , db has viral.1.1.genomic.phr, viral.1.1.genomic.pin, viral.1.1.genomic.pnd, viral.1.1.genomic.pni, viral.1.1.genomic.pog, viral.1.1.genomic.psd, viral.1.1.genomic.psi, viral.1.1.genomic.psq, viral.1.1.genomic.fasta. , made these files using command line
makeblastdb -in viral.1.1.genomic.fasta -out viral1.1.genomic -dbtype prot -parse_seqids
i don't know why keep getting error message saying no alias or index file found. have read other similar questions posted others don't seem finding answer problem. , try other tblast , blastx , both of them return similar error except said protein database instead of nucleotide
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