CODEWITHSUNDEEP
windowscmdbioinformaticsfastablast
user2487834
user2487834

Reputation: 23

blastdbcmd - Too many positional arguments <1>, the offending value: %f

I'm trying to use blastdbcmd - when I type the following on cmd

blastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txt

the following error pops up:

Error: Too many positional arguments <1>, the offending value: %f

I typed %f so that it's in Fasta format, and even after spending so much time on the internet to figure out, I still have no idea what to do for this error. Would you please be able to help me out?

Upvotes: 2

Views: 6681

Answers (4)

splaisan
splaisan

Reputation: 923

in my case it was a very difficult to spot look-alike for "-" after copy-pasting part of a command. Make sure the minus-signs are real minus signs!

Upvotes: 0

pcantalupo
pcantalupo

Reputation: 2226

Your problem is not with the -outfmt argument. It is that -entry_batch requires a file name. Also, you don't need to specify -outfmt '%f' since Fasta format is the default output.

Here is the command line that you want:

blastdbcmd.exe -db databaseBLAST -entry 'all' -out test_query.txt

Paul

Upvotes: 2

A.Mstt
A.Mstt

Reputation: 311

Maybe a little bit late, but I think this may be yet another case of UTF-8 versus ISO-latin finding a way to annoy:

I had the same problem with a different query using blastn, but the offending value was -db. I found out that it was an encoding problem with the "-" part of the command. I.e. if you are copy-pasting the commands from Mac or a pdf or so what looks like "%f" or "-" to us may be not. Try typing all the command instead of copy-pasting.

Upvotes: 3

Magoo
Magoo

Reputation: 80033

Pure guess : remove the quotes, double the % or more probably both.

%f is the default according to the documentation.

Upvotes: 0

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