Question: Message Error : Blastdbcmd
0
gravatar for florian.grosmaire
6 weeks ago by
florian.grosmaire0 wrote:

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

alignment sequence gene • 106 views
ADD COMMENTlink modified 6 weeks ago by GenoMax96k • written 6 weeks ago by florian.grosmaire0
0
gravatar for Pierre Lindenbaum
6 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

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

expand it before use

tar xvfz nr.00.tar.gz
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Pierre Lindenbaum134k
2

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by GenoMax96k

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 REPLYlink written 6 weeks ago by florian.grosmaire0
1

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

ADD REPLYlink written 6 weeks ago by GenoMax96k

Thank you very much !

ADD REPLYlink written 6 weeks ago by florian.grosmaire0
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