Message Error : Blastdbcmd

Question

[florian.grosmaire]

Hello, i try to use the blastdbcmd command and here is what i get

Command: blastdbcmd -db nr.00.tar.gz -entry name.txt -outfmt %f -out text1.fasta

Error message : BLAST Database error: No alias or index file found for nucleotide database [nr.00.tar.gz] in search path [/Users/macbook/Documents/Florian /BIOINFO/Git/Adrien_Bioinfo/Bioinfo-Axe2-Alignemements::]

Could you help me please ? I am not sure about the parameters to use with this blast fonctionality Thanks in advance

Answer 1

[Pierre Lindenbaum]

nr.00.tar.gz is 'just' a tar archive containing the files.

expand it before use

tar xvfz nr.00.tar.gz

[GenoMax]

florian.grosmaire : You will need to download and expand ALL nr files for this to work (38 pieces as of today).

[florian.grosmaire]

ok thanks, I'll do that Last question, I am not sure about the "entry" parameter. Does a text file containing sequences ID could be used ?

[GenoMax]

Use -entry_batch parameter with an input file with sequence ID.

[florian.grosmaire]

Thank you very much !