Question

Message Error : Blastdbcmd

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3.3 years ago

florian.grosmaire • 0

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

sequence gene alignment • 775 views

ADD COMMENT • link updated 3.3 years ago by GenoMax 141k • written 3.3 years ago by florian.grosmaire • 0

score 0 · Answer 1 · 2021-01-22

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3.3 years ago

Pierre Lindenbaum 161k

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

expand it before use

tar xvfz nr.00.tar.gz

ADD COMMENT • link 3.3 years ago by Pierre Lindenbaum 161k

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

ADD REPLY • link 3.3 years ago by GenoMax 141k

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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 ?

ADD REPLY • link 3.3 years ago by florian.grosmaire • 0

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

ADD REPLY • link 3.3 years ago by GenoMax 141k

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Thank you very much !

ADD REPLY • link 3.3 years ago by florian.grosmaire • 0